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Items: 1 to 20 of 76

1.

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.

2.

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.

PMID:
29978702
3.

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.

4.

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.

5.

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.

PMID:
29610270
6.

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.

7.

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]

8.

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.

PMID:
28936667
9.

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.

10.

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.

11.

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.

12.

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.

13.

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.

14.

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.

15.

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.

16.

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.

17.

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.

PMID:
27130639
18.

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.

19.

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.

20.

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.

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