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Items: 1 to 20 of 35

1.

A high-resolution map of human evolutionary constraint using 29 mammals.

Lindblad-Toh K, Garber M, Zuk O, Lin MF, Parker BJ, Washietl S, Kheradpour P, Ernst J, Jordan G, Mauceli E, Ward LD, Lowe CB, Holloway AK, Clamp M, Gnerre S, Alföldi J, Beal K, Chang J, Clawson H, Cuff J, Di Palma F, Fitzgerald S, Flicek P, Guttman M, Hubisz MJ, Jaffe DB, Jungreis I, Kent WJ, Kostka D, Lara M, Martins AL, Massingham T, Moltke I, Raney BJ, Rasmussen MD, Robinson J, Stark A, Vilella AJ, Wen J, Xie X, Zody MC; Broad Institute Sequencing Platform and Whole Genome Assembly Team., Baldwin J, Bloom T, Chin CW, Heiman D, Nicol R, Nusbaum C, Young S, Wilkinson J, Worley KC, Kovar CL, Muzny DM, Gibbs RA; Baylor College of Medicine Human Genome Sequencing Center Sequencing Team., Cree A, Dihn HH, Fowler G, Jhangiani S, Joshi V, Lee S, Lewis LR, Nazareth LV, Okwuonu G, Santibanez J, Warren WC, Mardis ER, Weinstock GM, Wilson RK; Genome Institute at Washington University., Delehaunty K, Dooling D, Fronik C, Fulton L, Fulton B, Graves T, Minx P, Sodergren E, Birney E, Margulies EH, Herrero J, Green ED, Haussler D, Siepel A, Goldman N, Pollard KS, Pedersen JS, Lander ES, Kellis M.

Nature. 2011 Oct 12;478(7370):476-82. doi: 10.1038/nature10530.

2.

The variant call format and VCFtools.

Danecek P, Auton A, Abecasis G, Albers CA, Banks E, DePristo MA, Handsaker RE, Lunter G, Marth GT, Sherry ST, McVean G, Durbin R; 1000 Genomes Project Analysis Group..

Bioinformatics. 2011 Aug 1;27(15):2156-8. doi: 10.1093/bioinformatics/btr330.

3.

Mapping and analysis of chromatin state dynamics in nine human cell types.

Ernst J, Kheradpour P, Mikkelsen TS, Shoresh N, Ward LD, Epstein CB, Zhang X, Wang L, Issner R, Coyne M, Ku M, Durham T, Kellis M, Bernstein BE.

Nature. 2011 May 5;473(7345):43-9. doi: 10.1038/nature09906.

4.

Identifying a high fraction of the human genome to be under selective constraint using GERP++.

Davydov EV, Goode DL, Sirota M, Cooper GM, Sidow A, Batzoglou S.

PLoS Comput Biol. 2010 Dec 2;6(12):e1001025. doi: 10.1371/journal.pcbi.1001025.

5.

Ensembl 2011.

Flicek P, Amode MR, Barrell D, Beal K, Brent S, Chen Y, Clapham P, Coates G, Fairley S, Fitzgerald S, Gordon L, Hendrix M, Hourlier T, Johnson N, Kähäri A, Keefe D, Keenan S, Kinsella R, Kokocinski F, Kulesha E, Larsson P, Longden I, McLaren W, Overduin B, Pritchard B, Riat HS, Rios D, Ritchie GR, Ruffier M, Schuster M, Sobral D, Spudich G, Tang YA, Trevanion S, Vandrovcova J, Vilella AJ, White S, Wilder SP, Zadissa A, Zamora J, Aken BL, Birney E, Cunningham F, Dunham I, Durbin R, Fernández-Suarez XM, Herrero J, Hubbard TJ, Parker A, Proctor G, Vogel J, Searle SM.

Nucleic Acids Res. 2011 Jan;39(Database issue):D800-6. doi: 10.1093/nar/gkq1064.

6.

A map of human genome variation from population-scale sequencing.

1000 Genomes Project Consortium., Abecasis GR, Altshuler D, Auton A, Brooks LD, Durbin RM, Gibbs RA, Hurles ME, McVean GA.

Nature. 2010 Oct 28;467(7319):1061-73. doi: 10.1038/nature09534. Erratum in: Nature. 2011 May 26;473(7348):544. Xue, Yali [added]; Cartwright, Reed A [added]; Altshuler, David L [corrected to Altshuler, David]; Kebbel, Andrew [corrected to Keebler, Jonathan]; Koko-Gonzales, Paula [corrected to Kokko-Gonzales, Paula]; Nickerson, Debbie A [corrected to Nickerson, Deborah A].

7.

is-rSNP: a novel technique for in silico regulatory SNP detection.

Macintyre G, Bailey J, Haviv I, Kowalczyk A.

Bioinformatics. 2010 Sep 15;26(18):i524-30. doi: 10.1093/bioinformatics/btq378.

8.

An 8q24 gene desert variant associated with prostate cancer risk confers differential in vivo activity to a MYC enhancer.

Wasserman NF, Aneas I, Nobrega MA.

Genome Res. 2010 Sep;20(9):1191-7. doi: 10.1101/gr.105361.110.

9.

Ensembl variation resources.

Chen Y, Cunningham F, Rios D, McLaren WM, Smith J, Pritchard B, Spudich GM, Brent S, Kulesha E, Marin-Garcia P, Smedley D, Birney E, Flicek P.

BMC Genomics. 2010 May 11;11:293. doi: 10.1186/1471-2164-11-293.

10.

Chemotherapeutic drug susceptibility associated SNPs are enriched in expression quantitative trait loci.

Gamazon ER, Huang RS, Cox NJ, Dolan ME.

Proc Natl Acad Sci U S A. 2010 May 18;107(20):9287-92. doi: 10.1073/pnas.1001827107.

11.

Trait-associated SNPs are more likely to be eQTLs: annotation to enhance discovery from GWAS.

Nicolae DL, Gamazon E, Zhang W, Duan S, Dolan ME, Cox NJ.

PLoS Genet. 2010 Apr 1;6(4):e1000888. doi: 10.1371/journal.pgen.1000888.

12.

A method and server for predicting damaging missense mutations.

Adzhubei IA, Schmidt S, Peshkin L, Ramensky VE, Gerasimova A, Bork P, Kondrashov AS, Sunyaev SR.

Nat Methods. 2010 Apr;7(4):248-9. doi: 10.1038/nmeth0410-248. No abstract available.

13.

BEDTools: a flexible suite of utilities for comparing genomic features.

Quinlan AR, Hall IM.

Bioinformatics. 2010 Mar 15;26(6):841-2. doi: 10.1093/bioinformatics/btq033.

14.

JASPAR 2010: the greatly expanded open-access database of transcription factor binding profiles.

Portales-Casamar E, Thongjuea S, Kwon AT, Arenillas D, Zhao X, Valen E, Yusuf D, Lenhard B, Wasserman WW, Sandelin A.

Nucleic Acids Res. 2010 Jan;38(Database issue):D105-10. doi: 10.1093/nar/gkp950.

15.

Genome-wide association study in a Chinese Han population identifies nine new susceptibility loci for systemic lupus erythematosus.

Han JW, Zheng HF, Cui Y, Sun LD, Ye DQ, Hu Z, Xu JH, Cai ZM, Huang W, Zhao GP, Xie HF, Fang H, Lu QJ, Xu JH, Li XP, Pan YF, Deng DQ, Zeng FQ, Ye ZZ, Zhang XY, Wang QW, Hao F, Ma L, Zuo XB, Zhou FS, Du WH, Cheng YL, Yang JQ, Shen SK, Li J, Sheng YJ, Zuo XX, Zhu WF, Gao F, Zhang PL, Guo Q, Li B, Gao M, Xiao FL, Quan C, Zhang C, Zhang Z, Zhu KJ, Li Y, Hu DY, Lu WS, Huang JL, Liu SX, Li H, Ren YQ, Wang ZX, Yang CJ, Wang PG, Zhou WM, Lv YM, Zhang AP, Zhang SQ, Lin D, Li Y, Low HQ, Shen M, Zhai ZF, Wang Y, Zhang FY, Yang S, Liu JJ, Zhang XJ.

Nat Genet. 2009 Nov;41(11):1234-7. doi: 10.1038/ng.472.

PMID:
19838193
16.

Identifying novel constrained elements by exploiting biased substitution patterns.

Garber M, Guttman M, Clamp M, Zody MC, Friedman N, Xie X.

Bioinformatics. 2009 Jun 15;25(12):i54-62. doi: 10.1093/bioinformatics/btp190.

17.

Potential etiologic and functional implications of genome-wide association loci for human diseases and traits.

Hindorff LA, Sethupathy P, Junkins HA, Ramos EM, Mehta JP, Collins FS, Manolio TA.

Proc Natl Acad Sci U S A. 2009 Jun 9;106(23):9362-7. doi: 10.1073/pnas.0903103106.

18.

Diversity and complexity in DNA recognition by transcription factors.

Badis G, Berger MF, Philippakis AA, Talukder S, Gehrke AR, Jaeger SA, Chan ET, Metzler G, Vedenko A, Chen X, Kuznetsov H, Wang CF, Coburn D, Newburger DE, Morris Q, Hughes TR, Bulyk ML.

Science. 2009 Jun 26;324(5935):1720-3. doi: 10.1126/science.1162327.

19.

SNPinfo: integrating GWAS and candidate gene information into functional SNP selection for genetic association studies.

Xu Z, Taylor JA.

Nucleic Acids Res. 2009 Jul;37(Web Server issue):W600-5. doi: 10.1093/nar/gkp290.

20.

SNAP: a web-based tool for identification and annotation of proxy SNPs using HapMap.

Johnson AD, Handsaker RE, Pulit SL, Nizzari MM, O'Donnell CJ, de Bakker PI.

Bioinformatics. 2008 Dec 15;24(24):2938-9. doi: 10.1093/bioinformatics/btn564.

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