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DMSO induces drastic changes in human cellular processes and epigenetic landscape in vitro.

Verheijen M, Lienhard M, Schrooders Y, Clayton O, Nudischer R, Boerno S, Timmermann B, Selevsek N, Schlapbach R, Gmuender H, Gotta S, Geraedts J, Herwig R, Kleinjans J, Caiment F.

Sci Rep. 2019 Mar 15;9(1):4641. doi: 10.1038/s41598-019-40660-0.


One step ahead: Innovation in core facilities.

Lippens S, D'Enfert C, Farkas L, Kehres A, Korn B, Morales M, Pepperkok R, Premvardhan L, Schlapbach R, Tiran A, Meder D, Van Minnebruggen G.

EMBO Rep. 2019 Apr;20(4). pii: e48017. doi: 10.15252/embr.201948017. Epub 2019 Mar 14. No abstract available.


Long fragments achieve lower base quality in Illumina paired-end sequencing.

Tan G, Opitz L, Schlapbach R, Rehrauer H.

Sci Rep. 2019 Feb 27;9(1):2856. doi: 10.1038/s41598-019-39076-7.


Pushing the limits of de novo genome assembly for complex prokaryotic genomes harboring very long, near identical repeats.

Schmid M, Frei D, Patrignani A, Schlapbach R, Frey JE, Remus-Emsermann MNP, Ahrens CH.

Nucleic Acids Res. 2018 Sep 28;46(17):8953-8965. doi: 10.1093/nar/gky726.


rawDiag: An R Package Supporting Rational LC-MS Method Optimization for Bottom-up Proteomics.

Trachsel C, Panse C, Kockmann T, Wolski WE, Grossmann J, Schlapbach R.

J Proteome Res. 2018 Aug 3;17(8):2908-2914. doi: 10.1021/acs.jproteome.8b00173. Epub 2018 Jul 24.


Pain-Associated Transcriptome Changes in Synovium of Knee Osteoarthritis Patients.

Bratus-Neuenschwander A, Castro-Giner F, Frank-Bertoncelj M, Aluri S, Fucentese SF, Schlapbach R, Sprott H.

Genes (Basel). 2018 Jul 4;9(7). pii: E338. doi: 10.3390/genes9070338.


Ca. Endozoicomonas cretensis: A Novel Fish Pathogen Characterized by Genome Plasticity.

Qi W, Cascarano MC, Schlapbach R, Katharios P, Vaughan L, Seth-Smith HMB.

Genome Biol Evol. 2018 Jun 1;10(6):1363-1374. doi: 10.1093/gbe/evy092.


Targeted Proteomics Guided by Label-free Quantitative Proteome Analysis in Saliva Reveal Transition Signatures from Health to Periodontal Disease.

Bostanci N, Selevsek N, Wolski W, Grossmann J, Bao K, Wahlander A, Trachsel C, Schlapbach R, Öztürk VÖ, Afacan B, Emingil G, Belibasakis GN.

Mol Cell Proteomics. 2018 Jul;17(7):1392-1409. doi: 10.1074/mcp.RA118.000718. Epub 2018 Apr 2.


The SysteMHC Atlas project.

Shao W, Pedrioli PGA, Wolski W, Scurtescu C, Schmid E, Vizcaíno JA, Courcelles M, Schuster H, Kowalewski D, Marino F, Arlehamn CSL, Vaughan K, Peters B, Sette A, Ottenhoff THM, Meijgaarden KE, Nieuwenhuizen N, Kaufmann SHE, Schlapbach R, Castle JC, Nesvizhskii AI, Nielsen M, Deutsch EW, Campbell DS, Moritz RL, Zubarev RA, Ytterberg AJ, Purcell AW, Marcilla M, Paradela A, Wang Q, Costello CE, Ternette N, van Veelen PA, van Els CACM, Heck AJR, de Souza GA, Sollid LM, Admon A, Stevanovic S, Rammensee HG, Thibault P, Perreault C, Bassani-Sternberg M, Aebersold R, Caron E.

Nucleic Acids Res. 2018 Jan 4;46(D1):D1237-D1247. doi: 10.1093/nar/gkx664.


Multiple hybrid de novo genome assembly of finger millet, an orphan allotetraploid crop.

Hatakeyama M, Aluri S, Balachadran MT, Sivarajan SR, Patrignani A, Grüter S, Poveda L, Shimizu-Inatsugi R, Baeten J, Francoijs KJ, Nataraja KN, Reddy YAN, Phadnis S, Ravikumar RL, Schlapbach R, Sreeman SM, Shimizu KK.

DNA Res. 2017 Sep 5. doi: 10.1093/dnares/dsx036. [Epub ahead of print]


RNA-Seq Data Analysis: From Raw Data Quality Control to Differential Expression Analysis.

Qi W, Schlapbach R, Rehrauer H.

Methods Mol Biol. 2017;1669:295-307. doi: 10.1007/978-1-4939-7286-9_23.


A model-based assay design to reproduce in vivo patterns of acute drug-induced toxicity.

Kuepfer L, Clayton O, Thiel C, Cordes H, Nudischer R, Blank LM, Baier V, Heymans S, Caiment F, Roth A, Fluri DA, Kelm JM, Castell J, Selevsek N, Schlapbach R, Keun H, Hynes J, Sarkans U, Gmuender H, Herwig R, Niederer S, Schuchhardt J, Segall M, Kleinjans J.

Arch Toxicol. 2018 Jan;92(1):553-555. doi: 10.1007/s00204-017-2041-7. Epub 2017 Aug 29. No abstract available.


Multi-laboratory assessment of reproducibility, qualitative and quantitative performance of SWATH-mass spectrometry.

Collins BC, Hunter CL, Liu Y, Schilling B, Rosenberger G, Bader SL, Chan DW, Gibson BW, Gingras AC, Held JM, Hirayama-Kurogi M, Hou G, Krisp C, Larsen B, Lin L, Liu S, Molloy MP, Moritz RL, Ohtsuki S, Schlapbach R, Selevsek N, Thomas SN, Tzeng SC, Zhang H, Aebersold R.

Nat Commun. 2017 Aug 21;8(1):291. doi: 10.1038/s41467-017-00249-5.


Precise Temporal Profiling of Signaling Complexes in Primary Cells Using SWATH Mass Spectrometry.

Caron E, Roncagalli R, Hase T, Wolski WE, Choi M, Menoita MG, Durand S, García-Blesa A, Fierro-Monti I, Sajic T, Heusel M, Weiss T, Malissen M, Schlapbach R, Collins BC, Ghosh S, Kitano H, Aebersold R, Malissen B, Gstaiger M.

Cell Rep. 2017 Mar 28;18(13):3219-3226. doi: 10.1016/j.celrep.2017.03.019.


Cell Cycle Constraints and Environmental Control of Local DNA Hypomethylation in α-Proteobacteria.

Ardissone S, Redder P, Russo G, Frandi A, Fumeaux C, Patrignani A, Schlapbach R, Falquet L, Viollier PH.

PLoS Genet. 2016 Dec 20;12(12):e1006499. doi: 10.1371/journal.pgen.1006499. eCollection 2016 Dec.


Prognostic value of cross-omics screening for kidney clear cell renal cancer survival.

Dimitrieva S, Schlapbach R, Rehrauer H.

Biol Direct. 2016 Dec 20;11(1):68.


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.

Meder D, Morales M, Pepperkok R, Schlapbach R, Tiran A, Van Minnebruggen G.

EMBO Rep. 2016 Aug;17(8):1088-93. doi: 10.15252/embr.201642857. Epub 2016 Jul 13. No abstract available.


SUSHI: an exquisite recipe for fully documented, reproducible and reusable NGS data analysis.

Hatakeyama M, Opitz L, Russo G, Qi W, Schlapbach R, Rehrauer H.

BMC Bioinformatics. 2016 Jun 2;17(1):228. doi: 10.1186/s12859-016-1104-8.


Host-Associated Genomic Features of the Novel Uncultured Intracellular Pathogen Ca. Ichthyocystis Revealed by Direct Sequencing of Epitheliocysts.

Qi W, Vaughan L, Katharios P, Schlapbach R, Seth-Smith HM.

Genome Biol Evol. 2016 Jun 13;8(6):1672-89. doi: 10.1093/gbe/evw111.


Targeted proteomics coming of age - SRM, PRM and DIA performance evaluated from a core facility perspective.

Kockmann T, Trachsel C, Panse C, Wahlander A, Selevsek N, Grossmann J, Wolski WE, Schlapbach R.

Proteomics. 2016 Aug;16(15-16):2183-92. doi: 10.1002/pmic.201500502. Epub 2016 Jun 8.


Highly sensitive, non-invasive detection of colorectal cancer mutations using single molecule, third generation sequencing.

Russo G, Patrignani A, Poveda L, Hoehn F, Scholtka B, Schlapbach R, Garvin AM.

Appl Transl Genom. 2015 Oct 16;7:32-9. doi: 10.1016/j.atg.2015.08.006. eCollection 2015 Dec.


Natural Genetic Variation Differentially Affects the Proteome and Transcriptome in Caenorhabditis elegans.

Kamkina P, Snoek LB, Grossmann J, Volkers RJ, Sterken MG, Daube M, Roschitzki B, Fortes C, Schlapbach R, Roth A, von Mering C, Hengartner MO, Schrimpf SP, Kammenga JE.

Mol Cell Proteomics. 2016 May;15(5):1670-80. doi: 10.1074/mcp.M115.052548. Epub 2016 Mar 4.


Emerging pathogens of gilthead seabream: characterisation and genomic analysis of novel intracellular β-proteobacteria.

Seth-Smith HM, Dourala N, Fehr A, Qi W, Katharios P, Ruetten M, Mateos JM, Nufer L, Weilenmann R, Ziegler U, Thomson NR, Schlapbach R, Vaughan L.

ISME J. 2016 Jul;10(7):1791-803. doi: 10.1038/ismej.2015.223. Epub 2016 Feb 5.


A Follow-Up of the Multicenter Collaborative Study on HIV-1 Drug Resistance and Tropism Testing Using 454 Ultra Deep Pyrosequencing.

St John EP, Simen BB, Turenchalk GS, Braverman MS, Abbate I, Aerssens J, Bouchez O, Gabriel C, Izopet J, Meixenberger K, Di Giallonardo F, Schlapbach R, Paredes R, Sakwa J, Schmitz-Agheguian GG, Thielen A, Victor M, Metzner KJ, Däumer MP; 454 HIV-1 Alpha Study Group.

PLoS One. 2016 Jan 12;11(1):e0146687. doi: 10.1371/journal.pone.0146687. eCollection 2016.


Environmental marine pathogen isolation using mesocosm culture of sharpsnout seabream: striking genomic and morphological features of novel Endozoicomonas sp.

Katharios P, Seth-Smith HM, Fehr A, Mateos JM, Qi W, Richter D, Nufer L, Ruetten M, Guevara Soto M, Ziegler U, Thomson NR, Schlapbach R, Vaughan L.

Sci Rep. 2015 Dec 7;5:17609. doi: 10.1038/srep17609.


Mass Spectrometric Proteome Analysis of Small Three-Dimensional Microtissues Allows for the Quantitative Description of Toxic Effects of Drugs.

Selevsek N, Schlapbach R.

Chimia (Aarau). 2015 Aug 19;69(7):494. doi: 10.2533/chimia.2015.494. No abstract available.


New insights into the performance of human whole-exome capture platforms.

Meienberg J, Zerjavic K, Keller I, Okoniewski M, Patrignani A, Ludin K, Xu Z, Steinmann B, Carrel T, Röthlisberger B, Schlapbach R, Bruggmann R, Matyas G.

Nucleic Acids Res. 2015 Jun 23;43(11):e76. doi: 10.1093/nar/gkv216. Epub 2015 Mar 27.


specL--an R/Bioconductor package to prepare peptide spectrum matches for use in targeted proteomics.

Panse C, Trachsel C, Grossmann J, Schlapbach R.

Bioinformatics. 2015 Jul 1;31(13):2228-31. doi: 10.1093/bioinformatics/btv105. Epub 2015 Feb 23.


The draft genome of Primula veris yields insights into the molecular basis of heterostyly.

Nowak MD, Russo G, Schlapbach R, Huu CN, Lenhard M, Conti E.

Genome Biol. 2015 Jan 24;16:12. doi: 10.1186/s13059-014-0567-z.


Shigella reroutes host cell central metabolism to obtain high-flux nutrient supply for vigorous intracellular growth.

Kentner D, Martano G, Callon M, Chiquet P, Brodmann M, Burton O, Wahlander A, Nanni P, Delmotte N, Grossmann J, Limenitakis J, Schlapbach R, Kiefer P, Vorholt JA, Hiller S, Bumann D.

Proc Natl Acad Sci U S A. 2014 Jul 8;111(27):9929-34. doi: 10.1073/pnas.1406694111. Epub 2014 Jun 23.


An international multicenter study on HIV-1 drug resistance testing by 454 ultra-deep pyrosequencing.

Simen BB, Braverman MS, Abbate I, Aerssens J, Bidet Y, Bouchez O, Gabriel C, Izopet J, Kessler HH, Stelzl E, Di Giallonardo F, Schlapbach R, Radonic A, Paredes R, Recordon-Pinson P, Sakwa J, St John EP, Schmitz-Agheguian GG, Metzner KJ, Däumer MP; 454 HIV Alphastudy Group.

J Virol Methods. 2014 Aug;204:31-7. doi: 10.1016/j.jviromet.2014.04.007. Epub 2014 Apr 13.


Blind spots of quantitative RNA-seq: the limits for assessing abundance, differential expression, and isoform switching.

Rehrauer H, Opitz L, Tan G, Sieverling L, Schlapbach R.

BMC Bioinformatics. 2013 Dec 24;14:370. doi: 10.1186/1471-2105-14-370.


Drop drying on surfaces determines chemical reactivity - the specific case of immobilization of oligonucleotides on microarrays.

Sobek J, Aquino C, Weigel W, Schlapbach R.

BMC Biophys. 2013 Jun 12;6:8. doi: 10.1186/2046-1682-6-8.


PTM MarkerFinder, a software tool to detect and validate spectra from peptides carrying post-translational modifications.

Nanni P, Panse C, Gehrig P, Mueller S, Grossmann J, Schlapbach R.

Proteomics. 2013 Aug;13(15):2251-5. doi: 10.1002/pmic.201300036. Epub 2013 Jul 1.


iTRAQ-Based and Label-Free Proteomics Approaches for Studies of Human Adenovirus Infections.

Trinh HV, Grossmann J, Gehrig P, Roschitzki B, Schlapbach R, Greber UF, Hemmi S.

Int J Proteomics. 2013;2013:581862. doi: 10.1155/2013/581862. Epub 2013 Mar 11.


Identification of a SIRT1 mutation in a family with type 1 diabetes.

Biason-Lauber A, Böni-Schnetzler M, Hubbard BP, Bouzakri K, Brunner A, Cavelti-Weder C, Keller C, Meyer-Böni M, Meier DT, Brorsson C, Timper K, Leibowitz G, Patrignani A, Bruggmann R, Boily G, Zulewski H, Geier A, Cermak JM, Elliott P, Ellis JL, Westphal C, Knobel U, Eloranta JJ, Kerr-Conte J, Pattou F, Konrad D, Matter CM, Fontana A, Rogler G, Schlapbach R, Regairaz C, Carballido JM, Glaser B, McBurney MW, Pociot F, Sinclair DA, Donath MY.

Cell Metab. 2013 Mar 5;17(3):448-455. doi: 10.1016/j.cmet.2013.02.001.


Precise breakpoint localization of large genomic deletions using PacBio and Illumina next-generation sequencers.

Okoniewski MJ, Meienberg J, Patrignani A, Szabelska A, Matyas G, Schlapbach R.

Biotechniques. 2013 Feb;54(2):98-100. doi: 10.2144/000113992.


PPINGUIN: Peptide Profiling Guided Identification of Proteins improves quantitation of iTRAQ ratios.

Bauer C, Kleinjung F, Rutishauser D, Panse C, Chadt A, Dreja T, Al-Hasani H, Reinert K, Schlapbach R, Schuchhardt J.

BMC Bioinformatics. 2012 Feb 16;13:34. doi: 10.1186/1471-2105-13-34.


Preferred analysis methods for single genomic regions in RNA sequencing revealed by processing the shape of coverage.

Okoniewski MJ, Leśniewska A, Szabelska A, Zyprych-Walczak J, Ryan M, Wachtel M, Morzy T, Schäfer B, Schlapbach R.

Nucleic Acids Res. 2012 May;40(9):e63. doi: 10.1093/nar/gkr1249. Epub 2011 Dec 30.


Life sciences data and application integration with B-fabric.

Türker C, Akal F, Schlapbach R.

J Integr Bioinform. 2011 Jul 20;8(2):159. doi: 10.2390/biecoll-jib-2011-159.


Myc-mediated repression of microRNA-34a promotes high-grade transformation of B-cell lymphoma by dysregulation of FoxP1.

Craig VJ, Cogliatti SB, Imig J, Renner C, Neuenschwander S, Rehrauer H, Schlapbach R, Dirnhofer S, Tzankov A, Müller A.

Blood. 2011 Jun 9;117(23):6227-36. doi: 10.1182/blood-2010-10-312231. Epub 2011 Apr 1.


Phosphoproteomic analysis reveals interconnected system-wide responses to perturbations of kinases and phosphatases in yeast.

Bodenmiller B, Wanka S, Kraft C, Urban J, Campbell D, Pedrioli PG, Gerrits B, Picotti P, Lam H, Vitek O, Brusniak MY, Roschitzki B, Zhang C, Shokat KM, Schlapbach R, Colman-Lerner A, Nolan GP, Nesvizhskii AI, Peter M, Loewith R, von Mering C, Aebersold R.

Sci Signal. 2010 Dec 21;3(153):rs4. doi: 10.1126/scisignal.2001182.


Implementation and evaluation of relative and absolute quantification in shotgun proteomics with label-free methods.

Grossmann J, Roschitzki B, Panse C, Fortes C, Barkow-Oesterreicher S, Rutishauser D, Schlapbach R.

J Proteomics. 2010 Aug 5;73(9):1740-6. doi: 10.1016/j.jprot.2010.05.011. Epub 2010 May 31.


Community proteogenomics reveals insights into the physiology of phyllosphere bacteria.

Delmotte N, Knief C, Chaffron S, Innerebner G, Roschitzki B, Schlapbach R, von Mering C, Vorholt JA.

Proc Natl Acad Sci U S A. 2009 Sep 22;106(38):16428-33. doi: 10.1073/pnas.0905240106. Epub 2009 Sep 4.


Development and experimental validation of a nifH oligonucleotide microarray to study diazotrophic communities in a glacier forefield.

Duc L, Neuenschwander S, Rehrauer H, Wagner U, Sobek J, Schlapbach R, Zeyer J.

Environ Microbiol. 2009 Aug;11(8):2179-89. doi: 10.1111/j.1462-2920.2009.01945.x. Epub 2009 May 18.


Phosphorylated serine and threonine residues promote site-specific fragmentation of singly charged, arginine-containing peptide ions.

Gehrig PM, Roschitzki B, Rutishauser D, Reiland S, Schlapbach R.

Rapid Commun Mass Spectrom. 2009 May;23(10):1435-45. doi: 10.1002/rcm.4019.


An integrated proteomics approach for studying the molecular pathogenesis of Dupuytren's disease.

Kraljevic Pavelic S, Sedic M, Hock K, Vucinic S, Jurisic D, Gehrig P, Scott M, Schlapbach R, Cacev T, Kapitanovic S, Pavelic K.

J Pathol. 2009 Mar;217(4):524-33. doi: 10.1002/path.2483.


PhosphoPep--a database of protein phosphorylation sites in model organisms.

Bodenmiller B, Campbell D, Gerrits B, Lam H, Jovanovic M, Picotti P, Schlapbach R, Aebersold R.

Nat Biotechnol. 2008 Dec;26(12):1339-40. doi: 10.1038/nbt1208-1339. No abstract available.


PhyloDetect: a likelihood-based strategy for detecting microorganisms with diagnostic microarrays.

Rehrauer H, Schönmann S, Eberl L, Schlapbach R.

Bioinformatics. 2008 Aug 15;24(16):i83-9. doi: 10.1093/bioinformatics/btn269.


Differential antiproliferative mechanisms of novel derivative of benzimidazo[1,2-alpha]quinoline in colon cancer cells depending on their p53 status.

Sedic M, Poznic M, Gehrig P, Scott M, Schlapbach R, Hranjec M, Karminski-Zamola G, Pavelic K, Kraljevic Pavelic S.

Mol Cancer Ther. 2008 Jul;7(7):2121-32. doi: 10.1158/1535-7163.MCT-07-2261.

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