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A public genome-scale lentiviral expression library of human ORFs.
Yang X, Boehm JS, Yang X, Salehi-Ashtiani K, Hao T, Shen Y, Lubonja R, Thomas SR, Alkan O, Bhimdi T, Green TM, Johannessen CM, Silver SJ, Nguyen C, Murray RR, Hieronymus H, Balcha D, Fan C, Lin C, Ghamsari L, Vidal M, Hahn WC, Hill DE, Root DE. Yang X, et al. Among authors: shen y. Nat Methods. 2011 Jun 26;8(8):659-61. doi: 10.1038/nmeth.1638. Nat Methods. 2011. PMID: 21706014 Free PMC article.
Metabolic network analysis integrated with transcript verification for sequenced genomes.
Manichaikul A, Ghamsari L, Hom EF, Lin C, Murray RR, Chang RL, Balaji S, Hao T, Shen Y, Chavali AK, Thiele I, Yang X, Fan C, Mello E, Hill DE, Vidal M, Salehi-Ashtiani K, Papin JA. Manichaikul A, et al. Among authors: shen y. Nat Methods. 2009 Aug;6(8):589-92. doi: 10.1038/nmeth.1348. Epub 2009 Jul 13. Nat Methods. 2009. PMID: 19597503 Free PMC article.
Large-scale RACE approach for proactive experimental definition of C. elegans ORFeome.
Salehi-Ashtiani K, Lin C, Hao T, Shen Y, Szeto D, Yang X, Ghamsari L, Lee H, Fan C, Murray RR, Milstein S, Svrzikapa N, Cusick ME, Roth FP, Hill DE, Vidal M. Salehi-Ashtiani K, et al. Among authors: shen y. Genome Res. 2009 Dec;19(12):2334-42. doi: 10.1101/gr.098640.109. Epub 2009 Oct 2. Genome Res. 2009. PMID: 19801531 Free PMC article.
Interpreting cancer genomes using systematic host network perturbations by tumour virus proteins.
Rozenblatt-Rosen O, Deo RC, Padi M, Adelmant G, Calderwood MA, Rolland T, Grace M, Dricot A, Askenazi M, Tavares M, Pevzner SJ, Abderazzaq F, Byrdsong D, Carvunis AR, Chen AA, Cheng J, Correll M, Duarte M, Fan C, Feltkamp MC, Ficarro SB, Franchi R, Garg BK, Gulbahce N, Hao T, Holthaus AM, James R, Korkhin A, Litovchick L, Mar JC, Pak TR, Rabello S, Rubio R, Shen Y, Singh S, Spangle JM, Tasan M, Wanamaker S, Webber JT, Roecklein-Canfield J, Johannsen E, Barabási AL, Beroukhim R, Kieff E, Cusick ME, Hill DE, Münger K, Marto JA, Quackenbush J, Roth FP, DeCaprio JA, Vidal M. Rozenblatt-Rosen O, et al. Among authors: shen y. Nature. 2012 Jul 26;487(7408):491-5. doi: 10.1038/nature11288. Nature. 2012. PMID: 22810586 Free PMC article.
Protein interaction network of alternatively spliced isoforms from brain links genetic risk factors for autism.
Corominas R, Yang X, Lin GN, Kang S, Shen Y, Ghamsari L, Broly M, Rodriguez M, Tam S, Wanamaker SA, Fan C, Yi S, Tasan M, Lemmens I, Kuang X, Zhao N, Malhotra D, Michaelson JJ, Vacic V, Calderwood MA, Roth FP, Tavernier J, Horvath S, Salehi-Ashtiani K, Korkin D, Sebat J, Hill DE, Hao T, Vidal M, Iakoucheva LM. Corominas R, et al. Among authors: shen y. Nat Commun. 2014 Apr 11;5:3650. doi: 10.1038/ncomms4650. Nat Commun. 2014. PMID: 24722188 Free PMC article.
A proteome-scale map of the human interactome network.
Rolland T, Taşan M, Charloteaux B, Pevzner SJ, Zhong Q, Sahni N, Yi S, Lemmens I, Fontanillo C, Mosca R, Kamburov A, Ghiassian SD, Yang X, Ghamsari L, Balcha D, Begg BE, Braun P, Brehme M, Broly MP, Carvunis AR, Convery-Zupan D, Corominas R, Coulombe-Huntington J, Dann E, Dreze M, Dricot A, Fan C, Franzosa E, Gebreab F, Gutierrez BJ, Hardy MF, Jin M, Kang S, Kiros R, Lin GN, Luck K, MacWilliams A, Menche J, Murray RR, Palagi A, Poulin MM, Rambout X, Rasla J, Reichert P, Romero V, Ruyssinck E, Sahalie JM, Scholz A, Shah AA, Sharma A, Shen Y, Spirohn K, Tam S, Tejeda AO, Wanamaker SA, Twizere JC, Vega K, Walsh J, Cusick ME, Xia Y, Barabási AL, Iakoucheva LM, Aloy P, De Las Rivas J, Tavernier J, Calderwood MA, Hill DE, Hao T, Roth FP, Vidal M. Rolland T, et al. Among authors: shen y. Cell. 2014 Nov 20;159(5):1212-1226. doi: 10.1016/j.cell.2014.10.050. Cell. 2014. PMID: 25416956 Free PMC article.
Widespread macromolecular interaction perturbations in human genetic disorders.
Sahni N, Yi S, Taipale M, Fuxman Bass JI, Coulombe-Huntington J, Yang F, Peng J, Weile J, Karras GI, Wang Y, Kovács IA, Kamburov A, Krykbaeva I, Lam MH, Tucker G, Khurana V, Sharma A, Liu YY, Yachie N, Zhong Q, Shen Y, Palagi A, San-Miguel A, Fan C, Balcha D, Dricot A, Jordan DM, Walsh JM, Shah AA, Yang X, Stoyanova AK, Leighton A, Calderwood MA, Jacob Y, Cusick ME, Salehi-Ashtiani K, Whitesell LJ, Sunyaev S, Berger B, Barabási AL, Charloteaux B, Hill DE, Hao T, Roth FP, Xia Y, Walhout AJM, Lindquist S, Vidal M. Sahni N, et al. Among authors: shen y. Cell. 2015 Apr 23;161(3):647-660. doi: 10.1016/j.cell.2015.04.013. Cell. 2015. PMID: 25910212 Free PMC article.
The Xenopus ORFeome: A resource that enables functional genomics.
Grant IM, Balcha D, Hao T, Shen Y, Trivedi P, Patrushev I, Fortriede JD, Karpinka JB, Liu L, Zorn AM, Stukenberg PT, Hill DE, Gilchrist MJ. Grant IM, et al. Among authors: shen y. Dev Biol. 2015 Dec 15;408(2):345-57. doi: 10.1016/j.ydbio.2015.09.004. Epub 2015 Sep 29. Dev Biol. 2015. PMID: 26391338 Free PMC article.
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