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Results: 18

1.

Abundance-based classifier for the prediction of mass spectrometric peptide detectability upon enrichment (PPA).

Muntel J, Boswell SA, Tang S, Ahmed S, Wapinski I, Foley G, Steen H, Springer M.

Mol Cell Proteomics. 2015 Feb;14(2):430-40. doi: 10.1074/mcp.M114.044321. Epub 2014 Dec 3.

PMID:
25473088
2.

Correction: Evolutionary principles of modular gene regulation in yeasts.

Thompson DA, Roy S, Chan M, Styczynski MP, Pfiffner J, French C, Socha A, Thielke A, Napolitano S, Muller P, Kellis M, Konieczka JH, Wapinski I, Regev A.

Elife. 2013 Jul 2;2:e01114. doi: 10.7554/eLife.01114.

3.

Evolutionary principles of modular gene regulation in yeasts.

Thompson DA, Roy S, Chan M, Styczynsky MP, Pfiffner J, French C, Socha A, Thielke A, Napolitano S, Muller P, Kellis M, Konieczka JH, Wapinski I, Regev A.

Elife. 2013 Jun 18;2:e00603. doi: 10.7554/eLife.00603. Erratum in: Elife. 2:2:e01114.

4.

Arboretum: reconstruction and analysis of the evolutionary history of condition-specific transcriptional modules.

Roy S, Wapinski I, Pfiffner J, French C, Socha A, Konieczka J, Habib N, Kellis M, Thompson D, Regev A.

Genome Res. 2013 Jun;23(6):1039-50. doi: 10.1101/gr.146233.112. Epub 2013 May 2.

5.

A functional selection model explains evolutionary robustness despite plasticity in regulatory networks.

Habib N, Wapinski I, Margalit H, Regev A, Friedman N.

Mol Syst Biol. 2012;8:619. doi: 10.1038/msb.2012.50.

6.

Proto-genes and de novo gene birth.

Carvunis AR, Rolland T, Wapinski I, Calderwood MA, Yildirim MA, Simonis N, Charloteaux B, Hidalgo CA, Barbette J, Santhanam B, Brar GA, Weissman JS, Regev A, Thierry-Mieg N, Cusick ME, Vidal M.

Nature. 2012 Jul 19;487(7407):370-4. doi: 10.1038/nature11184.

7.

Comparative analysis of Mycobacterium and related Actinomycetes yields insight into the evolution of Mycobacterium tuberculosis pathogenesis.

McGuire AM, Weiner B, Park ST, Wapinski I, Raman S, Dolganov G, Peterson M, Riley R, Zucker J, Abeel T, White J, Sisk P, Stolte C, Koehrsen M, Yamamoto RT, Iacobelli-Martinez M, Kidd MJ, Maer AM, Schoolnik GK, Regev A, Galagan J.

BMC Genomics. 2012 Mar 28;13:120. doi: 10.1186/1471-2164-13-120.

8.

Comparative functional genomics of the fission yeasts.

Rhind N, Chen Z, Yassour M, Thompson DA, Haas BJ, Habib N, Wapinski I, Roy S, Lin MF, Heiman DI, Young SK, Furuya K, Guo Y, Pidoux A, Chen HM, Robbertse B, Goldberg JM, Aoki K, Bayne EH, Berlin AM, Desjardins CA, Dobbs E, Dukaj L, Fan L, FitzGerald MG, French C, Gujja S, Hansen K, Keifenheim D, Levin JZ, Mosher RA, Müller CA, Pfiffner J, Priest M, Russ C, Smialowska A, Swoboda P, Sykes SM, Vaughn M, Vengrova S, Yoder R, Zeng Q, Allshire R, Baulcombe D, Birren BW, Brown W, Ekwall K, Kellis M, Leatherwood J, Levin H, Margalit H, Martienssen R, Nieduszynski CA, Spatafora JW, Friedman N, Dalgaard JZ, Baumann P, Niki H, Regev A, Nusbaum C.

Science. 2011 May 20;332(6032):930-6. doi: 10.1126/science.1203357. Epub 2011 Apr 21.

9.

Reconstructing gene histories in Ascomycota fungi.

Wapinski I, Regev A.

Methods Enzymol. 2010;470:447-85. doi: 10.1016/S0076-6879(10)70018-5. Epub 2010 Mar 1.

PMID:
20946821
10.

Comparative genomics reveals mobile pathogenicity chromosomes in Fusarium.

Ma LJ, van der Does HC, Borkovich KA, Coleman JJ, Daboussi MJ, Di Pietro A, Dufresne M, Freitag M, Grabherr M, Henrissat B, Houterman PM, Kang S, Shim WB, Woloshuk C, Xie X, Xu JR, Antoniw J, Baker SE, Bluhm BH, Breakspear A, Brown DW, Butchko RA, Chapman S, Coulson R, Coutinho PM, Danchin EG, Diener A, Gale LR, Gardiner DM, Goff S, Hammond-Kosack KE, Hilburn K, Hua-Van A, Jonkers W, Kazan K, Kodira CD, Koehrsen M, Kumar L, Lee YH, Li L, Manners JM, Miranda-Saavedra D, Mukherjee M, Park G, Park J, Park SY, Proctor RH, Regev A, Ruiz-Roldan MC, Sain D, Sakthikumar S, Sykes S, Schwartz DC, Turgeon BG, Wapinski I, Yoder O, Young S, Zeng Q, Zhou S, Galagan J, Cuomo CA, Kistler HC, Rep M.

Nature. 2010 Mar 18;464(7287):367-73. doi: 10.1038/nature08850.

11.

Gene duplication and the evolution of ribosomal protein gene regulation in yeast.

Wapinski I, Pfiffner J, French C, Socha A, Thompson DA, Regev A.

Proc Natl Acad Sci U S A. 2010 Mar 23;107(12):5505-10. doi: 10.1073/pnas.0911905107. Epub 2010 Mar 8.

12.

Overdispersion of the molecular clock varies between yeast, Drosophila and mammals.

Bedford T, Wapinski I, Hartl DL.

Genetics. 2008 Jun;179(2):977-84. doi: 10.1534/genetics.108.089185. Epub 2008 May 27.

13.

Revisiting the Saccharomyces cerevisiae predicted ORFeome.

Li QR, Carvunis AR, Yu H, Han JD, Zhong Q, Simonis N, Tam S, Hao T, Klitgord NJ, Dupuy D, Mou D, Wapinski I, Regev A, Hill DE, Cusick ME, Vidal M.

Genome Res. 2008 Aug;18(8):1294-303. doi: 10.1101/gr.076661.108. Epub 2008 May 23.

14.

Physiological and molecular evidence of heat acclimation memory: a lesson from thermal responses and ischemic cross-tolerance in the heart.

Tetievsky A, Cohen O, Eli-Berchoer L, Gerstenblith G, Stern MD, Wapinski I, Friedman N, Horowitz M.

Physiol Genomics. 2008 Jun 12;34(1):78-87. doi: 10.1152/physiolgenomics.00215.2007. Epub 2008 Apr 22.

15.

Natural history and evolutionary principles of gene duplication in fungi.

Wapinski I, Pfeffer A, Friedman N, Regev A.

Nature. 2007 Sep 6;449(7158):54-61.

PMID:
17805289
16.

Automatic genome-wide reconstruction of phylogenetic gene trees.

Wapinski I, Pfeffer A, Friedman N, Regev A.

Bioinformatics. 2007 Jul 1;23(13):i549-58.

17.

Stress-related genomic responses during the course of heat acclimation and its association with ischemic-reperfusion cross-tolerance.

Horowitz M, Eli-Berchoer L, Wapinski I, Friedman N, Kodesh E.

J Appl Physiol (1985). 2004 Oct;97(4):1496-507. Epub 2004 May 21.

18.

Support vector machine classification on the web.

Pavlidis P, Wapinski I, Noble WS.

Bioinformatics. 2004 Mar 1;20(4):586-7. Epub 2004 Jan 22.

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