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Abeyrathne, Priyanka

Goldie, Kenneth N; Abeyrathne, Priyanka; Kebbel, Fabian; Chami, Mohamed; Ringler, Philippe; Stahlberg, Henning (2014). Cryo-electron microscopy of membrane proteins. Methods in Molecular Biology, 1117:325-41.

Aebersold, R

Hofmann, A; Gerrits, B; Schmidt, A; Bock, T; Bausch-Fluck, D; Aebersold, R; Wollscheid, B (2010). Proteomic cell surface phenotyping of differentiating acute myeloid leukemia cells. Blood, 116(13):e26-34.

Aegerter, C M

Schluck, T; Aegerter, C M (2010). Photo-elastic properties of the wing imaginal disc of Drosophila. European Physical Journal E - Soft Matter and Biological Physics, 33(2):111-115.

Affolter, Markus

Hamaratoglu, Fisun; Morton de Lachapelle, Aitana; Pyrowolakis, George; Bergmann, Sven; Affolter, Markus (2011). Dpp signaling activity requires pentagone to scale with tissue size in the growing drosophila wing imaginal disc. PLoS Biology, 9:1-17.

Albericio, Fernando

van der Westen, Rebecca; Hosta-Rigau, Leticia; Sutherland, Duncan S; Goldie, Kenneth N; Albericio, Fernando; Postma, Almar; Städler, Brigitte (2012). Myoblast cell interaction with polydopamine coated liposomes. Biointerphases, 7(1-4):8.

Hosta-Rigau, Leticia; Jensen, Bettina E B; Fjeldsø, Kit S; Postma, Almar; Li, Guoxin; Goldie, Kenneth N; Albericio, Fernando; Zelikin, Alexander N; Städler, Brigitte (2012). Drug Delivery: Surface-Adhered Composite Poly(Vinyl Alcohol) Physical Hydrogels: Polymersome-Aided Delivery of Therapeutic Small Molecules. Advanced Healthcare Materials, 1(6):791-5.

Alitalo, Kari

Leppänen, Veli-Matti; Tvorogov, Denis; Kisko, Kaisa; Prota, Andrea E; Jeltsch, Michael; Anisimov, Andrey; Markovic-Mueller, Sandra; Stuttfeld, Edward; Goldie, Kenneth N; Ballmer-Hofer, Kurt; Alitalo, Kari (2013). Structural and mechanistic insights into VEGF receptor 3 ligand binding and activation. Proceedings of the National Academy of Sciences of the United States of America, 110(32):12960-12965.

Altmann, Karl-Heinz

Prota, Andrea E; Bargsten, Katja; Zurwerra, Didier; Field, Jessica J; Díaz, José Fernando; Altmann, Karl-Heinz; Steinmetz, Michel O (2013). Molecular Mechanism of Action of Microtubule-Stabilizing Anticancer Agents. Science, 339(6119):587-590.

Amstutz, M

Kudryashev, M; Stenta, M; Schmelz, S; Amstutz, M; Wiesand, U; Castano-Diez, D; Degiacomi, M T; Munnich, S; Bleck, C K; Kowal, J; Diepold, A; Heinz, D W; Dal Peraro, M; Cornelis, G R; Stahlberg, H (2013). In situ structural analysis of the Yersinia enterocolitica injectisome. eLife, 2:e00792-e00792.

Andersin, T

Bonhoure, N; Bounova, G; Bernasconi, D; Praz, V; Lammers, F; Canella, D; Willis, I M; Herr, W; Hernandez, N; Delorenzi, M; Hernandez, N; Delorenzi, M; Deplancke, B; Desvergne, B; Guex, N; Herr, W; Naef, F; Rougemont, J; Schibler, U; Andersin, T; Cousin, P; Gilardi, F; Gos, P; Lammers, F; Raghav, S; Villeneuve, D; Fabbretti, R; Vlegel, V; Xenarios, I; Migliavacca, E; Praz, V; David, F; Jarosz, Y; Kuznetsov, D; Liechti, R; Martin, O; Delafontaine, J; Cajan, J; Gustafson, K; Krier, I; Leleu, M; Molina, N; Naldi, A; Rib, L; Symul, L; Bounova, G (2014). Quantifying ChIP-seq data: a spiking method providing an internal reference for sample-to-sample normalization. Genome Research, 24(7):1157-1168.

Andreasen, Sidsel Ø

Andreasen, Sidsel Ø; Chong, Siow-Feng; Wohl, Benjamin M; Goldie, Kenneth N; Zelikin, Alexander N (2013). Poly(vinyl alcohol) physical hydrogel nanoparticles, not polymer solutions, exert inhibition of nitric oxide synthesis in cultured macrophages. Biomacromolecules, 14(5):1687-95.

Andres, C

Shapiguzov, A; Ingelsson, B; Samol, I; Andres, C; Kessler, F; Rochaix, J -D; Vener, A V; Goldschmidt-Clermont, M (2010). The PPH1 phosphatase is specifically involved in LHCII dephosphorylation and state transitions in Arabidopsis. Proceedings of the National Academy of Sciences of the United States of America, 107(10):4782-4787.

Anisimov, Andrey

Leppänen, Veli-Matti; Tvorogov, Denis; Kisko, Kaisa; Prota, Andrea E; Jeltsch, Michael; Anisimov, Andrey; Markovic-Mueller, Sandra; Stuttfeld, Edward; Goldie, Kenneth N; Ballmer-Hofer, Kurt; Alitalo, Kari (2013). Structural and mechanistic insights into VEGF receptor 3 ligand binding and activation. Proceedings of the National Academy of Sciences of the United States of America, 110(32):12960-12965.

Antoniadis, Helena

Tiwari, Neha; Meyer-Schaller, Nathalie; Arnold, Phil; Antoniadis, Helena; Pachkov, Mikhail; van Nimwegen, Erik; Christofori, Gerhard (2013). Klf4 is a transcriptional regulator of genes critical for EMT, including Jnk1 (Mapk8). PLoS ONE, 8(2):e57329.

Ares, Saúl

Schröter, Christian; Ares, Saúl; Morelli, Luis G; Isakova, Alina; Hens, Korneel; Soroldoni, Daniele; Gajewski, Martin; Jülicher, Frank; Maerkl, Sebastian J; Deplancke, Bart; Oates, Andrew C (2012). Topology and Dynamics of the Zebrafish Segmentation Clock Core Circuit. PLoS Biology, 10(7):1-20.

Arheit, Marcel

Kowal, Julia; Chami, Mohamed; Baumgartner, Paul; Arheit, Marcel; Chiu, Po-Lin; Rangl, Martina; Scheuring, Simon; Schröder, Gunnar F; Nimigean, Crina M; Stahlberg, Henning (2014). Ligand-induced structural changes in the cyclic nucleotide-modulated potassium channel MloK1. Nature Communications, 5:3106.

Arnaud, Lionel

Vayssier-Taussat, Muriel; Le Rhun, Danielle; Deng, Hong Kuan; Biville, Francis; Cescau, Sandra; Danchin, Antoine; Marignac, Geneviève; Lenaour, Evelyne; Boulouis, Henri Jean; Mavris, Maria; Arnaud, Lionel; Yang, Huanming; Wang, Jing; Quebatte, Maxime; Engel, Philipp; Saenz, Henri; Dehio, Christoph (2010). The Trw Type IV Secretion System of Bartonella Mediates Host-Specific Adhesion to Erythrocytes. PLoS Pathogens, 6(6):e1000946.

Arnold, Phil

Tiwari, Neha; Meyer-Schaller, Nathalie; Arnold, Phil; Antoniadis, Helena; Pachkov, Mikhail; van Nimwegen, Erik; Christofori, Gerhard (2013). Klf4 is a transcriptional regulator of genes critical for EMT, including Jnk1 (Mapk8). PLoS ONE, 8(2):e57329.

Tiwari, Neha; Tiwari, Vijay K; Waldmeier, Lorenz; Balwierz, Piotr J; Arnold, Phil; Pachkov, Mikhail; Meyer-Schaller, Nathalie; Schübeler, Dirk; van Nimwegen, Erik; Christofori, Gerhard (2013). Sox4 is a master regulator of epithelial-mesenchymal transition by controlling ezh2 expression and epigenetic reprogramming. Cancer Cell, 23(6):768-83.

Awile, Omar

Awile, Omar; Büyükkeçeci, Ferit; Reboux, Sylvain; Sbalzarini, Ivo F (2012). Fast neighbor lists for adaptive-resolution particle simulations. Computer Physics Communications, 183(5):1073-1081.

Awile, Omar; Demirel, Ömer; Sbalzarini, Ivo F; Simos, Theodore E; Psihoyios, George; Tsitouras, Ch (2010). Toward an Object-Oriented Core of the PPM Library. In: International Conference of Numerical Analysis and Applied Mathematics (ICNAAM), Rhodes, Greece, 19 September 2010 - 25 September 2010, 1313-1316.

Bailly-Bechet, Marc

Bailly-Bechet, Marc; Benecke, Arndt; Hardt, Wolf Dietrich; Lanza, Valentina; Sturm, Alexander; Zecchina, Riccardo (2011). An externally modulated, noise-driven switch for the regulation of SPI1 in Salmonella enterica serovar Typhimurium. Journal of Mathematical Biology, 63(4):637-662.

Bairoch, Amos

Mary, Camille; Duek, Paula; Salleron, Lisa; Tienz, Petra; Bumann, Dirk; Bairoch, Amos; Lane, Lydie (2012). Functional Identification of APIP as Human mtnB, a Key Enzyme in the Methionine Salvage Pathway. PLoS ONE, 7(12):e52877.

Balazs, Csaba

Smith, Kevin; Li, Yunpeng; Piccinini, Filippo; Csucs, Gabor; Balazs, Csaba; Bevilacqua, Alessandro; Horvath, Peter (2015). CIDRE: an illumination-correction method for optical microscopy. Nature Methods, 12(5):404-406.

Ballmer-Hofer, Kurt

Leppänen, Veli-Matti; Tvorogov, Denis; Kisko, Kaisa; Prota, Andrea E; Jeltsch, Michael; Anisimov, Andrey; Markovic-Mueller, Sandra; Stuttfeld, Edward; Goldie, Kenneth N; Ballmer-Hofer, Kurt; Alitalo, Kari (2013). Structural and mechanistic insights into VEGF receptor 3 ligand binding and activation. Proceedings of the National Academy of Sciences of the United States of America, 110(32):12960-12965.

Balwierz, Piotr J

Tiwari, Neha; Tiwari, Vijay K; Waldmeier, Lorenz; Balwierz, Piotr J; Arnold, Phil; Pachkov, Mikhail; Meyer-Schaller, Nathalie; Schübeler, Dirk; van Nimwegen, Erik; Christofori, Gerhard (2013). Sox4 is a master regulator of epithelial-mesenchymal transition by controlling ezh2 expression and epigenetic reprogramming. Cancer Cell, 23(6):768-83.

Bargsten, Katja

Prota, Andrea E; Bargsten, Katja; Zurwerra, Didier; Field, Jessica J; Díaz, José Fernando; Altmann, Karl-Heinz; Steinmetz, Michel O (2013). Molecular Mechanism of Action of Microtubule-Stabilizing Anticancer Agents. Science, 339(6119):587-590.

Barrett, Michael P

Limenitakis, Julien; Oppenheim, Rebecca D; Creek, Darren J; Foth, Bernardo J; Barrett, Michael P; Soldati-Favre, Dominique (2013). The 2-methylcitrate cycle is implicated in the detoxification of propionate in Toxoplasma gondii. Molecular Microbiology, 87(4):894-908.

Baruchet, Michaël

Gilardi, Federica; Migliavacca, Eugenia; Naldi, Aurélien; Baruchet, Michaël; Canella, Donatella; Le Martelot, Gwendal; Guex, Nicolas; Desvergne, Béatrice (2014). Genome-Wide Analysis of SREBP1 Activity around the Clock Reveals Its Combined Dependency on Nutrient and Circadian Signals. PLoS Genetics, 10(3):e1004155.

Barylyuk, Konstantin

Weidmann, Simon; Barylyuk, Konstantin; Nespovitaya, Nadezhda; Mädler, Stefanie; Zenobi, Renato (2013). A New, Modular Mass Calibrant for High-Mass MALDI-MS. Analytical Chemistry, 85:3425-3432.

Baudrimont, Antoine

Bonde, Marie Mi; Voegeli, Sylvia; Baudrimont, Antoine; Seraphin, Bertrand; Becskei, Attila (2014). Quantification of pre-mRNA escape rate and synergy in splicing. Nucleic Acids Research, 42(20):12847-12860.

Baum, Jake

Lemgruber, Leandro; Kudryashev, Mikhail; Dekiwadia, Chaitali; Riglar, David T; Baum, Jake; Stahlberg, Henning; Ralph, Stuart A; Frischknecht, Friedrich (2013). Cryo-electron tomography reveals four-membrane architecture of the Plasmodium apicoplast. Malaria Journal, 12:25.

Baumgartner, Paul

Kowal, Julia; Chami, Mohamed; Baumgartner, Paul; Arheit, Marcel; Chiu, Po-Lin; Rangl, Martina; Scheuring, Simon; Schröder, Gunnar F; Nimigean, Crina M; Stahlberg, Henning (2014). Ligand-induced structural changes in the cyclic nucleotide-modulated potassium channel MloK1. Nature Communications, 5:3106.

Bausch-Fluck, D

Hofmann, A; Gerrits, B; Schmidt, A; Bock, T; Bausch-Fluck, D; Aebersold, R; Wollscheid, B (2010). Proteomic cell surface phenotyping of differentiating acute myeloid leukemia cells. Blood, 116(13):e26-34.

Bayati, B

Bayati, B; Chatelain, P; Koumoutsakos, P (2009). D-leaping: Accelerating stochastic simulation algorithms for reactions with delays. Journal of Computational Physics, 228(16):5908-5916.

Rossinelli, D; Bayati, B; Koumoutsakos, P (2008). Accelerated stochastic and hybrid methods for spatial simulations of reaction-diffusion systems. Chemical Physics Letters, 451(1-3):136 - 140.

Bayer, E

Guenot, B; Bayer, E; Kierzkowski, D; Smith, R S; Mandel, T; Zadnikova, P; Benkova, E; Kuhlemeier, C (2012). PIN1-Independent Leaf Initiation in Arabidopsis. Plant Physiology, 159(4):1501-1510.

Bayer, E M

Smith, R S; Bayer, E M (2009). Auxin transport-feedback models of patterning in plants. Plant, Cell and Environment, 32(9):1258-1271.

Bayer, E M; Smith, R S; Mandel, T; Nakayama, N; Sauer, M; Prusinkiewicz, P; Kuhlemeier, C (2009). Integration of transport-based models for phyllotaxis and midvein formation. Genes and Development, 23(3):373-384.

Becskei, Attila

Bonde, Marie Mi; Voegeli, Sylvia; Baudrimont, Antoine; Seraphin, Bertrand; Becskei, Attila (2014). Quantification of pre-mRNA escape rate and synergy in splicing. Nucleic Acids Research, 42(20):12847-12860.

Beerenwinkel, Niko

Delgado-Eckert, Edgar; Ojosnegros, Samuel; Beerenwinkel, Niko (2011). The Evolution of Virulence in RNA Viruses under a Competition–Colonization Trade-Off. Bulletin of Mathematical Biology, 73(8):1881-1908.

Benecke, Arndt

Bailly-Bechet, Marc; Benecke, Arndt; Hardt, Wolf Dietrich; Lanza, Valentina; Sturm, Alexander; Zecchina, Riccardo (2011). An externally modulated, noise-driven switch for the regulation of SPI1 in Salmonella enterica serovar Typhimurium. Journal of Mathematical Biology, 63(4):637-662.

Benkova, E

Guenot, B; Bayer, E; Kierzkowski, D; Smith, R S; Mandel, T; Zadnikova, P; Benkova, E; Kuhlemeier, C (2012). PIN1-Independent Leaf Initiation in Arabidopsis. Plant Physiology, 159(4):1501-1510.

Bergdorf, M

Milde, F; Bergdorf, M; Koumoutsakos, P (2008). A hybrid model for three-dimensional simulations of sprouting angiogenesis. Biophysical journal, 95(7):3146-60.

Bergmann, Sven

Hamaratoglu, Fisun; Morton de Lachapelle, Aitana; Pyrowolakis, George; Bergmann, Sven; Affolter, Markus (2011). Dpp signaling activity requires pentagone to scale with tissue size in the growing drosophila wing imaginal disc. PLoS Biology, 9:1-17.

Bernard, Thomas

Bernard, Thomas; Bridge, Alan; Morgat, Anne; Moretti, Sébastien; Xenarios, Ioannis; Pagni, Marco (2014). Reconciliation of metabolites and biochemical reactions for metabolic networks. Briefings in Bioinformatics, 15(1):123-135.

Bernasconi, D

Bonhoure, N; Bounova, G; Bernasconi, D; Praz, V; Lammers, F; Canella, D; Willis, I M; Herr, W; Hernandez, N; Delorenzi, M; Hernandez, N; Delorenzi, M; Deplancke, B; Desvergne, B; Guex, N; Herr, W; Naef, F; Rougemont, J; Schibler, U; Andersin, T; Cousin, P; Gilardi, F; Gos, P; Lammers, F; Raghav, S; Villeneuve, D; Fabbretti, R; Vlegel, V; Xenarios, I; Migliavacca, E; Praz, V; David, F; Jarosz, Y; Kuznetsov, D; Liechti, R; Martin, O; Delafontaine, J; Cajan, J; Gustafson, K; Krier, I; Leleu, M; Molina, N; Naldi, A; Rib, L; Symul, L; Bounova, G (2014). Quantifying ChIP-seq data: a spiking method providing an internal reference for sample-to-sample normalization. Genome Research, 24(7):1157-1168.

Bevilacqua, Alessandro

Smith, Kevin; Li, Yunpeng; Piccinini, Filippo; Csucs, Gabor; Balazs, Csaba; Bevilacqua, Alessandro; Horvath, Peter (2015). CIDRE: an illumination-correction method for optical microscopy. Nature Methods, 12(5):404-406.

Bieri, Andrej

Ramakrishnan, Chandrasekhar; Bieri, Andrej; Sauter, Nora; Roizard, Sophie; Ringler, Philippe; Müller, Shirley A; Goldie, Kenneth N; Enimanev, Kaloyan; Stahlberg, Henning; Rinn, Bernd; Braun, Thomas (2014). openBEB: open biological experiment browser for correlative measurements. BMC Bioinformatics, 15:84.

Binda, Matteo

Dechant, Reinhard; Binda, Matteo; Lee, Sung Sik; Pelet, Serge; Winderickx, Joris; Peter, Matthias (2010). Cytosolic pH is a second messenger for glucose and regulates the PKA pathway through V‐ATPase. EMBO Journal Online, 29(15):2515-2526.

Biville, Francis

Vayssier-Taussat, Muriel; Le Rhun, Danielle; Deng, Hong Kuan; Biville, Francis; Cescau, Sandra; Danchin, Antoine; Marignac, Geneviève; Lenaour, Evelyne; Boulouis, Henri Jean; Mavris, Maria; Arnaud, Lionel; Yang, Huanming; Wang, Jing; Quebatte, Maxime; Engel, Philipp; Saenz, Henri; Dehio, Christoph (2010). The Trw Type IV Secretion System of Bartonella Mediates Host-Specific Adhesion to Erythrocytes. PLoS Pathogens, 6(6):e1000946.

Blanc, Mathieu

Blaskovic, Sanja; Blanc, Mathieu; van der Goot, F Gisou (2013). What does S-palmitoylation do to membrane proteins? FEBS Journal, 280(12):2766-2774.

Blaskovic, Sanja

Blaskovic, Sanja; Blanc, Mathieu; van der Goot, F Gisou (2013). What does S-palmitoylation do to membrane proteins? FEBS Journal, 280(12):2766-2774.

Bleck, C K

Kudryashev, M; Stenta, M; Schmelz, S; Amstutz, M; Wiesand, U; Castano-Diez, D; Degiacomi, M T; Munnich, S; Bleck, C K; Kowal, J; Diepold, A; Heinz, D W; Dal Peraro, M; Cornelis, G R; Stahlberg, H (2013). In situ structural analysis of the Yersinia enterocolitica injectisome. eLife, 2:e00792-e00792.

Bleck, Christopher Karl Ernst

Schmidt, Florian Ingo; Bleck, Christopher Karl Ernst; Helenius, Ari; Mercer, Jason (2011). Vaccinia extracellular virions enter cells by macropinocytosis and acid-activated membrane rupture. EMBO Journal Online, 30(17):3647-3661.

Bock, T

Hofmann, A; Gerrits, B; Schmidt, A; Bock, T; Bausch-Fluck, D; Aebersold, R; Wollscheid, B (2010). Proteomic cell surface phenotyping of differentiating acute myeloid leukemia cells. Blood, 116(13):e26-34.

Boekema, E J

Dudkina, N V; Kudryashev, M; Stahlberg, H; Boekema, E J (2011). Interaction of complexes I, III, and IV within the bovine respirasome by single particle cryoelectron tomography. Proceedings of the National Academy of Sciences of the United States of America, 108(37):15196-15200.

Bonde, Marie Mi

Bonde, Marie Mi; Voegeli, Sylvia; Baudrimont, Antoine; Seraphin, Bertrand; Becskei, Attila (2014). Quantification of pre-mRNA escape rate and synergy in splicing. Nucleic Acids Research, 42(20):12847-12860.

Bonhoure, N

Bonhoure, N; Bounova, G; Bernasconi, D; Praz, V; Lammers, F; Canella, D; Willis, I M; Herr, W; Hernandez, N; Delorenzi, M; Hernandez, N; Delorenzi, M; Deplancke, B; Desvergne, B; Guex, N; Herr, W; Naef, F; Rougemont, J; Schibler, U; Andersin, T; Cousin, P; Gilardi, F; Gos, P; Lammers, F; Raghav, S; Villeneuve, D; Fabbretti, R; Vlegel, V; Xenarios, I; Migliavacca, E; Praz, V; David, F; Jarosz, Y; Kuznetsov, D; Liechti, R; Martin, O; Delafontaine, J; Cajan, J; Gustafson, K; Krier, I; Leleu, M; Molina, N; Naldi, A; Rib, L; Symul, L; Bounova, G (2014). Quantifying ChIP-seq data: a spiking method providing an internal reference for sample-to-sample normalization. Genome Research, 24(7):1157-1168.

Boulouis, Henri Jean

Vayssier-Taussat, Muriel; Le Rhun, Danielle; Deng, Hong Kuan; Biville, Francis; Cescau, Sandra; Danchin, Antoine; Marignac, Geneviève; Lenaour, Evelyne; Boulouis, Henri Jean; Mavris, Maria; Arnaud, Lionel; Yang, Huanming; Wang, Jing; Quebatte, Maxime; Engel, Philipp; Saenz, Henri; Dehio, Christoph (2010). The Trw Type IV Secretion System of Bartonella Mediates Host-Specific Adhesion to Erythrocytes. PLoS Pathogens, 6(6):e1000946.

Bounova, G

Bonhoure, N; Bounova, G; Bernasconi, D; Praz, V; Lammers, F; Canella, D; Willis, I M; Herr, W; Hernandez, N; Delorenzi, M; Hernandez, N; Delorenzi, M; Deplancke, B; Desvergne, B; Guex, N; Herr, W; Naef, F; Rougemont, J; Schibler, U; Andersin, T; Cousin, P; Gilardi, F; Gos, P; Lammers, F; Raghav, S; Villeneuve, D; Fabbretti, R; Vlegel, V; Xenarios, I; Migliavacca, E; Praz, V; David, F; Jarosz, Y; Kuznetsov, D; Liechti, R; Martin, O; Delafontaine, J; Cajan, J; Gustafson, K; Krier, I; Leleu, M; Molina, N; Naldi, A; Rib, L; Symul, L; Bounova, G (2014). Quantifying ChIP-seq data: a spiking method providing an internal reference for sample-to-sample normalization. Genome Research, 24(7):1157-1168.

Bonhoure, N; Bounova, G; Bernasconi, D; Praz, V; Lammers, F; Canella, D; Willis, I M; Herr, W; Hernandez, N; Delorenzi, M; Hernandez, N; Delorenzi, M; Deplancke, B; Desvergne, B; Guex, N; Herr, W; Naef, F; Rougemont, J; Schibler, U; Andersin, T; Cousin, P; Gilardi, F; Gos, P; Lammers, F; Raghav, S; Villeneuve, D; Fabbretti, R; Vlegel, V; Xenarios, I; Migliavacca, E; Praz, V; David, F; Jarosz, Y; Kuznetsov, D; Liechti, R; Martin, O; Delafontaine, J; Cajan, J; Gustafson, K; Krier, I; Leleu, M; Molina, N; Naldi, A; Rib, L; Symul, L; Bounova, G (2014). Quantifying ChIP-seq data: a spiking method providing an internal reference for sample-to-sample normalization. Genome Research, 24(7):1157-1168.

Brankatschk, B

Brankatschk, B; Wichert, S P; Johnson, S D; Schaad, O; Rossner, M J; Gruenberg, J (2012). Regulation of the EGF Transcriptional Response by Endocytic Sorting. Science Signaling, 5(215):ra21.

Brankatschk, Ben

Brankatschk, Ben; Pons, Véronique; Parton, Robert G; Gruenberg, Jean (2011). Role of SNX16 in the dynamics of tubulo-cisternal membrane domains of late endosomes. PLoS ONE, 6(7):e21771.

Braun, Thomas

Giss, Dominic; Kemmerling, Simon; Dandey, Venkata; Stahlberg, Henning; Braun, Thomas (2014). Exploring the interactome: microfluidic isolation of proteins and interacting partners for quantitative analysis by electron microscopy. Analytical Chemistry, 86(10):4680-4687.

Ramakrishnan, Chandrasekhar; Bieri, Andrej; Sauter, Nora; Roizard, Sophie; Ringler, Philippe; Müller, Shirley A; Goldie, Kenneth N; Enimanev, Kaloyan; Stahlberg, Henning; Rinn, Bernd; Braun, Thomas (2014). openBEB: open biological experiment browser for correlative measurements. BMC Bioinformatics, 15:84.

Braybrook, S A

Chitwood, D H; Headland, L R; Ranjan, A; Martinez, C C; Braybrook, S A; Koenig, D P; Kuhlemeier, C; Smith, R S; Sinha, N R (2012). Leaf Asymmetry as a Developmental Constraint Imposed by Auxin-Dependent Phyllotactic Patterning. Plant Cell, 24(6):2318-2327.

Bridge, Alan

Bernard, Thomas; Bridge, Alan; Morgat, Anne; Moretti, Sébastien; Xenarios, Ioannis; Pagni, Marco (2014). Reconciliation of metabolites and biochemical reactions for metabolic networks. Briefings in Bioinformatics, 15(1):123-135.

Bumann, Dirk

Steeb, Benjamin; Claudi, Beatrice; Burton, Neil A; Tienz, Petra; Schmidt, Alexander; Farhan, Hesso; Mazé, Alain; Bumann, Dirk (2013). Parallel Exploitation of Diverse Host Nutrients Enhances Salmonella Virulence. PLoS Pathogens, 9(4):e1003301.

Mary, Camille; Duek, Paula; Salleron, Lisa; Tienz, Petra; Bumann, Dirk; Bairoch, Amos; Lane, Lydie (2012). Functional Identification of APIP as Human mtnB, a Key Enzyme in the Methionine Salvage Pathway. PLoS ONE, 7(12):e52877.

Burton, Neil A

Steeb, Benjamin; Claudi, Beatrice; Burton, Neil A; Tienz, Petra; Schmidt, Alexander; Farhan, Hesso; Mazé, Alain; Bumann, Dirk (2013). Parallel Exploitation of Diverse Host Nutrients Enhances Salmonella Virulence. PLoS Pathogens, 9(4):e1003301.

Busetto, Alberto Giovanni

Sunnåker, Mikael; Zamora-Sillero, Elias; Dechant, Reinhard; Ludwig, Christina; Busetto, Alberto Giovanni; Wagner, Andreas; Stelling, Joerg (2013). Automatic Generation of Predictive Dynamic Models Reveals Nuclear Phosphorylation as the Key Msn2 Control Mechanism. Science Signaling, 6(277):ra41.

Büyükkeçeci, Ferit

Awile, Omar; Büyükkeçeci, Ferit; Reboux, Sylvain; Sbalzarini, Ivo F (2012). Fast neighbor lists for adaptive-resolution particle simulations. Computer Physics Communications, 183(5):1073-1081.

Cajan, J

Bonhoure, N; Bounova, G; Bernasconi, D; Praz, V; Lammers, F; Canella, D; Willis, I M; Herr, W; Hernandez, N; Delorenzi, M; Hernandez, N; Delorenzi, M; Deplancke, B; Desvergne, B; Guex, N; Herr, W; Naef, F; Rougemont, J; Schibler, U; Andersin, T; Cousin, P; Gilardi, F; Gos, P; Lammers, F; Raghav, S; Villeneuve, D; Fabbretti, R; Vlegel, V; Xenarios, I; Migliavacca, E; Praz, V; David, F; Jarosz, Y; Kuznetsov, D; Liechti, R; Martin, O; Delafontaine, J; Cajan, J; Gustafson, K; Krier, I; Leleu, M; Molina, N; Naldi, A; Rib, L; Symul, L; Bounova, G (2014). Quantifying ChIP-seq data: a spiking method providing an internal reference for sample-to-sample normalization. Genome Research, 24(7):1157-1168.

Canella, D

Bonhoure, N; Bounova, G; Bernasconi, D; Praz, V; Lammers, F; Canella, D; Willis, I M; Herr, W; Hernandez, N; Delorenzi, M; Hernandez, N; Delorenzi, M; Deplancke, B; Desvergne, B; Guex, N; Herr, W; Naef, F; Rougemont, J; Schibler, U; Andersin, T; Cousin, P; Gilardi, F; Gos, P; Lammers, F; Raghav, S; Villeneuve, D; Fabbretti, R; Vlegel, V; Xenarios, I; Migliavacca, E; Praz, V; David, F; Jarosz, Y; Kuznetsov, D; Liechti, R; Martin, O; Delafontaine, J; Cajan, J; Gustafson, K; Krier, I; Leleu, M; Molina, N; Naldi, A; Rib, L; Symul, L; Bounova, G (2014). Quantifying ChIP-seq data: a spiking method providing an internal reference for sample-to-sample normalization. Genome Research, 24(7):1157-1168.

Canella, Donatella

Gilardi, Federica; Migliavacca, Eugenia; Naldi, Aurélien; Baruchet, Michaël; Canella, Donatella; Le Martelot, Gwendal; Guex, Nicolas; Desvergne, Béatrice (2014). Genome-Wide Analysis of SREBP1 Activity around the Clock Reveals Its Combined Dependency on Nutrient and Circadian Signals. PLoS Genetics, 10(3):e1004155.

Le Martelot, Gwendal; Canella, Donatella; Symul, Laura; Migliavacca, Eugenia; Gilardi, Federica; Liechti, Robin; Martin, Olivier; Harshman, Keith; Delorenzi, Mauro; Desvergne, Béatrice; Herr, Winship; Deplancke, Bart; Schibler, Ueli; Rougemont, Jacques; Guex, Nicolas; Hernandez, Nouria; Naef, Felix (2012). Genome-wide RNA polymerase II profiles and RNA accumulation reveal kinetics of transcription and associated epigenetic changes during diurnal cycles. PLoS Biology, 10(11):e1001442.

Cardini, Steven

Vonaesch, Pascale; Cardini, Steven; Sellin, Mikael E; Goud, Bruno; Hardt, Wolf-Dietrich; Schauer, Kristine (2013). Quantitative insights into actin rearrangements and bacterial target site selection fromSalmonella Typhimurium infection of micropatterned cells. Cellular Microbiology, 15(11):1851-1865.

Castano-Diez, D

Kudryashev, M; Stenta, M; Schmelz, S; Amstutz, M; Wiesand, U; Castano-Diez, D; Degiacomi, M T; Munnich, S; Bleck, C K; Kowal, J; Diepold, A; Heinz, D W; Dal Peraro, M; Cornelis, G R; Stahlberg, H (2013). In situ structural analysis of the Yersinia enterocolitica injectisome. eLife, 2:e00792-e00792.

Castaño-Díez, Daniel

Kudryashev, Mikhail; Castaño-Díez, Daniel; Stahlberg, Henning (2012). Limiting factors in single particle cryo electron tomography. Computational and Structural Biotechnology Journal, 1(2):online.

Cescau, Sandra

Vayssier-Taussat, Muriel; Le Rhun, Danielle; Deng, Hong Kuan; Biville, Francis; Cescau, Sandra; Danchin, Antoine; Marignac, Geneviève; Lenaour, Evelyne; Boulouis, Henri Jean; Mavris, Maria; Arnaud, Lionel; Yang, Huanming; Wang, Jing; Quebatte, Maxime; Engel, Philipp; Saenz, Henri; Dehio, Christoph (2010). The Trw Type IV Secretion System of Bartonella Mediates Host-Specific Adhesion to Erythrocytes. PLoS Pathogens, 6(6):e1000946.

Chami, Mohamed

Goldie, Kenneth N; Abeyrathne, Priyanka; Kebbel, Fabian; Chami, Mohamed; Ringler, Philippe; Stahlberg, Henning (2014). Cryo-electron microscopy of membrane proteins. Methods in Molecular Biology, 1117:325-41.

Kowal, Julia; Chami, Mohamed; Baumgartner, Paul; Arheit, Marcel; Chiu, Po-Lin; Rangl, Martina; Scheuring, Simon; Schröder, Gunnar F; Nimigean, Crina M; Stahlberg, Henning (2014). Ligand-induced structural changes in the cyclic nucleotide-modulated potassium channel MloK1. Nature Communications, 5:3106.

Chatelain, P

Bayati, B; Chatelain, P; Koumoutsakos, P (2009). D-leaping: Accelerating stochastic simulation algorithms for reactions with delays. Journal of Computational Physics, 228(16):5908-5916.

Mjolsness, E; Orendorff, D; Chatelain, P; Koumoutsakos, P (2009). An exact accelerated stochastic simulation algorithm. The Journal of chemical physics, 130(14):144110.

Cheng, Danni

Cheng, Danni; Jenner, Andrew M; Shui, Guanghou; Cheong, Wei Fun; Mitchell, Todd W; Nealon, Jessica R; Kim, Woojin S; McCann, Heather; Wenk, Markus R; Halliday, Glenda M; Garner, Brett (2011). Lipid pathway alterations in Parkinson's disease primary visual cortex. PLoS ONE, 6(2):e17299.

Cheong, Wei Fun

Cheng, Danni; Jenner, Andrew M; Shui, Guanghou; Cheong, Wei Fun; Mitchell, Todd W; Nealon, Jessica R; Kim, Woojin S; McCann, Heather; Wenk, Markus R; Halliday, Glenda M; Garner, Brett (2011). Lipid pathway alterations in Parkinson's disease primary visual cortex. PLoS ONE, 6(2):e17299.

Chitwood, D H

Chitwood, D H; Headland, L R; Ranjan, A; Martinez, C C; Braybrook, S A; Koenig, D P; Kuhlemeier, C; Smith, R S; Sinha, N R (2012). Leaf Asymmetry as a Developmental Constraint Imposed by Auxin-Dependent Phyllotactic Patterning. Plant Cell, 24(6):2318-2327.

Chiu, Po-Lin

Kowal, Julia; Chami, Mohamed; Baumgartner, Paul; Arheit, Marcel; Chiu, Po-Lin; Rangl, Martina; Scheuring, Simon; Schröder, Gunnar F; Nimigean, Crina M; Stahlberg, Henning (2014). Ligand-induced structural changes in the cyclic nucleotide-modulated potassium channel MloK1. Nature Communications, 5:3106.

Chong, Siow-Feng

Andreasen, Sidsel Ø; Chong, Siow-Feng; Wohl, Benjamin M; Goldie, Kenneth N; Zelikin, Alexander N (2013). Poly(vinyl alcohol) physical hydrogel nanoparticles, not polymer solutions, exert inhibition of nitric oxide synthesis in cultured macrophages. Biomacromolecules, 14(5):1687-95.

Christofori, Gerhard

Tiwari, Neha; Meyer-Schaller, Nathalie; Arnold, Phil; Antoniadis, Helena; Pachkov, Mikhail; van Nimwegen, Erik; Christofori, Gerhard (2013). Klf4 is a transcriptional regulator of genes critical for EMT, including Jnk1 (Mapk8). PLoS ONE, 8(2):e57329.

Tiwari, Neha; Tiwari, Vijay K; Waldmeier, Lorenz; Balwierz, Piotr J; Arnold, Phil; Pachkov, Mikhail; Meyer-Schaller, Nathalie; Schübeler, Dirk; van Nimwegen, Erik; Christofori, Gerhard (2013). Sox4 is a master regulator of epithelial-mesenchymal transition by controlling ezh2 expression and epigenetic reprogramming. Cancer Cell, 23(6):768-83.

Cinquemani, Eugenio

Cinquemani, Eugenio; Milias-Argeitis, Andreas; Summers, Sean; Lygeros, John (2008). Stochastic dynamics of genetic networks: modelling and parameter identification. Bioinformatics, 24(23):2748-2754.

Cioffi, Carla

Hermes, Jens P; Sander, Fabian; Peterle, Torsten; Cioffi, Carla; Ringler, Philippe; Pfohl, Thomas; Mayor, Marcel (2011). Direct control of the spatial arrangement of gold nanoparticles in organic-inorganic hybrid superstructures. Small, 7(7):920-9.

Claudi, Beatrice

Steeb, Benjamin; Claudi, Beatrice; Burton, Neil A; Tienz, Petra; Schmidt, Alexander; Farhan, Hesso; Mazé, Alain; Bumann, Dirk (2013). Parallel Exploitation of Diverse Host Nutrients Enhances Salmonella Virulence. PLoS Pathogens, 9(4):e1003301.

Conley, Gaurasundar M

Spühler, Isabelle A; Conley, Gaurasundar M; Scheffold, Frank; Sprecher, Simon G (2016). Super resolution imaging of genetically labeled synapses in drosophila brain tissue. Frontiers in Cellular Neuroscience:10:142.

Cornelis, G R

Kudryashev, M; Stenta, M; Schmelz, S; Amstutz, M; Wiesand, U; Castano-Diez, D; Degiacomi, M T; Munnich, S; Bleck, C K; Kowal, J; Diepold, A; Heinz, D W; Dal Peraro, M; Cornelis, G R; Stahlberg, H (2013). In situ structural analysis of the Yersinia enterocolitica injectisome. eLife, 2:e00792-e00792.

Cousin, P

Bonhoure, N; Bounova, G; Bernasconi, D; Praz, V; Lammers, F; Canella, D; Willis, I M; Herr, W; Hernandez, N; Delorenzi, M; Hernandez, N; Delorenzi, M; Deplancke, B; Desvergne, B; Guex, N; Herr, W; Naef, F; Rougemont, J; Schibler, U; Andersin, T; Cousin, P; Gilardi, F; Gos, P; Lammers, F; Raghav, S; Villeneuve, D; Fabbretti, R; Vlegel, V; Xenarios, I; Migliavacca, E; Praz, V; David, F; Jarosz, Y; Kuznetsov, D; Liechti, R; Martin, O; Delafontaine, J; Cajan, J; Gustafson, K; Krier, I; Leleu, M; Molina, N; Naldi, A; Rib, L; Symul, L; Bounova, G (2014). Quantifying ChIP-seq data: a spiking method providing an internal reference for sample-to-sample normalization. Genome Research, 24(7):1157-1168.

Creek, Darren J

Limenitakis, Julien; Oppenheim, Rebecca D; Creek, Darren J; Foth, Bernardo J; Barrett, Michael P; Soldati-Favre, Dominique (2013). The 2-methylcitrate cycle is implicated in the detoxification of propionate in Toxoplasma gondii. Molecular Microbiology, 87(4):894-908.

Cremonesi, Alessio

Soulard, Alexandre; Cremonesi, Alessio; Moes, Suzette; Schütz, Frédéric; Jenö, Paul; Hall, Michael N (2010). The Rapamycin-sensitive Phosphoproteome Reveals That TOR Controls Protein Kinase A Toward Some But Not All Substrates. Molecular Biology of the Cell, 21:3475-3486.

Crevecoeur, M

Samol, I; Shapiguzov, A; Ingelsson, B; Fucile, G; Crevecoeur, M; Vener, A V; Rochaix, J -D; Goldschmidt-Clermont, M (2012). Identification of a Photosystem II Phosphatase Involved in Light Acclimation in Arabidopsis. Plant Cell, 24(6):2596-2609.

Critchley, D R

Truttmann, M C; Misselwitz, B; Huser, S; Hardt, W-D; Critchley, D R; Dehio, C (2011). Bartonella henselae engages inside-out and outside-in signaling by integrin 1 and talin1 during invasome-mediated bacterial uptake. Journal of Cell Science, 124(21):3591-3602.

Csucs, Gabor

Smith, Kevin; Li, Yunpeng; Piccinini, Filippo; Csucs, Gabor; Balazs, Csaba; Bevilacqua, Alessandro; Horvath, Peter (2015). CIDRE: an illumination-correction method for optical microscopy. Nature Methods, 12(5):404-406.

Dal Peraro, M

Kudryashev, M; Stenta, M; Schmelz, S; Amstutz, M; Wiesand, U; Castano-Diez, D; Degiacomi, M T; Munnich, S; Bleck, C K; Kowal, J; Diepold, A; Heinz, D W; Dal Peraro, M; Cornelis, G R; Stahlberg, H (2013). In situ structural analysis of the Yersinia enterocolitica injectisome. eLife, 2:e00792-e00792.

Danchin, Antoine

Vayssier-Taussat, Muriel; Le Rhun, Danielle; Deng, Hong Kuan; Biville, Francis; Cescau, Sandra; Danchin, Antoine; Marignac, Geneviève; Lenaour, Evelyne; Boulouis, Henri Jean; Mavris, Maria; Arnaud, Lionel; Yang, Huanming; Wang, Jing; Quebatte, Maxime; Engel, Philipp; Saenz, Henri; Dehio, Christoph (2010). The Trw Type IV Secretion System of Bartonella Mediates Host-Specific Adhesion to Erythrocytes. PLoS Pathogens, 6(6):e1000946.

Dandey, Venkata

Giss, Dominic; Kemmerling, Simon; Dandey, Venkata; Stahlberg, Henning; Braun, Thomas (2014). Exploring the interactome: microfluidic isolation of proteins and interacting partners for quantitative analysis by electron microscopy. Analytical Chemistry, 86(10):4680-4687.

David, F

Bonhoure, N; Bounova, G; Bernasconi, D; Praz, V; Lammers, F; Canella, D; Willis, I M; Herr, W; Hernandez, N; Delorenzi, M; Hernandez, N; Delorenzi, M; Deplancke, B; Desvergne, B; Guex, N; Herr, W; Naef, F; Rougemont, J; Schibler, U; Andersin, T; Cousin, P; Gilardi, F; Gos, P; Lammers, F; Raghav, S; Villeneuve, D; Fabbretti, R; Vlegel, V; Xenarios, I; Migliavacca, E; Praz, V; David, F; Jarosz, Y; Kuznetsov, D; Liechti, R; Martin, O; Delafontaine, J; Cajan, J; Gustafson, K; Krier, I; Leleu, M; Molina, N; Naldi, A; Rib, L; Symul, L; Bounova, G (2014). Quantifying ChIP-seq data: a spiking method providing an internal reference for sample-to-sample normalization. Genome Research, 24(7):1157-1168.

David, Fabrice P A

Loizides-Mangold, Ursula; David, Fabrice P A; Nesatyy, Victor J; Kinoshita, Taroh; Riezman, Howard (2012). Glycosylphosphatidylinositol anchors regulate glycosphingolipid levels. Journal of Lipid Research, 53(8):1522-34.

De Strooper, Bart

Papadopoulou, Aikaterini S; Dooley, James; Linterman, Michelle A; Pierson, Wim; Ucar, Olga; Kyewski, Bruno; Zuklys, Saulius; Hollander, Georg A; Matthys, Patrick; Gray, Daniel H D; De Strooper, Bart; Liston, Adrian (2011). The thymic epithelial microRNA network elevates the threshold for infection-associated thymic involution via miR-29a mediated suppression of the IFN-α receptor. Nature Immunology, 13(2):181-187.

Dechant, Reinhard

Sunnåker, Mikael; Zamora-Sillero, Elias; Dechant, Reinhard; Ludwig, Christina; Busetto, Alberto Giovanni; Wagner, Andreas; Stelling, Joerg (2013). Automatic Generation of Predictive Dynamic Models Reveals Nuclear Phosphorylation as the Key Msn2 Control Mechanism. Science Signaling, 6(277):ra41.

Dechant, Reinhard; Binda, Matteo; Lee, Sung Sik; Pelet, Serge; Winderickx, Joris; Peter, Matthias (2010). Cytosolic pH is a second messenger for glucose and regulates the PKA pathway through V‐ATPase. EMBO Journal Online, 29(15):2515-2526.

Degiacomi, M T

Kudryashev, M; Stenta, M; Schmelz, S; Amstutz, M; Wiesand, U; Castano-Diez, D; Degiacomi, M T; Munnich, S; Bleck, C K; Kowal, J; Diepold, A; Heinz, D W; Dal Peraro, M; Cornelis, G R; Stahlberg, H (2013). In situ structural analysis of the Yersinia enterocolitica injectisome. eLife, 2:e00792-e00792.

Dehio, C

Truttmann, M C; Misselwitz, B; Huser, S; Hardt, W-D; Critchley, D R; Dehio, C (2011). Bartonella henselae engages inside-out and outside-in signaling by integrin 1 and talin1 during invasome-mediated bacterial uptake. Journal of Cell Science, 124(21):3591-3602.

Dehio, Christoph

Goepfert, Arnaud; Stanger, Frédéric V; Dehio, Christoph; Schirmer, Tilman (2013). Conserved Inhibitory Mechanism and Competent ATP Binding Mode for Adenylyltransferases with Fic Fold. PLoS ONE, 8(5):e64901.

Vayssier-Taussat, Muriel; Le Rhun, Danielle; Deng, Hong Kuan; Biville, Francis; Cescau, Sandra; Danchin, Antoine; Marignac, Geneviève; Lenaour, Evelyne; Boulouis, Henri Jean; Mavris, Maria; Arnaud, Lionel; Yang, Huanming; Wang, Jing; Quebatte, Maxime; Engel, Philipp; Saenz, Henri; Dehio, Christoph (2010). The Trw Type IV Secretion System of Bartonella Mediates Host-Specific Adhesion to Erythrocytes. PLoS Pathogens, 6(6):e1000946.

Dekiwadia, Chaitali

Lemgruber, Leandro; Kudryashev, Mikhail; Dekiwadia, Chaitali; Riglar, David T; Baum, Jake; Stahlberg, Henning; Ralph, Stuart A; Frischknecht, Friedrich (2013). Cryo-electron tomography reveals four-membrane architecture of the Plasmodium apicoplast. Malaria Journal, 12:25.

Delafontaine, J

Bonhoure, N; Bounova, G; Bernasconi, D; Praz, V; Lammers, F; Canella, D; Willis, I M; Herr, W; Hernandez, N; Delorenzi, M; Hernandez, N; Delorenzi, M; Deplancke, B; Desvergne, B; Guex, N; Herr, W; Naef, F; Rougemont, J; Schibler, U; Andersin, T; Cousin, P; Gilardi, F; Gos, P; Lammers, F; Raghav, S; Villeneuve, D; Fabbretti, R; Vlegel, V; Xenarios, I; Migliavacca, E; Praz, V; David, F; Jarosz, Y; Kuznetsov, D; Liechti, R; Martin, O; Delafontaine, J; Cajan, J; Gustafson, K; Krier, I; Leleu, M; Molina, N; Naldi, A; Rib, L; Symul, L; Bounova, G (2014). Quantifying ChIP-seq data: a spiking method providing an internal reference for sample-to-sample normalization. Genome Research, 24(7):1157-1168.

Delgado-Eckert, Edgar

Delgado-Eckert, Edgar; Ojosnegros, Samuel; Beerenwinkel, Niko (2011). The Evolution of Virulence in RNA Viruses under a Competition–Colonization Trade-Off. Bulletin of Mathematical Biology, 73(8):1881-1908.

Delgado-Gonzalo, R

Delgado-Gonzalo, R; Unser, M (2013). Spline-based framework for interactive segmentation in biomedical imaging. IRBM, 34(3):235-243.

Delgado-Gonzalo, R; Thévenaz, P; Unser, M (2012). Exponential splines and minimal-support bases for curve representation. Computer Aided Geometric Design, 29(2):109-128.

Delgado-Gonzalo, Ricard

Delgado-Gonzalo, Ricard; Thévenaz, Philippe; Seelamantula, Chandra Sekhar; Unser, Michael (2012). Snakes with an ellipse-reproducing property. IEEE transactions on image processing : a publication of the IEEE Signal Processing Society, 21(3):1258-71.

Delorenzi, M

Bonhoure, N; Bounova, G; Bernasconi, D; Praz, V; Lammers, F; Canella, D; Willis, I M; Herr, W; Hernandez, N; Delorenzi, M; Hernandez, N; Delorenzi, M; Deplancke, B; Desvergne, B; Guex, N; Herr, W; Naef, F; Rougemont, J; Schibler, U; Andersin, T; Cousin, P; Gilardi, F; Gos, P; Lammers, F; Raghav, S; Villeneuve, D; Fabbretti, R; Vlegel, V; Xenarios, I; Migliavacca, E; Praz, V; David, F; Jarosz, Y; Kuznetsov, D; Liechti, R; Martin, O; Delafontaine, J; Cajan, J; Gustafson, K; Krier, I; Leleu, M; Molina, N; Naldi, A; Rib, L; Symul, L; Bounova, G (2014). Quantifying ChIP-seq data: a spiking method providing an internal reference for sample-to-sample normalization. Genome Research, 24(7):1157-1168.

Bonhoure, N; Bounova, G; Bernasconi, D; Praz, V; Lammers, F; Canella, D; Willis, I M; Herr, W; Hernandez, N; Delorenzi, M; Hernandez, N; Delorenzi, M; Deplancke, B; Desvergne, B; Guex, N; Herr, W; Naef, F; Rougemont, J; Schibler, U; Andersin, T; Cousin, P; Gilardi, F; Gos, P; Lammers, F; Raghav, S; Villeneuve, D; Fabbretti, R; Vlegel, V; Xenarios, I; Migliavacca, E; Praz, V; David, F; Jarosz, Y; Kuznetsov, D; Liechti, R; Martin, O; Delafontaine, J; Cajan, J; Gustafson, K; Krier, I; Leleu, M; Molina, N; Naldi, A; Rib, L; Symul, L; Bounova, G (2014). Quantifying ChIP-seq data: a spiking method providing an internal reference for sample-to-sample normalization. Genome Research, 24(7):1157-1168.

Delorenzi, Mauro

Le Martelot, Gwendal; Canella, Donatella; Symul, Laura; Migliavacca, Eugenia; Gilardi, Federica; Liechti, Robin; Martin, Olivier; Harshman, Keith; Delorenzi, Mauro; Desvergne, Béatrice; Herr, Winship; Deplancke, Bart; Schibler, Ueli; Rougemont, Jacques; Guex, Nicolas; Hernandez, Nouria; Naef, Felix (2012). Genome-wide RNA polymerase II profiles and RNA accumulation reveal kinetics of transcription and associated epigenetic changes during diurnal cycles. PLoS Biology, 10(11):e1001442.

Demirel, Ömer

Awile, Omar; Demirel, Ömer; Sbalzarini, Ivo F; Simos, Theodore E; Psihoyios, George; Tsitouras, Ch (2010). Toward an Object-Oriented Core of the PPM Library. In: International Conference of Numerical Analysis and Applied Mathematics (ICNAAM), Rhodes, Greece, 19 September 2010 - 25 September 2010, 1313-1316.

Deng, Hong Kuan

Vayssier-Taussat, Muriel; Le Rhun, Danielle; Deng, Hong Kuan; Biville, Francis; Cescau, Sandra; Danchin, Antoine; Marignac, Geneviève; Lenaour, Evelyne; Boulouis, Henri Jean; Mavris, Maria; Arnaud, Lionel; Yang, Huanming; Wang, Jing; Quebatte, Maxime; Engel, Philipp; Saenz, Henri; Dehio, Christoph (2010). The Trw Type IV Secretion System of Bartonella Mediates Host-Specific Adhesion to Erythrocytes. PLoS Pathogens, 6(6):e1000946.

Deplancke, B

Bonhoure, N; Bounova, G; Bernasconi, D; Praz, V; Lammers, F; Canella, D; Willis, I M; Herr, W; Hernandez, N; Delorenzi, M; Hernandez, N; Delorenzi, M; Deplancke, B; Desvergne, B; Guex, N; Herr, W; Naef, F; Rougemont, J; Schibler, U; Andersin, T; Cousin, P; Gilardi, F; Gos, P; Lammers, F; Raghav, S; Villeneuve, D; Fabbretti, R; Vlegel, V; Xenarios, I; Migliavacca, E; Praz, V; David, F; Jarosz, Y; Kuznetsov, D; Liechti, R; Martin, O; Delafontaine, J; Cajan, J; Gustafson, K; Krier, I; Leleu, M; Molina, N; Naldi, A; Rib, L; Symul, L; Bounova, G (2014). Quantifying ChIP-seq data: a spiking method providing an internal reference for sample-to-sample normalization. Genome Research, 24(7):1157-1168.

Deplancke, Bart

Simicevic, Jovan; Schmid, Adrien W; Gilardoni, Paola A; Zoller, Benjamin; Raghav, Sunil K; Krier, Irina; Gubelmann, Carinne; Lisacek, Frédérique; Naef, Felix; Moniatte, Marc; Deplancke, Bart (2013). Absolute quantification of transcription factors during cellular differentiation using multiplexed targeted proteomics. Nature Methods, 10(6):570-576.

Rockel, Sylvie; Geertz, Marcel; Hens, Korneel; Deplancke, Bart; Maerkl, Sebastian J (2012). iSLIM: a comprehensive approach to mapping and characterizing gene regulatory networks. Nucleic Acids Research:1-8.

Schröter, Christian; Ares, Saúl; Morelli, Luis G; Isakova, Alina; Hens, Korneel; Soroldoni, Daniele; Gajewski, Martin; Jülicher, Frank; Maerkl, Sebastian J; Deplancke, Bart; Oates, Andrew C (2012). Topology and Dynamics of the Zebrafish Segmentation Clock Core Circuit. PLoS Biology, 10(7):1-20.

Le Martelot, Gwendal; Canella, Donatella; Symul, Laura; Migliavacca, Eugenia; Gilardi, Federica; Liechti, Robin; Martin, Olivier; Harshman, Keith; Delorenzi, Mauro; Desvergne, Béatrice; Herr, Winship; Deplancke, Bart; Schibler, Ueli; Rougemont, Jacques; Guex, Nicolas; Hernandez, Nouria; Naef, Felix (2012). Genome-wide RNA polymerase II profiles and RNA accumulation reveal kinetics of transcription and associated epigenetic changes during diurnal cycles. PLoS Biology, 10(11):e1001442.

Desvergne, B

Bonhoure, N; Bounova, G; Bernasconi, D; Praz, V; Lammers, F; Canella, D; Willis, I M; Herr, W; Hernandez, N; Delorenzi, M; Hernandez, N; Delorenzi, M; Deplancke, B; Desvergne, B; Guex, N; Herr, W; Naef, F; Rougemont, J; Schibler, U; Andersin, T; Cousin, P; Gilardi, F; Gos, P; Lammers, F; Raghav, S; Villeneuve, D; Fabbretti, R; Vlegel, V; Xenarios, I; Migliavacca, E; Praz, V; David, F; Jarosz, Y; Kuznetsov, D; Liechti, R; Martin, O; Delafontaine, J; Cajan, J; Gustafson, K; Krier, I; Leleu, M; Molina, N; Naldi, A; Rib, L; Symul, L; Bounova, G (2014). Quantifying ChIP-seq data: a spiking method providing an internal reference for sample-to-sample normalization. Genome Research, 24(7):1157-1168.

Desvergne, Béatrice

Gilardi, Federica; Migliavacca, Eugenia; Naldi, Aurélien; Baruchet, Michaël; Canella, Donatella; Le Martelot, Gwendal; Guex, Nicolas; Desvergne, Béatrice (2014). Genome-Wide Analysis of SREBP1 Activity around the Clock Reveals Its Combined Dependency on Nutrient and Circadian Signals. PLoS Genetics, 10(3):e1004155.

Le Martelot, Gwendal; Canella, Donatella; Symul, Laura; Migliavacca, Eugenia; Gilardi, Federica; Liechti, Robin; Martin, Olivier; Harshman, Keith; Delorenzi, Mauro; Desvergne, Béatrice; Herr, Winship; Deplancke, Bart; Schibler, Ueli; Rougemont, Jacques; Guex, Nicolas; Hernandez, Nouria; Naef, Felix (2012). Genome-wide RNA polymerase II profiles and RNA accumulation reveal kinetics of transcription and associated epigenetic changes during diurnal cycles. PLoS Biology, 10(11):e1001442.

Diepold, A

Kudryashev, M; Stenta, M; Schmelz, S; Amstutz, M; Wiesand, U; Castano-Diez, D; Degiacomi, M T; Munnich, S; Bleck, C K; Kowal, J; Diepold, A; Heinz, D W; Dal Peraro, M; Cornelis, G R; Stahlberg, H (2013). In situ structural analysis of the Yersinia enterocolitica injectisome. eLife, 2:e00792-e00792.

Dooley, James

Papadopoulou, Aikaterini S; Dooley, James; Linterman, Michelle A; Pierson, Wim; Ucar, Olga; Kyewski, Bruno; Zuklys, Saulius; Hollander, Georg A; Matthys, Patrick; Gray, Daniel H D; De Strooper, Bart; Liston, Adrian (2011). The thymic epithelial microRNA network elevates the threshold for infection-associated thymic involution via miR-29a mediated suppression of the IFN-α receptor. Nature Immunology, 13(2):181-187.

Dudkina, N V

Dudkina, N V; Kudryashev, M; Stahlberg, H; Boekema, E J (2011). Interaction of complexes I, III, and IV within the bovine respirasome by single particle cryoelectron tomography. Proceedings of the National Academy of Sciences of the United States of America, 108(37):15196-15200.

Duek, Paula

Mary, Camille; Duek, Paula; Salleron, Lisa; Tienz, Petra; Bumann, Dirk; Bairoch, Amos; Lane, Lydie (2012). Functional Identification of APIP as Human mtnB, a Key Enzyme in the Methionine Salvage Pathway. PLoS ONE, 7(12):e52877.

Díaz, José Fernando

Prota, Andrea E; Bargsten, Katja; Zurwerra, Didier; Field, Jessica J; Díaz, José Fernando; Altmann, Karl-Heinz; Steinmetz, Michel O (2013). Molecular Mechanism of Action of Microtubule-Stabilizing Anticancer Agents. Science, 339(6119):587-590.

Efremov, Roman G

Polyansky, Anton A; Ramaswamy, Rajesh; Volynsky, Pavel E; Sbalzarini, Ivo F; Marrink, Siewert J; Efremov, Roman G (2010). Antimicrobial Peptides Induce Growth of Phosphatidylglycerol Domains in a Model Bacterial Membrane. Journal of Physical Chemistry Letters, 1(20):3108-3111.

Engel, Philipp

Vayssier-Taussat, Muriel; Le Rhun, Danielle; Deng, Hong Kuan; Biville, Francis; Cescau, Sandra; Danchin, Antoine; Marignac, Geneviève; Lenaour, Evelyne; Boulouis, Henri Jean; Mavris, Maria; Arnaud, Lionel; Yang, Huanming; Wang, Jing; Quebatte, Maxime; Engel, Philipp; Saenz, Henri; Dehio, Christoph (2010). The Trw Type IV Secretion System of Bartonella Mediates Host-Specific Adhesion to Erythrocytes. PLoS Pathogens, 6(6):e1000946.

Enimanev, Kaloyan

Ramakrishnan, Chandrasekhar; Bieri, Andrej; Sauter, Nora; Roizard, Sophie; Ringler, Philippe; Müller, Shirley A; Goldie, Kenneth N; Enimanev, Kaloyan; Stahlberg, Henning; Rinn, Bernd; Braun, Thomas (2014). openBEB: open biological experiment browser for correlative measurements. BMC Bioinformatics, 15:84.

Ewers, Helge

Schoen, Ingmar; Ries, Jonas; Klotzsch, Enrico; Ewers, Helge; Vogel, Viola (2011). Binding-activated localization microscopy of DNA structures. Nano letters, 11(9):4008-4011.

Fabbretti, R

Bonhoure, N; Bounova, G; Bernasconi, D; Praz, V; Lammers, F; Canella, D; Willis, I M; Herr, W; Hernandez, N; Delorenzi, M; Hernandez, N; Delorenzi, M; Deplancke, B; Desvergne, B; Guex, N; Herr, W; Naef, F; Rougemont, J; Schibler, U; Andersin, T; Cousin, P; Gilardi, F; Gos, P; Lammers, F; Raghav, S; Villeneuve, D; Fabbretti, R; Vlegel, V; Xenarios, I; Migliavacca, E; Praz, V; David, F; Jarosz, Y; Kuznetsov, D; Liechti, R; Martin, O; Delafontaine, J; Cajan, J; Gustafson, K; Krier, I; Leleu, M; Molina, N; Naldi, A; Rib, L; Symul, L; Bounova, G (2014). Quantifying ChIP-seq data: a spiking method providing an internal reference for sample-to-sample normalization. Genome Research, 24(7):1157-1168.

Farhan, Hesso

Steeb, Benjamin; Claudi, Beatrice; Burton, Neil A; Tienz, Petra; Schmidt, Alexander; Farhan, Hesso; Mazé, Alain; Bumann, Dirk (2013). Parallel Exploitation of Diverse Host Nutrients Enhances Salmonella Virulence. PLoS Pathogens, 9(4):e1003301.

Felekis, D

Routier-Kierzkowska, A -L; Weber, A; Kochova, P; Felekis, D; Nelson, B J; Kuhlemeier, C; Smith, R S (2012). Cellular Force Microscopy for in Vivo Measurements of Plant Tissue Mechanics. Plant Physiology, 158(4):1514-1522.

Feller, Chrystel

Feller, Chrystel; Gabriel, Jean-Pierre; Mazza, Christian; Yerly, Florence (2014). Pattern formation in auxin flux. Journal of Mathematical Biology, 68(4):879-909.

Fidalgo, Luis M

Woodruff, Kristina; Fidalgo, Luis M; Gobaa, Samy; Lutolf, Matthias P; Maerkl, Sebastian J (2013). Live Mammalian Cell Arrays. Nature Methods, 10(6):550-552.

Field, Jessica J

Prota, Andrea E; Bargsten, Katja; Zurwerra, Didier; Field, Jessica J; Díaz, José Fernando; Altmann, Karl-Heinz; Steinmetz, Michel O (2013). Molecular Mechanism of Action of Microtubule-Stabilizing Anticancer Agents. Science, 339(6119):587-590.

Fivaz, M

Lim, L; Jackson-Lewis, V; Wong, L C; Shui, G H; Goh, A X H; Kesavapany, S; Jenner, A M; Fivaz, M; Przedborski, S; Wenk, M R (2012). Lanosterol induces mitochondrial uncoupling and protects dopaminergic neurons from cell death in a model for Parkinson's disease. Cell Death and Differentiation, 19(3):416-27.

Fjeldsø, Kit S

Hosta-Rigau, Leticia; Jensen, Bettina E B; Fjeldsø, Kit S; Postma, Almar; Li, Guoxin; Goldie, Kenneth N; Albericio, Fernando; Zelikin, Alexander N; Städler, Brigitte (2012). Drug Delivery: Surface-Adhered Composite Poly(Vinyl Alcohol) Physical Hydrogels: Polymersome-Aided Delivery of Therapeutic Small Molecules. Advanced Healthcare Materials, 1(6):791-5.

Foth, Bernardo J

Limenitakis, Julien; Oppenheim, Rebecca D; Creek, Darren J; Foth, Bernardo J; Barrett, Michael P; Soldati-Favre, Dominique (2013). The 2-methylcitrate cycle is implicated in the detoxification of propionate in Toxoplasma gondii. Molecular Microbiology, 87(4):894-908.

Frischknecht, Friedrich

Lemgruber, Leandro; Kudryashev, Mikhail; Dekiwadia, Chaitali; Riglar, David T; Baum, Jake; Stahlberg, Henning; Ralph, Stuart A; Frischknecht, Friedrich (2013). Cryo-electron tomography reveals four-membrane architecture of the Plasmodium apicoplast. Malaria Journal, 12:25.

Fucile, G

Samol, I; Shapiguzov, A; Ingelsson, B; Fucile, G; Crevecoeur, M; Vener, A V; Rochaix, J -D; Goldschmidt-Clermont, M (2012). Identification of a Photosystem II Phosphatase Involved in Light Acclimation in Arabidopsis. Plant Cell, 24(6):2596-2609.

Gabriel, Jean-Pierre

Feller, Chrystel; Gabriel, Jean-Pierre; Mazza, Christian; Yerly, Florence (2014). Pattern formation in auxin flux. Journal of Mathematical Biology, 68(4):879-909.

Gajewski, Martin

Schröter, Christian; Ares, Saúl; Morelli, Luis G; Isakova, Alina; Hens, Korneel; Soroldoni, Daniele; Gajewski, Martin; Jülicher, Frank; Maerkl, Sebastian J; Deplancke, Bart; Oates, Andrew C (2012). Topology and Dynamics of the Zebrafish Segmentation Clock Core Circuit. PLoS Biology, 10(7):1-20.

Ganguly, Arnab

Koeppl, Heinz; Zechner, Christoph; Ganguly, Arnab; Pelet, Serge; Peter, Matthias (2012). Accounting for extrinsic variability in the estimation of stochastic rate constants. International Journal of Robust and Nonlinear Control, 22(10):1103-1119.

Garner, Brett

Cheng, Danni; Jenner, Andrew M; Shui, Guanghou; Cheong, Wei Fun; Mitchell, Todd W; Nealon, Jessica R; Kim, Woojin S; McCann, Heather; Wenk, Markus R; Halliday, Glenda M; Garner, Brett (2011). Lipid pathway alterations in Parkinson's disease primary visual cortex. PLoS ONE, 6(2):e17299.

Geertz, Marcel

Rockel, Sylvie; Geertz, Marcel; Hens, Korneel; Deplancke, Bart; Maerkl, Sebastian J (2012). iSLIM: a comprehensive approach to mapping and characterizing gene regulatory networks. Nucleic Acids Research:1-8.

Geertz, Marcel; Shore, David; Maerkl, Sebastian J (2012). Massively parallel measurements of molecular interaction kinetics on a microfluidic platform. Proceedings of the National Academy of Sciences of the United States of America, 109(41):16540-16545.

Geertz, Marcel; Rockel, Sylvie; Maerkl, Sebastian J (2012). A high-throughput microfluidic method for generating and characterizing transcription factor mutant libraries. Methods in Molecular Biology, 813:107-123.

Geertz, Marcel; Maerkl, Sebastian J (2010). Experimental strategies for studying transcription factor-DNA binding specificities. Briefings in Functional Genomics:1-12.

Gerrits, B

Hofmann, A; Gerrits, B; Schmidt, A; Bock, T; Bausch-Fluck, D; Aebersold, R; Wollscheid, B (2010). Proteomic cell surface phenotyping of differentiating acute myeloid leukemia cells. Blood, 116(13):e26-34.

Gilardi, F

Bonhoure, N; Bounova, G; Bernasconi, D; Praz, V; Lammers, F; Canella, D; Willis, I M; Herr, W; Hernandez, N; Delorenzi, M; Hernandez, N; Delorenzi, M; Deplancke, B; Desvergne, B; Guex, N; Herr, W; Naef, F; Rougemont, J; Schibler, U; Andersin, T; Cousin, P; Gilardi, F; Gos, P; Lammers, F; Raghav, S; Villeneuve, D; Fabbretti, R; Vlegel, V; Xenarios, I; Migliavacca, E; Praz, V; David, F; Jarosz, Y; Kuznetsov, D; Liechti, R; Martin, O; Delafontaine, J; Cajan, J; Gustafson, K; Krier, I; Leleu, M; Molina, N; Naldi, A; Rib, L; Symul, L; Bounova, G (2014). Quantifying ChIP-seq data: a spiking method providing an internal reference for sample-to-sample normalization. Genome Research, 24(7):1157-1168.

Gilardi, Federica

Gilardi, Federica; Migliavacca, Eugenia; Naldi, Aurélien; Baruchet, Michaël; Canella, Donatella; Le Martelot, Gwendal; Guex, Nicolas; Desvergne, Béatrice (2014). Genome-Wide Analysis of SREBP1 Activity around the Clock Reveals Its Combined Dependency on Nutrient and Circadian Signals. PLoS Genetics, 10(3):e1004155.

Le Martelot, Gwendal; Canella, Donatella; Symul, Laura; Migliavacca, Eugenia; Gilardi, Federica; Liechti, Robin; Martin, Olivier; Harshman, Keith; Delorenzi, Mauro; Desvergne, Béatrice; Herr, Winship; Deplancke, Bart; Schibler, Ueli; Rougemont, Jacques; Guex, Nicolas; Hernandez, Nouria; Naef, Felix (2012). Genome-wide RNA polymerase II profiles and RNA accumulation reveal kinetics of transcription and associated epigenetic changes during diurnal cycles. PLoS Biology, 10(11):e1001442.

Gilardoni, Paola A

Simicevic, Jovan; Schmid, Adrien W; Gilardoni, Paola A; Zoller, Benjamin; Raghav, Sunil K; Krier, Irina; Gubelmann, Carinne; Lisacek, Frédérique; Naef, Felix; Moniatte, Marc; Deplancke, Bart (2013). Absolute quantification of transcription factors during cellular differentiation using multiplexed targeted proteomics. Nature Methods, 10(6):570-576.

Giss, Dominic

Giss, Dominic; Kemmerling, Simon; Dandey, Venkata; Stahlberg, Henning; Braun, Thomas (2014). Exploring the interactome: microfluidic isolation of proteins and interacting partners for quantitative analysis by electron microscopy. Analytical Chemistry, 86(10):4680-4687.

Gobaa, Samy

Woodruff, Kristina; Fidalgo, Luis M; Gobaa, Samy; Lutolf, Matthias P; Maerkl, Sebastian J (2013). Live Mammalian Cell Arrays. Nature Methods, 10(6):550-552.

Gobet, Cédric

Quinodoz, Mathieu; Gobet, Cédric; Naef, Felix; Gustafson, Kyle B (2014). Characteristic bimodal profiles of RNA polymerase II at thousands of active mammalian promoters. Genome Biology, 15(6):R85.

Goepfert, Arnaud

Goepfert, Arnaud; Stanger, Frédéric V; Dehio, Christoph; Schirmer, Tilman (2013). Conserved Inhibitory Mechanism and Competent ATP Binding Mode for Adenylyltransferases with Fic Fold. PLoS ONE, 8(5):e64901.

Goh, A X H

Lim, L; Jackson-Lewis, V; Wong, L C; Shui, G H; Goh, A X H; Kesavapany, S; Jenner, A M; Fivaz, M; Przedborski, S; Wenk, M R (2012). Lanosterol induces mitochondrial uncoupling and protects dopaminergic neurons from cell death in a model for Parkinson's disease. Cell Death and Differentiation, 19(3):416-27.

Goldie, Kenneth N

Goldie, Kenneth N; Abeyrathne, Priyanka; Kebbel, Fabian; Chami, Mohamed; Ringler, Philippe; Stahlberg, Henning (2014). Cryo-electron microscopy of membrane proteins. Methods in Molecular Biology, 1117:325-41.

Ramakrishnan, Chandrasekhar; Bieri, Andrej; Sauter, Nora; Roizard, Sophie; Ringler, Philippe; Müller, Shirley A; Goldie, Kenneth N; Enimanev, Kaloyan; Stahlberg, Henning; Rinn, Bernd; Braun, Thomas (2014). openBEB: open biological experiment browser for correlative measurements. BMC Bioinformatics, 15:84.

Leppänen, Veli-Matti; Tvorogov, Denis; Kisko, Kaisa; Prota, Andrea E; Jeltsch, Michael; Anisimov, Andrey; Markovic-Mueller, Sandra; Stuttfeld, Edward; Goldie, Kenneth N; Ballmer-Hofer, Kurt; Alitalo, Kari (2013). Structural and mechanistic insights into VEGF receptor 3 ligand binding and activation. Proceedings of the National Academy of Sciences of the United States of America, 110(32):12960-12965.

Andreasen, Sidsel Ø; Chong, Siow-Feng; Wohl, Benjamin M; Goldie, Kenneth N; Zelikin, Alexander N (2013). Poly(vinyl alcohol) physical hydrogel nanoparticles, not polymer solutions, exert inhibition of nitric oxide synthesis in cultured macrophages. Biomacromolecules, 14(5):1687-95.

van der Westen, Rebecca; Hosta-Rigau, Leticia; Sutherland, Duncan S; Goldie, Kenneth N; Albericio, Fernando; Postma, Almar; Städler, Brigitte (2012). Myoblast cell interaction with polydopamine coated liposomes. Biointerphases, 7(1-4):8.

Hosta-Rigau, Leticia; Jensen, Bettina E B; Fjeldsø, Kit S; Postma, Almar; Li, Guoxin; Goldie, Kenneth N; Albericio, Fernando; Zelikin, Alexander N; Städler, Brigitte (2012). Drug Delivery: Surface-Adhered Composite Poly(Vinyl Alcohol) Physical Hydrogels: Polymersome-Aided Delivery of Therapeutic Small Molecules. Advanced Healthcare Materials, 1(6):791-5.

Goldschmidt-Clermont, M

Samol, I; Shapiguzov, A; Ingelsson, B; Fucile, G; Crevecoeur, M; Vener, A V; Rochaix, J -D; Goldschmidt-Clermont, M (2012). Identification of a Photosystem II Phosphatase Involved in Light Acclimation in Arabidopsis. Plant Cell, 24(6):2596-2609.

Shapiguzov, A; Ingelsson, B; Samol, I; Andres, C; Kessler, F; Rochaix, J -D; Vener, A V; Goldschmidt-Clermont, M (2010). The PPH1 phosphatase is specifically involved in LHCII dephosphorylation and state transitions in Arabidopsis. Proceedings of the National Academy of Sciences of the United States of America, 107(10):4782-4787.

González-Segredo, Nélido

Ramaswamy, Rajesh; Sbalzarini, Ivo F; González-Segredo, Nélido (2011). Noise-Induced Modulation of the Relaxation Kinetics around a Non-Equilibrium Steady State of Non-Linear Chemical Reaction Networks. PLoS ONE, 6(1):e16045.

Gos, P

Bonhoure, N; Bounova, G; Bernasconi, D; Praz, V; Lammers, F; Canella, D; Willis, I M; Herr, W; Hernandez, N; Delorenzi, M; Hernandez, N; Delorenzi, M; Deplancke, B; Desvergne, B; Guex, N; Herr, W; Naef, F; Rougemont, J; Schibler, U; Andersin, T; Cousin, P; Gilardi, F; Gos, P; Lammers, F; Raghav, S; Villeneuve, D; Fabbretti, R; Vlegel, V; Xenarios, I; Migliavacca, E; Praz, V; David, F; Jarosz, Y; Kuznetsov, D; Liechti, R; Martin, O; Delafontaine, J; Cajan, J; Gustafson, K; Krier, I; Leleu, M; Molina, N; Naldi, A; Rib, L; Symul, L; Bounova, G (2014). Quantifying ChIP-seq data: a spiking method providing an internal reference for sample-to-sample normalization. Genome Research, 24(7):1157-1168.

Goud, Bruno

Vonaesch, Pascale; Cardini, Steven; Sellin, Mikael E; Goud, Bruno; Hardt, Wolf-Dietrich; Schauer, Kristine (2013). Quantitative insights into actin rearrangements and bacterial target site selection fromSalmonella Typhimurium infection of micropatterned cells. Cellular Microbiology, 15(11):1851-1865.

Gray, Daniel H D

Papadopoulou, Aikaterini S; Dooley, James; Linterman, Michelle A; Pierson, Wim; Ucar, Olga; Kyewski, Bruno; Zuklys, Saulius; Hollander, Georg A; Matthys, Patrick; Gray, Daniel H D; De Strooper, Bart; Liston, Adrian (2011). The thymic epithelial microRNA network elevates the threshold for infection-associated thymic involution via miR-29a mediated suppression of the IFN-α receptor. Nature Immunology, 13(2):181-187.

Gruenberg, J

Brankatschk, B; Wichert, S P; Johnson, S D; Schaad, O; Rossner, M J; Gruenberg, J (2012). Regulation of the EGF Transcriptional Response by Endocytic Sorting. Science Signaling, 5(215):ra21.

Gruenberg, Jean

Brankatschk, Ben; Pons, Véronique; Parton, Robert G; Gruenberg, Jean (2011). Role of SNX16 in the dynamics of tubulo-cisternal membrane domains of late endosomes. PLoS ONE, 6(7):e21771.

Gubelmann, Carinne

Simicevic, Jovan; Schmid, Adrien W; Gilardoni, Paola A; Zoller, Benjamin; Raghav, Sunil K; Krier, Irina; Gubelmann, Carinne; Lisacek, Frédérique; Naef, Felix; Moniatte, Marc; Deplancke, Bart (2013). Absolute quantification of transcription factors during cellular differentiation using multiplexed targeted proteomics. Nature Methods, 10(6):570-576.

Guenot, B

Guenot, B; Bayer, E; Kierzkowski, D; Smith, R S; Mandel, T; Zadnikova, P; Benkova, E; Kuhlemeier, C (2012). PIN1-Independent Leaf Initiation in Arabidopsis. Plant Physiology, 159(4):1501-1510.

Guex, N

Bonhoure, N; Bounova, G; Bernasconi, D; Praz, V; Lammers, F; Canella, D; Willis, I M; Herr, W; Hernandez, N; Delorenzi, M; Hernandez, N; Delorenzi, M; Deplancke, B; Desvergne, B; Guex, N; Herr, W; Naef, F; Rougemont, J; Schibler, U; Andersin, T; Cousin, P; Gilardi, F; Gos, P; Lammers, F; Raghav, S; Villeneuve, D; Fabbretti, R; Vlegel, V; Xenarios, I; Migliavacca, E; Praz, V; David, F; Jarosz, Y; Kuznetsov, D; Liechti, R; Martin, O; Delafontaine, J; Cajan, J; Gustafson, K; Krier, I; Leleu, M; Molina, N; Naldi, A; Rib, L; Symul, L; Bounova, G (2014). Quantifying ChIP-seq data: a spiking method providing an internal reference for sample-to-sample normalization. Genome Research, 24(7):1157-1168.

Guex, Nicolas

Gilardi, Federica; Migliavacca, Eugenia; Naldi, Aurélien; Baruchet, Michaël; Canella, Donatella; Le Martelot, Gwendal; Guex, Nicolas; Desvergne, Béatrice (2014). Genome-Wide Analysis of SREBP1 Activity around the Clock Reveals Its Combined Dependency on Nutrient and Circadian Signals. PLoS Genetics, 10(3):e1004155.

Le Martelot, Gwendal; Canella, Donatella; Symul, Laura; Migliavacca, Eugenia; Gilardi, Federica; Liechti, Robin; Martin, Olivier; Harshman, Keith; Delorenzi, Mauro; Desvergne, Béatrice; Herr, Winship; Deplancke, Bart; Schibler, Ueli; Rougemont, Jacques; Guex, Nicolas; Hernandez, Nouria; Naef, Felix (2012). Genome-wide RNA polymerase II profiles and RNA accumulation reveal kinetics of transcription and associated epigenetic changes during diurnal cycles. PLoS Biology, 10(11):e1001442.

Gustafson, K

Bonhoure, N; Bounova, G; Bernasconi, D; Praz, V; Lammers, F; Canella, D; Willis, I M; Herr, W; Hernandez, N; Delorenzi, M; Hernandez, N; Delorenzi, M; Deplancke, B; Desvergne, B; Guex, N; Herr, W; Naef, F; Rougemont, J; Schibler, U; Andersin, T; Cousin, P; Gilardi, F; Gos, P; Lammers, F; Raghav, S; Villeneuve, D; Fabbretti, R; Vlegel, V; Xenarios, I; Migliavacca, E; Praz, V; David, F; Jarosz, Y; Kuznetsov, D; Liechti, R; Martin, O; Delafontaine, J; Cajan, J; Gustafson, K; Krier, I; Leleu, M; Molina, N; Naldi, A; Rib, L; Symul, L; Bounova, G (2014). Quantifying ChIP-seq data: a spiking method providing an internal reference for sample-to-sample normalization. Genome Research, 24(7):1157-1168.

Gustafson, Kyle B

Quinodoz, Mathieu; Gobet, Cédric; Naef, Felix; Gustafson, Kyle B (2014). Characteristic bimodal profiles of RNA polymerase II at thousands of active mammalian promoters. Genome Biology, 15(6):R85.

Hall, Michael N

Shimobayash, Mitsugu; Oppliger, Wolfgang; Moes, Suzette; Jenö, Paul; Hall, Michael N (2013). TORC1-regulated protein kinase Npr1 phosphorylates Orm to stimulate complex sphingolipid synthesis. Molecular Biology of the Cell, 24:870-881.

Loewith, Robbie; Hall, Michael N (2011). Target of Rapamycin (TOR) in Nutrient Signaling and Growth Control. Genetics, 189:1177 -1201.

Zinzalla, Vittoria; Stracka, Daniele; Oppliger, Wolfgang; Hall, Michael N (2011). Activation of mTORC2 by Association with the Ribosome. Cell, 144:757-768.

Soulard, Alexandre; Cremonesi, Alessio; Moes, Suzette; Schütz, Frédéric; Jenö, Paul; Hall, Michael N (2010). The Rapamycin-sensitive Phosphoproteome Reveals That TOR Controls Protein Kinase A Toward Some But Not All Substrates. Molecular Biology of the Cell, 21:3475-3486.

Halliday, Glenda M

Cheng, Danni; Jenner, Andrew M; Shui, Guanghou; Cheong, Wei Fun; Mitchell, Todd W; Nealon, Jessica R; Kim, Woojin S; McCann, Heather; Wenk, Markus R; Halliday, Glenda M; Garner, Brett (2011). Lipid pathway alterations in Parkinson's disease primary visual cortex. PLoS ONE, 6(2):e17299.

Hamaratoglu, Fisun

Hamaratoglu, Fisun; Morton de Lachapelle, Aitana; Pyrowolakis, George; Bergmann, Sven; Affolter, Markus (2011). Dpp signaling activity requires pentagone to scale with tissue size in the growing drosophila wing imaginal disc. PLoS Biology, 9:1-17.

Hardt, W-D

Truttmann, M C; Misselwitz, B; Huser, S; Hardt, W-D; Critchley, D R; Dehio, C (2011). Bartonella henselae engages inside-out and outside-in signaling by integrin 1 and talin1 during invasome-mediated bacterial uptake. Journal of Cell Science, 124(21):3591-3602.

Hardt, Wolf Dietrich

Bailly-Bechet, Marc; Benecke, Arndt; Hardt, Wolf Dietrich; Lanza, Valentina; Sturm, Alexander; Zecchina, Riccardo (2011). An externally modulated, noise-driven switch for the regulation of SPI1 in Salmonella enterica serovar Typhimurium. Journal of Mathematical Biology, 63(4):637-662.

Hardt, Wolf-Dietrich

Vonaesch, Pascale; Cardini, Steven; Sellin, Mikael E; Goud, Bruno; Hardt, Wolf-Dietrich; Schauer, Kristine (2013). Quantitative insights into actin rearrangements and bacterial target site selection fromSalmonella Typhimurium infection of micropatterned cells. Cellular Microbiology, 15(11):1851-1865.

Harshman, Keith

Le Martelot, Gwendal; Canella, Donatella; Symul, Laura; Migliavacca, Eugenia; Gilardi, Federica; Liechti, Robin; Martin, Olivier; Harshman, Keith; Delorenzi, Mauro; Desvergne, Béatrice; Herr, Winship; Deplancke, Bart; Schibler, Ueli; Rougemont, Jacques; Guex, Nicolas; Hernandez, Nouria; Naef, Felix (2012). Genome-wide RNA polymerase II profiles and RNA accumulation reveal kinetics of transcription and associated epigenetic changes during diurnal cycles. PLoS Biology, 10(11):e1001442.

Headland, L R

Chitwood, D H; Headland, L R; Ranjan, A; Martinez, C C; Braybrook, S A; Koenig, D P; Kuhlemeier, C; Smith, R S; Sinha, N R (2012). Leaf Asymmetry as a Developmental Constraint Imposed by Auxin-Dependent Phyllotactic Patterning. Plant Cell, 24(6):2318-2327.

Heinemann, Matthias

Kotte, Oliver; Heinemann, Matthias (2009). A divide-and-conquer approach to analyze underdetermined biochemical models. Bioinformatics, 25(4):519-525.

Heinz, D W

Kudryashev, M; Stenta, M; Schmelz, S; Amstutz, M; Wiesand, U; Castano-Diez, D; Degiacomi, M T; Munnich, S; Bleck, C K; Kowal, J; Diepold, A; Heinz, D W; Dal Peraro, M; Cornelis, G R; Stahlberg, H (2013). In situ structural analysis of the Yersinia enterocolitica injectisome. eLife, 2:e00792-e00792.

Helenius, Ari

Schmidt, Florian Ingo; Bleck, Christopher Karl Ernst; Helenius, Ari; Mercer, Jason (2011). Vaccinia extracellular virions enter cells by macropinocytosis and acid-activated membrane rupture. EMBO Journal Online, 30(17):3647-3661.

Helmuth, Jo A

Helmuth, Jo A; Paul, Grégory; Sbalzarini, Ivo F (2010). Beyond co-localization: inferring spatial interactions between sub-cellular structures from microscopy images. BMC Bioinformatics, 11(1):372.

Hens, Korneel

Rockel, Sylvie; Geertz, Marcel; Hens, Korneel; Deplancke, Bart; Maerkl, Sebastian J (2012). iSLIM: a comprehensive approach to mapping and characterizing gene regulatory networks. Nucleic Acids Research:1-8.

Schröter, Christian; Ares, Saúl; Morelli, Luis G; Isakova, Alina; Hens, Korneel; Soroldoni, Daniele; Gajewski, Martin; Jülicher, Frank; Maerkl, Sebastian J; Deplancke, Bart; Oates, Andrew C (2012). Topology and Dynamics of the Zebrafish Segmentation Clock Core Circuit. PLoS Biology, 10(7):1-20.

Hermes, Jens P

Hermes, Jens P; Sander, Fabian; Peterle, Torsten; Cioffi, Carla; Ringler, Philippe; Pfohl, Thomas; Mayor, Marcel (2011). Direct control of the spatial arrangement of gold nanoparticles in organic-inorganic hybrid superstructures. Small, 7(7):920-9.

Hernandez, N

Bonhoure, N; Bounova, G; Bernasconi, D; Praz, V; Lammers, F; Canella, D; Willis, I M; Herr, W; Hernandez, N; Delorenzi, M; Hernandez, N; Delorenzi, M; Deplancke, B; Desvergne, B; Guex, N; Herr, W; Naef, F; Rougemont, J; Schibler, U; Andersin, T; Cousin, P; Gilardi, F; Gos, P; Lammers, F; Raghav, S; Villeneuve, D; Fabbretti, R; Vlegel, V; Xenarios, I; Migliavacca, E; Praz, V; David, F; Jarosz, Y; Kuznetsov, D; Liechti, R; Martin, O; Delafontaine, J; Cajan, J; Gustafson, K; Krier, I; Leleu, M; Molina, N; Naldi, A; Rib, L; Symul, L; Bounova, G (2014). Quantifying ChIP-seq data: a spiking method providing an internal reference for sample-to-sample normalization. Genome Research, 24(7):1157-1168.

Bonhoure, N; Bounova, G; Bernasconi, D; Praz, V; Lammers, F; Canella, D; Willis, I M; Herr, W; Hernandez, N; Delorenzi, M; Hernandez, N; Delorenzi, M; Deplancke, B; Desvergne, B; Guex, N; Herr, W; Naef, F; Rougemont, J; Schibler, U; Andersin, T; Cousin, P; Gilardi, F; Gos, P; Lammers, F; Raghav, S; Villeneuve, D; Fabbretti, R; Vlegel, V; Xenarios, I; Migliavacca, E; Praz, V; David, F; Jarosz, Y; Kuznetsov, D; Liechti, R; Martin, O; Delafontaine, J; Cajan, J; Gustafson, K; Krier, I; Leleu, M; Molina, N; Naldi, A; Rib, L; Symul, L; Bounova, G (2014). Quantifying ChIP-seq data: a spiking method providing an internal reference for sample-to-sample normalization. Genome Research, 24(7):1157-1168.

Hernandez, Nouria

Le Martelot, Gwendal; Canella, Donatella; Symul, Laura; Migliavacca, Eugenia; Gilardi, Federica; Liechti, Robin; Martin, Olivier; Harshman, Keith; Delorenzi, Mauro; Desvergne, Béatrice; Herr, Winship; Deplancke, Bart; Schibler, Ueli; Rougemont, Jacques; Guex, Nicolas; Hernandez, Nouria; Naef, Felix (2012). Genome-wide RNA polymerase II profiles and RNA accumulation reveal kinetics of transcription and associated epigenetic changes during diurnal cycles. PLoS Biology, 10(11):e1001442.

Herr, W

Bonhoure, N; Bounova, G; Bernasconi, D; Praz, V; Lammers, F; Canella, D; Willis, I M; Herr, W; Hernandez, N; Delorenzi, M; Hernandez, N; Delorenzi, M; Deplancke, B; Desvergne, B; Guex, N; Herr, W; Naef, F; Rougemont, J; Schibler, U; Andersin, T; Cousin, P; Gilardi, F; Gos, P; Lammers, F; Raghav, S; Villeneuve, D; Fabbretti, R; Vlegel, V; Xenarios, I; Migliavacca, E; Praz, V; David, F; Jarosz, Y; Kuznetsov, D; Liechti, R; Martin, O; Delafontaine, J; Cajan, J; Gustafson, K; Krier, I; Leleu, M; Molina, N; Naldi, A; Rib, L; Symul, L; Bounova, G (2014). Quantifying ChIP-seq data: a spiking method providing an internal reference for sample-to-sample normalization. Genome Research, 24(7):1157-1168.

Bonhoure, N; Bounova, G; Bernasconi, D; Praz, V; Lammers, F; Canella, D; Willis, I M; Herr, W; Hernandez, N; Delorenzi, M; Hernandez, N; Delorenzi, M; Deplancke, B; Desvergne, B; Guex, N; Herr, W; Naef, F; Rougemont, J; Schibler, U; Andersin, T; Cousin, P; Gilardi, F; Gos, P; Lammers, F; Raghav, S; Villeneuve, D; Fabbretti, R; Vlegel, V; Xenarios, I; Migliavacca, E; Praz, V; David, F; Jarosz, Y; Kuznetsov, D; Liechti, R; Martin, O; Delafontaine, J; Cajan, J; Gustafson, K; Krier, I; Leleu, M; Molina, N; Naldi, A; Rib, L; Symul, L; Bounova, G (2014). Quantifying ChIP-seq data: a spiking method providing an internal reference for sample-to-sample normalization. Genome Research, 24(7):1157-1168.

Herr, Winship

Le Martelot, Gwendal; Canella, Donatella; Symul, Laura; Migliavacca, Eugenia; Gilardi, Federica; Liechti, Robin; Martin, Olivier; Harshman, Keith; Delorenzi, Mauro; Desvergne, Béatrice; Herr, Winship; Deplancke, Bart; Schibler, Ueli; Rougemont, Jacques; Guex, Nicolas; Hernandez, Nouria; Naef, Felix (2012). Genome-wide RNA polymerase II profiles and RNA accumulation reveal kinetics of transcription and associated epigenetic changes during diurnal cycles. PLoS Biology, 10(11):e1001442.

Herrmann, Hans J

Munglani, Gautam; Vetter, Roman; Wittel, Falk K; Herrmann, Hans J (2015). Orthotropic rotation-free thin shell elements. Computational Mechanics, 56(5):785-793.

Hofmann, A

Hofmann, A; Gerrits, B; Schmidt, A; Bock, T; Bausch-Fluck, D; Aebersold, R; Wollscheid, B (2010). Proteomic cell surface phenotyping of differentiating acute myeloid leukemia cells. Blood, 116(13):e26-34.

Hollander, Georg A

Papadopoulou, Aikaterini S; Dooley, James; Linterman, Michelle A; Pierson, Wim; Ucar, Olga; Kyewski, Bruno; Zuklys, Saulius; Hollander, Georg A; Matthys, Patrick; Gray, Daniel H D; De Strooper, Bart; Liston, Adrian (2011). The thymic epithelial microRNA network elevates the threshold for infection-associated thymic involution via miR-29a mediated suppression of the IFN-α receptor. Nature Immunology, 13(2):181-187.

Horvath, Peter

Smith, Kevin; Li, Yunpeng; Piccinini, Filippo; Csucs, Gabor; Balazs, Csaba; Bevilacqua, Alessandro; Horvath, Peter (2015). CIDRE: an illumination-correction method for optical microscopy. Nature Methods, 12(5):404-406.

Hosta-Rigau, Leticia

van der Westen, Rebecca; Hosta-Rigau, Leticia; Sutherland, Duncan S; Goldie, Kenneth N; Albericio, Fernando; Postma, Almar; Städler, Brigitte (2012). Myoblast cell interaction with polydopamine coated liposomes. Biointerphases, 7(1-4):8.

Hosta-Rigau, Leticia; Jensen, Bettina E B; Fjeldsø, Kit S; Postma, Almar; Li, Guoxin; Goldie, Kenneth N; Albericio, Fernando; Zelikin, Alexander N; Städler, Brigitte (2012). Drug Delivery: Surface-Adhered Composite Poly(Vinyl Alcohol) Physical Hydrogels: Polymersome-Aided Delivery of Therapeutic Small Molecules. Advanced Healthcare Materials, 1(6):791-5.

Huser, S

Truttmann, M C; Misselwitz, B; Huser, S; Hardt, W-D; Critchley, D R; Dehio, C (2011). Bartonella henselae engages inside-out and outside-in signaling by integrin 1 and talin1 during invasome-mediated bacterial uptake. Journal of Cell Science, 124(21):3591-3602.

Ingelsson, B

Samol, I; Shapiguzov, A; Ingelsson, B; Fucile, G; Crevecoeur, M; Vener, A V; Rochaix, J -D; Goldschmidt-Clermont, M (2012). Identification of a Photosystem II Phosphatase Involved in Light Acclimation in Arabidopsis. Plant Cell, 24(6):2596-2609.

Shapiguzov, A; Ingelsson, B; Samol, I; Andres, C; Kessler, F; Rochaix, J -D; Vener, A V; Goldschmidt-Clermont, M (2010). The PPH1 phosphatase is specifically involved in LHCII dephosphorylation and state transitions in Arabidopsis. Proceedings of the National Academy of Sciences of the United States of America, 107(10):4782-4787.

Isakova, Alina

Schröter, Christian; Ares, Saúl; Morelli, Luis G; Isakova, Alina; Hens, Korneel; Soroldoni, Daniele; Gajewski, Martin; Jülicher, Frank; Maerkl, Sebastian J; Deplancke, Bart; Oates, Andrew C (2012). Topology and Dynamics of the Zebrafish Segmentation Clock Core Circuit. PLoS Biology, 10(7):1-20.

Jackson-Lewis, V

Lim, L; Jackson-Lewis, V; Wong, L C; Shui, G H; Goh, A X H; Kesavapany, S; Jenner, A M; Fivaz, M; Przedborski, S; Wenk, M R (2012). Lanosterol induces mitochondrial uncoupling and protects dopaminergic neurons from cell death in a model for Parkinson's disease. Cell Death and Differentiation, 19(3):416-27.

Jarosz, Y

Bonhoure, N; Bounova, G; Bernasconi, D; Praz, V; Lammers, F; Canella, D; Willis, I M; Herr, W; Hernandez, N; Delorenzi, M; Hernandez, N; Delorenzi, M; Deplancke, B; Desvergne, B; Guex, N; Herr, W; Naef, F; Rougemont, J; Schibler, U; Andersin, T; Cousin, P; Gilardi, F; Gos, P; Lammers, F; Raghav, S; Villeneuve, D; Fabbretti, R; Vlegel, V; Xenarios, I; Migliavacca, E; Praz, V; David, F; Jarosz, Y; Kuznetsov, D; Liechti, R; Martin, O; Delafontaine, J; Cajan, J; Gustafson, K; Krier, I; Leleu, M; Molina, N; Naldi, A; Rib, L; Symul, L; Bounova, G (2014). Quantifying ChIP-seq data: a spiking method providing an internal reference for sample-to-sample normalization. Genome Research, 24(7):1157-1168.

Jeltsch, Michael

Leppänen, Veli-Matti; Tvorogov, Denis; Kisko, Kaisa; Prota, Andrea E; Jeltsch, Michael; Anisimov, Andrey; Markovic-Mueller, Sandra; Stuttfeld, Edward; Goldie, Kenneth N; Ballmer-Hofer, Kurt; Alitalo, Kari (2013). Structural and mechanistic insights into VEGF receptor 3 ligand binding and activation. Proceedings of the National Academy of Sciences of the United States of America, 110(32):12960-12965.

Jenner, A M

Lim, L; Jackson-Lewis, V; Wong, L C; Shui, G H; Goh, A X H; Kesavapany, S; Jenner, A M; Fivaz, M; Przedborski, S; Wenk, M R (2012). Lanosterol induces mitochondrial uncoupling and protects dopaminergic neurons from cell death in a model for Parkinson's disease. Cell Death and Differentiation, 19(3):416-27.

Jenner, Andrew M

Cheng, Danni; Jenner, Andrew M; Shui, Guanghou; Cheong, Wei Fun; Mitchell, Todd W; Nealon, Jessica R; Kim, Woojin S; McCann, Heather; Wenk, Markus R; Halliday, Glenda M; Garner, Brett (2011). Lipid pathway alterations in Parkinson's disease primary visual cortex. PLoS ONE, 6(2):e17299.

Jensen, Bettina E B

Hosta-Rigau, Leticia; Jensen, Bettina E B; Fjeldsø, Kit S; Postma, Almar; Li, Guoxin; Goldie, Kenneth N; Albericio, Fernando; Zelikin, Alexander N; Städler, Brigitte (2012). Drug Delivery: Surface-Adhered Composite Poly(Vinyl Alcohol) Physical Hydrogels: Polymersome-Aided Delivery of Therapeutic Small Molecules. Advanced Healthcare Materials, 1(6):791-5.

Jenö, Paul

Shimobayash, Mitsugu; Oppliger, Wolfgang; Moes, Suzette; Jenö, Paul; Hall, Michael N (2013). TORC1-regulated protein kinase Npr1 phosphorylates Orm to stimulate complex sphingolipid synthesis. Molecular Biology of the Cell, 24:870-881.

Soulard, Alexandre; Cremonesi, Alessio; Moes, Suzette; Schütz, Frédéric; Jenö, Paul; Hall, Michael N (2010). The Rapamycin-sensitive Phosphoproteome Reveals That TOR Controls Protein Kinase A Toward Some But Not All Substrates. Molecular Biology of the Cell, 21:3475-3486.

Johnson, S D

Brankatschk, B; Wichert, S P; Johnson, S D; Schaad, O; Rossner, M J; Gruenberg, J (2012). Regulation of the EGF Transcriptional Response by Endocytic Sorting. Science Signaling, 5(215):ra21.

Jülicher, Frank

Schröter, Christian; Ares, Saúl; Morelli, Luis G; Isakova, Alina; Hens, Korneel; Soroldoni, Daniele; Gajewski, Martin; Jülicher, Frank; Maerkl, Sebastian J; Deplancke, Bart; Oates, Andrew C (2012). Topology and Dynamics of the Zebrafish Segmentation Clock Core Circuit. PLoS Biology, 10(7):1-20.

Kebbel, Fabian

Goldie, Kenneth N; Abeyrathne, Priyanka; Kebbel, Fabian; Chami, Mohamed; Ringler, Philippe; Stahlberg, Henning (2014). Cryo-electron microscopy of membrane proteins. Methods in Molecular Biology, 1117:325-41.

Kemmerling, Simon

Giss, Dominic; Kemmerling, Simon; Dandey, Venkata; Stahlberg, Henning; Braun, Thomas (2014). Exploring the interactome: microfluidic isolation of proteins and interacting partners for quantitative analysis by electron microscopy. Analytical Chemistry, 86(10):4680-4687.

Kesavapany, S

Lim, L; Jackson-Lewis, V; Wong, L C; Shui, G H; Goh, A X H; Kesavapany, S; Jenner, A M; Fivaz, M; Przedborski, S; Wenk, M R (2012). Lanosterol induces mitochondrial uncoupling and protects dopaminergic neurons from cell death in a model for Parkinson's disease. Cell Death and Differentiation, 19(3):416-27.

Kessler, F

Shapiguzov, A; Ingelsson, B; Samol, I; Andres, C; Kessler, F; Rochaix, J -D; Vener, A V; Goldschmidt-Clermont, M (2010). The PPH1 phosphatase is specifically involved in LHCII dephosphorylation and state transitions in Arabidopsis. Proceedings of the National Academy of Sciences of the United States of America, 107(10):4782-4787.

Kiefer, P

Kiefer, P; Schmitt, U; Vorholt, J A (2013). eMZed: an open source framework in Python for rapid and interactive development of LC/MS data analysis workflows. Bioinformatics, 29(7):963-964.

Kierzkowski, D

Guenot, B; Bayer, E; Kierzkowski, D; Smith, R S; Mandel, T; Zadnikova, P; Benkova, E; Kuhlemeier, C (2012). PIN1-Independent Leaf Initiation in Arabidopsis. Plant Physiology, 159(4):1501-1510.

Kim, Woojin S

Cheng, Danni; Jenner, Andrew M; Shui, Guanghou; Cheong, Wei Fun; Mitchell, Todd W; Nealon, Jessica R; Kim, Woojin S; McCann, Heather; Wenk, Markus R; Halliday, Glenda M; Garner, Brett (2011). Lipid pathway alterations in Parkinson's disease primary visual cortex. PLoS ONE, 6(2):e17299.

Kinoshita, Taroh

Loizides-Mangold, Ursula; David, Fabrice P A; Nesatyy, Victor J; Kinoshita, Taroh; Riezman, Howard (2012). Glycosylphosphatidylinositol anchors regulate glycosphingolipid levels. Journal of Lipid Research, 53(8):1522-34.

Kisko, Kaisa

Leppänen, Veli-Matti; Tvorogov, Denis; Kisko, Kaisa; Prota, Andrea E; Jeltsch, Michael; Anisimov, Andrey; Markovic-Mueller, Sandra; Stuttfeld, Edward; Goldie, Kenneth N; Ballmer-Hofer, Kurt; Alitalo, Kari (2013). Structural and mechanistic insights into VEGF receptor 3 ligand binding and activation. Proceedings of the National Academy of Sciences of the United States of America, 110(32):12960-12965.

Klotzsch, Enrico

Schoen, Ingmar; Ries, Jonas; Klotzsch, Enrico; Ewers, Helge; Vogel, Viola (2011). Binding-activated localization microscopy of DNA structures. Nano letters, 11(9):4008-4011.

Kochova, P

Routier-Kierzkowska, A -L; Weber, A; Kochova, P; Felekis, D; Nelson, B J; Kuhlemeier, C; Smith, R S (2012). Cellular Force Microscopy for in Vivo Measurements of Plant Tissue Mechanics. Plant Physiology, 158(4):1514-1522.

Koenig, D P

Chitwood, D H; Headland, L R; Ranjan, A; Martinez, C C; Braybrook, S A; Koenig, D P; Kuhlemeier, C; Smith, R S; Sinha, N R (2012). Leaf Asymmetry as a Developmental Constraint Imposed by Auxin-Dependent Phyllotactic Patterning. Plant Cell, 24(6):2318-2327.

Koeppl, Heinz

Koeppl, Heinz; Zechner, Christoph; Ganguly, Arnab; Pelet, Serge; Peter, Matthias (2012). Accounting for extrinsic variability in the estimation of stochastic rate constants. International Journal of Robust and Nonlinear Control, 22(10):1103-1119.

Kotte, Oliver

Kotte, Oliver; Heinemann, Matthias (2009). A divide-and-conquer approach to analyze underdetermined biochemical models. Bioinformatics, 25(4):519-525.

Koumoutsakos, P

Bayati, B; Chatelain, P; Koumoutsakos, P (2009). D-leaping: Accelerating stochastic simulation algorithms for reactions with delays. Journal of Computational Physics, 228(16):5908-5916.

Mjolsness, E; Orendorff, D; Chatelain, P; Koumoutsakos, P (2009). An exact accelerated stochastic simulation algorithm. The Journal of chemical physics, 130(14):144110.

Milde, F; Bergdorf, M; Koumoutsakos, P (2008). A hybrid model for three-dimensional simulations of sprouting angiogenesis. Biophysical journal, 95(7):3146-60.

Rossinelli, D; Bayati, B; Koumoutsakos, P (2008). Accelerated stochastic and hybrid methods for spatial simulations of reaction-diffusion systems. Chemical Physics Letters, 451(1-3):136 - 140.

Kowal, J

Kudryashev, M; Stenta, M; Schmelz, S; Amstutz, M; Wiesand, U; Castano-Diez, D; Degiacomi, M T; Munnich, S; Bleck, C K; Kowal, J; Diepold, A; Heinz, D W; Dal Peraro, M; Cornelis, G R; Stahlberg, H (2013). In situ structural analysis of the Yersinia enterocolitica injectisome. eLife, 2:e00792-e00792.

Kowal, Julia

Kowal, Julia; Chami, Mohamed; Baumgartner, Paul; Arheit, Marcel; Chiu, Po-Lin; Rangl, Martina; Scheuring, Simon; Schröder, Gunnar F; Nimigean, Crina M; Stahlberg, Henning (2014). Ligand-induced structural changes in the cyclic nucleotide-modulated potassium channel MloK1. Nature Communications, 5:3106.

Krier, I

Bonhoure, N; Bounova, G; Bernasconi, D; Praz, V; Lammers, F; Canella, D; Willis, I M; Herr, W; Hernandez, N; Delorenzi, M; Hernandez, N; Delorenzi, M; Deplancke, B; Desvergne, B; Guex, N; Herr, W; Naef, F; Rougemont, J; Schibler, U; Andersin, T; Cousin, P; Gilardi, F; Gos, P; Lammers, F; Raghav, S; Villeneuve, D; Fabbretti, R; Vlegel, V; Xenarios, I; Migliavacca, E; Praz, V; David, F; Jarosz, Y; Kuznetsov, D; Liechti, R; Martin, O; Delafontaine, J; Cajan, J; Gustafson, K; Krier, I; Leleu, M; Molina, N; Naldi, A; Rib, L; Symul, L; Bounova, G (2014). Quantifying ChIP-seq data: a spiking method providing an internal reference for sample-to-sample normalization. Genome Research, 24(7):1157-1168.

Krier, Irina

Simicevic, Jovan; Schmid, Adrien W; Gilardoni, Paola A; Zoller, Benjamin; Raghav, Sunil K; Krier, Irina; Gubelmann, Carinne; Lisacek, Frédérique; Naef, Felix; Moniatte, Marc; Deplancke, Bart (2013). Absolute quantification of transcription factors during cellular differentiation using multiplexed targeted proteomics. Nature Methods, 10(6):570-576.

Kudryashev, M

Kudryashev, M; Stenta, M; Schmelz, S; Amstutz, M; Wiesand, U; Castano-Diez, D; Degiacomi, M T; Munnich, S; Bleck, C K; Kowal, J; Diepold, A; Heinz, D W; Dal Peraro, M; Cornelis, G R; Stahlberg, H (2013). In situ structural analysis of the Yersinia enterocolitica injectisome. eLife, 2:e00792-e00792.

Dudkina, N V; Kudryashev, M; Stahlberg, H; Boekema, E J (2011). Interaction of complexes I, III, and IV within the bovine respirasome by single particle cryoelectron tomography. Proceedings of the National Academy of Sciences of the United States of America, 108(37):15196-15200.

Kudryashev, Mikhail

Lemgruber, Leandro; Kudryashev, Mikhail; Dekiwadia, Chaitali; Riglar, David T; Baum, Jake; Stahlberg, Henning; Ralph, Stuart A; Frischknecht, Friedrich (2013). Cryo-electron tomography reveals four-membrane architecture of the Plasmodium apicoplast. Malaria Journal, 12:25.

Kudryashev, Mikhail; Castaño-Díez, Daniel; Stahlberg, Henning (2012). Limiting factors in single particle cryo electron tomography. Computational and Structural Biotechnology Journal, 1(2):online.

Kuhlemeier, C

Routier-Kierzkowska, A -L; Weber, A; Kochova, P; Felekis, D; Nelson, B J; Kuhlemeier, C; Smith, R S (2012). Cellular Force Microscopy for in Vivo Measurements of Plant Tissue Mechanics. Plant Physiology, 158(4):1514-1522.

Chitwood, D H; Headland, L R; Ranjan, A; Martinez, C C; Braybrook, S A; Koenig, D P; Kuhlemeier, C; Smith, R S; Sinha, N R (2012). Leaf Asymmetry as a Developmental Constraint Imposed by Auxin-Dependent Phyllotactic Patterning. Plant Cell, 24(6):2318-2327.

Guenot, B; Bayer, E; Kierzkowski, D; Smith, R S; Mandel, T; Zadnikova, P; Benkova, E; Kuhlemeier, C (2012). PIN1-Independent Leaf Initiation in Arabidopsis. Plant Physiology, 159(4):1501-1510.

Bayer, E M; Smith, R S; Mandel, T; Nakayama, N; Sauer, M; Prusinkiewicz, P; Kuhlemeier, C (2009). Integration of transport-based models for phyllotaxis and midvein formation. Genes and Development, 23(3):373-384.

Kuznetsov, D

Bonhoure, N; Bounova, G; Bernasconi, D; Praz, V; Lammers, F; Canella, D; Willis, I M; Herr, W; Hernandez, N; Delorenzi, M; Hernandez, N; Delorenzi, M; Deplancke, B; Desvergne, B; Guex, N; Herr, W; Naef, F; Rougemont, J; Schibler, U; Andersin, T; Cousin, P; Gilardi, F; Gos, P; Lammers, F; Raghav, S; Villeneuve, D; Fabbretti, R; Vlegel, V; Xenarios, I; Migliavacca, E; Praz, V; David, F; Jarosz, Y; Kuznetsov, D; Liechti, R; Martin, O; Delafontaine, J; Cajan, J; Gustafson, K; Krier, I; Leleu, M; Molina, N; Naldi, A; Rib, L; Symul, L; Bounova, G (2014). Quantifying ChIP-seq data: a spiking method providing an internal reference for sample-to-sample normalization. Genome Research, 24(7):1157-1168.

Kyewski, Bruno

Papadopoulou, Aikaterini S; Dooley, James; Linterman, Michelle A; Pierson, Wim; Ucar, Olga; Kyewski, Bruno; Zuklys, Saulius; Hollander, Georg A; Matthys, Patrick; Gray, Daniel H D; De Strooper, Bart; Liston, Adrian (2011). The thymic epithelial microRNA network elevates the threshold for infection-associated thymic involution via miR-29a mediated suppression of the IFN-α receptor. Nature Immunology, 13(2):181-187.

Lammers, F

Bonhoure, N; Bounova, G; Bernasconi, D; Praz, V; Lammers, F; Canella, D; Willis, I M; Herr, W; Hernandez, N; Delorenzi, M; Hernandez, N; Delorenzi, M; Deplancke, B; Desvergne, B; Guex, N; Herr, W; Naef, F; Rougemont, J; Schibler, U; Andersin, T; Cousin, P; Gilardi, F; Gos, P; Lammers, F; Raghav, S; Villeneuve, D; Fabbretti, R; Vlegel, V; Xenarios, I; Migliavacca, E; Praz, V; David, F; Jarosz, Y; Kuznetsov, D; Liechti, R; Martin, O; Delafontaine, J; Cajan, J; Gustafson, K; Krier, I; Leleu, M; Molina, N; Naldi, A; Rib, L; Symul, L; Bounova, G (2014). Quantifying ChIP-seq data: a spiking method providing an internal reference for sample-to-sample normalization. Genome Research, 24(7):1157-1168.

Bonhoure, N; Bounova, G; Bernasconi, D; Praz, V; Lammers, F; Canella, D; Willis, I M; Herr, W; Hernandez, N; Delorenzi, M; Hernandez, N; Delorenzi, M; Deplancke, B; Desvergne, B; Guex, N; Herr, W; Naef, F; Rougemont, J; Schibler, U; Andersin, T; Cousin, P; Gilardi, F; Gos, P; Lammers, F; Raghav, S; Villeneuve, D; Fabbretti, R; Vlegel, V; Xenarios, I; Migliavacca, E; Praz, V; David, F; Jarosz, Y; Kuznetsov, D; Liechti, R; Martin, O; Delafontaine, J; Cajan, J; Gustafson, K; Krier, I; Leleu, M; Molina, N; Naldi, A; Rib, L; Symul, L; Bounova, G (2014). Quantifying ChIP-seq data: a spiking method providing an internal reference for sample-to-sample normalization. Genome Research, 24(7):1157-1168.

Lane, Lydie

Mary, Camille; Duek, Paula; Salleron, Lisa; Tienz, Petra; Bumann, Dirk; Bairoch, Amos; Lane, Lydie (2012). Functional Identification of APIP as Human mtnB, a Key Enzyme in the Methionine Salvage Pathway. PLoS ONE, 7(12):e52877.

Lanza, Valentina

Bailly-Bechet, Marc; Benecke, Arndt; Hardt, Wolf Dietrich; Lanza, Valentina; Sturm, Alexander; Zecchina, Riccardo (2011). An externally modulated, noise-driven switch for the regulation of SPI1 in Salmonella enterica serovar Typhimurium. Journal of Mathematical Biology, 63(4):637-662.

Le Martelot, Gwendal

Gilardi, Federica; Migliavacca, Eugenia; Naldi, Aurélien; Baruchet, Michaël; Canella, Donatella; Le Martelot, Gwendal; Guex, Nicolas; Desvergne, Béatrice (2014). Genome-Wide Analysis of SREBP1 Activity around the Clock Reveals Its Combined Dependency on Nutrient and Circadian Signals. PLoS Genetics, 10(3):e1004155.

Le Martelot, Gwendal; Canella, Donatella; Symul, Laura; Migliavacca, Eugenia; Gilardi, Federica; Liechti, Robin; Martin, Olivier; Harshman, Keith; Delorenzi, Mauro; Desvergne, Béatrice; Herr, Winship; Deplancke, Bart; Schibler, Ueli; Rougemont, Jacques; Guex, Nicolas; Hernandez, Nouria; Naef, Felix (2012). Genome-wide RNA polymerase II profiles and RNA accumulation reveal kinetics of transcription and associated epigenetic changes during diurnal cycles. PLoS Biology, 10(11):e1001442.

Le Rhun, Danielle

Vayssier-Taussat, Muriel; Le Rhun, Danielle; Deng, Hong Kuan; Biville, Francis; Cescau, Sandra; Danchin, Antoine; Marignac, Geneviève; Lenaour, Evelyne; Boulouis, Henri Jean; Mavris, Maria; Arnaud, Lionel; Yang, Huanming; Wang, Jing; Quebatte, Maxime; Engel, Philipp; Saenz, Henri; Dehio, Christoph (2010). The Trw Type IV Secretion System of Bartonella Mediates Host-Specific Adhesion to Erythrocytes. PLoS Pathogens, 6(6):e1000946.

Lee, Sung Sik

Dechant, Reinhard; Binda, Matteo; Lee, Sung Sik; Pelet, Serge; Winderickx, Joris; Peter, Matthias (2010). Cytosolic pH is a second messenger for glucose and regulates the PKA pathway through V‐ATPase. EMBO Journal Online, 29(15):2515-2526.

Leleu, M

Bonhoure, N; Bounova, G; Bernasconi, D; Praz, V; Lammers, F; Canella, D; Willis, I M; Herr, W; Hernandez, N; Delorenzi, M; Hernandez, N; Delorenzi, M; Deplancke, B; Desvergne, B; Guex, N; Herr, W; Naef, F; Rougemont, J; Schibler, U; Andersin, T; Cousin, P; Gilardi, F; Gos, P; Lammers, F; Raghav, S; Villeneuve, D; Fabbretti, R; Vlegel, V; Xenarios, I; Migliavacca, E; Praz, V; David, F; Jarosz, Y; Kuznetsov, D; Liechti, R; Martin, O; Delafontaine, J; Cajan, J; Gustafson, K; Krier, I; Leleu, M; Molina, N; Naldi, A; Rib, L; Symul, L; Bounova, G (2014). Quantifying ChIP-seq data: a spiking method providing an internal reference for sample-to-sample normalization. Genome Research, 24(7):1157-1168.

Lemgruber, Leandro

Lemgruber, Leandro; Kudryashev, Mikhail; Dekiwadia, Chaitali; Riglar, David T; Baum, Jake; Stahlberg, Henning; Ralph, Stuart A; Frischknecht, Friedrich (2013). Cryo-electron tomography reveals four-membrane architecture of the Plasmodium apicoplast. Malaria Journal, 12:25.

Lenaour, Evelyne

Vayssier-Taussat, Muriel; Le Rhun, Danielle; Deng, Hong Kuan; Biville, Francis; Cescau, Sandra; Danchin, Antoine; Marignac, Geneviève; Lenaour, Evelyne; Boulouis, Henri Jean; Mavris, Maria; Arnaud, Lionel; Yang, Huanming; Wang, Jing; Quebatte, Maxime; Engel, Philipp; Saenz, Henri; Dehio, Christoph (2010). The Trw Type IV Secretion System of Bartonella Mediates Host-Specific Adhesion to Erythrocytes. PLoS Pathogens, 6(6):e1000946.

Leppänen, Veli-Matti

Leppänen, Veli-Matti; Tvorogov, Denis; Kisko, Kaisa; Prota, Andrea E; Jeltsch, Michael; Anisimov, Andrey; Markovic-Mueller, Sandra; Stuttfeld, Edward; Goldie, Kenneth N; Ballmer-Hofer, Kurt; Alitalo, Kari (2013). Structural and mechanistic insights into VEGF receptor 3 ligand binding and activation. Proceedings of the National Academy of Sciences of the United States of America, 110(32):12960-12965.

Li, Guoxin

Hosta-Rigau, Leticia; Jensen, Bettina E B; Fjeldsø, Kit S; Postma, Almar; Li, Guoxin; Goldie, Kenneth N; Albericio, Fernando; Zelikin, Alexander N; Städler, Brigitte (2012). Drug Delivery: Surface-Adhered Composite Poly(Vinyl Alcohol) Physical Hydrogels: Polymersome-Aided Delivery of Therapeutic Small Molecules. Advanced Healthcare Materials, 1(6):791-5.

Li, Yunpeng

Smith, Kevin; Li, Yunpeng; Piccinini, Filippo; Csucs, Gabor; Balazs, Csaba; Bevilacqua, Alessandro; Horvath, Peter (2015). CIDRE: an illumination-correction method for optical microscopy. Nature Methods, 12(5):404-406.

Liechti, R

Bonhoure, N; Bounova, G; Bernasconi, D; Praz, V; Lammers, F; Canella, D; Willis, I M; Herr, W; Hernandez, N; Delorenzi, M; Hernandez, N; Delorenzi, M; Deplancke, B; Desvergne, B; Guex, N; Herr, W; Naef, F; Rougemont, J; Schibler, U; Andersin, T; Cousin, P; Gilardi, F; Gos, P; Lammers, F; Raghav, S; Villeneuve, D; Fabbretti, R; Vlegel, V; Xenarios, I; Migliavacca, E; Praz, V; David, F; Jarosz, Y; Kuznetsov, D; Liechti, R; Martin, O; Delafontaine, J; Cajan, J; Gustafson, K; Krier, I; Leleu, M; Molina, N; Naldi, A; Rib, L; Symul, L; Bounova, G (2014). Quantifying ChIP-seq data: a spiking method providing an internal reference for sample-to-sample normalization. Genome Research, 24(7):1157-1168.

Liechti, Robin

Le Martelot, Gwendal; Canella, Donatella; Symul, Laura; Migliavacca, Eugenia; Gilardi, Federica; Liechti, Robin; Martin, Olivier; Harshman, Keith; Delorenzi, Mauro; Desvergne, Béatrice; Herr, Winship; Deplancke, Bart; Schibler, Ueli; Rougemont, Jacques; Guex, Nicolas; Hernandez, Nouria; Naef, Felix (2012). Genome-wide RNA polymerase II profiles and RNA accumulation reveal kinetics of transcription and associated epigenetic changes during diurnal cycles. PLoS Biology, 10(11):e1001442.

Lim, L

Lim, L; Jackson-Lewis, V; Wong, L C; Shui, G H; Goh, A X H; Kesavapany, S; Jenner, A M; Fivaz, M; Przedborski, S; Wenk, M R (2012). Lanosterol induces mitochondrial uncoupling and protects dopaminergic neurons from cell death in a model for Parkinson's disease. Cell Death and Differentiation, 19(3):416-27.

Limenitakis, Julien

Limenitakis, Julien; Oppenheim, Rebecca D; Creek, Darren J; Foth, Bernardo J; Barrett, Michael P; Soldati-Favre, Dominique (2013). The 2-methylcitrate cycle is implicated in the detoxification of propionate in Toxoplasma gondii. Molecular Microbiology, 87(4):894-908.

Linterman, Michelle A

Papadopoulou, Aikaterini S; Dooley, James; Linterman, Michelle A; Pierson, Wim; Ucar, Olga; Kyewski, Bruno; Zuklys, Saulius; Hollander, Georg A; Matthys, Patrick; Gray, Daniel H D; De Strooper, Bart; Liston, Adrian (2011). The thymic epithelial microRNA network elevates the threshold for infection-associated thymic involution via miR-29a mediated suppression of the IFN-α receptor. Nature Immunology, 13(2):181-187.

Lisacek, Frédérique

Simicevic, Jovan; Schmid, Adrien W; Gilardoni, Paola A; Zoller, Benjamin; Raghav, Sunil K; Krier, Irina; Gubelmann, Carinne; Lisacek, Frédérique; Naef, Felix; Moniatte, Marc; Deplancke, Bart (2013). Absolute quantification of transcription factors during cellular differentiation using multiplexed targeted proteomics. Nature Methods, 10(6):570-576.

Liston, Adrian

Papadopoulou, Aikaterini S; Dooley, James; Linterman, Michelle A; Pierson, Wim; Ucar, Olga; Kyewski, Bruno; Zuklys, Saulius; Hollander, Georg A; Matthys, Patrick; Gray, Daniel H D; De Strooper, Bart; Liston, Adrian (2011). The thymic epithelial microRNA network elevates the threshold for infection-associated thymic involution via miR-29a mediated suppression of the IFN-α receptor. Nature Immunology, 13(2):181-187.

Loewith, Robbie

Loewith, Robbie; Hall, Michael N (2011). Target of Rapamycin (TOR) in Nutrient Signaling and Growth Control. Genetics, 189:1177 -1201.

Loizides-Mangold, Ursula

Loizides-Mangold, Ursula; David, Fabrice P A; Nesatyy, Victor J; Kinoshita, Taroh; Riezman, Howard (2012). Glycosylphosphatidylinositol anchors regulate glycosphingolipid levels. Journal of Lipid Research, 53(8):1522-34.

Ludwig, Christina

Sunnåker, Mikael; Zamora-Sillero, Elias; Dechant, Reinhard; Ludwig, Christina; Busetto, Alberto Giovanni; Wagner, Andreas; Stelling, Joerg (2013). Automatic Generation of Predictive Dynamic Models Reveals Nuclear Phosphorylation as the Key Msn2 Control Mechanism. Science Signaling, 6(277):ra41.

Lutolf, Matthias P

Woodruff, Kristina; Fidalgo, Luis M; Gobaa, Samy; Lutolf, Matthias P; Maerkl, Sebastian J (2013). Live Mammalian Cell Arrays. Nature Methods, 10(6):550-552.

Lygeros, John

Cinquemani, Eugenio; Milias-Argeitis, Andreas; Summers, Sean; Lygeros, John (2008). Stochastic dynamics of genetic networks: modelling and parameter identification. Bioinformatics, 24(23):2748-2754.

Maerkl, Sebastian J

Woodruff, Kristina; Fidalgo, Luis M; Gobaa, Samy; Lutolf, Matthias P; Maerkl, Sebastian J (2013). Live Mammalian Cell Arrays. Nature Methods, 10(6):550-552.

Rockel, Sylvie; Geertz, Marcel; Hens, Korneel; Deplancke, Bart; Maerkl, Sebastian J (2012). iSLIM: a comprehensive approach to mapping and characterizing gene regulatory networks. Nucleic Acids Research:1-8.

Geertz, Marcel; Shore, David; Maerkl, Sebastian J (2012). Massively parallel measurements of molecular interaction kinetics on a microfluidic platform. Proceedings of the National Academy of Sciences of the United States of America, 109(41):16540-16545.

Schröter, Christian; Ares, Saúl; Morelli, Luis G; Isakova, Alina; Hens, Korneel; Soroldoni, Daniele; Gajewski, Martin; Jülicher, Frank; Maerkl, Sebastian J; Deplancke, Bart; Oates, Andrew C (2012). Topology and Dynamics of the Zebrafish Segmentation Clock Core Circuit. PLoS Biology, 10(7):1-20.

Rajkumar, Arun S; Maerkl, Sebastian J (2012). Rapid Synthesis Of Defined Eukaryotic Promoter Libraries. ACS Synthetic Biology, 1:483-490.

Geertz, Marcel; Rockel, Sylvie; Maerkl, Sebastian J (2012). A high-throughput microfluidic method for generating and characterizing transcription factor mutant libraries. Methods in Molecular Biology, 813:107-123.

Maerkl, Sebastian J (2011). Next generation microfluidic platforms for high-throughput protein biochemistry. Current Opinion in Biotechnology, 22(1):59-65.

Geertz, Marcel; Maerkl, Sebastian J (2010). Experimental strategies for studying transcription factor-DNA binding specificities. Briefings in Functional Genomics:1-12.

Maerkl, Sebastian J (2009). Microfluidic High-Throughput Screening. Integrative Biology, 1:19-29.

Mandel, T

Guenot, B; Bayer, E; Kierzkowski, D; Smith, R S; Mandel, T; Zadnikova, P; Benkova, E; Kuhlemeier, C (2012). PIN1-Independent Leaf Initiation in Arabidopsis. Plant Physiology, 159(4):1501-1510.

Bayer, E M; Smith, R S; Mandel, T; Nakayama, N; Sauer, M; Prusinkiewicz, P; Kuhlemeier, C (2009). Integration of transport-based models for phyllotaxis and midvein formation. Genes and Development, 23(3):373-384.

Marignac, Geneviève

Vayssier-Taussat, Muriel; Le Rhun, Danielle; Deng, Hong Kuan; Biville, Francis; Cescau, Sandra; Danchin, Antoine; Marignac, Geneviève; Lenaour, Evelyne; Boulouis, Henri Jean; Mavris, Maria; Arnaud, Lionel; Yang, Huanming; Wang, Jing; Quebatte, Maxime; Engel, Philipp; Saenz, Henri; Dehio, Christoph (2010). The Trw Type IV Secretion System of Bartonella Mediates Host-Specific Adhesion to Erythrocytes. PLoS Pathogens, 6(6):e1000946.

Markovic-Mueller, Sandra

Leppänen, Veli-Matti; Tvorogov, Denis; Kisko, Kaisa; Prota, Andrea E; Jeltsch, Michael; Anisimov, Andrey; Markovic-Mueller, Sandra; Stuttfeld, Edward; Goldie, Kenneth N; Ballmer-Hofer, Kurt; Alitalo, Kari (2013). Structural and mechanistic insights into VEGF receptor 3 ligand binding and activation. Proceedings of the National Academy of Sciences of the United States of America, 110(32):12960-12965.

Marrink, Siewert J

Polyansky, Anton A; Ramaswamy, Rajesh; Volynsky, Pavel E; Sbalzarini, Ivo F; Marrink, Siewert J; Efremov, Roman G (2010). Antimicrobial Peptides Induce Growth of Phosphatidylglycerol Domains in a Model Bacterial Membrane. Journal of Physical Chemistry Letters, 1(20):3108-3111.

Martin, O

Bonhoure, N; Bounova, G; Bernasconi, D; Praz, V; Lammers, F; Canella, D; Willis, I M; Herr, W; Hernandez, N; Delorenzi, M; Hernandez, N; Delorenzi, M; Deplancke, B; Desvergne, B; Guex, N; Herr, W; Naef, F; Rougemont, J; Schibler, U; Andersin, T; Cousin, P; Gilardi, F; Gos, P; Lammers, F; Raghav, S; Villeneuve, D; Fabbretti, R; Vlegel, V; Xenarios, I; Migliavacca, E; Praz, V; David, F; Jarosz, Y; Kuznetsov, D; Liechti, R; Martin, O; Delafontaine, J; Cajan, J; Gustafson, K; Krier, I; Leleu, M; Molina, N; Naldi, A; Rib, L; Symul, L; Bounova, G (2014). Quantifying ChIP-seq data: a spiking method providing an internal reference for sample-to-sample normalization. Genome Research, 24(7):1157-1168.

Martin, Olivier

Le Martelot, Gwendal; Canella, Donatella; Symul, Laura; Migliavacca, Eugenia; Gilardi, Federica; Liechti, Robin; Martin, Olivier; Harshman, Keith; Delorenzi, Mauro; Desvergne, Béatrice; Herr, Winship; Deplancke, Bart; Schibler, Ueli; Rougemont, Jacques; Guex, Nicolas; Hernandez, Nouria; Naef, Felix (2012). Genome-wide RNA polymerase II profiles and RNA accumulation reveal kinetics of transcription and associated epigenetic changes during diurnal cycles. PLoS Biology, 10(11):e1001442.

Martinez, C C

Chitwood, D H; Headland, L R; Ranjan, A; Martinez, C C; Braybrook, S A; Koenig, D P; Kuhlemeier, C; Smith, R S; Sinha, N R (2012). Leaf Asymmetry as a Developmental Constraint Imposed by Auxin-Dependent Phyllotactic Patterning. Plant Cell, 24(6):2318-2327.

Mary, Camille

Mary, Camille; Duek, Paula; Salleron, Lisa; Tienz, Petra; Bumann, Dirk; Bairoch, Amos; Lane, Lydie (2012). Functional Identification of APIP as Human mtnB, a Key Enzyme in the Methionine Salvage Pathway. PLoS ONE, 7(12):e52877.

Matthys, Patrick

Papadopoulou, Aikaterini S; Dooley, James; Linterman, Michelle A; Pierson, Wim; Ucar, Olga; Kyewski, Bruno; Zuklys, Saulius; Hollander, Georg A; Matthys, Patrick; Gray, Daniel H D; De Strooper, Bart; Liston, Adrian (2011). The thymic epithelial microRNA network elevates the threshold for infection-associated thymic involution via miR-29a mediated suppression of the IFN-α receptor. Nature Immunology, 13(2):181-187.

Mavris, Maria

Vayssier-Taussat, Muriel; Le Rhun, Danielle; Deng, Hong Kuan; Biville, Francis; Cescau, Sandra; Danchin, Antoine; Marignac, Geneviève; Lenaour, Evelyne; Boulouis, Henri Jean; Mavris, Maria; Arnaud, Lionel; Yang, Huanming; Wang, Jing; Quebatte, Maxime; Engel, Philipp; Saenz, Henri; Dehio, Christoph (2010). The Trw Type IV Secretion System of Bartonella Mediates Host-Specific Adhesion to Erythrocytes. PLoS Pathogens, 6(6):e1000946.

Mayor, Marcel

Hermes, Jens P; Sander, Fabian; Peterle, Torsten; Cioffi, Carla; Ringler, Philippe; Pfohl, Thomas; Mayor, Marcel (2011). Direct control of the spatial arrangement of gold nanoparticles in organic-inorganic hybrid superstructures. Small, 7(7):920-9.

Mazza, Christian

Feller, Chrystel; Gabriel, Jean-Pierre; Mazza, Christian; Yerly, Florence (2014). Pattern formation in auxin flux. Journal of Mathematical Biology, 68(4):879-909.

Mazé, Alain

Steeb, Benjamin; Claudi, Beatrice; Burton, Neil A; Tienz, Petra; Schmidt, Alexander; Farhan, Hesso; Mazé, Alain; Bumann, Dirk (2013). Parallel Exploitation of Diverse Host Nutrients Enhances Salmonella Virulence. PLoS Pathogens, 9(4):e1003301.

McCann, Heather

Cheng, Danni; Jenner, Andrew M; Shui, Guanghou; Cheong, Wei Fun; Mitchell, Todd W; Nealon, Jessica R; Kim, Woojin S; McCann, Heather; Wenk, Markus R; Halliday, Glenda M; Garner, Brett (2011). Lipid pathway alterations in Parkinson's disease primary visual cortex. PLoS ONE, 6(2):e17299.

Mercer, Jason

Schmidt, Florian Ingo; Bleck, Christopher Karl Ernst; Helenius, Ari; Mercer, Jason (2011). Vaccinia extracellular virions enter cells by macropinocytosis and acid-activated membrane rupture. EMBO Journal Online, 30(17):3647-3661.

Meyer-Schaller, Nathalie

Tiwari, Neha; Meyer-Schaller, Nathalie; Arnold, Phil; Antoniadis, Helena; Pachkov, Mikhail; van Nimwegen, Erik; Christofori, Gerhard (2013). Klf4 is a transcriptional regulator of genes critical for EMT, including Jnk1 (Mapk8). PLoS ONE, 8(2):e57329.

Tiwari, Neha; Tiwari, Vijay K; Waldmeier, Lorenz; Balwierz, Piotr J; Arnold, Phil; Pachkov, Mikhail; Meyer-Schaller, Nathalie; Schübeler, Dirk; van Nimwegen, Erik; Christofori, Gerhard (2013). Sox4 is a master regulator of epithelial-mesenchymal transition by controlling ezh2 expression and epigenetic reprogramming. Cancer Cell, 23(6):768-83.

Migliavacca, E

Bonhoure, N; Bounova, G; Bernasconi, D; Praz, V; Lammers, F; Canella, D; Willis, I M; Herr, W; Hernandez, N; Delorenzi, M; Hernandez, N; Delorenzi, M; Deplancke, B; Desvergne, B; Guex, N; Herr, W; Naef, F; Rougemont, J; Schibler, U; Andersin, T; Cousin, P; Gilardi, F; Gos, P; Lammers, F; Raghav, S; Villeneuve, D; Fabbretti, R; Vlegel, V; Xenarios, I; Migliavacca, E; Praz, V; David, F; Jarosz, Y; Kuznetsov, D; Liechti, R; Martin, O; Delafontaine, J; Cajan, J; Gustafson, K; Krier, I; Leleu, M; Molina, N; Naldi, A; Rib, L; Symul, L; Bounova, G (2014). Quantifying ChIP-seq data: a spiking method providing an internal reference for sample-to-sample normalization. Genome Research, 24(7):1157-1168.

Migliavacca, Eugenia

Gilardi, Federica; Migliavacca, Eugenia; Naldi, Aurélien; Baruchet, Michaël; Canella, Donatella; Le Martelot, Gwendal; Guex, Nicolas; Desvergne, Béatrice (2014). Genome-Wide Analysis of SREBP1 Activity around the Clock Reveals Its Combined Dependency on Nutrient and Circadian Signals. PLoS Genetics, 10(3):e1004155.

Le Martelot, Gwendal; Canella, Donatella; Symul, Laura; Migliavacca, Eugenia; Gilardi, Federica; Liechti, Robin; Martin, Olivier; Harshman, Keith; Delorenzi, Mauro; Desvergne, Béatrice; Herr, Winship; Deplancke, Bart; Schibler, Ueli; Rougemont, Jacques; Guex, Nicolas; Hernandez, Nouria; Naef, Felix (2012). Genome-wide RNA polymerase II profiles and RNA accumulation reveal kinetics of transcription and associated epigenetic changes during diurnal cycles. PLoS Biology, 10(11):e1001442.

Milde, F

Milde, F; Bergdorf, M; Koumoutsakos, P (2008). A hybrid model for three-dimensional simulations of sprouting angiogenesis. Biophysical journal, 95(7):3146-60.

Milias-Argeitis, Andreas

Cinquemani, Eugenio; Milias-Argeitis, Andreas; Summers, Sean; Lygeros, John (2008). Stochastic dynamics of genetic networks: modelling and parameter identification. Bioinformatics, 24(23):2748-2754.

Misselwitz, B

Truttmann, M C; Misselwitz, B; Huser, S; Hardt, W-D; Critchley, D R; Dehio, C (2011). Bartonella henselae engages inside-out and outside-in signaling by integrin 1 and talin1 during invasome-mediated bacterial uptake. Journal of Cell Science, 124(21):3591-3602.

Mitchell, Todd W

Cheng, Danni; Jenner, Andrew M; Shui, Guanghou; Cheong, Wei Fun; Mitchell, Todd W; Nealon, Jessica R; Kim, Woojin S; McCann, Heather; Wenk, Markus R; Halliday, Glenda M; Garner, Brett (2011). Lipid pathway alterations in Parkinson's disease primary visual cortex. PLoS ONE, 6(2):e17299.

Mjolsness, E

Mjolsness, E; Orendorff, D; Chatelain, P; Koumoutsakos, P (2009). An exact accelerated stochastic simulation algorithm. The Journal of chemical physics, 130(14):144110.

Moes, Suzette

Shimobayash, Mitsugu; Oppliger, Wolfgang; Moes, Suzette; Jenö, Paul; Hall, Michael N (2013). TORC1-regulated protein kinase Npr1 phosphorylates Orm to stimulate complex sphingolipid synthesis. Molecular Biology of the Cell, 24:870-881.

Soulard, Alexandre; Cremonesi, Alessio; Moes, Suzette; Schütz, Frédéric; Jenö, Paul; Hall, Michael N (2010). The Rapamycin-sensitive Phosphoproteome Reveals That TOR Controls Protein Kinase A Toward Some But Not All Substrates. Molecular Biology of the Cell, 21:3475-3486.

Moharana, Kedar

Moharana, Kedar; Zabeau, Lennart; Peelman, Frank; Ringler, Philippe; Stahlberg, Henning; Tavernier, Jan; Savvides, Savvas N (2014). Structural and mechanistic paradigm of leptin receptor activation revealed by complexes with wild-type and antagonist leptins. Structure, 22(6):866-877.

Molina, N

Bonhoure, N; Bounova, G; Bernasconi, D; Praz, V; Lammers, F; Canella, D; Willis, I M; Herr, W; Hernandez, N; Delorenzi, M; Hernandez, N; Delorenzi, M; Deplancke, B; Desvergne, B; Guex, N; Herr, W; Naef, F; Rougemont, J; Schibler, U; Andersin, T; Cousin, P; Gilardi, F; Gos, P; Lammers, F; Raghav, S; Villeneuve, D; Fabbretti, R; Vlegel, V; Xenarios, I; Migliavacca, E; Praz, V; David, F; Jarosz, Y; Kuznetsov, D; Liechti, R; Martin, O; Delafontaine, J; Cajan, J; Gustafson, K; Krier, I; Leleu, M; Molina, N; Naldi, A; Rib, L; Symul, L; Bounova, G (2014). Quantifying ChIP-seq data: a spiking method providing an internal reference for sample-to-sample normalization. Genome Research, 24(7):1157-1168.

Moniatte, Marc

Simicevic, Jovan; Schmid, Adrien W; Gilardoni, Paola A; Zoller, Benjamin; Raghav, Sunil K; Krier, Irina; Gubelmann, Carinne; Lisacek, Frédérique; Naef, Felix; Moniatte, Marc; Deplancke, Bart (2013). Absolute quantification of transcription factors during cellular differentiation using multiplexed targeted proteomics. Nature Methods, 10(6):570-576.

Morelli, Luis G

Schröter, Christian; Ares, Saúl; Morelli, Luis G; Isakova, Alina; Hens, Korneel; Soroldoni, Daniele; Gajewski, Martin; Jülicher, Frank; Maerkl, Sebastian J; Deplancke, Bart; Oates, Andrew C (2012). Topology and Dynamics of the Zebrafish Segmentation Clock Core Circuit. PLoS Biology, 10(7):1-20.

Moretti, Sébastien

Bernard, Thomas; Bridge, Alan; Morgat, Anne; Moretti, Sébastien; Xenarios, Ioannis; Pagni, Marco (2014). Reconciliation of metabolites and biochemical reactions for metabolic networks. Briefings in Bioinformatics, 15(1):123-135.

Morgat, Anne

Bernard, Thomas; Bridge, Alan; Morgat, Anne; Moretti, Sébastien; Xenarios, Ioannis; Pagni, Marco (2014). Reconciliation of metabolites and biochemical reactions for metabolic networks. Briefings in Bioinformatics, 15(1):123-135.

Morton de Lachapelle, Aitana

Hamaratoglu, Fisun; Morton de Lachapelle, Aitana; Pyrowolakis, George; Bergmann, Sven; Affolter, Markus (2011). Dpp signaling activity requires pentagone to scale with tissue size in the growing drosophila wing imaginal disc. PLoS Biology, 9:1-17.

Munglani, Gautam

Munglani, Gautam; Vetter, Roman; Wittel, Falk K; Herrmann, Hans J (2015). Orthotropic rotation-free thin shell elements. Computational Mechanics, 56(5):785-793.

Munnich, S

Kudryashev, M; Stenta, M; Schmelz, S; Amstutz, M; Wiesand, U; Castano-Diez, D; Degiacomi, M T; Munnich, S; Bleck, C K; Kowal, J; Diepold, A; Heinz, D W; Dal Peraro, M; Cornelis, G R; Stahlberg, H (2013). In situ structural analysis of the Yersinia enterocolitica injectisome. eLife, 2:e00792-e00792.

Mädler, Stefanie

Weidmann, Simon; Barylyuk, Konstantin; Nespovitaya, Nadezhda; Mädler, Stefanie; Zenobi, Renato (2013). A New, Modular Mass Calibrant for High-Mass MALDI-MS. Analytical Chemistry, 85:3425-3432.

Müller, Shirley A

Ramakrishnan, Chandrasekhar; Bieri, Andrej; Sauter, Nora; Roizard, Sophie; Ringler, Philippe; Müller, Shirley A; Goldie, Kenneth N; Enimanev, Kaloyan; Stahlberg, Henning; Rinn, Bernd; Braun, Thomas (2014). openBEB: open biological experiment browser for correlative measurements. BMC Bioinformatics, 15:84.

Nadal-Ribelles, M

Pelet, S; Rudolf, F; Nadal-Ribelles, M; de Nadal, E; Posas, F; Peter, M (2011). Transient activation of the HOG MAPK pathway regulates bimodal gene expression. Science, 332(6030):732-735.

Naef, F

Bonhoure, N; Bounova, G; Bernasconi, D; Praz, V; Lammers, F; Canella, D; Willis, I M; Herr, W; Hernandez, N; Delorenzi, M; Hernandez, N; Delorenzi, M; Deplancke, B; Desvergne, B; Guex, N; Herr, W; Naef, F; Rougemont, J; Schibler, U; Andersin, T; Cousin, P; Gilardi, F; Gos, P; Lammers, F; Raghav, S; Villeneuve, D; Fabbretti, R; Vlegel, V; Xenarios, I; Migliavacca, E; Praz, V; David, F; Jarosz, Y; Kuznetsov, D; Liechti, R; Martin, O; Delafontaine, J; Cajan, J; Gustafson, K; Krier, I; Leleu, M; Molina, N; Naldi, A; Rib, L; Symul, L; Bounova, G (2014). Quantifying ChIP-seq data: a spiking method providing an internal reference for sample-to-sample normalization. Genome Research, 24(7):1157-1168.

Naef, Felix

Quinodoz, Mathieu; Gobet, Cédric; Naef, Felix; Gustafson, Kyle B (2014). Characteristic bimodal profiles of RNA polymerase II at thousands of active mammalian promoters. Genome Biology, 15(6):R85.

Simicevic, Jovan; Schmid, Adrien W; Gilardoni, Paola A; Zoller, Benjamin; Raghav, Sunil K; Krier, Irina; Gubelmann, Carinne; Lisacek, Frédérique; Naef, Felix; Moniatte, Marc; Deplancke, Bart (2013). Absolute quantification of transcription factors during cellular differentiation using multiplexed targeted proteomics. Nature Methods, 10(6):570-576.

Le Martelot, Gwendal; Canella, Donatella; Symul, Laura; Migliavacca, Eugenia; Gilardi, Federica; Liechti, Robin; Martin, Olivier; Harshman, Keith; Delorenzi, Mauro; Desvergne, Béatrice; Herr, Winship; Deplancke, Bart; Schibler, Ueli; Rougemont, Jacques; Guex, Nicolas; Hernandez, Nouria; Naef, Felix (2012). Genome-wide RNA polymerase II profiles and RNA accumulation reveal kinetics of transcription and associated epigenetic changes during diurnal cycles. PLoS Biology, 10(11):e1001442.

Nakayama, N

Bayer, E M; Smith, R S; Mandel, T; Nakayama, N; Sauer, M; Prusinkiewicz, P; Kuhlemeier, C (2009). Integration of transport-based models for phyllotaxis and midvein formation. Genes and Development, 23(3):373-384.

Naldi, A

Bonhoure, N; Bounova, G; Bernasconi, D; Praz, V; Lammers, F; Canella, D; Willis, I M; Herr, W; Hernandez, N; Delorenzi, M; Hernandez, N; Delorenzi, M; Deplancke, B; Desvergne, B; Guex, N; Herr, W; Naef, F; Rougemont, J; Schibler, U; Andersin, T; Cousin, P; Gilardi, F; Gos, P; Lammers, F; Raghav, S; Villeneuve, D; Fabbretti, R; Vlegel, V; Xenarios, I; Migliavacca, E; Praz, V; David, F; Jarosz, Y; Kuznetsov, D; Liechti, R; Martin, O; Delafontaine, J; Cajan, J; Gustafson, K; Krier, I; Leleu, M; Molina, N; Naldi, A; Rib, L; Symul, L; Bounova, G (2014). Quantifying ChIP-seq data: a spiking method providing an internal reference for sample-to-sample normalization. Genome Research, 24(7):1157-1168.

Naldi, Aurélien

Gilardi, Federica; Migliavacca, Eugenia; Naldi, Aurélien; Baruchet, Michaël; Canella, Donatella; Le Martelot, Gwendal; Guex, Nicolas; Desvergne, Béatrice (2014). Genome-Wide Analysis of SREBP1 Activity around the Clock Reveals Its Combined Dependency on Nutrient and Circadian Signals. PLoS Genetics, 10(3):e1004155.

Nealon, Jessica R

Cheng, Danni; Jenner, Andrew M; Shui, Guanghou; Cheong, Wei Fun; Mitchell, Todd W; Nealon, Jessica R; Kim, Woojin S; McCann, Heather; Wenk, Markus R; Halliday, Glenda M; Garner, Brett (2011). Lipid pathway alterations in Parkinson's disease primary visual cortex. PLoS ONE, 6(2):e17299.

Nelson, B J

Routier-Kierzkowska, A -L; Weber, A; Kochova, P; Felekis, D; Nelson, B J; Kuhlemeier, C; Smith, R S (2012). Cellular Force Microscopy for in Vivo Measurements of Plant Tissue Mechanics. Plant Physiology, 158(4):1514-1522.

Nesatyy, Victor J

Loizides-Mangold, Ursula; David, Fabrice P A; Nesatyy, Victor J; Kinoshita, Taroh; Riezman, Howard (2012). Glycosylphosphatidylinositol anchors regulate glycosphingolipid levels. Journal of Lipid Research, 53(8):1522-34.

Nespovitaya, Nadezhda

Weidmann, Simon; Barylyuk, Konstantin; Nespovitaya, Nadezhda; Mädler, Stefanie; Zenobi, Renato (2013). A New, Modular Mass Calibrant for High-Mass MALDI-MS. Analytical Chemistry, 85:3425-3432.

Nimigean, Crina M

Kowal, Julia; Chami, Mohamed; Baumgartner, Paul; Arheit, Marcel; Chiu, Po-Lin; Rangl, Martina; Scheuring, Simon; Schröder, Gunnar F; Nimigean, Crina M; Stahlberg, Henning (2014). Ligand-induced structural changes in the cyclic nucleotide-modulated potassium channel MloK1. Nature Communications, 5:3106.

Oates, Andrew C

Schröter, Christian; Ares, Saúl; Morelli, Luis G; Isakova, Alina; Hens, Korneel; Soroldoni, Daniele; Gajewski, Martin; Jülicher, Frank; Maerkl, Sebastian J; Deplancke, Bart; Oates, Andrew C (2012). Topology and Dynamics of the Zebrafish Segmentation Clock Core Circuit. PLoS Biology, 10(7):1-20.

Ojosnegros, Samuel

Delgado-Eckert, Edgar; Ojosnegros, Samuel; Beerenwinkel, Niko (2011). The Evolution of Virulence in RNA Viruses under a Competition–Colonization Trade-Off. Bulletin of Mathematical Biology, 73(8):1881-1908.

Oppenheim, Rebecca D

Limenitakis, Julien; Oppenheim, Rebecca D; Creek, Darren J; Foth, Bernardo J; Barrett, Michael P; Soldati-Favre, Dominique (2013). The 2-methylcitrate cycle is implicated in the detoxification of propionate in Toxoplasma gondii. Molecular Microbiology, 87(4):894-908.

Oppliger, Wolfgang

Shimobayash, Mitsugu; Oppliger, Wolfgang; Moes, Suzette; Jenö, Paul; Hall, Michael N (2013). TORC1-regulated protein kinase Npr1 phosphorylates Orm to stimulate complex sphingolipid synthesis. Molecular Biology of the Cell, 24:870-881.

Zinzalla, Vittoria; Stracka, Daniele; Oppliger, Wolfgang; Hall, Michael N (2011). Activation of mTORC2 by Association with the Ribosome. Cell, 144:757-768.

Orendorff, D

Mjolsness, E; Orendorff, D; Chatelain, P; Koumoutsakos, P (2009). An exact accelerated stochastic simulation algorithm. The Journal of chemical physics, 130(14):144110.

Pachkov, Mikhail

Tiwari, Neha; Meyer-Schaller, Nathalie; Arnold, Phil; Antoniadis, Helena; Pachkov, Mikhail; van Nimwegen, Erik; Christofori, Gerhard (2013). Klf4 is a transcriptional regulator of genes critical for EMT, including Jnk1 (Mapk8). PLoS ONE, 8(2):e57329.

Tiwari, Neha; Tiwari, Vijay K; Waldmeier, Lorenz; Balwierz, Piotr J; Arnold, Phil; Pachkov, Mikhail; Meyer-Schaller, Nathalie; Schübeler, Dirk; van Nimwegen, Erik; Christofori, Gerhard (2013). Sox4 is a master regulator of epithelial-mesenchymal transition by controlling ezh2 expression and epigenetic reprogramming. Cancer Cell, 23(6):768-83.

Pagni, Marco

Bernard, Thomas; Bridge, Alan; Morgat, Anne; Moretti, Sébastien; Xenarios, Ioannis; Pagni, Marco (2014). Reconciliation of metabolites and biochemical reactions for metabolic networks. Briefings in Bioinformatics, 15(1):123-135.

Papadopoulou, Aikaterini S

Papadopoulou, Aikaterini S; Dooley, James; Linterman, Michelle A; Pierson, Wim; Ucar, Olga; Kyewski, Bruno; Zuklys, Saulius; Hollander, Georg A; Matthys, Patrick; Gray, Daniel H D; De Strooper, Bart; Liston, Adrian (2011). The thymic epithelial microRNA network elevates the threshold for infection-associated thymic involution via miR-29a mediated suppression of the IFN-α receptor. Nature Immunology, 13(2):181-187.

Parton, Robert G

Brankatschk, Ben; Pons, Véronique; Parton, Robert G; Gruenberg, Jean (2011). Role of SNX16 in the dynamics of tubulo-cisternal membrane domains of late endosomes. PLoS ONE, 6(7):e21771.

Paul, Grégory

Helmuth, Jo A; Paul, Grégory; Sbalzarini, Ivo F (2010). Beyond co-localization: inferring spatial interactions between sub-cellular structures from microscopy images. BMC Bioinformatics, 11(1):372.

Peelman, Frank

Moharana, Kedar; Zabeau, Lennart; Peelman, Frank; Ringler, Philippe; Stahlberg, Henning; Tavernier, Jan; Savvides, Savvas N (2014). Structural and mechanistic paradigm of leptin receptor activation revealed by complexes with wild-type and antagonist leptins. Structure, 22(6):866-877.

Pelet, S

Pelet, S; Rudolf, F; Nadal-Ribelles, M; de Nadal, E; Posas, F; Peter, M (2011). Transient activation of the HOG MAPK pathway regulates bimodal gene expression. Science, 332(6030):732-735.

Pelet, Serge

Koeppl, Heinz; Zechner, Christoph; Ganguly, Arnab; Pelet, Serge; Peter, Matthias (2012). Accounting for extrinsic variability in the estimation of stochastic rate constants. International Journal of Robust and Nonlinear Control, 22(10):1103-1119.

Pelet, Serge; Peter, Matthias (2011). Fluorescent-Based Quantitative Measurements of Signal Transduction in Single Cells. In: Koeppl, Heinz; Densmore, Douglas; Setti, Gianluca; di Bernardo, Mario. Design and Analysis of Biomolecular Circuits: Engineering Approaches to Systems and Synthetic Biology. New York, USA: Springer, 369-394.

Dechant, Reinhard; Binda, Matteo; Lee, Sung Sik; Pelet, Serge; Winderickx, Joris; Peter, Matthias (2010). Cytosolic pH is a second messenger for glucose and regulates the PKA pathway through V‐ATPase. EMBO Journal Online, 29(15):2515-2526.

Peter, M

Pelet, S; Rudolf, F; Nadal-Ribelles, M; de Nadal, E; Posas, F; Peter, M (2011). Transient activation of the HOG MAPK pathway regulates bimodal gene expression. Science, 332(6030):732-735.

Peter, Matthias

Koeppl, Heinz; Zechner, Christoph; Ganguly, Arnab; Pelet, Serge; Peter, Matthias (2012). Accounting for extrinsic variability in the estimation of stochastic rate constants. International Journal of Robust and Nonlinear Control, 22(10):1103-1119.

Pelet, Serge; Peter, Matthias (2011). Fluorescent-Based Quantitative Measurements of Signal Transduction in Single Cells. In: Koeppl, Heinz; Densmore, Douglas; Setti, Gianluca; di Bernardo, Mario. Design and Analysis of Biomolecular Circuits: Engineering Approaches to Systems and Synthetic Biology. New York, USA: Springer, 369-394.

Dechant, Reinhard; Binda, Matteo; Lee, Sung Sik; Pelet, Serge; Winderickx, Joris; Peter, Matthias (2010). Cytosolic pH is a second messenger for glucose and regulates the PKA pathway through V‐ATPase. EMBO Journal Online, 29(15):2515-2526.

Peterle, Torsten

Hermes, Jens P; Sander, Fabian; Peterle, Torsten; Cioffi, Carla; Ringler, Philippe; Pfohl, Thomas; Mayor, Marcel (2011). Direct control of the spatial arrangement of gold nanoparticles in organic-inorganic hybrid superstructures. Small, 7(7):920-9.

Pfohl, Thomas

Hermes, Jens P; Sander, Fabian; Peterle, Torsten; Cioffi, Carla; Ringler, Philippe; Pfohl, Thomas; Mayor, Marcel (2011). Direct control of the spatial arrangement of gold nanoparticles in organic-inorganic hybrid superstructures. Small, 7(7):920-9.

Piccinini, Filippo

Smith, Kevin; Li, Yunpeng; Piccinini, Filippo; Csucs, Gabor; Balazs, Csaba; Bevilacqua, Alessandro; Horvath, Peter (2015). CIDRE: an illumination-correction method for optical microscopy. Nature Methods, 12(5):404-406.

Pierson, Wim

Papadopoulou, Aikaterini S; Dooley, James; Linterman, Michelle A; Pierson, Wim; Ucar, Olga; Kyewski, Bruno; Zuklys, Saulius; Hollander, Georg A; Matthys, Patrick; Gray, Daniel H D; De Strooper, Bart; Liston, Adrian (2011). The thymic epithelial microRNA network elevates the threshold for infection-associated thymic involution via miR-29a mediated suppression of the IFN-α receptor. Nature Immunology, 13(2):181-187.

Polyansky, Anton A

Polyansky, Anton A; Ramaswamy, Rajesh; Volynsky, Pavel E; Sbalzarini, Ivo F; Marrink, Siewert J; Efremov, Roman G (2010). Antimicrobial Peptides Induce Growth of Phosphatidylglycerol Domains in a Model Bacterial Membrane. Journal of Physical Chemistry Letters, 1(20):3108-3111.

Pons, Véronique

Brankatschk, Ben; Pons, Véronique; Parton, Robert G; Gruenberg, Jean (2011). Role of SNX16 in the dynamics of tubulo-cisternal membrane domains of late endosomes. PLoS ONE, 6(7):e21771.

Posas, F

Pelet, S; Rudolf, F; Nadal-Ribelles, M; de Nadal, E; Posas, F; Peter, M (2011). Transient activation of the HOG MAPK pathway regulates bimodal gene expression. Science, 332(6030):732-735.

Postma, Almar

van der Westen, Rebecca; Hosta-Rigau, Leticia; Sutherland, Duncan S; Goldie, Kenneth N; Albericio, Fernando; Postma, Almar; Städler, Brigitte (2012). Myoblast cell interaction with polydopamine coated liposomes. Biointerphases, 7(1-4):8.

Hosta-Rigau, Leticia; Jensen, Bettina E B; Fjeldsø, Kit S; Postma, Almar; Li, Guoxin; Goldie, Kenneth N; Albericio, Fernando; Zelikin, Alexander N; Städler, Brigitte (2012). Drug Delivery: Surface-Adhered Composite Poly(Vinyl Alcohol) Physical Hydrogels: Polymersome-Aided Delivery of Therapeutic Small Molecules. Advanced Healthcare Materials, 1(6):791-5.

Praz, V

Bonhoure, N; Bounova, G; Bernasconi, D; Praz, V; Lammers, F; Canella, D; Willis, I M; Herr, W; Hernandez, N; Delorenzi, M; Hernandez, N; Delorenzi, M; Deplancke, B; Desvergne, B; Guex, N; Herr, W; Naef, F; Rougemont, J; Schibler, U; Andersin, T; Cousin, P; Gilardi, F; Gos, P; Lammers, F; Raghav, S; Villeneuve, D; Fabbretti, R; Vlegel, V; Xenarios, I; Migliavacca, E; Praz, V; David, F; Jarosz, Y; Kuznetsov, D; Liechti, R; Martin, O; Delafontaine, J; Cajan, J; Gustafson, K; Krier, I; Leleu, M; Molina, N; Naldi, A; Rib, L; Symul, L; Bounova, G (2014). Quantifying ChIP-seq data: a spiking method providing an internal reference for sample-to-sample normalization. Genome Research, 24(7):1157-1168.

Bonhoure, N; Bounova, G; Bernasconi, D; Praz, V; Lammers, F; Canella, D; Willis, I M; Herr, W; Hernandez, N; Delorenzi, M; Hernandez, N; Delorenzi, M; Deplancke, B; Desvergne, B; Guex, N; Herr, W; Naef, F; Rougemont, J; Schibler, U; Andersin, T; Cousin, P; Gilardi, F; Gos, P; Lammers, F; Raghav, S; Villeneuve, D; Fabbretti, R; Vlegel, V; Xenarios, I; Migliavacca, E; Praz, V; David, F; Jarosz, Y; Kuznetsov, D; Liechti, R; Martin, O; Delafontaine, J; Cajan, J; Gustafson, K; Krier, I; Leleu, M; Molina, N; Naldi, A; Rib, L; Symul, L; Bounova, G (2014). Quantifying ChIP-seq data: a spiking method providing an internal reference for sample-to-sample normalization. Genome Research, 24(7):1157-1168.

Prota, Andrea E

Leppänen, Veli-Matti; Tvorogov, Denis; Kisko, Kaisa; Prota, Andrea E; Jeltsch, Michael; Anisimov, Andrey; Markovic-Mueller, Sandra; Stuttfeld, Edward; Goldie, Kenneth N; Ballmer-Hofer, Kurt; Alitalo, Kari (2013). Structural and mechanistic insights into VEGF receptor 3 ligand binding and activation. Proceedings of the National Academy of Sciences of the United States of America, 110(32):12960-12965.

Prota, Andrea E; Bargsten, Katja; Zurwerra, Didier; Field, Jessica J; Díaz, José Fernando; Altmann, Karl-Heinz; Steinmetz, Michel O (2013). Molecular Mechanism of Action of Microtubule-Stabilizing Anticancer Agents. Science, 339(6119):587-590.

Prusinkiewicz, P

Bayer, E M; Smith, R S; Mandel, T; Nakayama, N; Sauer, M; Prusinkiewicz, P; Kuhlemeier, C (2009). Integration of transport-based models for phyllotaxis and midvein formation. Genes and Development, 23(3):373-384.

Przedborski, S

Lim, L; Jackson-Lewis, V; Wong, L C; Shui, G H; Goh, A X H; Kesavapany, S; Jenner, A M; Fivaz, M; Przedborski, S; Wenk, M R (2012). Lanosterol induces mitochondrial uncoupling and protects dopaminergic neurons from cell death in a model for Parkinson's disease. Cell Death and Differentiation, 19(3):416-27.

Psihoyios, George

Awile, Omar; Demirel, Ömer; Sbalzarini, Ivo F; Simos, Theodore E; Psihoyios, George; Tsitouras, Ch (2010). Toward an Object-Oriented Core of the PPM Library. In: International Conference of Numerical Analysis and Applied Mathematics (ICNAAM), Rhodes, Greece, 19 September 2010 - 25 September 2010, 1313-1316.

Pyrowolakis, George

Hamaratoglu, Fisun; Morton de Lachapelle, Aitana; Pyrowolakis, George; Bergmann, Sven; Affolter, Markus (2011). Dpp signaling activity requires pentagone to scale with tissue size in the growing drosophila wing imaginal disc. PLoS Biology, 9:1-17.

Quebatte, Maxime

Vayssier-Taussat, Muriel; Le Rhun, Danielle; Deng, Hong Kuan; Biville, Francis; Cescau, Sandra; Danchin, Antoine; Marignac, Geneviève; Lenaour, Evelyne; Boulouis, Henri Jean; Mavris, Maria; Arnaud, Lionel; Yang, Huanming; Wang, Jing; Quebatte, Maxime; Engel, Philipp; Saenz, Henri; Dehio, Christoph (2010). The Trw Type IV Secretion System of Bartonella Mediates Host-Specific Adhesion to Erythrocytes. PLoS Pathogens, 6(6):e1000946.

Quinodoz, Mathieu

Quinodoz, Mathieu; Gobet, Cédric; Naef, Felix; Gustafson, Kyle B (2014). Characteristic bimodal profiles of RNA polymerase II at thousands of active mammalian promoters. Genome Biology, 15(6):R85.

Raghav, S

Bonhoure, N; Bounova, G; Bernasconi, D; Praz, V; Lammers, F; Canella, D; Willis, I M; Herr, W; Hernandez, N; Delorenzi, M; Hernandez, N; Delorenzi, M; Deplancke, B; Desvergne, B; Guex, N; Herr, W; Naef, F; Rougemont, J; Schibler, U; Andersin, T; Cousin, P; Gilardi, F; Gos, P; Lammers, F; Raghav, S; Villeneuve, D; Fabbretti, R; Vlegel, V; Xenarios, I; Migliavacca, E; Praz, V; David, F; Jarosz, Y; Kuznetsov, D; Liechti, R; Martin, O; Delafontaine, J; Cajan, J; Gustafson, K; Krier, I; Leleu, M; Molina, N; Naldi, A; Rib, L; Symul, L; Bounova, G (2014). Quantifying ChIP-seq data: a spiking method providing an internal reference for sample-to-sample normalization. Genome Research, 24(7):1157-1168.

Raghav, Sunil K

Simicevic, Jovan; Schmid, Adrien W; Gilardoni, Paola A; Zoller, Benjamin; Raghav, Sunil K; Krier, Irina; Gubelmann, Carinne; Lisacek, Frédérique; Naef, Felix; Moniatte, Marc; Deplancke, Bart (2013). Absolute quantification of transcription factors during cellular differentiation using multiplexed targeted proteomics. Nature Methods, 10(6):570-576.

Rajkumar, Arun S

Rajkumar, Arun S; Maerkl, Sebastian J (2012). Rapid Synthesis Of Defined Eukaryotic Promoter Libraries. ACS Synthetic Biology, 1:483-490.

Ralph, Stuart A

Lemgruber, Leandro; Kudryashev, Mikhail; Dekiwadia, Chaitali; Riglar, David T; Baum, Jake; Stahlberg, Henning; Ralph, Stuart A; Frischknecht, Friedrich (2013). Cryo-electron tomography reveals four-membrane architecture of the Plasmodium apicoplast. Malaria Journal, 12:25.

Ramakrishnan, Chandrasekhar

Ramakrishnan, Chandrasekhar; Bieri, Andrej; Sauter, Nora; Roizard, Sophie; Ringler, Philippe; Müller, Shirley A; Goldie, Kenneth N; Enimanev, Kaloyan; Stahlberg, Henning; Rinn, Bernd; Braun, Thomas (2014). openBEB: open biological experiment browser for correlative measurements. BMC Bioinformatics, 15:84.

Ramaswamy, Rajesh

Ramaswamy, Rajesh; Sbalzarini, Ivo F (2011). Exact on-lattice stochastic reaction-diffusion simulations using partial-propensity methods. Journal of Chemical Physics, 135(24):244103.

Ramaswamy, Rajesh; Sbalzarini, Ivo F; González-Segredo, Nélido (2011). Noise-Induced Modulation of the Relaxation Kinetics around a Non-Equilibrium Steady State of Non-Linear Chemical Reaction Networks. PLoS ONE, 6(1):e16045.

Ramaswamy, Rajesh; Sbalzarini, Ivo F (2010). A partial-propensity variant of the composition-rejection stochastic simulation algorithm for chemical reaction networks. The Journal of chemical physics, 132(4):044102.

Polyansky, Anton A; Ramaswamy, Rajesh; Volynsky, Pavel E; Sbalzarini, Ivo F; Marrink, Siewert J; Efremov, Roman G (2010). Antimicrobial Peptides Induce Growth of Phosphatidylglycerol Domains in a Model Bacterial Membrane. Journal of Physical Chemistry Letters, 1(20):3108-3111.

Rangl, Martina

Kowal, Julia; Chami, Mohamed; Baumgartner, Paul; Arheit, Marcel; Chiu, Po-Lin; Rangl, Martina; Scheuring, Simon; Schröder, Gunnar F; Nimigean, Crina M; Stahlberg, Henning (2014). Ligand-induced structural changes in the cyclic nucleotide-modulated potassium channel MloK1. Nature Communications, 5:3106.

Ranjan, A

Chitwood, D H; Headland, L R; Ranjan, A; Martinez, C C; Braybrook, S A; Koenig, D P; Kuhlemeier, C; Smith, R S; Sinha, N R (2012). Leaf Asymmetry as a Developmental Constraint Imposed by Auxin-Dependent Phyllotactic Patterning. Plant Cell, 24(6):2318-2327.

Reboux, Sylvain

Reboux, Sylvain; Schrader, Birte; Sbalzarini, Ivo F (2012). A self-organizing Lagrangian particle method for adaptive-resolution advection–diffusion simulations. Journal of Computational Physics, 231(9):3623-3646.

Awile, Omar; Büyükkeçeci, Ferit; Reboux, Sylvain; Sbalzarini, Ivo F (2012). Fast neighbor lists for adaptive-resolution particle simulations. Computer Physics Communications, 183(5):1073-1081.

Rib, L

Bonhoure, N; Bounova, G; Bernasconi, D; Praz, V; Lammers, F; Canella, D; Willis, I M; Herr, W; Hernandez, N; Delorenzi, M; Hernandez, N; Delorenzi, M; Deplancke, B; Desvergne, B; Guex, N; Herr, W; Naef, F; Rougemont, J; Schibler, U; Andersin, T; Cousin, P; Gilardi, F; Gos, P; Lammers, F; Raghav, S; Villeneuve, D; Fabbretti, R; Vlegel, V; Xenarios, I; Migliavacca, E; Praz, V; David, F; Jarosz, Y; Kuznetsov, D; Liechti, R; Martin, O; Delafontaine, J; Cajan, J; Gustafson, K; Krier, I; Leleu, M; Molina, N; Naldi, A; Rib, L; Symul, L; Bounova, G (2014). Quantifying ChIP-seq data: a spiking method providing an internal reference for sample-to-sample normalization. Genome Research, 24(7):1157-1168.

Ries, Jonas

Schoen, Ingmar; Ries, Jonas; Klotzsch, Enrico; Ewers, Helge; Vogel, Viola (2011). Binding-activated localization microscopy of DNA structures. Nano letters, 11(9):4008-4011.

Riezman, Howard

Loizides-Mangold, Ursula; David, Fabrice P A; Nesatyy, Victor J; Kinoshita, Taroh; Riezman, Howard (2012). Glycosylphosphatidylinositol anchors regulate glycosphingolipid levels. Journal of Lipid Research, 53(8):1522-34.

Riglar, David T

Lemgruber, Leandro; Kudryashev, Mikhail; Dekiwadia, Chaitali; Riglar, David T; Baum, Jake; Stahlberg, Henning; Ralph, Stuart A; Frischknecht, Friedrich (2013). Cryo-electron tomography reveals four-membrane architecture of the Plasmodium apicoplast. Malaria Journal, 12:25.

Ringler, Philippe

Goldie, Kenneth N; Abeyrathne, Priyanka; Kebbel, Fabian; Chami, Mohamed; Ringler, Philippe; Stahlberg, Henning (2014). Cryo-electron microscopy of membrane proteins. Methods in Molecular Biology, 1117:325-41.

Moharana, Kedar; Zabeau, Lennart; Peelman, Frank; Ringler, Philippe; Stahlberg, Henning; Tavernier, Jan; Savvides, Savvas N (2014). Structural and mechanistic paradigm of leptin receptor activation revealed by complexes with wild-type and antagonist leptins. Structure, 22(6):866-877.

Ramakrishnan, Chandrasekhar; Bieri, Andrej; Sauter, Nora; Roizard, Sophie; Ringler, Philippe; Müller, Shirley A; Goldie, Kenneth N; Enimanev, Kaloyan; Stahlberg, Henning; Rinn, Bernd; Braun, Thomas (2014). openBEB: open biological experiment browser for correlative measurements. BMC Bioinformatics, 15:84.

Hermes, Jens P; Sander, Fabian; Peterle, Torsten; Cioffi, Carla; Ringler, Philippe; Pfohl, Thomas; Mayor, Marcel (2011). Direct control of the spatial arrangement of gold nanoparticles in organic-inorganic hybrid superstructures. Small, 7(7):920-9.

Rinn, Bernd

Ramakrishnan, Chandrasekhar; Bieri, Andrej; Sauter, Nora; Roizard, Sophie; Ringler, Philippe; Müller, Shirley A; Goldie, Kenneth N; Enimanev, Kaloyan; Stahlberg, Henning; Rinn, Bernd; Braun, Thomas (2014). openBEB: open biological experiment browser for correlative measurements. BMC Bioinformatics, 15:84.

Rochaix, J -D

Samol, I; Shapiguzov, A; Ingelsson, B; Fucile, G; Crevecoeur, M; Vener, A V; Rochaix, J -D; Goldschmidt-Clermont, M (2012). Identification of a Photosystem II Phosphatase Involved in Light Acclimation in Arabidopsis. Plant Cell, 24(6):2596-2609.

Shapiguzov, A; Ingelsson, B; Samol, I; Andres, C; Kessler, F; Rochaix, J -D; Vener, A V; Goldschmidt-Clermont, M (2010). The PPH1 phosphatase is specifically involved in LHCII dephosphorylation and state transitions in Arabidopsis. Proceedings of the National Academy of Sciences of the United States of America, 107(10):4782-4787.

Rockel, Sylvie

Rockel, Sylvie; Geertz, Marcel; Hens, Korneel; Deplancke, Bart; Maerkl, Sebastian J (2012). iSLIM: a comprehensive approach to mapping and characterizing gene regulatory networks. Nucleic Acids Research:1-8.

Geertz, Marcel; Rockel, Sylvie; Maerkl, Sebastian J (2012). A high-throughput microfluidic method for generating and characterizing transcription factor mutant libraries. Methods in Molecular Biology, 813:107-123.

Roizard, Sophie

Ramakrishnan, Chandrasekhar; Bieri, Andrej; Sauter, Nora; Roizard, Sophie; Ringler, Philippe; Müller, Shirley A; Goldie, Kenneth N; Enimanev, Kaloyan; Stahlberg, Henning; Rinn, Bernd; Braun, Thomas (2014). openBEB: open biological experiment browser for correlative measurements. BMC Bioinformatics, 15:84.

Rossinelli, D

Rossinelli, D; Bayati, B; Koumoutsakos, P (2008). Accelerated stochastic and hybrid methods for spatial simulations of reaction-diffusion systems. Chemical Physics Letters, 451(1-3):136 - 140.

Rossner, M J

Brankatschk, B; Wichert, S P; Johnson, S D; Schaad, O; Rossner, M J; Gruenberg, J (2012). Regulation of the EGF Transcriptional Response by Endocytic Sorting. Science Signaling, 5(215):ra21.

Rougemont, J

Bonhoure, N; Bounova, G; Bernasconi, D; Praz, V; Lammers, F; Canella, D; Willis, I M; Herr, W; Hernandez, N; Delorenzi, M; Hernandez, N; Delorenzi, M; Deplancke, B; Desvergne, B; Guex, N; Herr, W; Naef, F; Rougemont, J; Schibler, U; Andersin, T; Cousin, P; Gilardi, F; Gos, P; Lammers, F; Raghav, S; Villeneuve, D; Fabbretti, R; Vlegel, V; Xenarios, I; Migliavacca, E; Praz, V; David, F; Jarosz, Y; Kuznetsov, D; Liechti, R; Martin, O; Delafontaine, J; Cajan, J; Gustafson, K; Krier, I; Leleu, M; Molina, N; Naldi, A; Rib, L; Symul, L; Bounova, G (2014). Quantifying ChIP-seq data: a spiking method providing an internal reference for sample-to-sample normalization. Genome Research, 24(7):1157-1168.

Rougemont, Jacques

Le Martelot, Gwendal; Canella, Donatella; Symul, Laura; Migliavacca, Eugenia; Gilardi, Federica; Liechti, Robin; Martin, Olivier; Harshman, Keith; Delorenzi, Mauro; Desvergne, Béatrice; Herr, Winship; Deplancke, Bart; Schibler, Ueli; Rougemont, Jacques; Guex, Nicolas; Hernandez, Nouria; Naef, Felix (2012). Genome-wide RNA polymerase II profiles and RNA accumulation reveal kinetics of transcription and associated epigenetic changes during diurnal cycles. PLoS Biology, 10(11):e1001442.

Routier-Kierzkowska, A -L

Routier-Kierzkowska, A -L; Weber, A; Kochova, P; Felekis, D; Nelson, B J; Kuhlemeier, C; Smith, R S (2012). Cellular Force Microscopy for in Vivo Measurements of Plant Tissue Mechanics. Plant Physiology, 158(4):1514-1522.

Rudolf, F

Pelet, S; Rudolf, F; Nadal-Ribelles, M; de Nadal, E; Posas, F; Peter, M (2011). Transient activation of the HOG MAPK pathway regulates bimodal gene expression. Science, 332(6030):732-735.

Saenz, Henri

Vayssier-Taussat, Muriel; Le Rhun, Danielle; Deng, Hong Kuan; Biville, Francis; Cescau, Sandra; Danchin, Antoine; Marignac, Geneviève; Lenaour, Evelyne; Boulouis, Henri Jean; Mavris, Maria; Arnaud, Lionel; Yang, Huanming; Wang, Jing; Quebatte, Maxime; Engel, Philipp; Saenz, Henri; Dehio, Christoph (2010). The Trw Type IV Secretion System of Bartonella Mediates Host-Specific Adhesion to Erythrocytes. PLoS Pathogens, 6(6):e1000946.

Salleron, Lisa

Mary, Camille; Duek, Paula; Salleron, Lisa; Tienz, Petra; Bumann, Dirk; Bairoch, Amos; Lane, Lydie (2012). Functional Identification of APIP as Human mtnB, a Key Enzyme in the Methionine Salvage Pathway. PLoS ONE, 7(12):e52877.

Samol, I

Samol, I; Shapiguzov, A; Ingelsson, B; Fucile, G; Crevecoeur, M; Vener, A V; Rochaix, J -D; Goldschmidt-Clermont, M (2012). Identification of a Photosystem II Phosphatase Involved in Light Acclimation in Arabidopsis. Plant Cell, 24(6):2596-2609.

Shapiguzov, A; Ingelsson, B; Samol, I; Andres, C; Kessler, F; Rochaix, J -D; Vener, A V; Goldschmidt-Clermont, M (2010). The PPH1 phosphatase is specifically involved in LHCII dephosphorylation and state transitions in Arabidopsis. Proceedings of the National Academy of Sciences of the United States of America, 107(10):4782-4787.

Sander, Fabian

Hermes, Jens P; Sander, Fabian; Peterle, Torsten; Cioffi, Carla; Ringler, Philippe; Pfohl, Thomas; Mayor, Marcel (2011). Direct control of the spatial arrangement of gold nanoparticles in organic-inorganic hybrid superstructures. Small, 7(7):920-9.

Sauer, M

Bayer, E M; Smith, R S; Mandel, T; Nakayama, N; Sauer, M; Prusinkiewicz, P; Kuhlemeier, C (2009). Integration of transport-based models for phyllotaxis and midvein formation. Genes and Development, 23(3):373-384.

Sauer, Uwe

Sévin, Daniel C; Sauer, Uwe (2014). Ubiquinone accumulation improves osmotic-stress tolerance in Escherichia coli. Nature Chemical Biology, 10(4):266-272.

Sauter, Nora

Ramakrishnan, Chandrasekhar; Bieri, Andrej; Sauter, Nora; Roizard, Sophie; Ringler, Philippe; Müller, Shirley A; Goldie, Kenneth N; Enimanev, Kaloyan; Stahlberg, Henning; Rinn, Bernd; Braun, Thomas (2014). openBEB: open biological experiment browser for correlative measurements. BMC Bioinformatics, 15:84.

Savvides, Savvas N

Moharana, Kedar; Zabeau, Lennart; Peelman, Frank; Ringler, Philippe; Stahlberg, Henning; Tavernier, Jan; Savvides, Savvas N (2014). Structural and mechanistic paradigm of leptin receptor activation revealed by complexes with wild-type and antagonist leptins. Structure, 22(6):866-877.

Sbalzarini, Ivo F

Sbalzarini, Ivo F (2013). Modeling and simulation of biological systems from image data. BioEssays, 35(5):482-490.

Reboux, Sylvain; Schrader, Birte; Sbalzarini, Ivo F (2012). A self-organizing Lagrangian particle method for adaptive-resolution advection–diffusion simulations. Journal of Computational Physics, 231(9):3623-3646.

Awile, Omar; Büyükkeçeci, Ferit; Reboux, Sylvain; Sbalzarini, Ivo F (2012). Fast neighbor lists for adaptive-resolution particle simulations. Computer Physics Communications, 183(5):1073-1081.

Ramaswamy, Rajesh; Sbalzarini, Ivo F (2011). Exact on-lattice stochastic reaction-diffusion simulations using partial-propensity methods. Journal of Chemical Physics, 135(24):244103.

Ramaswamy, Rajesh; Sbalzarini, Ivo F; González-Segredo, Nélido (2011). Noise-Induced Modulation of the Relaxation Kinetics around a Non-Equilibrium Steady State of Non-Linear Chemical Reaction Networks. PLoS ONE, 6(1):e16045.

Awile, Omar; Demirel, Ömer; Sbalzarini, Ivo F; Simos, Theodore E; Psihoyios, George; Tsitouras, Ch (2010). Toward an Object-Oriented Core of the PPM Library. In: International Conference of Numerical Analysis and Applied Mathematics (ICNAAM), Rhodes, Greece, 19 September 2010 - 25 September 2010, 1313-1316.

Ramaswamy, Rajesh; Sbalzarini, Ivo F (2010). A partial-propensity variant of the composition-rejection stochastic simulation algorithm for chemical reaction networks. The Journal of chemical physics, 132(4):044102.

Polyansky, Anton A; Ramaswamy, Rajesh; Volynsky, Pavel E; Sbalzarini, Ivo F; Marrink, Siewert J; Efremov, Roman G (2010). Antimicrobial Peptides Induce Growth of Phosphatidylglycerol Domains in a Model Bacterial Membrane. Journal of Physical Chemistry Letters, 1(20):3108-3111.

Helmuth, Jo A; Paul, Grégory; Sbalzarini, Ivo F (2010). Beyond co-localization: inferring spatial interactions between sub-cellular structures from microscopy images. BMC Bioinformatics, 11(1):372.

Schaad, O

Brankatschk, B; Wichert, S P; Johnson, S D; Schaad, O; Rossner, M J; Gruenberg, J (2012). Regulation of the EGF Transcriptional Response by Endocytic Sorting. Science Signaling, 5(215):ra21.

Schauer, Kristine

Vonaesch, Pascale; Cardini, Steven; Sellin, Mikael E; Goud, Bruno; Hardt, Wolf-Dietrich; Schauer, Kristine (2013). Quantitative insights into actin rearrangements and bacterial target site selection fromSalmonella Typhimurium infection of micropatterned cells. Cellular Microbiology, 15(11):1851-1865.

Scheffold, Frank

Spühler, Isabelle A; Conley, Gaurasundar M; Scheffold, Frank; Sprecher, Simon G (2016). Super resolution imaging of genetically labeled synapses in drosophila brain tissue. Frontiers in Cellular Neuroscience:10:142.

Scheuring, Simon

Kowal, Julia; Chami, Mohamed; Baumgartner, Paul; Arheit, Marcel; Chiu, Po-Lin; Rangl, Martina; Scheuring, Simon; Schröder, Gunnar F; Nimigean, Crina M; Stahlberg, Henning (2014). Ligand-induced structural changes in the cyclic nucleotide-modulated potassium channel MloK1. Nature Communications, 5:3106.

Schibler, U

Bonhoure, N; Bounova, G; Bernasconi, D; Praz, V; Lammers, F; Canella, D; Willis, I M; Herr, W; Hernandez, N; Delorenzi, M; Hernandez, N; Delorenzi, M; Deplancke, B; Desvergne, B; Guex, N; Herr, W; Naef, F; Rougemont, J; Schibler, U; Andersin, T; Cousin, P; Gilardi, F; Gos, P; Lammers, F; Raghav, S; Villeneuve, D; Fabbretti, R; Vlegel, V; Xenarios, I; Migliavacca, E; Praz, V; David, F; Jarosz, Y; Kuznetsov, D; Liechti, R; Martin, O; Delafontaine, J; Cajan, J; Gustafson, K; Krier, I; Leleu, M; Molina, N; Naldi, A; Rib, L; Symul, L; Bounova, G (2014). Quantifying ChIP-seq data: a spiking method providing an internal reference for sample-to-sample normalization. Genome Research, 24(7):1157-1168.

Schibler, Ueli

Le Martelot, Gwendal; Canella, Donatella; Symul, Laura; Migliavacca, Eugenia; Gilardi, Federica; Liechti, Robin; Martin, Olivier; Harshman, Keith; Delorenzi, Mauro; Desvergne, Béatrice; Herr, Winship; Deplancke, Bart; Schibler, Ueli; Rougemont, Jacques; Guex, Nicolas; Hernandez, Nouria; Naef, Felix (2012). Genome-wide RNA polymerase II profiles and RNA accumulation reveal kinetics of transcription and associated epigenetic changes during diurnal cycles. PLoS Biology, 10(11):e1001442.

Schirmer, Tilman

Goepfert, Arnaud; Stanger, Frédéric V; Dehio, Christoph; Schirmer, Tilman (2013). Conserved Inhibitory Mechanism and Competent ATP Binding Mode for Adenylyltransferases with Fic Fold. PLoS ONE, 8(5):e64901.

Schluck, T

Schluck, T; Aegerter, C M (2010). Photo-elastic properties of the wing imaginal disc of Drosophila. European Physical Journal E - Soft Matter and Biological Physics, 33(2):111-115.

Schmelz, S

Kudryashev, M; Stenta, M; Schmelz, S; Amstutz, M; Wiesand, U; Castano-Diez, D; Degiacomi, M T; Munnich, S; Bleck, C K; Kowal, J; Diepold, A; Heinz, D W; Dal Peraro, M; Cornelis, G R; Stahlberg, H (2013). In situ structural analysis of the Yersinia enterocolitica injectisome. eLife, 2:e00792-e00792.

Schmid, Adrien W

Simicevic, Jovan; Schmid, Adrien W; Gilardoni, Paola A; Zoller, Benjamin; Raghav, Sunil K; Krier, Irina; Gubelmann, Carinne; Lisacek, Frédérique; Naef, Felix; Moniatte, Marc; Deplancke, Bart (2013). Absolute quantification of transcription factors during cellular differentiation using multiplexed targeted proteomics. Nature Methods, 10(6):570-576.

Schmidt, A

Hofmann, A; Gerrits, B; Schmidt, A; Bock, T; Bausch-Fluck, D; Aebersold, R; Wollscheid, B (2010). Proteomic cell surface phenotyping of differentiating acute myeloid leukemia cells. Blood, 116(13):e26-34.

Schmidt, Alexander

Steeb, Benjamin; Claudi, Beatrice; Burton, Neil A; Tienz, Petra; Schmidt, Alexander; Farhan, Hesso; Mazé, Alain; Bumann, Dirk (2013). Parallel Exploitation of Diverse Host Nutrients Enhances Salmonella Virulence. PLoS Pathogens, 9(4):e1003301.

Schmidt, Florian Ingo

Schmidt, Florian Ingo; Bleck, Christopher Karl Ernst; Helenius, Ari; Mercer, Jason (2011). Vaccinia extracellular virions enter cells by macropinocytosis and acid-activated membrane rupture. EMBO Journal Online, 30(17):3647-3661.

Schmitt, U

Kiefer, P; Schmitt, U; Vorholt, J A (2013). eMZed: an open source framework in Python for rapid and interactive development of LC/MS data analysis workflows. Bioinformatics, 29(7):963-964.

Schoen, Ingmar

Schoen, Ingmar; Ries, Jonas; Klotzsch, Enrico; Ewers, Helge; Vogel, Viola (2011). Binding-activated localization microscopy of DNA structures. Nano letters, 11(9):4008-4011.

Schrader, Birte

Reboux, Sylvain; Schrader, Birte; Sbalzarini, Ivo F (2012). A self-organizing Lagrangian particle method for adaptive-resolution advection–diffusion simulations. Journal of Computational Physics, 231(9):3623-3646.

Schröder, Gunnar F

Kowal, Julia; Chami, Mohamed; Baumgartner, Paul; Arheit, Marcel; Chiu, Po-Lin; Rangl, Martina; Scheuring, Simon; Schröder, Gunnar F; Nimigean, Crina M; Stahlberg, Henning (2014). Ligand-induced structural changes in the cyclic nucleotide-modulated potassium channel MloK1. Nature Communications, 5:3106.

Schröter, Christian

Schröter, Christian; Ares, Saúl; Morelli, Luis G; Isakova, Alina; Hens, Korneel; Soroldoni, Daniele; Gajewski, Martin; Jülicher, Frank; Maerkl, Sebastian J; Deplancke, Bart; Oates, Andrew C (2012). Topology and Dynamics of the Zebrafish Segmentation Clock Core Circuit. PLoS Biology, 10(7):1-20.

Schübeler, Dirk

Tiwari, Neha; Tiwari, Vijay K; Waldmeier, Lorenz; Balwierz, Piotr J; Arnold, Phil; Pachkov, Mikhail; Meyer-Schaller, Nathalie; Schübeler, Dirk; van Nimwegen, Erik; Christofori, Gerhard (2013). Sox4 is a master regulator of epithelial-mesenchymal transition by controlling ezh2 expression and epigenetic reprogramming. Cancer Cell, 23(6):768-83.

Schütz, Frédéric

Soulard, Alexandre; Cremonesi, Alessio; Moes, Suzette; Schütz, Frédéric; Jenö, Paul; Hall, Michael N (2010). The Rapamycin-sensitive Phosphoproteome Reveals That TOR Controls Protein Kinase A Toward Some But Not All Substrates. Molecular Biology of the Cell, 21:3475-3486.

Seelamantula, Chandra Sekhar

Delgado-Gonzalo, Ricard; Thévenaz, Philippe; Seelamantula, Chandra Sekhar; Unser, Michael (2012). Snakes with an ellipse-reproducing property. IEEE transactions on image processing : a publication of the IEEE Signal Processing Society, 21(3):1258-71.

Sellin, Mikael E

Vonaesch, Pascale; Cardini, Steven; Sellin, Mikael E; Goud, Bruno; Hardt, Wolf-Dietrich; Schauer, Kristine (2013). Quantitative insights into actin rearrangements and bacterial target site selection fromSalmonella Typhimurium infection of micropatterned cells. Cellular Microbiology, 15(11):1851-1865.

Seraphin, Bertrand

Bonde, Marie Mi; Voegeli, Sylvia; Baudrimont, Antoine; Seraphin, Bertrand; Becskei, Attila (2014). Quantification of pre-mRNA escape rate and synergy in splicing. Nucleic Acids Research, 42(20):12847-12860.

Shapiguzov, A

Samol, I; Shapiguzov, A; Ingelsson, B; Fucile, G; Crevecoeur, M; Vener, A V; Rochaix, J -D; Goldschmidt-Clermont, M (2012). Identification of a Photosystem II Phosphatase Involved in Light Acclimation in Arabidopsis. Plant Cell, 24(6):2596-2609.

Shapiguzov, A; Ingelsson, B; Samol, I; Andres, C; Kessler, F; Rochaix, J -D; Vener, A V; Goldschmidt-Clermont, M (2010). The PPH1 phosphatase is specifically involved in LHCII dephosphorylation and state transitions in Arabidopsis. Proceedings of the National Academy of Sciences of the United States of America, 107(10):4782-4787.

Shimobayash, Mitsugu

Shimobayash, Mitsugu; Oppliger, Wolfgang; Moes, Suzette; Jenö, Paul; Hall, Michael N (2013). TORC1-regulated protein kinase Npr1 phosphorylates Orm to stimulate complex sphingolipid synthesis. Molecular Biology of the Cell, 24:870-881.

Shore, David

Geertz, Marcel; Shore, David; Maerkl, Sebastian J (2012). Massively parallel measurements of molecular interaction kinetics on a microfluidic platform. Proceedings of the National Academy of Sciences of the United States of America, 109(41):16540-16545.

Shui, G H

Lim, L; Jackson-Lewis, V; Wong, L C; Shui, G H; Goh, A X H; Kesavapany, S; Jenner, A M; Fivaz, M; Przedborski, S; Wenk, M R (2012). Lanosterol induces mitochondrial uncoupling and protects dopaminergic neurons from cell death in a model for Parkinson's disease. Cell Death and Differentiation, 19(3):416-27.

Shui, Guanghou

Cheng, Danni; Jenner, Andrew M; Shui, Guanghou; Cheong, Wei Fun; Mitchell, Todd W; Nealon, Jessica R; Kim, Woojin S; McCann, Heather; Wenk, Markus R; Halliday, Glenda M; Garner, Brett (2011). Lipid pathway alterations in Parkinson's disease primary visual cortex. PLoS ONE, 6(2):e17299.

Simicevic, Jovan

Simicevic, Jovan; Schmid, Adrien W; Gilardoni, Paola A; Zoller, Benjamin; Raghav, Sunil K; Krier, Irina; Gubelmann, Carinne; Lisacek, Frédérique; Naef, Felix; Moniatte, Marc; Deplancke, Bart (2013). Absolute quantification of transcription factors during cellular differentiation using multiplexed targeted proteomics. Nature Methods, 10(6):570-576.

Simos, Theodore E

Awile, Omar; Demirel, Ömer; Sbalzarini, Ivo F; Simos, Theodore E; Psihoyios, George; Tsitouras, Ch (2010). Toward an Object-Oriented Core of the PPM Library. In: International Conference of Numerical Analysis and Applied Mathematics (ICNAAM), Rhodes, Greece, 19 September 2010 - 25 September 2010, 1313-1316.

Sinha, N R

Chitwood, D H; Headland, L R; Ranjan, A; Martinez, C C; Braybrook, S A; Koenig, D P; Kuhlemeier, C; Smith, R S; Sinha, N R (2012). Leaf Asymmetry as a Developmental Constraint Imposed by Auxin-Dependent Phyllotactic Patterning. Plant Cell, 24(6):2318-2327.

Smith, Kevin

Smith, Kevin; Li, Yunpeng; Piccinini, Filippo; Csucs, Gabor; Balazs, Csaba; Bevilacqua, Alessandro; Horvath, Peter (2015). CIDRE: an illumination-correction method for optical microscopy. Nature Methods, 12(5):404-406.

Smith, R S

Routier-Kierzkowska, A -L; Weber, A; Kochova, P; Felekis, D; Nelson, B J; Kuhlemeier, C; Smith, R S (2012). Cellular Force Microscopy for in Vivo Measurements of Plant Tissue Mechanics. Plant Physiology, 158(4):1514-1522.

Chitwood, D H; Headland, L R; Ranjan, A; Martinez, C C; Braybrook, S A; Koenig, D P; Kuhlemeier, C; Smith, R S; Sinha, N R (2012). Leaf Asymmetry as a Developmental Constraint Imposed by Auxin-Dependent Phyllotactic Patterning. Plant Cell, 24(6):2318-2327.

Guenot, B; Bayer, E; Kierzkowski, D; Smith, R S; Mandel, T; Zadnikova, P; Benkova, E; Kuhlemeier, C (2012). PIN1-Independent Leaf Initiation in Arabidopsis. Plant Physiology, 159(4):1501-1510.

Smith, R S; Bayer, E M (2009). Auxin transport-feedback models of patterning in plants. Plant, Cell and Environment, 32(9):1258-1271.

Bayer, E M; Smith, R S; Mandel, T; Nakayama, N; Sauer, M; Prusinkiewicz, P; Kuhlemeier, C (2009). Integration of transport-based models for phyllotaxis and midvein formation. Genes and Development, 23(3):373-384.

Soldati-Favre, Dominique

Limenitakis, Julien; Oppenheim, Rebecca D; Creek, Darren J; Foth, Bernardo J; Barrett, Michael P; Soldati-Favre, Dominique (2013). The 2-methylcitrate cycle is implicated in the detoxification of propionate in Toxoplasma gondii. Molecular Microbiology, 87(4):894-908.

Soroldoni, Daniele

Schröter, Christian; Ares, Saúl; Morelli, Luis G; Isakova, Alina; Hens, Korneel; Soroldoni, Daniele; Gajewski, Martin; Jülicher, Frank; Maerkl, Sebastian J; Deplancke, Bart; Oates, Andrew C (2012). Topology and Dynamics of the Zebrafish Segmentation Clock Core Circuit. PLoS Biology, 10(7):1-20.

Soulard, Alexandre

Soulard, Alexandre; Cremonesi, Alessio; Moes, Suzette; Schütz, Frédéric; Jenö, Paul; Hall, Michael N (2010). The Rapamycin-sensitive Phosphoproteome Reveals That TOR Controls Protein Kinase A Toward Some But Not All Substrates. Molecular Biology of the Cell, 21:3475-3486.

Sprecher, Simon G

Spühler, Isabelle A; Conley, Gaurasundar M; Scheffold, Frank; Sprecher, Simon G (2016). Super resolution imaging of genetically labeled synapses in drosophila brain tissue. Frontiers in Cellular Neuroscience:10:142.

Spühler, Isabelle A

Spühler, Isabelle A; Conley, Gaurasundar M; Scheffold, Frank; Sprecher, Simon G (2016). Super resolution imaging of genetically labeled synapses in drosophila brain tissue. Frontiers in Cellular Neuroscience:10:142.

Stahlberg, H

Kudryashev, M; Stenta, M; Schmelz, S; Amstutz, M; Wiesand, U; Castano-Diez, D; Degiacomi, M T; Munnich, S; Bleck, C K; Kowal, J; Diepold, A; Heinz, D W; Dal Peraro, M; Cornelis, G R; Stahlberg, H (2013). In situ structural analysis of the Yersinia enterocolitica injectisome. eLife, 2:e00792-e00792.

Dudkina, N V; Kudryashev, M; Stahlberg, H; Boekema, E J (2011). Interaction of complexes I, III, and IV within the bovine respirasome by single particle cryoelectron tomography. Proceedings of the National Academy of Sciences of the United States of America, 108(37):15196-15200.

Stahlberg, Henning

Goldie, Kenneth N; Abeyrathne, Priyanka; Kebbel, Fabian; Chami, Mohamed; Ringler, Philippe; Stahlberg, Henning (2014). Cryo-electron microscopy of membrane proteins. Methods in Molecular Biology, 1117:325-41.

Giss, Dominic; Kemmerling, Simon; Dandey, Venkata; Stahlberg, Henning; Braun, Thomas (2014). Exploring the interactome: microfluidic isolation of proteins and interacting partners for quantitative analysis by electron microscopy. Analytical Chemistry, 86(10):4680-4687.

Kowal, Julia; Chami, Mohamed; Baumgartner, Paul; Arheit, Marcel; Chiu, Po-Lin; Rangl, Martina; Scheuring, Simon; Schröder, Gunnar F; Nimigean, Crina M; Stahlberg, Henning (2014). Ligand-induced structural changes in the cyclic nucleotide-modulated potassium channel MloK1. Nature Communications, 5:3106.

Moharana, Kedar; Zabeau, Lennart; Peelman, Frank; Ringler, Philippe; Stahlberg, Henning; Tavernier, Jan; Savvides, Savvas N (2014). Structural and mechanistic paradigm of leptin receptor activation revealed by complexes with wild-type and antagonist leptins. Structure, 22(6):866-877.

Ramakrishnan, Chandrasekhar; Bieri, Andrej; Sauter, Nora; Roizard, Sophie; Ringler, Philippe; Müller, Shirley A; Goldie, Kenneth N; Enimanev, Kaloyan; Stahlberg, Henning; Rinn, Bernd; Braun, Thomas (2014). openBEB: open biological experiment browser for correlative measurements. BMC Bioinformatics, 15:84.

Lemgruber, Leandro; Kudryashev, Mikhail; Dekiwadia, Chaitali; Riglar, David T; Baum, Jake; Stahlberg, Henning; Ralph, Stuart A; Frischknecht, Friedrich (2013). Cryo-electron tomography reveals four-membrane architecture of the Plasmodium apicoplast. Malaria Journal, 12:25.

Kudryashev, Mikhail; Castaño-Díez, Daniel; Stahlberg, Henning (2012). Limiting factors in single particle cryo electron tomography. Computational and Structural Biotechnology Journal, 1(2):online.

Stanger, Frédéric V

Goepfert, Arnaud; Stanger, Frédéric V; Dehio, Christoph; Schirmer, Tilman (2013). Conserved Inhibitory Mechanism and Competent ATP Binding Mode for Adenylyltransferases with Fic Fold. PLoS ONE, 8(5):e64901.

Steeb, Benjamin

Steeb, Benjamin; Claudi, Beatrice; Burton, Neil A; Tienz, Petra; Schmidt, Alexander; Farhan, Hesso; Mazé, Alain; Bumann, Dirk (2013). Parallel Exploitation of Diverse Host Nutrients Enhances Salmonella Virulence. PLoS Pathogens, 9(4):e1003301.

Steinmetz, Michel O

Prota, Andrea E; Bargsten, Katja; Zurwerra, Didier; Field, Jessica J; Díaz, José Fernando; Altmann, Karl-Heinz; Steinmetz, Michel O (2013). Molecular Mechanism of Action of Microtubule-Stabilizing Anticancer Agents. Science, 339(6119):587-590.

Stelling, Joerg

Sunnåker, Mikael; Zamora-Sillero, Elias; Dechant, Reinhard; Ludwig, Christina; Busetto, Alberto Giovanni; Wagner, Andreas; Stelling, Joerg (2013). Automatic Generation of Predictive Dynamic Models Reveals Nuclear Phosphorylation as the Key Msn2 Control Mechanism. Science Signaling, 6(277):ra41.

Stenta, M

Kudryashev, M; Stenta, M; Schmelz, S; Amstutz, M; Wiesand, U; Castano-Diez, D; Degiacomi, M T; Munnich, S; Bleck, C K; Kowal, J; Diepold, A; Heinz, D W; Dal Peraro, M; Cornelis, G R; Stahlberg, H (2013). In situ structural analysis of the Yersinia enterocolitica injectisome. eLife, 2:e00792-e00792.

Stracka, Daniele

Zinzalla, Vittoria; Stracka, Daniele; Oppliger, Wolfgang; Hall, Michael N (2011). Activation of mTORC2 by Association with the Ribosome. Cell, 144:757-768.

Sturm, Alexander

Bailly-Bechet, Marc; Benecke, Arndt; Hardt, Wolf Dietrich; Lanza, Valentina; Sturm, Alexander; Zecchina, Riccardo (2011). An externally modulated, noise-driven switch for the regulation of SPI1 in Salmonella enterica serovar Typhimurium. Journal of Mathematical Biology, 63(4):637-662.

Stuttfeld, Edward

Leppänen, Veli-Matti; Tvorogov, Denis; Kisko, Kaisa; Prota, Andrea E; Jeltsch, Michael; Anisimov, Andrey; Markovic-Mueller, Sandra; Stuttfeld, Edward; Goldie, Kenneth N; Ballmer-Hofer, Kurt; Alitalo, Kari (2013). Structural and mechanistic insights into VEGF receptor 3 ligand binding and activation. Proceedings of the National Academy of Sciences of the United States of America, 110(32):12960-12965.

Städler, Brigitte

van der Westen, Rebecca; Hosta-Rigau, Leticia; Sutherland, Duncan S; Goldie, Kenneth N; Albericio, Fernando; Postma, Almar; Städler, Brigitte (2012). Myoblast cell interaction with polydopamine coated liposomes. Biointerphases, 7(1-4):8.

Hosta-Rigau, Leticia; Jensen, Bettina E B; Fjeldsø, Kit S; Postma, Almar; Li, Guoxin; Goldie, Kenneth N; Albericio, Fernando; Zelikin, Alexander N; Städler, Brigitte (2012). Drug Delivery: Surface-Adhered Composite Poly(Vinyl Alcohol) Physical Hydrogels: Polymersome-Aided Delivery of Therapeutic Small Molecules. Advanced Healthcare Materials, 1(6):791-5.

Summers, Sean

Cinquemani, Eugenio; Milias-Argeitis, Andreas; Summers, Sean; Lygeros, John (2008). Stochastic dynamics of genetic networks: modelling and parameter identification. Bioinformatics, 24(23):2748-2754.

Sunnåker, Mikael

Sunnåker, Mikael; Zamora-Sillero, Elias; Dechant, Reinhard; Ludwig, Christina; Busetto, Alberto Giovanni; Wagner, Andreas; Stelling, Joerg (2013). Automatic Generation of Predictive Dynamic Models Reveals Nuclear Phosphorylation as the Key Msn2 Control Mechanism. Science Signaling, 6(277):ra41.

Sutherland, Duncan S

van der Westen, Rebecca; Hosta-Rigau, Leticia; Sutherland, Duncan S; Goldie, Kenneth N; Albericio, Fernando; Postma, Almar; Städler, Brigitte (2012). Myoblast cell interaction with polydopamine coated liposomes. Biointerphases, 7(1-4):8.

Symul, L

Bonhoure, N; Bounova, G; Bernasconi, D; Praz, V; Lammers, F; Canella, D; Willis, I M; Herr, W; Hernandez, N; Delorenzi, M; Hernandez, N; Delorenzi, M; Deplancke, B; Desvergne, B; Guex, N; Herr, W; Naef, F; Rougemont, J; Schibler, U; Andersin, T; Cousin, P; Gilardi, F; Gos, P; Lammers, F; Raghav, S; Villeneuve, D; Fabbretti, R; Vlegel, V; Xenarios, I; Migliavacca, E; Praz, V; David, F; Jarosz, Y; Kuznetsov, D; Liechti, R; Martin, O; Delafontaine, J; Cajan, J; Gustafson, K; Krier, I; Leleu, M; Molina, N; Naldi, A; Rib, L; Symul, L; Bounova, G (2014). Quantifying ChIP-seq data: a spiking method providing an internal reference for sample-to-sample normalization. Genome Research, 24(7):1157-1168.

Symul, Laura

Le Martelot, Gwendal; Canella, Donatella; Symul, Laura; Migliavacca, Eugenia; Gilardi, Federica; Liechti, Robin; Martin, Olivier; Harshman, Keith; Delorenzi, Mauro; Desvergne, Béatrice; Herr, Winship; Deplancke, Bart; Schibler, Ueli; Rougemont, Jacques; Guex, Nicolas; Hernandez, Nouria; Naef, Felix (2012). Genome-wide RNA polymerase II profiles and RNA accumulation reveal kinetics of transcription and associated epigenetic changes during diurnal cycles. PLoS Biology, 10(11):e1001442.

Szabad, János

Szabad, János (2010). Putting together rather than taking apart. EMBO Reports, 11(12):904-906.

Sévin, Daniel C

Sévin, Daniel C; Sauer, Uwe (2014). Ubiquinone accumulation improves osmotic-stress tolerance in Escherichia coli. Nature Chemical Biology, 10(4):266-272.

Tavernier, Jan

Moharana, Kedar; Zabeau, Lennart; Peelman, Frank; Ringler, Philippe; Stahlberg, Henning; Tavernier, Jan; Savvides, Savvas N (2014). Structural and mechanistic paradigm of leptin receptor activation revealed by complexes with wild-type and antagonist leptins. Structure, 22(6):866-877.

Thévenaz, P

Delgado-Gonzalo, R; Thévenaz, P; Unser, M (2012). Exponential splines and minimal-support bases for curve representation. Computer Aided Geometric Design, 29(2):109-128.

Thévenaz, Philippe

Delgado-Gonzalo, Ricard; Thévenaz, Philippe; Seelamantula, Chandra Sekhar; Unser, Michael (2012). Snakes with an ellipse-reproducing property. IEEE transactions on image processing : a publication of the IEEE Signal Processing Society, 21(3):1258-71.

Tienz, Petra

Steeb, Benjamin; Claudi, Beatrice; Burton, Neil A; Tienz, Petra; Schmidt, Alexander; Farhan, Hesso; Mazé, Alain; Bumann, Dirk (2013). Parallel Exploitation of Diverse Host Nutrients Enhances Salmonella Virulence. PLoS Pathogens, 9(4):e1003301.

Mary, Camille; Duek, Paula; Salleron, Lisa; Tienz, Petra; Bumann, Dirk; Bairoch, Amos; Lane, Lydie (2012). Functional Identification of APIP as Human mtnB, a Key Enzyme in the Methionine Salvage Pathway. PLoS ONE, 7(12):e52877.

Tiwari, Neha

Tiwari, Neha; Meyer-Schaller, Nathalie; Arnold, Phil; Antoniadis, Helena; Pachkov, Mikhail; van Nimwegen, Erik; Christofori, Gerhard (2013). Klf4 is a transcriptional regulator of genes critical for EMT, including Jnk1 (Mapk8). PLoS ONE, 8(2):e57329.

Tiwari, Neha; Tiwari, Vijay K; Waldmeier, Lorenz; Balwierz, Piotr J; Arnold, Phil; Pachkov, Mikhail; Meyer-Schaller, Nathalie; Schübeler, Dirk; van Nimwegen, Erik; Christofori, Gerhard (2013). Sox4 is a master regulator of epithelial-mesenchymal transition by controlling ezh2 expression and epigenetic reprogramming. Cancer Cell, 23(6):768-83.

Tiwari, Vijay K

Tiwari, Neha; Tiwari, Vijay K; Waldmeier, Lorenz; Balwierz, Piotr J; Arnold, Phil; Pachkov, Mikhail; Meyer-Schaller, Nathalie; Schübeler, Dirk; van Nimwegen, Erik; Christofori, Gerhard (2013). Sox4 is a master regulator of epithelial-mesenchymal transition by controlling ezh2 expression and epigenetic reprogramming. Cancer Cell, 23(6):768-83.

Truttmann, M C

Truttmann, M C; Misselwitz, B; Huser, S; Hardt, W-D; Critchley, D R; Dehio, C (2011). Bartonella henselae engages inside-out and outside-in signaling by integrin 1 and talin1 during invasome-mediated bacterial uptake. Journal of Cell Science, 124(21):3591-3602.

Tsitouras, Ch

Awile, Omar; Demirel, Ömer; Sbalzarini, Ivo F; Simos, Theodore E; Psihoyios, George; Tsitouras, Ch (2010). Toward an Object-Oriented Core of the PPM Library. In: International Conference of Numerical Analysis and Applied Mathematics (ICNAAM), Rhodes, Greece, 19 September 2010 - 25 September 2010, 1313-1316.

Tvorogov, Denis

Leppänen, Veli-Matti; Tvorogov, Denis; Kisko, Kaisa; Prota, Andrea E; Jeltsch, Michael; Anisimov, Andrey; Markovic-Mueller, Sandra; Stuttfeld, Edward; Goldie, Kenneth N; Ballmer-Hofer, Kurt; Alitalo, Kari (2013). Structural and mechanistic insights into VEGF receptor 3 ligand binding and activation. Proceedings of the National Academy of Sciences of the United States of America, 110(32):12960-12965.

Ucar, Olga

Papadopoulou, Aikaterini S; Dooley, James; Linterman, Michelle A; Pierson, Wim; Ucar, Olga; Kyewski, Bruno; Zuklys, Saulius; Hollander, Georg A; Matthys, Patrick; Gray, Daniel H D; De Strooper, Bart; Liston, Adrian (2011). The thymic epithelial microRNA network elevates the threshold for infection-associated thymic involution via miR-29a mediated suppression of the IFN-α receptor. Nature Immunology, 13(2):181-187.

Unser, M

Delgado-Gonzalo, R; Unser, M (2013). Spline-based framework for interactive segmentation in biomedical imaging. IRBM, 34(3):235-243.

Delgado-Gonzalo, R; Thévenaz, P; Unser, M (2012). Exponential splines and minimal-support bases for curve representation. Computer Aided Geometric Design, 29(2):109-128.

Unser, Michael

Delgado-Gonzalo, Ricard; Thévenaz, Philippe; Seelamantula, Chandra Sekhar; Unser, Michael (2012). Snakes with an ellipse-reproducing property. IEEE transactions on image processing : a publication of the IEEE Signal Processing Society, 21(3):1258-71.

Vayssier-Taussat, Muriel

Vayssier-Taussat, Muriel; Le Rhun, Danielle; Deng, Hong Kuan; Biville, Francis; Cescau, Sandra; Danchin, Antoine; Marignac, Geneviève; Lenaour, Evelyne; Boulouis, Henri Jean; Mavris, Maria; Arnaud, Lionel; Yang, Huanming; Wang, Jing; Quebatte, Maxime; Engel, Philipp; Saenz, Henri; Dehio, Christoph (2010). The Trw Type IV Secretion System of Bartonella Mediates Host-Specific Adhesion to Erythrocytes. PLoS Pathogens, 6(6):e1000946.

Vener, A V

Samol, I; Shapiguzov, A; Ingelsson, B; Fucile, G; Crevecoeur, M; Vener, A V; Rochaix, J -D; Goldschmidt-Clermont, M (2012). Identification of a Photosystem II Phosphatase Involved in Light Acclimation in Arabidopsis. Plant Cell, 24(6):2596-2609.

Shapiguzov, A; Ingelsson, B; Samol, I; Andres, C; Kessler, F; Rochaix, J -D; Vener, A V; Goldschmidt-Clermont, M (2010). The PPH1 phosphatase is specifically involved in LHCII dephosphorylation and state transitions in Arabidopsis. Proceedings of the National Academy of Sciences of the United States of America, 107(10):4782-4787.

Vetter, Roman

Munglani, Gautam; Vetter, Roman; Wittel, Falk K; Herrmann, Hans J (2015). Orthotropic rotation-free thin shell elements. Computational Mechanics, 56(5):785-793.

Villeneuve, D

Bonhoure, N; Bounova, G; Bernasconi, D; Praz, V; Lammers, F; Canella, D; Willis, I M; Herr, W; Hernandez, N; Delorenzi, M; Hernandez, N; Delorenzi, M; Deplancke, B; Desvergne, B; Guex, N; Herr, W; Naef, F; Rougemont, J; Schibler, U; Andersin, T; Cousin, P; Gilardi, F; Gos, P; Lammers, F; Raghav, S; Villeneuve, D; Fabbretti, R; Vlegel, V; Xenarios, I; Migliavacca, E; Praz, V; David, F; Jarosz, Y; Kuznetsov, D; Liechti, R; Martin, O; Delafontaine, J; Cajan, J; Gustafson, K; Krier, I; Leleu, M; Molina, N; Naldi, A; Rib, L; Symul, L; Bounova, G (2014). Quantifying ChIP-seq data: a spiking method providing an internal reference for sample-to-sample normalization. Genome Research, 24(7):1157-1168.

Vlegel, V

Bonhoure, N; Bounova, G; Bernasconi, D; Praz, V; Lammers, F; Canella, D; Willis, I M; Herr, W; Hernandez, N; Delorenzi, M; Hernandez, N; Delorenzi, M; Deplancke, B; Desvergne, B; Guex, N; Herr, W; Naef, F; Rougemont, J; Schibler, U; Andersin, T; Cousin, P; Gilardi, F; Gos, P; Lammers, F; Raghav, S; Villeneuve, D; Fabbretti, R; Vlegel, V; Xenarios, I; Migliavacca, E; Praz, V; David, F; Jarosz, Y; Kuznetsov, D; Liechti, R; Martin, O; Delafontaine, J; Cajan, J; Gustafson, K; Krier, I; Leleu, M; Molina, N; Naldi, A; Rib, L; Symul, L; Bounova, G (2014). Quantifying ChIP-seq data: a spiking method providing an internal reference for sample-to-sample normalization. Genome Research, 24(7):1157-1168.

Voegeli, Sylvia

Bonde, Marie Mi; Voegeli, Sylvia; Baudrimont, Antoine; Seraphin, Bertrand; Becskei, Attila (2014). Quantification of pre-mRNA escape rate and synergy in splicing. Nucleic Acids Research, 42(20):12847-12860.

Vogel, Viola

Schoen, Ingmar; Ries, Jonas; Klotzsch, Enrico; Ewers, Helge; Vogel, Viola (2011). Binding-activated localization microscopy of DNA structures. Nano letters, 11(9):4008-4011.

Volynsky, Pavel E

Polyansky, Anton A; Ramaswamy, Rajesh; Volynsky, Pavel E; Sbalzarini, Ivo F; Marrink, Siewert J; Efremov, Roman G (2010). Antimicrobial Peptides Induce Growth of Phosphatidylglycerol Domains in a Model Bacterial Membrane. Journal of Physical Chemistry Letters, 1(20):3108-3111.

Vonaesch, Pascale

Vonaesch, Pascale; Cardini, Steven; Sellin, Mikael E; Goud, Bruno; Hardt, Wolf-Dietrich; Schauer, Kristine (2013). Quantitative insights into actin rearrangements and bacterial target site selection fromSalmonella Typhimurium infection of micropatterned cells. Cellular Microbiology, 15(11):1851-1865.

Vorholt, J A

Kiefer, P; Schmitt, U; Vorholt, J A (2013). eMZed: an open source framework in Python for rapid and interactive development of LC/MS data analysis workflows. Bioinformatics, 29(7):963-964.

Wagner, Andreas

Sunnåker, Mikael; Zamora-Sillero, Elias; Dechant, Reinhard; Ludwig, Christina; Busetto, Alberto Giovanni; Wagner, Andreas; Stelling, Joerg (2013). Automatic Generation of Predictive Dynamic Models Reveals Nuclear Phosphorylation as the Key Msn2 Control Mechanism. Science Signaling, 6(277):ra41.

Waldmeier, Lorenz

Tiwari, Neha; Tiwari, Vijay K; Waldmeier, Lorenz; Balwierz, Piotr J; Arnold, Phil; Pachkov, Mikhail; Meyer-Schaller, Nathalie; Schübeler, Dirk; van Nimwegen, Erik; Christofori, Gerhard (2013). Sox4 is a master regulator of epithelial-mesenchymal transition by controlling ezh2 expression and epigenetic reprogramming. Cancer Cell, 23(6):768-83.

Wang, Jing

Vayssier-Taussat, Muriel; Le Rhun, Danielle; Deng, Hong Kuan; Biville, Francis; Cescau, Sandra; Danchin, Antoine; Marignac, Geneviève; Lenaour, Evelyne; Boulouis, Henri Jean; Mavris, Maria; Arnaud, Lionel; Yang, Huanming; Wang, Jing; Quebatte, Maxime; Engel, Philipp; Saenz, Henri; Dehio, Christoph (2010). The Trw Type IV Secretion System of Bartonella Mediates Host-Specific Adhesion to Erythrocytes. PLoS Pathogens, 6(6):e1000946.

Weber, A

Routier-Kierzkowska, A -L; Weber, A; Kochova, P; Felekis, D; Nelson, B J; Kuhlemeier, C; Smith, R S (2012). Cellular Force Microscopy for in Vivo Measurements of Plant Tissue Mechanics. Plant Physiology, 158(4):1514-1522.

Weidmann, Simon

Weidmann, Simon; Barylyuk, Konstantin; Nespovitaya, Nadezhda; Mädler, Stefanie; Zenobi, Renato (2013). A New, Modular Mass Calibrant for High-Mass MALDI-MS. Analytical Chemistry, 85:3425-3432.

Wenk, M R

Lim, L; Jackson-Lewis, V; Wong, L C; Shui, G H; Goh, A X H; Kesavapany, S; Jenner, A M; Fivaz, M; Przedborski, S; Wenk, M R (2012). Lanosterol induces mitochondrial uncoupling and protects dopaminergic neurons from cell death in a model for Parkinson's disease. Cell Death and Differentiation, 19(3):416-27.

Wenk, Markus R

Cheng, Danni; Jenner, Andrew M; Shui, Guanghou; Cheong, Wei Fun; Mitchell, Todd W; Nealon, Jessica R; Kim, Woojin S; McCann, Heather; Wenk, Markus R; Halliday, Glenda M; Garner, Brett (2011). Lipid pathway alterations in Parkinson's disease primary visual cortex. PLoS ONE, 6(2):e17299.

Wichert, S P

Brankatschk, B; Wichert, S P; Johnson, S D; Schaad, O; Rossner, M J; Gruenberg, J (2012). Regulation of the EGF Transcriptional Response by Endocytic Sorting. Science Signaling, 5(215):ra21.

Wiesand, U

Kudryashev, M; Stenta, M; Schmelz, S; Amstutz, M; Wiesand, U; Castano-Diez, D; Degiacomi, M T; Munnich, S; Bleck, C K; Kowal, J; Diepold, A; Heinz, D W; Dal Peraro, M; Cornelis, G R; Stahlberg, H (2013). In situ structural analysis of the Yersinia enterocolitica injectisome. eLife, 2:e00792-e00792.

Willis, I M

Bonhoure, N; Bounova, G; Bernasconi, D; Praz, V; Lammers, F; Canella, D; Willis, I M; Herr, W; Hernandez, N; Delorenzi, M; Hernandez, N; Delorenzi, M; Deplancke, B; Desvergne, B; Guex, N; Herr, W; Naef, F; Rougemont, J; Schibler, U; Andersin, T; Cousin, P; Gilardi, F; Gos, P; Lammers, F; Raghav, S; Villeneuve, D; Fabbretti, R; Vlegel, V; Xenarios, I; Migliavacca, E; Praz, V; David, F; Jarosz, Y; Kuznetsov, D; Liechti, R; Martin, O; Delafontaine, J; Cajan, J; Gustafson, K; Krier, I; Leleu, M; Molina, N; Naldi, A; Rib, L; Symul, L; Bounova, G (2014). Quantifying ChIP-seq data: a spiking method providing an internal reference for sample-to-sample normalization. Genome Research, 24(7):1157-1168.

Winderickx, Joris

Dechant, Reinhard; Binda, Matteo; Lee, Sung Sik; Pelet, Serge; Winderickx, Joris; Peter, Matthias (2010). Cytosolic pH is a second messenger for glucose and regulates the PKA pathway through V‐ATPase. EMBO Journal Online, 29(15):2515-2526.

Wittel, Falk K

Munglani, Gautam; Vetter, Roman; Wittel, Falk K; Herrmann, Hans J (2015). Orthotropic rotation-free thin shell elements. Computational Mechanics, 56(5):785-793.

Wohl, Benjamin M

Andreasen, Sidsel Ø; Chong, Siow-Feng; Wohl, Benjamin M; Goldie, Kenneth N; Zelikin, Alexander N (2013). Poly(vinyl alcohol) physical hydrogel nanoparticles, not polymer solutions, exert inhibition of nitric oxide synthesis in cultured macrophages. Biomacromolecules, 14(5):1687-95.

Wollscheid, B

Hofmann, A; Gerrits, B; Schmidt, A; Bock, T; Bausch-Fluck, D; Aebersold, R; Wollscheid, B (2010). Proteomic cell surface phenotyping of differentiating acute myeloid leukemia cells. Blood, 116(13):e26-34.

Wong, L C

Lim, L; Jackson-Lewis, V; Wong, L C; Shui, G H; Goh, A X H; Kesavapany, S; Jenner, A M; Fivaz, M; Przedborski, S; Wenk, M R (2012). Lanosterol induces mitochondrial uncoupling and protects dopaminergic neurons from cell death in a model for Parkinson's disease. Cell Death and Differentiation, 19(3):416-27.

Woodruff, Kristina

Woodruff, Kristina; Fidalgo, Luis M; Gobaa, Samy; Lutolf, Matthias P; Maerkl, Sebastian J (2013). Live Mammalian Cell Arrays. Nature Methods, 10(6):550-552.

Xenarios, I

Bonhoure, N; Bounova, G; Bernasconi, D; Praz, V; Lammers, F; Canella, D; Willis, I M; Herr, W; Hernandez, N; Delorenzi, M; Hernandez, N; Delorenzi, M; Deplancke, B; Desvergne, B; Guex, N; Herr, W; Naef, F; Rougemont, J; Schibler, U; Andersin, T; Cousin, P; Gilardi, F; Gos, P; Lammers, F; Raghav, S; Villeneuve, D; Fabbretti, R; Vlegel, V; Xenarios, I; Migliavacca, E; Praz, V; David, F; Jarosz, Y; Kuznetsov, D; Liechti, R; Martin, O; Delafontaine, J; Cajan, J; Gustafson, K; Krier, I; Leleu, M; Molina, N; Naldi, A; Rib, L; Symul, L; Bounova, G (2014). Quantifying ChIP-seq data: a spiking method providing an internal reference for sample-to-sample normalization. Genome Research, 24(7):1157-1168.

Xenarios, Ioannis

Bernard, Thomas; Bridge, Alan; Morgat, Anne; Moretti, Sébastien; Xenarios, Ioannis; Pagni, Marco (2014). Reconciliation of metabolites and biochemical reactions for metabolic networks. Briefings in Bioinformatics, 15(1):123-135.

Yang, Huanming

Vayssier-Taussat, Muriel; Le Rhun, Danielle; Deng, Hong Kuan; Biville, Francis; Cescau, Sandra; Danchin, Antoine; Marignac, Geneviève; Lenaour, Evelyne; Boulouis, Henri Jean; Mavris, Maria; Arnaud, Lionel; Yang, Huanming; Wang, Jing; Quebatte, Maxime; Engel, Philipp; Saenz, Henri; Dehio, Christoph (2010). The Trw Type IV Secretion System of Bartonella Mediates Host-Specific Adhesion to Erythrocytes. PLoS Pathogens, 6(6):e1000946.

Yerly, Florence

Feller, Chrystel; Gabriel, Jean-Pierre; Mazza, Christian; Yerly, Florence (2014). Pattern formation in auxin flux. Journal of Mathematical Biology, 68(4):879-909.

Zabeau, Lennart

Moharana, Kedar; Zabeau, Lennart; Peelman, Frank; Ringler, Philippe; Stahlberg, Henning; Tavernier, Jan; Savvides, Savvas N (2014). Structural and mechanistic paradigm of leptin receptor activation revealed by complexes with wild-type and antagonist leptins. Structure, 22(6):866-877.

Zadnikova, P

Guenot, B; Bayer, E; Kierzkowski, D; Smith, R S; Mandel, T; Zadnikova, P; Benkova, E; Kuhlemeier, C (2012). PIN1-Independent Leaf Initiation in Arabidopsis. Plant Physiology, 159(4):1501-1510.

Zamora-Sillero, Elias

Sunnåker, Mikael; Zamora-Sillero, Elias; Dechant, Reinhard; Ludwig, Christina; Busetto, Alberto Giovanni; Wagner, Andreas; Stelling, Joerg (2013). Automatic Generation of Predictive Dynamic Models Reveals Nuclear Phosphorylation as the Key Msn2 Control Mechanism. Science Signaling, 6(277):ra41.

Zecchina, Riccardo

Bailly-Bechet, Marc; Benecke, Arndt; Hardt, Wolf Dietrich; Lanza, Valentina; Sturm, Alexander; Zecchina, Riccardo (2011). An externally modulated, noise-driven switch for the regulation of SPI1 in Salmonella enterica serovar Typhimurium. Journal of Mathematical Biology, 63(4):637-662.

Zechner, Christoph

Koeppl, Heinz; Zechner, Christoph; Ganguly, Arnab; Pelet, Serge; Peter, Matthias (2012). Accounting for extrinsic variability in the estimation of stochastic rate constants. International Journal of Robust and Nonlinear Control, 22(10):1103-1119.

Zelikin, Alexander N

Andreasen, Sidsel Ø; Chong, Siow-Feng; Wohl, Benjamin M; Goldie, Kenneth N; Zelikin, Alexander N (2013). Poly(vinyl alcohol) physical hydrogel nanoparticles, not polymer solutions, exert inhibition of nitric oxide synthesis in cultured macrophages. Biomacromolecules, 14(5):1687-95.

Hosta-Rigau, Leticia; Jensen, Bettina E B; Fjeldsø, Kit S; Postma, Almar; Li, Guoxin; Goldie, Kenneth N; Albericio, Fernando; Zelikin, Alexander N; Städler, Brigitte (2012). Drug Delivery: Surface-Adhered Composite Poly(Vinyl Alcohol) Physical Hydrogels: Polymersome-Aided Delivery of Therapeutic Small Molecules. Advanced Healthcare Materials, 1(6):791-5.

Zenobi, Renato

Weidmann, Simon; Barylyuk, Konstantin; Nespovitaya, Nadezhda; Mädler, Stefanie; Zenobi, Renato (2013). A New, Modular Mass Calibrant for High-Mass MALDI-MS. Analytical Chemistry, 85:3425-3432.

Zinzalla, Vittoria

Zinzalla, Vittoria; Stracka, Daniele; Oppliger, Wolfgang; Hall, Michael N (2011). Activation of mTORC2 by Association with the Ribosome. Cell, 144:757-768.

Zoller, Benjamin

Simicevic, Jovan; Schmid, Adrien W; Gilardoni, Paola A; Zoller, Benjamin; Raghav, Sunil K; Krier, Irina; Gubelmann, Carinne; Lisacek, Frédérique; Naef, Felix; Moniatte, Marc; Deplancke, Bart (2013). Absolute quantification of transcription factors during cellular differentiation using multiplexed targeted proteomics. Nature Methods, 10(6):570-576.

Zuklys, Saulius

Papadopoulou, Aikaterini S; Dooley, James; Linterman, Michelle A; Pierson, Wim; Ucar, Olga; Kyewski, Bruno; Zuklys, Saulius; Hollander, Georg A; Matthys, Patrick; Gray, Daniel H D; De Strooper, Bart; Liston, Adrian (2011). The thymic epithelial microRNA network elevates the threshold for infection-associated thymic involution via miR-29a mediated suppression of the IFN-α receptor. Nature Immunology, 13(2):181-187.

Zurwerra, Didier

Prota, Andrea E; Bargsten, Katja; Zurwerra, Didier; Field, Jessica J; Díaz, José Fernando; Altmann, Karl-Heinz; Steinmetz, Michel O (2013). Molecular Mechanism of Action of Microtubule-Stabilizing Anticancer Agents. Science, 339(6119):587-590.

de Nadal, E

Pelet, S; Rudolf, F; Nadal-Ribelles, M; de Nadal, E; Posas, F; Peter, M (2011). Transient activation of the HOG MAPK pathway regulates bimodal gene expression. Science, 332(6030):732-735.

van Nimwegen, Erik

Tiwari, Neha; Meyer-Schaller, Nathalie; Arnold, Phil; Antoniadis, Helena; Pachkov, Mikhail; van Nimwegen, Erik; Christofori, Gerhard (2013). Klf4 is a transcriptional regulator of genes critical for EMT, including Jnk1 (Mapk8). PLoS ONE, 8(2):e57329.

Tiwari, Neha; Tiwari, Vijay K; Waldmeier, Lorenz; Balwierz, Piotr J; Arnold, Phil; Pachkov, Mikhail; Meyer-Schaller, Nathalie; Schübeler, Dirk; van Nimwegen, Erik; Christofori, Gerhard (2013). Sox4 is a master regulator of epithelial-mesenchymal transition by controlling ezh2 expression and epigenetic reprogramming. Cancer Cell, 23(6):768-83.

van der Goot, F Gisou

Blaskovic, Sanja; Blanc, Mathieu; van der Goot, F Gisou (2013). What does S-palmitoylation do to membrane proteins? FEBS Journal, 280(12):2766-2774.

van der Westen, Rebecca

van der Westen, Rebecca; Hosta-Rigau, Leticia; Sutherland, Duncan S; Goldie, Kenneth N;