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Items: 1 to 20 of 22

1.

Consent Codes: Upholding Standard Data Use Conditions.

Dyke SO, Philippakis AA, Rambla De Argila J, Paltoo DN, Luetkemeier ES, Knoppers BM, Brookes AJ, Spalding JD, Thompson M, Roos M, Boycott KM, Brudno M, Hurles M, Rehm HL, Matern A, Fiume M, Sherry ST.

PLoS Genet. 2016 Jan 21;12(1):e1005772. doi: 10.1371/journal.pgen.1005772. eCollection 2016 Jan.

2.

The Matchmaker Exchange: a platform for rare disease gene discovery.

Philippakis AA, Azzariti DR, Beltran S, Brookes AJ, Brownstein CA, Brudno M, Brunner HG, Buske OJ, Carey K, Doll C, Dumitriu S, Dyke SO, den Dunnen JT, Firth HV, Gibbs RA, Girdea M, Gonzalez M, Haendel MA, Hamosh A, Holm IA, Huang L, Hurles ME, Hutton B, Krier JB, Misyura A, Mungall CJ, Paschall J, Paten B, Robinson PN, Schiettecatte F, Sobreira NL, Swaminathan GJ, Taschner PE, Terry SF, Washington NL, Züchner S, Boycott KM, Rehm HL.

Hum Mutat. 2015 Oct;36(10):915-21. doi: 10.1002/humu.22858.

PMID:
26295439
3.

The 1000 Genomes Project: data management and community access.

Clarke L, Zheng-Bradley X, Smith R, Kulesha E, Xiao C, Toneva I, Vaughan B, Preuss D, Leinonen R, Shumway M, Sherry S, Flicek P; 1000 Genomes Project Consortium.

Nat Methods. 2012 Apr 27;9(5):459-62. doi: 10.1038/nmeth.1974.

4.

Cardiac amyloidosis mimicking hypertrophic cardiomyopathy with obstruction: treatment with disopyramide.

Philippakis AA, Falk RH.

Circulation. 2012 Apr 10;125(14):1821-4. doi: 10.1161/CIRCULATIONAHA.111.064246. No abstract available.

5.

The functional spectrum of low-frequency coding variation.

Marth GT, Yu F, Indap AR, Garimella K, Gravel S, Leong WF, Tyler-Smith C, Bainbridge M, Blackwell T, Zheng-Bradley X, Chen Y, Challis D, Clarke L, Ball EV, Cibulskis K, Cooper DN, Fulton B, Hartl C, Koboldt D, Muzny D, Smith R, Sougnez C, Stewart C, Ward A, Yu J, Xue Y, Altshuler D, Bustamante CD, Clark AG, Daly M, DePristo M, Flicek P, Gabriel S, Mardis E, Palotie A, Gibbs R; 1000 Genomes Project.

Genome Biol. 2011 Sep 14;12(9):R84. doi: 10.1186/gb-2011-12-9-r84.

6.

Comparing strategies to fine-map the association of common SNPs at chromosome 9p21 with type 2 diabetes and myocardial infarction.

Shea J, Agarwala V, Philippakis AA, Maguire J, Banks E, Depristo M, Thomson B, Guiducci C, Onofrio RC, Kathiresan S, Gabriel S, Burtt NP, Daly MJ, Groop L, Altshuler D; Myocardial Infarction Genetics Consortium.

Nat Genet. 2011 Jul 24;43(8):801-5. doi: 10.1038/ng.871.

7.

Demographic history and rare allele sharing among human populations.

Gravel S, Henn BM, Gutenkunst RN, Indap AR, Marth GT, Clark AG, Yu F, Gibbs RA; 1000 Genomes Project, Bustamante CD.

Proc Natl Acad Sci U S A. 2011 Jul 19;108(29):11983-8. doi: 10.1073/pnas.1019276108. Epub 2011 Jul 5.

8.

A framework for variation discovery and genotyping using next-generation DNA sequencing data.

DePristo MA, Banks E, Poplin R, Garimella KV, Maguire JR, Hartl C, Philippakis AA, del Angel G, Rivas MA, Hanna M, McKenna A, Fennell TJ, Kernytsky AM, Sivachenko AY, Cibulskis K, Gabriel SB, Altshuler D, Daly MJ.

Nat Genet. 2011 May;43(5):491-8. doi: 10.1038/ng.806. Epub 2011 Apr 10.

9.

Mapping copy number variation by population-scale genome sequencing.

Mills RE, Walter K, Stewart C, Handsaker RE, Chen K, Alkan C, Abyzov A, Yoon SC, Ye K, Cheetham RK, Chinwalla A, Conrad DF, Fu Y, Grubert F, Hajirasouliha I, Hormozdiari F, Iakoucheva LM, Iqbal Z, Kang S, Kidd JM, Konkel MK, Korn J, Khurana E, Kural D, Lam HY, Leng J, Li R, Li Y, Lin CY, Luo R, Mu XJ, Nemesh J, Peckham HE, Rausch T, Scally A, Shi X, Stromberg MP, Stütz AM, Urban AE, Walker JA, Wu J, Zhang Y, Zhang ZD, Batzer MA, Ding L, Marth GT, McVean G, Sebat J, Snyder M, Wang J, Ye K, Eichler EE, Gerstein MB, Hurles ME, Lee C, McCarroll SA, Korbel JO; 1000 Genomes Project.

Nature. 2011 Feb 3;470(7332):59-65. doi: 10.1038/nature09708.

10.

Diversity of human copy number variation and multicopy genes.

Sudmant PH, Kitzman JO, Antonacci F, Alkan C, Malig M, Tsalenko A, Sampas N, Bruhn L, Shendure J; 1000 Genomes Project, Eichler EE.

Science. 2010 Oct 29;330(6004):641-6. doi: 10.1126/science.1197005.

11.

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].

12.

Multi-step control of muscle diversity by Hox proteins in the Drosophila embryo.

Enriquez J, Boukhatmi H, Dubois L, Philippakis AA, Bulyk ML, Michelson AM, Crozatier M, Vincent A.

Development. 2010 Feb;137(3):457-66. doi: 10.1242/dev.045286. Epub 2010 Jan 7.

13.

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. Epub 2009 May 14.

14.

High-resolution DNA-binding specificity analysis of yeast transcription factors.

Zhu C, Byers KJ, McCord RP, Shi Z, Berger MF, Newburger DE, Saulrieta K, Smith Z, Shah MV, Radhakrishnan M, Philippakis AA, Hu Y, De Masi F, Pacek M, Rolfs A, Murthy T, Labaer J, Bulyk ML.

Genome Res. 2009 Apr;19(4):556-66. doi: 10.1101/gr.090233.108. Epub 2009 Jan 21.

15.

Predicting the binding preference of transcription factors to individual DNA k-mers.

Alleyne TM, Peña-Castillo L, Badis G, Talukder S, Berger MF, Gehrke AR, Philippakis AA, Bulyk ML, Morris QD, Hughes TR.

Bioinformatics. 2009 Apr 15;25(8):1012-8. doi: 10.1093/bioinformatics/btn645. Epub 2008 Dec 16.

16.

Design of compact, universal DNA microarrays for protein binding microarray experiments.

Philippakis AA, Qureshi AM, Berger MF, Bulyk ML.

J Comput Biol. 2008 Sep;15(7):655-65. doi: 10.1089/cmb.2007.0114.

17.

Variation in homeodomain DNA binding revealed by high-resolution analysis of sequence preferences.

Berger MF, Badis G, Gehrke AR, Talukder S, Philippakis AA, Peña-Castillo L, Alleyne TM, Mnaimneh S, Botvinnik OB, Chan ET, Khalid F, Zhang W, Newburger D, Jaeger SA, Morris QD, Bulyk ML, Hughes TR.

Cell. 2008 Jun 27;133(7):1266-76. doi: 10.1016/j.cell.2008.05.024.

18.

Systematic identification of mammalian regulatory motifs' target genes and functions.

Warner JB, Philippakis AA, Jaeger SA, He FS, Lin J, Bulyk ML.

Nat Methods. 2008 Apr;5(4):347-53. doi: 10.1038/nmeth.1188. Epub 2008 Mar 2.

19.

Inferring condition-specific transcription factor function from DNA binding and gene expression data.

McCord RP, Berger MF, Philippakis AA, Bulyk ML.

Mol Syst Biol. 2007;3:100. Epub 2007 Apr 17. Erratum in: Mol Syst Biol. 2010;6:362.

20.

Compact, universal DNA microarrays to comprehensively determine transcription-factor binding site specificities.

Berger MF, Philippakis AA, Qureshi AM, He FS, Estep PW 3rd, Bulyk ML.

Nat Biotechnol. 2006 Nov;24(11):1429-35. Epub 2006 Sep 24.

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