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Loizides-Mangold, Ursula (2013). On the future of mass-spectrometry-based lipidomics. FEBS Journal, 280:2817-2829.
Paul, Grégory; Cardinale, Janick; Sbalzarini, Ivo F (2013). Coupling Image Restoration and Segmentation: A Generalized Linear Model/Bregman Perspective. International Journal of Computer Vision, 104(1):69-93.
Sbalzarini, Ivo F (2013). Modeling and simulation of biological systems from image data. BioEssays, 35(5):482-490.
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.
Blaskovic, Sanja; Blanc, Mathieu; van der Goot, F Gisou (2013). What does S-palmitoylation do to membrane proteins? FEBS Journal, 280(12):2766-2774.
Yakimovich, A; Gumpert, H; Burckhardt, C J; Lutschg, V A; Jurgeit, A; Sbalzarini, I F; Greber, U F (2012). Cell-free transmission of human adenovirus by passive mass transfer in cell culture simulated in a computer model. Journal of Virology, 86(18):10123-10137.
Snijder, Berend; Sacher, Raphael; Rämö, Pauli; Liberali, Prisca; Mench, Karin; Wolfrum, Nina; Burleigh, Laura; Scott, Cameron C; Verheije, Monique H; Mercer, Jason; Moese, Stefan; Heger, Thomas; Theusner, Kristina; Jurgeit, Andreas; Lamparter, David; Balistreri, Giuseppe; Schelhaas, Mario; De Haan, Cornelis A M; Marjomäki, Varpu; Hyypiä, Timo; Rottier, Peter J M; Sodeik, Beate; Marsh, Mark; Gruenberg, Jean; Amara, Ali; Greber, Urs; Helenius, Ari; Pelkmans, Lucas (2012). Single-cell analysis of population context advances RNAi screening at multiple levels. Molecular Systems Biology, 8(579):1-18.
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.
Cardinale, J; Paul, G; Sbalzarini, I F (2012). Discrete region competition for unknown numbers of connected regions. IEEE transactions on image processing : a publication of the IEEE Signal Processing Society, 21(8):3531-3545.
Ramaswamy, Rajesh; González-Segredo, Nélido; Sbalzarini, Ivo F; Grima, Ramon (2012). Discreteness-induced concentration inversion in mesoscopic chemical systems. Nature Communications, 3:779.
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.
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.
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.
Lakkaraju, Asvin K K; Abrami, Laurence; Lemmin, Thomas; Blaskovic, Sanja; Kunz, Béatrice; Kihara, Akio; Dal Peraro, Matteo; van der Goot, Françoise Gisou (2012). Palmitoylated calnexin is a key component of the ribosome-translocon complex. The EMBO Journal, 31(7):1823-35.
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.
Ramaswamy, Rajesh; Sbalzarini, Ivo F (2011). A partial-propensity formulation of the stochastic simulation algorithm for chemical reaction networks with delays. Journal of Chemical Physics, 134(1):014106.
Lissina, Elena; Young, Brian; Urbanus, Malene L; Guan, Xue Li; Lowenson, Jonathan; Hoon, Shawn; Baryshnikova, Anastasia; Riezman, Isabelle; Michaut, Magali; Riezman, Howard; Cowen, Leah E; Wenk, Markus R; Clarke, Steven G; Giaever, Guri; Nislow, Corey (2011). A systems biology approach reveals the role of a novel methyltransferase in response to chemical stress and lipid homeostasis. PLoS Genetics, 7(10):e1002332.
Burckhardt, C J; Suomalainen, M; Schoenenberger, P; Boucke, K; Hemmi, S; Greber, U F (2011). Drifting Motions of the Adenovirus Receptor CAR and Immobile Integrins Initiate Virus Uncoating and Membrane Lytic Protein Exposure. Cell Host & Microbe, 10(2):105-117.
Ramaswamy, Rajesh; Sbalzarini, Ivo F (2011). Exact on-lattice stochastic reaction-diffusion simulations using partial-propensity methods. Journal of Chemical Physics, 135(24):244103.
Helmuth, Jo A; Reboux, Sylvain; Sbalzarini, Ivo F (2011). Exact stochastic simulations of intra-cellular transport by mechanically coupled molecular motors. Journal of Computer Science, 2(4):324-334.
Müller, Christian L; Ramaswamy, Rajesh; Sbalzarini, Ivo F (2011). Global Parameter Identification of Stochastic Reaction Networks from Single Trajectories. In: Goryanin, Igor I; Goryachev, Andrew B. Advances in Systems Biology. New York, NY: Springer, 477-498.
Ambühl, Mark E; Brepsant, Charles; Meister, Jean-Jacques; Verkhovsky, Alexander B; Sbalzarini, Ivo F (2011). High-resolution cell outline segmentation and tracking from phase-contrast microscopy images. Journal of Microscopy, 245(2):161-170.
Ramaswamy, Rajesh; Sbalzarini, Ivo F (2011). Intrinsic noise alters the frequency spectrum of mesoscopic oscillatory chemical reaction systems. Scientific Reports, 1:154.
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.
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.
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.
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. American Institute of Physics, 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.
Schrader, Birte; Reboux, Sylvain; Sbalzarini, Ivo F (2010). Discretization correction of general integral PSE Operators for particle methods. Journal of Computational Physics, 229(11):4159-4182.
Wenk, Markus R (2010). Lipidomics: new tools and applications. Cell, 143(6):888-95.
Köhler, K; Brunner, E; Xue, L Guan; Boucke, K; Greber, U F; Mohanty, S; Barth, J M I; Wenk, M R; Hafen, E (2009). A combined proteomic and genetic analysis identifies a role for the lipid desaturase Desat1 in starvation-induced autophagy in Drosophila. Autophagy, 5(7):980-990.
Cardinale, Janick; Rauch, Alexander; Barral, Yves; Székely, Gábor; Sbalzarini, Ivo F (2009). Bayesian image analysis with on-line confidence estimates and its application to microtubule tracking. In: IEEE International Symposium on Biomedical Imaging: From Nano to Macro, Boston, MA, 28 June 2009 - 1 July 2009, 1091-1094.
Menuz, V; Howell, K S; Gentina, S; Epstein, S; Riezman, I; Fornallaz-Mulhauser, M; Hengartner, M O; Gomez, M; Riezman, H; Martinou, J C (2009). Protection of C. elegans from anoxia by HYL-2 ceramide synthase. Science, 324(5925):381-384.
Ramaswamy, Rajesh; González-Segredo, Nélido; Sbalzarini, Ivo F (2009). A new class of highly efficient exact stochastic simulation algorithms for chemical reaction networks. The Journal of chemical physics, 130(24):244104.
Helmuth, Jo A; Sbalzarini, Ivo F (2009). Deconvolving Active Contours for Fluorescence Microscopy Images. Lecture Notes in Computer Science, 5875:544-553.
Guan, Xue Li; Souza, Cleiton M; Pichler, Harald; Dewhurst, Gisèle; Schaad, Olivier; Kajiwara, Kentaro; Wakabayashi, Hirotomo; Ivanova, Tanya; Castillon, Guillaume A; Piccolis, Manuele; Abe, Fumiyoshi; Loewith, Robbie; Funato, Kouichi; Wenk, Markus R; Riezman, Howard (2009). Functional interactions between sphingolipids and sterols in biological membranes regulating cell physiology. Molecular Biology of the Cell, 20(7):2083-95.
