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The MicroArray Quality Control (MAQC)-II study of common practices for the development and validation of microarray-based predictive models.
Shi L, Campbell G, Jones WD, Campagne F, Wen Z, Walker SJ, Su Z, Chu TM, Goodsaid FM, Pusztai L, Shaughnessy JD Jr, Oberthuer A, Thomas RS, Paules RS, Fielden M, Barlogie B, Chen W, Du P, Fischer M, Furlanello C, Gallas BD, Ge X, Megherbi DB, Symmans WF, Wang MD, Zhang J, Bitter H, Brors B, Bushel PR, Bylesjo M, Chen M, Cheng J, Cheng J, Chou J, Davison TS, Delorenzi M, Deng Y, Devanarayan V, Dix DJ, Dopazo J, Dorff KC, Elloumi F, Fan J, Fan S, Fan X, Fang H, Gonzaludo N, Hess KR, Hong H, Huan J, Irizarry RA, Judson R, Juraeva D, Lababidi S, Lambert CG, Li L, Li Y, Li Z, Lin SM, Liu G, Lobenhofer EK, Luo J, Luo W, McCall MN, Nikolsky Y, Pennello GA, Perkins RG, Philip R, Popovici V, Price ND, Qian F, Scherer A, Shi T, Shi W, Sung J, Thierry-Mieg D, Thierry-Mieg J, Thodima V, Trygg J, Vishnuvajjala L, Wang SJ, Wu J, Wu Y, Xie Q, Yousef WA, Zhang L, Zhang X, Zhong S, Zhou Y, Zhu S, Arasappan D, Bao W, Lucas AB, Berthold F, Brennan RJ, Buness A, Catalano JG, Chang C, Chen R, Cheng Y, Cui J, Czika W, Demichelis F, Deng X, Dosymbekov D, Eils R, Feng Y, Fostel J, Fulmer-Smentek S, Fuscoe JC, Gatto L, Ge W, Goldstein DR, Guo L, Halbert DN, Han J, Harris SC, Hatzis C, Herman D, Hua… See abstract for full author list ➔ Shi L, et al. Among authors: gatto l. Nat Biotechnol. 2010 Aug;28(8):827-38. doi: 10.1038/nbt.1665. Epub 2010 Jul 30. Nat Biotechnol. 2010. PMID: 20676074 Free PMC article.
Orchestrating high-throughput genomic analysis with Bioconductor.
Huber W, Carey VJ, Gentleman R, Anders S, Carlson M, Carvalho BS, Bravo HC, Davis S, Gatto L, Girke T, Gottardo R, Hahne F, Hansen KD, Irizarry RA, Lawrence M, Love MI, MacDonald J, Obenchain V, Oleś AK, Pagès H, Reyes A, Shannon P, Smyth GK, Tenenbaum D, Waldron L, Morgan M. Huber W, et al. Among authors: gatto l. Nat Methods. 2015 Feb;12(2):115-21. doi: 10.1038/nmeth.3252. Nat Methods. 2015. PMID: 25633503 Free PMC article. Review.
Organelle proteomics experimental designs and analysis.
Gatto L, Vizcaíno JA, Hermjakob H, Huber W, Lilley KS. Gatto L, et al. Proteomics. 2010 Nov;10(22):3957-69. doi: 10.1002/pmic.201000244. Epub 2010 Nov 2. Proteomics. 2010. PMID: 21080489 Review.
A cross-platform toolkit for mass spectrometry and proteomics.
Chambers MC, Maclean B, Burke R, Amodei D, Ruderman DL, Neumann S, Gatto L, Fischer B, Pratt B, Egertson J, Hoff K, Kessner D, Tasman N, Shulman N, Frewen B, Baker TA, Brusniak MY, Paulse C, Creasy D, Flashner L, Kani K, Moulding C, Seymour SL, Nuwaysir LM, Lefebvre B, Kuhlmann F, Roark J, Rainer P, Detlev S, Hemenway T, Huhmer A, Langridge J, Connolly B, Chadick T, Holly K, Eckels J, Deutsch EW, Moritz RL, Katz JE, Agus DB, MacCoss M, Tabb DL, Mallick P. Chambers MC, et al. Among authors: gatto l. Nat Biotechnol. 2012 Oct;30(10):918-20. doi: 10.1038/nbt.2377. Nat Biotechnol. 2012. PMID: 23051804 Free PMC article.
Using R and Bioconductor for proteomics data analysis.
Gatto L, Christoforou A. Gatto L, et al. Biochim Biophys Acta. 2014 Jan;1844(1 Pt A):42-51. doi: 10.1016/j.bbapap.2013.04.032. Epub 2013 May 18. Biochim Biophys Acta. 2014. PMID: 23692960 Review.
Using hyperLOPIT to perform high-resolution mapping of the spatial proteome.
Mulvey CM, Breckels LM, Geladaki A, Britovšek NK, Nightingale DJH, Christoforou A, Elzek M, Deery MJ, Gatto L, Lilley KS. Mulvey CM, et al. Among authors: gatto l. Nat Protoc. 2017 Jun;12(6):1110-1135. doi: 10.1038/nprot.2017.026. Epub 2017 May 4. Nat Protoc. 2017. PMID: 28471460
ProteomeXchange provides globally coordinated proteomics data submission and dissemination.
Vizcaíno JA, Deutsch EW, Wang R, Csordas A, Reisinger F, Ríos D, Dianes JA, Sun Z, Farrah T, Bandeira N, Binz PA, Xenarios I, Eisenacher M, Mayer G, Gatto L, Campos A, Chalkley RJ, Kraus HJ, Albar JP, Martinez-Bartolomé S, Apweiler R, Omenn GS, Martens L, Jones AR, Hermjakob H. Vizcaíno JA, et al. Among authors: gatto l. Nat Biotechnol. 2014 Mar;32(3):223-6. doi: 10.1038/nbt.2839. Nat Biotechnol. 2014. PMID: 24727771 Free PMC article. No abstract available.
BioContainers: an open-source and community-driven framework for software standardization.
da Veiga Leprevost F, Grüning BA, Alves Aflitos S, Röst HL, Uszkoreit J, Barsnes H, Vaudel M, Moreno P, Gatto L, Weber J, Bai M, Jimenez RC, Sachsenberg T, Pfeuffer J, Vera Alvarez R, Griss J, Nesvizhskii AI, Perez-Riverol Y. da Veiga Leprevost F, et al. Among authors: gatto l. Bioinformatics. 2017 Aug 15;33(16):2580-2582. doi: 10.1093/bioinformatics/btx192. Bioinformatics. 2017. PMID: 28379341 Free PMC article.
420 results