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Results: 1 to 20 of 464

1.

Comparative analysis of regulatory information and circuits across distant species.

Boyle AP, Araya CL, Brdlik C, Cayting P, Cheng C, Cheng Y, Gardner K, Hillier LW, Janette J, Jiang L, Kasper D, Kawli T, Kheradpour P, Kundaje A, Li JJ, Ma L, Niu W, Rehm EJ, Rozowsky J, Slattery M, Spokony R, Terrell R, Vafeados D, Wang D, Weisdepp P, Wu YC, Xie D, Yan KK, Feingold EA, Good PJ, Pazin MJ, Huang H, Bickel PJ, Brenner SE, Reinke V, Waterston RH, Gerstein M, White KP, Kellis M, Snyder M.

Nature. 2014 Aug 28;512(7515):453-6. doi: 10.1038/nature13668.

PMID:
25164757
[PubMed - in process]
2.

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.

PMID:
25164755
[PubMed - in process]
3.

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.

PMID:
25157146
[PubMed - in process]
Free Article
4.

Cellular superspreaders: an epidemiological perspective on HIV infection inside the body.

Talbert-Slagle K, Atkins KE, Yan KK, Khurana E, Gerstein M, Bradley EH, Berg D, Galvani AP, Townsend JP.

PLoS Pathog. 2014 May 8;10(5):e1004092. doi: 10.1371/journal.ppat.1004092. eCollection 2014 May. No abstract available.

PMID:
24811311
[PubMed - in process]
Free PMC Article
5.

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.

PMID:
24759409
[PubMed - indexed for MEDLINE]
6.

Defining functional DNA elements in the human genome.

Kellis M, Wold B, Snyder MP, Bernstein BE, Kundaje A, Marinov GK, Ward LD, Birney E, Crawford GE, Dekker J, Dunham I, Elnitski LL, Farnham PJ, Feingold EA, Gerstein M, Giddings MC, Gilbert DM, Gingeras TR, Green ED, Guigo R, Hubbard T, Kent J, Lieb JD, Myers RM, Pazin MJ, Ren B, Stamatoyannopoulos JA, Weng Z, White KP, Hardison RC.

Proc Natl Acad Sci U S A. 2014 Apr 29;111(17):6131-8. doi: 10.1073/pnas.1318948111. Epub 2014 Apr 21. Review.

PMID:
24753594
[PubMed - indexed for MEDLINE]
Free PMC Article
7.

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.

PMID:
24695229
[PubMed - indexed for MEDLINE]
8.

A15: predicting macrophage activation syndrome in pediatric systemic lupus erythematosus patients at diagnosis.

Gerstein M, Sukhdeo S, Levy DM, Feldman BM, Benseler SM, Ng LW, Abdelhaleem M, Silverman ED, Hiraki L.

Arthritis Rheumatol. 2014 Mar;66 Suppl 11:S25. doi: 10.1002/art.38431.

PMID:
24677941
[PubMed - in process]
9.

Identification of a major determinant for serine-threonine kinase phosphoacceptor specificity.

Chen C, Ha BH, Thévenin AF, Lou HJ, Zhang R, Yip KY, Peterson JR, Gerstein M, Kim PM, Filippakopoulos P, Knapp S, Boggon TJ, Turk BE.

Mol Cell. 2014 Jan 9;53(1):140-7. doi: 10.1016/j.molcel.2013.11.013. Epub 2013 Dec 26.

PMID:
24374310
[PubMed - indexed for MEDLINE]
Free PMC Article
10.

Integrative annotation of variants from 1092 humans: application to cancer genomics.

Khurana E, Fu Y, Colonna V, Mu XJ, Kang HM, Lappalainen T, Sboner A, Lochovsky L, Chen J, Harmanci A, Das J, Abyzov A, Balasubramanian S, Beal K, Chakravarty D, Challis D, Chen Y, Clarke D, Clarke L, Cunningham F, Evani US, Flicek P, Fragoza R, Garrison E, Gibbs R, Gümüs ZH, Herrero J, Kitabayashi N, Kong Y, Lage K, Liluashvili V, Lipkin SM, MacArthur DG, Marth G, Muzny D, Pers TH, Ritchie GR, Rosenfeld JA, Sisu C, Wei X, Wilson M, Xue Y, Yu F; 1000 Genomes Project Consortium, Dermitzakis ET, Yu H, Rubin MA, Tyler-Smith C, Gerstein M.

Science. 2013 Oct 4;342(6154):1235587. doi: 10.1126/science.1235587.

PMID:
24092746
[PubMed - indexed for MEDLINE]
Free PMC Article
11.

Analysis of variable retroduplications in human populations suggests coupling of retrotransposition to cell division.

Abyzov A, Iskow R, Gokcumen O, Radke DW, Balasubramanian S, Pei B, Habegger L; 1000 Genomes Project Consortium, Lee C, Gerstein M.

Genome Res. 2013 Dec;23(12):2042-52. doi: 10.1101/gr.154625.113. Epub 2013 Sep 11.

PMID:
24026178
[PubMed - indexed for MEDLINE]
Free PMC Article
12.

Identification of yeast cell cycle regulated genes based on genomic features.

Cheng C, Fu Y, Shen L, Gerstein M.

BMC Syst Biol. 2013 Jul 29;7:70. doi: 10.1186/1752-0509-7-70.

PMID:
23895232
[PubMed - indexed for MEDLINE]
Free PMC Article
13.

Identification of genes critical for resistance to infection by West Nile virus using RNA-Seq analysis.

Qian F, Chung L, Zheng W, Bruno V, Alexander RP, Wang Z, Wang X, Kurscheid S, Zhao H, Fikrig E, Gerstein M, Snyder M, Montgomery RR.

Viruses. 2013 Jul 8;5(7):1664-81. doi: 10.3390/v5071664.

PMID:
23881275
[PubMed - indexed for MEDLINE]
Free PMC Article
14.

Transcriptomic and phylogenetic analysis of a bacterial cell cycle reveals strong associations between gene co-expression and evolution.

Fang G, Passalacqua KD, Hocking J, Llopis PM, Gerstein M, Bergman NH, Jacobs-Wagner C.

BMC Genomics. 2013 Jul 5;14:450. doi: 10.1186/1471-2164-14-450.

PMID:
23829427
[PubMed - indexed for MEDLINE]
Free PMC Article
15.

Machine learning and genome annotation: a match meant to be?

Yip KY, Cheng C, Gerstein M.

Genome Biol. 2013 May 29;14(5):205. doi: 10.1186/gb-2013-14-5-205.

PMID:
23731483
[PubMed - in process]
Free PMC Article
16.

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.

PMID:
23651518
[PubMed - in process]
Free PMC Article
17.

Pentraxin 3 is a marker of early joint inflammation in patients with juvenile idiopathic arthritis.

Padeh S, Farzam N, Chayen G, Gerstein M, Berkun Y.

Immunol Res. 2013 Jul;56(2-3):444-50. doi: 10.1007/s12026-013-8417-8.

PMID:
23579776
[PubMed - indexed for MEDLINE]
18.

Interpretation of genomic variants using a unified biological network approach.

Khurana E, Fu Y, Chen J, Gerstein M.

PLoS Comput Biol. 2013;9(3):e1002886. doi: 10.1371/journal.pcbi.1002886. Epub 2013 Mar 7.

PMID:
23505346
[PubMed - indexed for MEDLINE]
Free PMC Article
19.

The origin, evolution, and functional impact of short insertion-deletion variants identified in 179 human genomes.

Montgomery SB, Goode DL, Kvikstad E, Albers CA, Zhang ZD, Mu XJ, Ananda G, Howie B, Karczewski KJ, Smith KS, Anaya V, Richardson R, Davis J; 1000 Genomes Project Consortium, MacArthur DG, Sidow A, Duret L, Gerstein M, Makova KD, Marchini J, McVean G, Lunter G.

Genome Res. 2013 May;23(5):749-61. doi: 10.1101/gr.148718.112. Epub 2013 Mar 11.

PMID:
23478400
[PubMed - indexed for MEDLINE]
Free PMC Article
20.

Accurate identification and analysis of human mRNA isoforms using deep long read sequencing.

Tilgner H, Raha D, Habegger L, Mohiuddin M, Gerstein M, Snyder M.

G3 (Bethesda). 2013 Mar;3(3):387-97. doi: 10.1534/g3.112.004812. Epub 2013 Mar 1.

PMID:
23450794
[PubMed - indexed for MEDLINE]
Free PMC Article

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