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Schmid, Michael; Frei, Daniel; Patrignani, Andrea; Schlapbach, Ralph; Frey, Jürg E; Remus-Emsermann, Mitja N P; Ahrens, Christian H (2018). Pushing the limits of de novo genome assembly for complex prokaryotic genomes harboring very long, near identical repeats. Nucleic Acids Research, 46(17):8953-8965.

Bratus-Neuenschwander, Anna; Castro-Giner, Francesc; Frank-Bertoncelj, Mojca; Aluri, Sirisha; Fucentese, Sandro F; Schlapbach, Ralph; Sprott, Haiko (2018). Pain-Associated Transcriptome Changes in Synovium of Knee Osteoarthritis Patients. Genes, 9(7):E338.

Qi, Weihong; Cascarano, Maria Chiara; Schlapbach, Ralph; Katharios, Pantelis; Vaughan, Lloyd; Seth-Smith, Helena M B (2018). Ca. Endozoicomonas cretensis: A Novel Fish Pathogen Characterized by Genome Plasticity. Genome Biology and Evolution, 10(6):1363-1374.

Shao, Wenguang; Pedrioli, Patrick G A; Wolski, Witold; Scurtescu, Cristian; Schmid, Emanuel; Vizcaíno, Juan A; Courcelles, Mathieu; Schuster, Heiko; Kowalewski, Daniel; Marino, Fabio; Arlehamn, Cecilia S L; Vaughan, Kerrie; Peters, Bjoern; Sette, Alessandro; Ottenhoff, Tom H M; Meijgaarden, Krista E; Nieuwenhuizen, Natalie; Kaufmann, Stefan H E; Schlapbach, Ralph; Castle, John C; Nesvizhskii, Alexey I; Nielsen, Morten; Deutsch, Eric W; Campbell, David S; Moritz, Robert L; Zubarev, Roman A; Ytterberg, Anders Jimmy; Purcell, Anthony W; Marcilla, Miguel; Paradela, Alberto; et al (2018). The SysteMHC Atlas project. Nucleic Acids Research, 46(D1):D1237-D1247.

Hatakeyama, Masaomi; Aluri, Sirisha; Balachadran, Mathi Thumilan; Sivarajan, Sajeevan Radha; Patrignani, Andrea; Grüter, Simon; Poveda, Lucy; Shimizu-Inatsugi, Rie; Baeten, John; Francoijs, Kees-Jan; Nataraja, Karaba N; Reddy, Yellodu A Nanja; Phadnis, Shamprasad; Ravikumar, Ramapura L; Schlapbach, Ralph; Sreeman, Sheshshayee M; Shimizu, Kentaro K (2018). Multiple hybrid de novo genome assembly of finger millet, an orphan allotetraploid crop. DNA Research, 25(1):39-47.

Trachsel, Christian; Panse, Christian; Kockmann, Tobias; Wolski, Witold Eryk; Grossmann, Jonas; Schlapbach, Ralph (2018). rawDiag - an R package supporting rational LC-MS method optimization for bottom-up proteomics. bioRxiv 304485, University of Zurich.

Caron, Etienne; Roncagalli, Romain; Hase, Takeshi; Wolski, Witold E; Choi, Meena; Menoita, Marisa G; Durand, Stephane; García-Blesa, Antonio; Fierro-Monti, Ivo; Sajic, Tatjana; Heusel, Moritz; Weiss, Tobias; Malissen, Marie; Schlapbach, Ralph; Collins, Ben C; Ghosh, Samik; Kitano, Hiroaki; Aebersold, Ruedi; Malissen, Bernard; Gstaiger, Matthias (2017). Precise Temporal Profiling of Signaling Complexes in Primary Cells Using SWATH Mass Spectrometry. Cell Reports, 18(13):3219-3226.

Qi, Weihong; Schlapbach, Ralph; Rehrauer, Hubert (2017). RNA-Seq Data Analysis: From Raw Data Quality Control to Differential Expression Analysis. Methods in Molecular Biology, 1669:295-307.

Dimitrieva, Slavica; Schlapbach, Ralph; Rehrauer, Hubert (2016). Prognostic value of cross-omics screening for kidney clear cell renal cancer survival. Biology Direct, 11(1):68.

Ardissone, Silvia; Redder, Peter; Russo, Giancarlo; Frandi, Antonio; Fumeaux, Coralie; Patrignani, Andrea; Schlapbach, Ralph; Falquet, Laurent; Viollier, Patrick H (2016). Cell cycle constraints and environmental control of local DNA hypomethylation in α-proteobacteria. PLoS Genetics, 12(12):e1006499.

Meder, Doris; Morales, Mònica; Pepperkok, Rainer; Schlapbach, Ralph; Tiran, Andreas; Van Minnebruggen, Geert (2016). Institutional core facilities: prerequisite for breakthroughs in the life sciences: Core facilities play an increasingly important role in biomedical research by providing scientists access to sophisticated technology and expertise. EMBO Reports, 17(8):1088-1093.

Kockmann, Tobias; Trachsel, Christian; Panse, Christian; Wahlander, Asa; Selevsek, Nathalie; Grossmann, Jonas; Wolski, Witold E; Schlapbach, Ralph (2016). Targeted proteomics coming of age - SRM, PRM and DIA performance evaluated from a core facility perspective. Proteomics, 16(15-16):2183-2192.

Seth-Smith, Helena M B; Dourala, Nancy; Fehr, Alexander; Qi, Weihong; Katharios, Pantelis; Ruetten, Maja; Mateos, José M; Nufer, Lisbeth; Weilenmann, Roseline; Ziegler, Urs; Thomson, Nicholas R; Schlapbach, Ralph; Vaughan, Lloyd (2016). Emerging pathogens of gilthead seabream: characterisation and genomic analysis of novel intracellular β-proteobacteria. The ISME journal, 10(7):1791-1803.

Qi, Weihong; Vaughan, Lloyd; Katharios, Pantelis; Schlapbach, Ralph; Seth-Smith, Helena M B (2016). Host-associated genomic features of the novel uncultured intracellular pathogen ca. ichthyocystis revealed by direct sequencing of epitheliocysts. Genome Biology and Evolution, 8(6):1672-1689.

Hatakeyama, Masaomi; Opitz, Lennart; Russo, Giancarlo; Qi, Weihong; Schlapbach, Ralph; Rehrauer, Hubert (2016). SUSHI: an exquisite recipe for fully documented, reproducible and reusable NGS data analysis. BMC Bioinformatics, 17(1):228.

St John, Elizabeth P; Simen, Birgitte B; Turenchalk, Gregory S; Braverman, Michael S; Abbate, Isabella; Aerssens, Jeroen; Bouchez, Olivier; Gabriel, Christian; Izopet, Jacques; Meixenberger, Karolin; Di Giallonardo, Francesca; Schlapbach, Ralph; Paredes, Roger; Sakwa, James; Schmitz-Agheguian, Gudrun G; Thielen, Alexander; Victor, Martin; Metzner, Karin J; Däumer, Martin P (2016). A follow-up of the multicenter collaborative study on HIV-1 drug resistance and tropism testing using 454 ultra deep pyrosequencing. PLoS ONE, 11(1):e0146687.

Kamkina, Polina; Snoek, L Basten; Grossmann, Jonas; Volkers, Rita J M; Sterken, Mark G; Daube, Michael; Roschitzki, Bernd; Fortes, Claudia; Schlapbach, Ralph; Roth, Alexander; von Mering, Christian; Hengartner, Michael O; Schrimpf, Sabine P; Kammenga, Jan E (2016). Natural genetic variation differentially affects the proteome and transcriptome in Caenorhabditis elegans. Molecular & Cellular Proteomics, 15(5):1670-1680.

Sobek, Jens; Rehrauer, Hubert; Schauer, Stefan; Fischer, David; Patrignani, Andrea; Landgraf, Stephan; Korlach, Jonas; Schlapbach, Ralph (2016). Single-molecule DNA hybridisation studied by using a modified DNA sequencer: a comparison with surface plasmon resonance data. Methods and applications in fluorescence, 4(1):1-17.

Katharios, Pantelis; Seth-Smith, Helena MB; Fehr, Alexander; Mateos, José María; Qi, Weihong; Richter, Denis; Nufer, Lisbeth; Ruetten, Maja; Guevara Soto, Maricruz; Ziegler, Urs; Thomson, Nicholas R; Schlapbach, Ralph; Vaughan, Lloyd (2015). Environmental marine pathogen isolation using mesocosm culture of sharpsnout seabream: striking genomic and morphological features of novel Endozoicomonas sp. Scientific Reports, 5:onlie.

Meienberg, Janine; Zerjavic, Katja; Keller, Irene; Okoniewski, Michal; Patrignani, Andrea; Ludin, Katja; Xu, Zhenyu; Steinmann, Beat; Carrel, Thierry; Röthlisberger, Benno; Schlapbach, Ralph; Bruggmann, Rémy; Matyas, Gabor (2015). New insights into the performance of human whole-exome capture platforms. Nucleic Acids Research, 43(11):e76.

Panse, Christian; Trachsel, Christian; Grossmann, Jonas; Schlapbach, Ralph (2015). specL - An R/Bioconductor package to prepare peptide spectrum matches for use in targeted proteomics. Bioinformatics, 31(13):2228-2231.

Russo, Giancarlo; Patrignani, Andrea; Poveda, Lucy; Hoehn, Frederic; Scholtka, Bettina; Schlapbach, Ralph; Garvin, Alex M (2015). Highly sensitive, non-invasive detection of colorectal cancer mutations using single molecule, third generation sequencing. Applied and Translational Genomics, 7:32-39.

Nowak, Michael D; Russo, Giancarlo; Schlapbach, Ralph; Huu, Cuong Nguyen; Lenhard, Michael; Conti, Elena (2015). The draft genome of Primula veris yields insights into the molecular basis of heterostyly. Genome Biology, 16:12.

Kentner, David; Martano, Giuseppe; Callon, Morgane; Chiquet, Petra; Brodmann, Maj; Burton, Olga; Wahlander, Asa; Nanni, Paolo; Delmotte, Nathanaël; Grossmann, Jonas; Limenitakis, Julien; Schlapbach, Ralph; Kiefer, Patrick; Vorholt, Julia A; Hiller, Sebastian; Bumann, Dirk (2014). Shigella reroutes host cell central metabolism to obtain high-flux nutrient supply for vigorous intracellular growth. Proceedings of the National Academy of Sciences of the United States of America, 111(27):9929-9934.

Simen, Birgitte B; Braverman, Michael S; Abbate, Isabella; Aerssens, Jeroen; Bidet, Yannick; Bouchez, Olivier; Gabriel, Christian; Izopet, Jacques; Kessler, Harald H; Stelzl, Evelyn; Di Giallonardo, Francesca; Schlapbach, Ralph; Radonic, Aleksander; Paredes, Roger; Recordon-Pinson, Patricia; Sakwa, James; St John, Elizabeth P; Schmitz-Agheguian, Gudrun G; Metzner, Karin J; Däumer, Martin P (2014). An international multicenter study on HIV-1 drug resistance testing by 454 ultra-deep pyrosequencing. Journal of Virological Methods, 204:31-37.

Drissner, David; Gekenidis, Maria-Theresia; Schlapbach, Ralph; Brunisholz, René (2014). When Time-to-Result Matters: Identification of Microbes Based on MALDI-TOF Protein and Peptide Profiling. CHIMIA International Journal for Chemistry, 68(6):453.

Trinh, Hung V; Grossmann, Jonas; Gehrig, Peter; Roschitzki, Bernd; Schlapbach, Ralph; Greber, Urs F; Hemmi, Silvio (2013). iTRAQ-based and label-free proteomics approaches for studies of human adenovirus infections. International Journal of Proteomics, 2013:581862.

Biason-Lauber, Anna; Böni-Schnetzler, Marianne; Hubbard, Basil P; Bouzakri, Karim; Brunner, Andrea; Cavelti-Weder, Claudia; Keller, Cornelia; Meyer-Böni, Monika; Meier, Daniel T; Brorsson, Caroline; Timper, Katharina; Leibowitz, Gil; Patrignani, Andrea; Bruggmann, Remy; Boily, Gino; Zulewski, Henryk; Geier, Andreas; Cermak, Jennifer M; Elliott, Peter; Ellis, James L; Westphal, Christoph; Knobel, Urs; Eloranta, Jyrki J; Kerr-Conte, Julie; Pattou, François; Konrad, Daniel; Matter, Christian M; Fontana, Adriano; Rogler, Gerhard; Schlapbach, Ralph; Regairaz, Camille; Carballido, José M; Glaser, Benjamin; McBurney, Michael W; Pociot, Flemming; Sinclair, David A; Donath, Marc Y (2013). Identification of a SIRT1 mutation in a family with type 1 Diabetes. Cell Metabolism, 17(3):448-455.

Sobek, Jens; Schauer, Stefan; Rehrauer, Hubert; Fischer, David; Patrignani, Andrea; Landgraf, Stephan; Schlapbach, Ralph (2013). Single molecule interactions studied by using a modified DNA sequencer: a comparison with surface plasmon resonance. In: SPIE, San Francisco, 2 February 2013 - 2 February 2013, 85960Y.

Rehrauer, Hubert; Opitz, Lennart; Tan, Ge; Sieverling, Lina; Schlapbach, Ralph (2013). Blind spots of quantitative RNA-seq: the limits for assessing abundance, differential expression, and isoform switching. BMC Bioinformatics, 14:370.

Sobek, Jens; Aquino, Catharine; Weigel, Wilfried; Schlapbach, Ralph (2013). Drop drying on surfaces determines chemical reactivity - the specific case of immobilization of oligonucleotides on microarrays. BMC Biophysics, 6:8.

Nanni, Paolo; Panse, Christian; Gehrig, Peter; Mueller, Susanne; Grossmann, Jonas; Schlapbach, Ralph (2013). PTM MarkerFinder, a software tool to detect and validate spectra from peptides carrying post-translational modifications. Proteomics, 13(15):2251-2255.

Okoniewski, Michal J; Meienberg, Janine; Patrignani, Andrea; Szabelska, Alicja; Matyas, Gabor; Schlapbach, Ralph (2013). Precise breakpoint localization of large genomic deletions using PacBio and Illumina next-generation sequencers. BioTechniques, 54(2):98-100.

Bauer, Chris; Kleinjung, Frank; Rutishauser, Dorothea; Panse, Christian; Chadt, Alexandra; Dreja, Tanja; Al-Hasani, Hadi; Reinert, Knut; Schlapbach, Ralph; Schuchhardt, Johannes (2012). PPINGUIN: Peptide Profiling Guided Identification of Proteins improves quantitation of iTRAQ ratios. BMC Bioinformatics, 13:34.

Spanaus, Katharina-Susanne; Kronenberg, Florian; Ritz, Eberhard; Schlapbach, Ralph; Fliser, Danilo; Hersberger, Martin; Kollerits, Barbara; König, Paul; von Eckardstein, Arnold (2007). B-type natriuretic peptide concentrations predict the progression of nondiabetic chronic kidney disease: the Mild-to-Moderate Kidney Disease Study. Clinical Chemistry, 53(7):1264-1272.

This list was generated on Wed Jun 26 16:28:03 2019 CEST.