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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
[PubMed - in process]
Free Article
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.

PMID:
23840936
[PubMed - in process]
Free PMC Article
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.

PMID:
23795289
[PubMed - in process]
Free PMC Article
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.

PMID:
23640720
[PubMed - indexed for MEDLINE]
Free PMC Article
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.

PMID:
23089682
[PubMed - indexed for MEDLINE]
Free PMC Article
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.

PMID:
22722833
[PubMed - indexed for MEDLINE]
Free PMC Article
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.

PMID:
22452820
[PubMed - indexed for MEDLINE]
Free PMC Article
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.

PMID:
21511999
[PubMed - indexed for MEDLINE]
Free PMC Article
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
[PubMed - indexed for MEDLINE]
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.

PMID:
20237561
[PubMed - indexed for MEDLINE]
Free PMC Article
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.

PMID:
20212107
[PubMed - indexed for MEDLINE]
Free PMC Article
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.

PMID:
18505862
[PubMed - indexed for MEDLINE]
Free PMC Article
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.

PMID:
18502943
[PubMed - indexed for MEDLINE]
Free PMC Article
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.

PMID:
18430807
[PubMed - indexed for MEDLINE]
Free Article
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
[PubMed - indexed for MEDLINE]
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.

PMID:
17646342
[PubMed - indexed for MEDLINE]
Free Article
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.

PMID:
15155711
[PubMed - indexed for MEDLINE]
Free Article
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.

PMID:
14990457
[PubMed - indexed for MEDLINE]
Free Article
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