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Items: 1 to 50 of 126

1.

Reliability of Whole-Exome Sequencing for Assessing Intratumor Genetic Heterogeneity.

Shi W, Ng CKY, Lim RS, Jiang T, Kumar S, Li X, Wali VB, Piscuoglio S, Gerstein MB, Chagpar AB, Weigelt B, Pusztai L, Reis-Filho JS, Hatzis C.

Cell Rep. 2018 Nov 6;25(6):1446-1457. doi: 10.1016/j.celrep.2018.10.046.

2.

Isoform-Level Interpretation of High-Throughput Proteomics Data Enabled by Deep Integration with RNA-seq.

Carlyle BC, Kitchen RR, Zhang J, Wilson RS, Lam TT, Rozowsky JS, Williams KR, Sestan N, Gerstein MB, Nairn AC.

J Proteome Res. 2018 Oct 5;17(10):3431-3444. doi: 10.1021/acs.jproteome.8b00310. Epub 2018 Sep 6.

PMID:
30125121
3.

Gene names can confound most-searched listings.

Gerstein MB, Navarro FCP.

Nature. 2018 Jan 25;553(7689):405. doi: 10.1038/d41586-018-01077-3. No abstract available.

PMID:
29368714
4.

A multiregional proteomic survey of the postnatal human brain.

Carlyle BC, Kitchen RR, Kanyo JE, Voss EZ, Pletikos M, Sousa AMM, Lam TT, Gerstein MB, Sestan N, Nairn AC.

Nat Neurosci. 2017 Dec;20(12):1787-1795. doi: 10.1038/s41593-017-0011-2. Epub 2017 Nov 13.

5.

Molecular and cellular reorganization of neural circuits in the human lineage.

Sousa AMM, Zhu Y, Raghanti MA, Kitchen RR, Onorati M, Tebbenkamp ATN, Stutz B, Meyer KA, Li M, Kawasawa YI, Liu F, Perez RG, Mele M, Carvalho T, Skarica M, Gulden FO, Pletikos M, Shibata A, Stephenson AR, Edler MK, Ely JJ, Elsworth JD, Horvath TL, Hof PR, Hyde TM, Kleinman JE, Weinberger DR, Reimers M, Lifton RP, Mane SM, Noonan JP, State MW, Lein ES, Knowles JA, Marques-Bonet T, Sherwood CC, Gerstein MB, Sestan N.

Science. 2017 Nov 24;358(6366):1027-1032. doi: 10.1126/science.aan3456.

6.

Gaining comprehensive biological insight into the transcriptome by performing a broad-spectrum RNA-seq analysis.

Sahraeian SME, Mohiyuddin M, Sebra R, Tilgner H, Afshar PT, Au KF, Bani Asadi N, Gerstein MB, Wong WH, Snyder MP, Schadt E, Lam HYK.

Nat Commun. 2017 Jul 5;8(1):59. doi: 10.1038/s41467-017-00050-4.

7.

Landscape and variation of novel retroduplications in 26 human populations.

Zhang Y, Li S, Abyzov A, Gerstein MB.

PLoS Comput Biol. 2017 Jun 29;13(6):e1005567. doi: 10.1371/journal.pcbi.1005567. eCollection 2017 Jun.

8.

Dynamic RNA-protein interactions underlie the zebrafish maternal-to-zygotic transition.

Despic V, Dejung M, Gu M, Krishnan J, Zhang J, Herzel L, Straube K, Gerstein MB, Butter F, Neugebauer KM.

Genome Res. 2017 Jul;27(7):1184-1194. doi: 10.1101/gr.215954.116. Epub 2017 Apr 5.

9.

Whole-genome analysis of papillary kidney cancer finds significant noncoding alterations.

Li S, Shuch BM, Gerstein MB.

PLoS Genet. 2017 Mar 30;13(3):e1006685. doi: 10.1371/journal.pgen.1006685. eCollection 2017 Mar.

10.

Pangolin genomes and the evolution of mammalian scales and immunity.

Choo SW, Rayko M, Tan TK, Hari R, Komissarov A, Wee WY, Yurchenko AA, Kliver S, Tamazian G, Antunes A, Wilson RK, Warren WC, Koepfli KP, Minx P, Krasheninnikova K, Kotze A, Dalton DL, Vermaak E, Paterson IC, Dobrynin P, Sitam FT, Rovie-Ryan JJ, Johnson WE, Yusoff AM, Luo SJ, Karuppannan KV, Fang G, Zheng D, Gerstein MB, Lipovich L, O'Brien SJ, Wong GJ.

Genome Res. 2016 Oct;26(10):1312-1322. Epub 2016 Aug 10.

11.

Extending gene ontology in the context of extracellular RNA and vesicle communication.

Cheung KH, Keerthikumar S, Roncaglia P, Subramanian SL, Roth ME, Samuel M, Anand S, Gangoda L, Gould S, Alexander R, Galas D, Gerstein MB, Hill AF, Kitchen RR, Lötvall J, Patel T, Procaccini DC, Quesenberry P, Rozowsky J, Raffai RL, Shypitsyna A, Su AI, Théry C, Vickers K, Wauben MH, Mathivanan S, Milosavljevic A, Laurent LC.

J Biomed Semantics. 2016 Apr 12;7:19. doi: 10.1186/s13326-016-0061-5. eCollection 2016.

12.

Understanding genome structural variations.

Abyzov A, Li S, Gerstein MB.

Oncotarget. 2016 Feb 16;7(7):7370-1. doi: 10.18632/oncotarget.6485. No abstract available.

13.

The PsychENCODE project.

PsychENCODE Consortium, Akbarian S, Liu C, Knowles JA, Vaccarino FM, Farnham PJ, Crawford GE, Jaffe AE, Pinto D, Dracheva S, Geschwind DH, Mill J, Nairn AC, Abyzov A, Pochareddy S, Prabhakar S, Weissman S, Sullivan PF, State MW, Weng Z, Peters MA, White KP, Gerstein MB, Amiri A, Armoskus C, Ashley-Koch AE, Bae T, Beckel-Mitchener A, Berman BP, Coetzee GA, Coppola G, Francoeur N, Fromer M, Gao R, Grennan K, Herstein J, Kavanagh DH, Ivanov NA, Jiang Y, Kitchen RR, Kozlenkov A, Kundakovic M, Li M, Li Z, Liu S, Mangravite LM, Mattei E, Markenscoff-Papadimitriou E, Navarro FC, North N, Omberg L, Panchision D, Parikshak N, Poschmann J, Price AJ, Purcaro M, Reddy TE, Roussos P, Schreiner S, Scuderi S, Sebra R, Shibata M, Shieh AW, Skarica M, Sun W, Swarup V, Thomas A, Tsuji J, van Bakel H, Wang D, Wang Y, Wang K, Werling DM, Willsey AJ, Witt H, Won H, Wong CC, Wray GA, Wu EY, Xu X, Yao L, Senthil G, Lehner T, Sklar P, Sestan N.

Nat Neurosci. 2015 Dec;18(12):1707-12. doi: 10.1038/nn.4156. Review. No abstract available.

14.

An integrated map of structural variation in 2,504 human genomes.

Sudmant PH, Rausch T, Gardner EJ, Handsaker RE, Abyzov A, Huddleston J, Zhang Y, Ye K, Jun G, Fritz MH, Konkel MK, Malhotra A, Stütz AM, Shi X, Casale FP, Chen J, Hormozdiari F, Dayama G, Chen K, Malig M, Chaisson MJP, Walter K, Meiers S, Kashin S, Garrison E, Auton A, Lam HYK, Mu XJ, Alkan C, Antaki D, Bae T, Cerveira E, Chines P, Chong Z, Clarke L, Dal E, Ding L, Emery S, Fan X, Gujral M, Kahveci F, Kidd JM, Kong Y, Lameijer EW, McCarthy S, Flicek P, Gibbs RA, Marth G, Mason CE, Menelaou A, Muzny DM, Nelson BJ, Noor A, Parrish NF, Pendleton M, Quitadamo A, Raeder B, Schadt EE, Romanovitch M, Schlattl A, Sebra R, Shabalin AA, Untergasser A, Walker JA, Wang M, Yu F, Zhang C, Zhang J, Zheng-Bradley X, Zhou W, Zichner T, Sebat J, Batzer MA, McCarroll SA; 1000 Genomes Project Consortium, Mills RE, Gerstein MB, Bashir A, Stegle O, Devine SE, Lee C, Eichler EE, Korbel JO.

Nature. 2015 Oct 1;526(7571):75-81. doi: 10.1038/nature15394.

15.

Leveraging long read sequencing from a single individual to provide a comprehensive resource for benchmarking variant calling methods.

Mu JC, Tootoonchi Afshar P, Mohiyuddin M, Chen X, Li J, Bani Asadi N, Gerstein MB, Wong WH, Lam HY.

Sci Rep. 2015 Sep 28;5:14493. doi: 10.1038/srep14493.

16.

An ensemble approach to accurately detect somatic mutations using SomaticSeq.

Fang LT, Afshar PT, Chhibber A, Mohiyuddin M, Fan Y, Mu JC, Gibeling G, Barr S, Asadi NB, Gerstein MB, Koboldt DC, Wang W, Wong WH, Lam HY.

Genome Biol. 2015 Sep 17;16:197. doi: 10.1186/s13059-015-0758-2.

17.

Erratum: analysis of deletion breakpoints from 1,092 humans reveals details of mutation mechanisms.

Abyzov A, Li S, Kim DR, Mohiyuddin M, Stütz AM, Parrish NF, Mu XJ, Clark W, Chen K, Hurles M, Korbel JO, Lam HY, Lee C, Gerstein MB.

Nat Commun. 2015 Sep 8;6:8389. doi: 10.1038/ncomms9389. No abstract available.

PMID:
26346554
18.

Tracking Distinct RNA Populations Using Efficient and Reversible Covalent Chemistry.

Duffy EE, Rutenberg-Schoenberg M, Stark CD, Kitchen RR, Gerstein MB, Simon MD.

Mol Cell. 2015 Sep 3;59(5):858-66. doi: 10.1016/j.molcel.2015.07.023.

19.

Integration of extracellular RNA profiling data using metadata, biomedical ontologies and Linked Data technologies.

Subramanian SL, Kitchen RR, Alexander R, Carter BS, Cheung KH, Laurent LC, Pico A, Roberts LR, Roth ME, Rozowsky JS, Su AI, Gerstein MB, Milosavljevic A.

J Extracell Vesicles. 2015 Aug 28;4:27497. doi: 10.3402/jev.v4.27497. eCollection 2015.

20.

Analysis of deletion breakpoints from 1,092 humans reveals details of mutation mechanisms.

Abyzov A, Li S, Kim DR, Mohiyuddin M, Stütz AM, Parrish NF, Mu XJ, Clark W, Chen K, Hurles M, Korbel JO, Lam HY, Lee C, Gerstein MB.

Nat Commun. 2015 Jun 1;6:7256. doi: 10.1038/ncomms8256. Erratum in: Nat Commun. 2015;6:8389.

21.

Loregic: a method to characterize the cooperative logic of regulatory factors.

Wang D, Yan KK, Sisu C, Cheng C, Rozowsky J, Meyerson W, Gerstein MB.

PLoS Comput Biol. 2015 Apr 17;11(4):e1004132. doi: 10.1371/journal.pcbi.1004132. eCollection 2015 Apr.

22.

MetaSV: an accurate and integrative structural-variant caller for next generation sequencing.

Mohiyuddin M, Mu JC, Li J, Bani Asadi N, Gerstein MB, Abyzov A, Wong WH, Lam HY.

Bioinformatics. 2015 Aug 15;31(16):2741-4. doi: 10.1093/bioinformatics/btv204. Epub 2015 Apr 10.

23.

VarSim: a high-fidelity simulation and validation framework for high-throughput genome sequencing with cancer applications.

Mu JC, Mohiyuddin M, Li J, Bani Asadi N, Gerstein MB, Abyzov A, Wong WH, Lam HY.

Bioinformatics. 2015 May 1;31(9):1469-71. doi: 10.1093/bioinformatics/btu828. Epub 2014 Dec 17.

24.

Decoding neuroproteomics: integrating the genome, translatome and functional anatomy.

Kitchen RR, Rozowsky JS, Gerstein MB, Nairn AC.

Nat Neurosci. 2014 Nov;17(11):1491-9. doi: 10.1038/nn.3829. Epub 2014 Oct 28. Review.

25.

Characterization of stress-responsive lncRNAs in Arabidopsis thaliana by integrating expression, epigenetic and structural features.

Di C, Yuan J, Wu Y, Li J, Lin H, Hu L, Zhang T, Qi Y, Gerstein MB, Guo Y, Lu ZJ.

Plant J. 2014 Dec;80(5):848-61. doi: 10.1111/tpj.12679. Epub 2014 Oct 21.

26.

Comparative analysis of the transcriptome across distant species.

Gerstein MB, Rozowsky J, Yan KK, Wang D, Cheng C, Brown JB, Davis CA, Hillier L, Sisu C, Li JJ, Pei B, Harmanci AO, Duff MO, Djebali S, Alexander RP, Alver BH, Auerbach R, Bell K, Bickel PJ, Boeck ME, Boley NP, Booth BW, Cherbas L, Cherbas P, Di C, Dobin A, Drenkow J, Ewing B, Fang G, Fastuca M, Feingold EA, Frankish A, Gao G, Good PJ, Guigó R, Hammonds A, Harrow J, Hoskins RA, Howald C, Hu L, Huang H, Hubbard TJ, Huynh C, Jha S, Kasper D, Kato M, Kaufman TC, Kitchen RR, Ladewig E, Lagarde J, Lai E, Leng J, Lu Z, MacCoss M, May G, McWhirter R, Merrihew G, Miller DM, Mortazavi A, Murad R, Oliver B, Olson S, Park PJ, Pazin MJ, Perrimon N, Pervouchine D, Reinke V, Reymond A, Robinson G, Samsonova A, Saunders GI, Schlesinger F, Sethi A, Slack FJ, Spencer WC, Stoiber MH, Strasbourger P, Tanzer A, Thompson OA, Wan KH, Wang G, Wang H, Watkins KL, Wen J, Wen K, Xue C, Yang L, Yip K, Zaleski C, Zhang Y, Zheng H, Brenner SE, Graveley BR, Celniker SE, Gingeras TR, Waterston R.

Nature. 2014 Aug 28;512(7515):445-8. doi: 10.1038/nature13424.

27.

Comparative analysis of pseudogenes across three phyla.

Sisu C, Pei B, Leng J, Frankish A, Zhang Y, Balasubramanian S, Harte R, Wang D, Rutenberg-Schoenberg M, Clark W, Diekhans M, Rozowsky J, Hubbard T, Harrow J, Gerstein MB.

Proc Natl Acad Sci U S A. 2014 Sep 16;111(37):13361-6. doi: 10.1073/pnas.1407293111. Epub 2014 Aug 25.

28.

Guidelines for investigating causality of sequence variants in human disease.

MacArthur DG, Manolio TA, Dimmock DP, Rehm HL, Shendure J, Abecasis GR, Adams DR, Altman RB, Antonarakis SE, Ashley EA, Barrett JC, Biesecker LG, Conrad DF, Cooper GM, Cox NJ, Daly MJ, Gerstein MB, Goldstein DB, Hirschhorn JN, Leal SM, Pennacchio LA, Stamatoyannopoulos JA, Sunyaev SR, Valle D, Voight BF, Winckler W, Gunter C.

Nature. 2014 Apr 24;508(7497):469-76. doi: 10.1038/nature13127.

29.

Transcriptional landscape of the prenatal human brain.

Miller JA, Ding SL, Sunkin SM, Smith KA, Ng L, Szafer A, Ebbert A, Riley ZL, Royall JJ, Aiona K, Arnold JM, Bennet C, Bertagnolli D, Brouner K, Butler S, Caldejon S, Carey A, Cuhaciyan C, Dalley RA, Dee N, Dolbeare TA, Facer BA, Feng D, Fliss TP, Gee G, Goldy J, Gourley L, Gregor BW, Gu G, Howard RE, Jochim JM, Kuan CL, Lau C, Lee CK, Lee F, Lemon TA, Lesnar P, McMurray B, Mastan N, Mosqueda N, Naluai-Cecchini T, Ngo NK, Nyhus J, Oldre A, Olson E, Parente J, Parker PD, Parry SE, Stevens A, Pletikos M, Reding M, Roll K, Sandman D, Sarreal M, Shapouri S, Shapovalova NV, Shen EH, Sjoquist N, Slaughterbeck CR, Smith M, Sodt AJ, Williams D, Zöllei L, Fischl B, Gerstein MB, Geschwind DH, Glass IA, Hawrylycz MJ, Hevner RF, Huang H, Jones AR, Knowles JA, Levitt P, Phillips JW, Sestan N, Wohnoutka P, Dang C, Bernard A, Hohmann JG, Lein ES.

Nature. 2014 Apr 10;508(7495):199-206. doi: 10.1038/nature13185. Epub 2014 Apr 2.

30.

Sixty years of genome biology.

Doolittle WF, Fraser P, Gerstein MB, Graveley BR, Henikoff S, Huttenhower C, Oshlack A, Ponting CP, Rinn JL, Schatz MC, Ule J, Weigel D, Weinstock GM.

Genome Biol. 2013 Apr 25;14(4):113. doi: 10.1186/gb-2013-14-4-113.

31.

Epigenetic repression of miR-31 disrupts androgen receptor homeostasis and contributes to prostate cancer progression.

Lin PC, Chiu YL, Banerjee S, Park K, Mosquera JM, Giannopoulou E, Alves P, Tewari AK, Gerstein MB, Beltran H, Melnick AM, Elemento O, Demichelis F, Rubin MA.

Cancer Res. 2013 Feb 1;73(3):1232-44. doi: 10.1158/0008-5472.CAN-12-2968. Epub 2012 Dec 11.

32.

Architecture of the human regulatory network derived from ENCODE data.

Gerstein MB, Kundaje A, Hariharan M, Landt SG, Yan KK, Cheng C, Mu XJ, Khurana E, Rozowsky J, Alexander R, Min R, Alves P, Abyzov A, Addleman N, Bhardwaj N, Boyle AP, Cayting P, Charos A, Chen DZ, Cheng Y, Clarke D, Eastman C, Euskirchen G, Frietze S, Fu Y, Gertz J, Grubert F, Harmanci A, Jain P, Kasowski M, Lacroute P, Leng JJ, Lian J, Monahan H, O'Geen H, Ouyang Z, Partridge EC, Patacsil D, Pauli F, Raha D, Ramirez L, Reddy TE, Reed B, Shi M, Slifer T, Wang J, Wu L, Yang X, Yip KY, Zilberman-Schapira G, Batzoglou S, Sidow A, Farnham PJ, Myers RM, Weissman SM, Snyder M.

Nature. 2012 Sep 6;489(7414):91-100. doi: 10.1038/nature11245.

33.

The GENCODE pseudogene resource.

Pei B, Sisu C, Frankish A, Howald C, Habegger L, Mu XJ, Harte R, Balasubramanian S, Tanzer A, Diekhans M, Reymond A, Hubbard TJ, Harrow J, Gerstein MB.

Genome Biol. 2012 Sep 26;13(9):R51. doi: 10.1186/gb-2012-13-9-r51.

34.

Chromatin state signatures associated with tissue-specific gene expression and enhancer activity in the embryonic limb.

Cotney J, Leng J, Oh S, DeMare LE, Reilly SK, Gerstein MB, Noonan JP.

Genome Res. 2012 Jun;22(6):1069-80. doi: 10.1101/gr.129817.111. Epub 2012 Mar 15.

35.

Detecting and annotating genetic variations using the HugeSeq pipeline.

Lam HY, Pan C, Clark MJ, Lacroute P, Chen R, Haraksingh R, O'Huallachain M, Gerstein MB, Kidd JM, Bustamante CD, Snyder M.

Nat Biotechnol. 2012 Mar 7;30(3):226-9. doi: 10.1038/nbt.2134. No abstract available.

36.

Genomic analysis of the hydrocarbon-producing, cellulolytic, endophytic fungus Ascocoryne sarcoides.

Gianoulis TA, Griffin MA, Spakowicz DJ, Dunican BF, Alpha CJ, Sboner A, Sismour AM, Kodira C, Egholm M, Church GM, Gerstein MB, Strobel SA.

PLoS Genet. 2012;8(3):e1002558. doi: 10.1371/journal.pgen.1002558. Epub 2012 Mar 1.

37.

Molecular characterization of neuroendocrine prostate cancer and identification of new drug targets.

Beltran H, Rickman DS, Park K, Chae SS, Sboner A, MacDonald TY, Wang Y, Sheikh KL, Terry S, Tagawa ST, Dhir R, Nelson JB, de la Taille A, Allory Y, Gerstein MB, Perner S, Pienta KJ, Chinnaiyan AM, Wang Y, Collins CC, Gleave ME, Demichelis F, Nanus DM, Rubin MA.

Cancer Discov. 2011 Nov;1(6):487-95. doi: 10.1158/2159-8290.CD-11-0130.

38.

A systematic survey of loss-of-function variants in human protein-coding genes.

MacArthur DG, Balasubramanian S, Frankish A, Huang N, Morris J, Walter K, Jostins L, Habegger L, Pickrell JK, Montgomery SB, Albers CA, Zhang ZD, Conrad DF, Lunter G, Zheng H, Ayub Q, DePristo MA, Banks E, Hu M, Handsaker RE, Rosenfeld JA, Fromer M, Jin M, Mu XJ, Khurana E, Ye K, Kay M, Saunders GI, Suner MM, Hunt T, Barnes IH, Amid C, Carvalho-Silva DR, Bignell AH, Snow C, Yngvadottir B, Bumpstead S, Cooper DN, Xue Y, Romero IG; 1000 Genomes Project Consortium, Wang J, Li Y, Gibbs RA, McCarroll SA, Dermitzakis ET, Pritchard JK, Barrett JC, Harrow J, Hurles ME, Gerstein MB, Tyler-Smith C.

Science. 2012 Feb 17;335(6070):823-8. doi: 10.1126/science.1215040. Erratum in: Science. 2012 Apr 20;336(6079):296.

39.

Novel insights through the integration of structural and functional genomics data with protein networks.

Clarke D, Bhardwaj N, Gerstein MB.

J Struct Biol. 2012 Sep;179(3):320-6. doi: 10.1016/j.jsb.2012.02.001. Epub 2012 Feb 11.

40.

Performance comparison of whole-genome sequencing platforms.

Lam HY, Clark MJ, Chen R, Chen R, Natsoulis G, O'Huallachain M, Dewey FE, Habegger L, Ashley EA, Gerstein MB, Butte AJ, Ji HP, Snyder M.

Nat Biotechnol. 2011 Dec 18;30(1):78-82. doi: 10.1038/nbt.2065. Erratum in: Nat Biotechnol. 2012 Jun;30(6):562.

41.

Genome-wide analysis of chromatin features identifies histone modification sensitive and insensitive yeast transcription factors.

Cheng C, Shou C, Yip KY, Gerstein MB.

Genome Biol. 2011 Nov 7;12(11):R111. doi: 10.1186/gb-2011-12-11-r111.

42.

Predicting protein ligand binding motions with the conformation explorer.

Flores SC, Gerstein MB.

BMC Bioinformatics. 2011 Oct 27;12:417. doi: 10.1186/1471-2105-12-417.

43.

Identification of a disease-defining gene fusion in epithelioid hemangioendothelioma.

Tanas MR, Sboner A, Oliveira AM, Erickson-Johnson MR, Hespelt J, Hanwright PJ, Flanagan J, Luo Y, Fenwick K, Natrajan R, Mitsopoulos C, Zvelebil M, Hoch BL, Weiss SW, Debiec-Rychter M, Sciot R, West RB, Lazar AJ, Ashworth A, Reis-Filho JS, Lord CJ, Gerstein MB, Rubin MA, Rubin BP.

Sci Transl Med. 2011 Aug 31;3(98):98ra82. doi: 10.1126/scitranslmed.3002409.

44.

The real cost of sequencing: higher than you think!

Sboner A, Mu XJ, Greenbaum D, Auerbach RK, Gerstein MB.

Genome Biol. 2011 Aug 25;12(8):125. doi: 10.1186/gb-2011-12-8-125.

45.

Integration of protein motions with molecular networks reveals different mechanisms for permanent and transient interactions.

Bhardwaj N, Abyzov A, Clarke D, Shou C, Gerstein MB.

Protein Sci. 2011 Oct;20(10):1745-54. doi: 10.1002/pro.710. Epub 2011 Sep 15.

46.

The reality of pervasive transcription.

Clark MB, Amaral PP, Schlesinger FJ, Dinger ME, Taft RJ, Rinn JL, Ponting CP, Stadler PF, Morris KV, Morillon A, Rozowsky JS, Gerstein MB, Wahlestedt C, Hayashizaki Y, Carninci P, Gingeras TR, Mattick JS.

PLoS Biol. 2011 Jul;9(7):e1000625; discussion e1001102. doi: 10.1371/journal.pbio.1000625. Epub 2011 Jul 12. No abstract available.

47.

Analysis of genomic variation in non-coding elements using population-scale sequencing data from the 1000 Genomes Project.

Mu XJ, Lu ZJ, Kong Y, Lam HY, Gerstein MB.

Nucleic Acids Res. 2011 Sep 1;39(16):7058-76. doi: 10.1093/nar/gkr342. Epub 2011 May 19.

48.

The CRIT framework for identifying cross patterns in systems biology and application to chemogenomics.

Gianoulis TA, Agarwal A, Snyder M, Gerstein MB.

Genome Biol. 2011;12(3):R32. doi: 10.1186/gb-2011-12-3-r32. Epub 2011 Mar 31.

49.

Diverse roles and interactions of the SWI/SNF chromatin remodeling complex revealed using global approaches.

Euskirchen GM, Auerbach RK, Davidov E, Gianoulis TA, Zhong G, Rozowsky J, Bhardwaj N, Gerstein MB, Snyder M.

PLoS Genet. 2011 Mar;7(3):e1002008. doi: 10.1371/journal.pgen.1002008. Epub 2011 Mar 3.

50.

The genomic complexity of primary human prostate cancer.

Berger MF, Lawrence MS, Demichelis F, Drier Y, Cibulskis K, Sivachenko AY, Sboner A, Esgueva R, Pflueger D, Sougnez C, Onofrio R, Carter SL, Park K, Habegger L, Ambrogio L, Fennell T, Parkin M, Saksena G, Voet D, Ramos AH, Pugh TJ, Wilkinson J, Fisher S, Winckler W, Mahan S, Ardlie K, Baldwin J, Simons JW, Kitabayashi N, MacDonald TY, Kantoff PW, Chin L, Gabriel SB, Gerstein MB, Golub TR, Meyerson M, Tewari A, Lander ES, Getz G, Rubin MA, Garraway LA.

Nature. 2011 Feb 10;470(7333):214-20. doi: 10.1038/nature09744.

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