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Results: 1 to 20 of 69

1.

Unrestricted modification search reveals lysine methylation as major modification induced by tissue formalin fixation and paraffin-embedding.

Zhang Y, Muller M, Xu B, Yoshida Y, Horlacher O, Nikitin F, Garessus S, Magdeldin S, Kinoshita N, Fujinaka H, Yaoita E, Hasegawa M, Lisacek F, Yamamoto T.

Proteomics. 2015 Mar 30. doi: 10.1002/pmic.201400454. [Epub ahead of print]

PMID:
25825003
2.

Uncovering intense protein diversification in a cone snail venom gland using an integrative venomics approach.

Biass D, Violette A, Hulo N, Lisacek F, Favreau P, Stöcklin R.

J Proteome Res. 2015 Feb 6;14(2):628-38. doi: 10.1021/pr500583u. Epub 2015 Jan 22.

PMID:
25536169
3.

Pathway analysis and transcriptomics improve protein identification by shotgun proteomics from samples comprising small number of cells--a benchmarking study.

Sun J, Zhang GL, Li S, Ivanov AR, Fenyo D, Lisacek F, Murthy SK, Karger BL, Brusic V.

BMC Genomics. 2014;15 Suppl 9:S1. doi: 10.1186/1471-2164-15-S9-S1. Epub 2014 Dec 8.

4.

Processing strategies and software solutions for data-independent acquisition in mass spectrometry.

Bilbao A, Varesio E, Luban J, Strambio-De-Castillia C, Hopfgartner G, Müller M, Lisacek F.

Proteomics. 2015 Mar;15(5-6):964-80. doi: 10.1002/pmic.201400323. Epub 2015 Feb 2.

PMID:
25430050
5.

Animal board invited review: advances in proteomics for animal and food sciences.

Almeida AM, Bassols A, Bendixen E, Bhide M, Ceciliani F, Cristobal S, Eckersall PD, Hollung K, Lisacek F, Mazzucchelli G, McLaughlin M, Miller I, Nally JE, Plowman J, Renaut J, Rodrigues P, Roncada P, Staric J, Turk R.

Animal. 2015 Jan;9(1):1-17. doi: 10.1017/S1751731114002602. Epub 2014 Oct 31.

6.

GlycoDigest: a tool for the targeted use of exoglycosidase digestions in glycan structure determination.

Gotz L, Abrahams JL, Mariethoz J, Rudd PM, Karlsson NG, Packer NH, Campbell MP, Lisacek F.

Bioinformatics. 2014 Nov 1;30(21):3131-3. doi: 10.1093/bioinformatics/btu425. Epub 2014 Jul 10.

PMID:
25015990
7.

Fifteen years SIB Swiss Institute of Bioinformatics: life science databases, tools and support.

Stockinger H, Altenhoff AM, Arnold K, Bairoch A, Bastian F, Bergmann S, Bougueleret L, Bucher P, Delorenzi M, Lane L, Le Mercier P, Lisacek F, Michielin O, Palagi PM, Rougemont J, Schwede T, von Mering C, van Nimwegen E, Walther D, Xenarios I, Zavolan M, Zdobnov EM, Zoete V, Appel RD.

Nucleic Acids Res. 2014 Jul;42(Web Server issue):W436-41. doi: 10.1093/nar/gku380. Epub 2014 May 3.

8.

NETTAB 2012 on "Integrated Bio-Search".

Romano P, Lisacek F, Masseroli M.

BMC Bioinformatics. 2014;15 Suppl 1:S1. doi: 10.1186/1471-2105-15-S1-S1. Epub 2014 Jan 10.

9.

Toolboxes for a standardised and systematic study of glycans.

Campbell MP, Ranzinger R, Lütteke T, Mariethoz J, Hayes CA, Zhang J, Akune Y, Aoki-Kinoshita KF, Damerell D, Carta G, York WS, Haslam SM, Narimatsu H, Rudd PM, Karlsson NG, Packer NH, Lisacek F.

BMC Bioinformatics. 2014;15 Suppl 1:S9. doi: 10.1186/1471-2105-15-S1-S9. Epub 2014 Jan 10.

10.

Integrated Bio-Search: challenges and trends for the integration, search and comprehensive processing of biological information.

Masseroli M, Mons B, Bongcam-Rudloff E, Ceri S, Kel A, Rechenmann F, Lisacek F, Romano P.

BMC Bioinformatics. 2014;15 Suppl 1:S2. doi: 10.1186/1471-2105-15-S1-S2. Epub 2014 Jan 10. Review.

11.

UniCarbKB: building a knowledge platform for glycoproteomics.

Campbell MP, Peterson R, Mariethoz J, Gasteiger E, Akune Y, Aoki-Kinoshita KF, Lisacek F, Packer NH.

Nucleic Acids Res. 2014 Jan;42(Database issue):D215-21. doi: 10.1093/nar/gkt1128. Epub 2013 Nov 13.

12.

Comparative analysis of Leishmania exoproteomes: implication for host-pathogen interactions.

Peysselon F, Launay G, Lisacek F, Duclos B, Ricard-Blum S.

Biochim Biophys Acta. 2013 Dec;1834(12):2653-62. doi: 10.1016/j.bbapap.2013.09.015. Epub 2013 Oct 1.

PMID:
24096101
13.

Clustering and filtering tandem mass spectra acquired in data-independent mode.

Pak H, Nikitin F, Gluck F, Lisacek F, Scherl A, Muller M.

J Am Soc Mass Spectrom. 2013 Dec;24(12):1862-71. doi: 10.1007/s13361-013-0720-z. Epub 2013 Sep 5.

PMID:
24006250
14.

SugarBind database (SugarBindDB): a resource of pathogen lectins and corresponding glycan targets.

Shakhsheer B, Anderson M, Khatib K, Tadoori L, Joshi L, Lisacek F, Hirschman L, Mullen E.

J Mol Recognit. 2013 Sep;26(9):426-31. doi: 10.1002/jmr.2285.

PMID:
23836470
15.

Absolute quantification of transcription factors during cellular differentiation using multiplexed targeted proteomics.

Simicevic J, Schmid AW, Gilardoni PA, Zoller B, Raghav SK, Krier I, Gubelmann C, Lisacek F, Naef F, Moniatte M, Deplancke B.

Nat Methods. 2013 Jun;10(6):570-6. doi: 10.1038/nmeth.2441. Epub 2013 Apr 14.

PMID:
23584187
16.

Position-specific scoring matrix and hidden Markov model complement each other for the prediction of conopeptide superfamilies.

Koua D, Laht S, Kaplinski L, Stöcklin R, Remm M, Favreau P, Lisacek F.

Biochim Biophys Acta. 2013 Apr;1834(4):717-24. doi: 10.1016/j.bbapap.2012.12.015. Epub 2013 Jan 22.

PMID:
23352837
17.

EasyProt--an easy-to-use graphical platform for proteomics data analysis.

Gluck F, Hoogland C, Antinori P, Robin X, Nikitin F, Zufferey A, Pasquarello C, Fétaud V, Dayon L, Müller M, Lisacek F, Geiser L, Hochstrasser D, Sanchez JC, Scherl A.

J Proteomics. 2013 Feb 21;79:146-60. doi: 10.1016/j.jprot.2012.12.012. Epub 2012 Dec 28.

PMID:
23277275
18.

ConoDictor: a tool for prediction of conopeptide superfamilies.

Koua D, Brauer A, Laht S, Kaplinski L, Favreau P, Remm M, Lisacek F, Stöcklin R.

Nucleic Acids Res. 2012 Jul;40(Web Server issue):W238-41. doi: 10.1093/nar/gks337. Epub 2012 May 31.

19.

Identification and classification of conopeptides using profile Hidden Markov Models.

Laht S, Koua D, Kaplinski L, Lisacek F, Stöcklin R, Remm M.

Biochim Biophys Acta. 2012 Mar;1824(3):488-92. doi: 10.1016/j.bbapap.2011.12.004. Epub 2011 Dec 30.

PMID:
22244925
20.

UniCarbKB: putting the pieces together for glycomics research.

Campbell MP, Hayes CA, Struwe WB, Wilkins MR, Aoki-Kinoshita KF, Harvey DJ, Rudd PM, Kolarich D, Lisacek F, Karlsson NG, Packer NH.

Proteomics. 2011 Nov;11(21):4117-21. doi: 10.1002/pmic.201100302. Epub 2011 Sep 19.

PMID:
21898825
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