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Items: 36

1.

A framework for the detection of de novo mutations in family-based sequencing data.

Francioli LC, Cretu-Stancu M, Garimella KV, Fromer M, Kloosterman WP; Genome of the Netherlands consortium, Samocha KE, Neale BM, Daly MJ, Banks E, DePristo MA, de Bakker PI.

Eur J Hum Genet. 2017 Feb;25(2):227-233. doi: 10.1038/ejhg.2016.147. Epub 2016 Nov 23.

2.

Exome sequencing identifies rare LDLR and APOA5 alleles conferring risk for myocardial infarction.

Do R, Stitziel NO, Won HH, Jørgensen AB, Duga S, Angelica Merlini P, Kiezun A, Farrall M, Goel A, Zuk O, Guella I, Asselta R, Lange LA, Peloso GM, Auer PL; NHLBI Exome Sequencing Project, Girelli D, Martinelli N, Farlow DN, DePristo MA, Roberts R, Stewart AF, Saleheen D, Danesh J, Epstein SE, Sivapalaratnam S, Hovingh GK, Kastelein JJ, Samani NJ, Schunkert H, Erdmann J, Shah SH, Kraus WE, Davies R, Nikpay M, Johansen CT, Wang J, Hegele RA, Hechter E, Marz W, Kleber ME, Huang J, Johnson AD, Li M, Burke GL, Gross M, Liu Y, Assimes TL, Heiss G, Lange EM, Folsom AR, Taylor HA, Olivieri O, Hamsten A, Clarke R, Reilly DF, Yin W, Rivas MA, Donnelly P, Rossouw JE, Psaty BM, Herrington DM, Wilson JG, Rich SS, Bamshad MJ, Tracy RP, Cupples LA, Rader DJ, Reilly MP, Spertus JA, Cresci S, Hartiala J, Tang WH, Hazen SL, Allayee H, Reiner AP, Carlson CS, Kooperberg C, Jackson RD, Boerwinkle E, Lander ES, Schwartz SM, Siscovick DS, McPherson R, Tybjaerg-Hansen A, Abecasis GR, Watkins H, Nickerson DA, Ardissino D, Sunyaev SR, O'Donnell CJ, Altshuler D, Gabriel S, Kathiresan S.

Nature. 2015 Feb 5;518(7537):102-6. doi: 10.1038/nature13917. Epub 2014 Dec 10.

3.

From FastQ data to high confidence variant calls: the Genome Analysis Toolkit best practices pipeline.

Van der Auwera GA, Carneiro MO, Hartl C, Poplin R, Del Angel G, Levy-Moonshine A, Jordan T, Shakir K, Roazen D, Thibault J, Banks E, Garimella KV, Altshuler D, Gabriel S, DePristo MA.

Curr Protoc Bioinformatics. 2013;43:11.10.1-33. doi: 10.1002/0471250953.bi1110s43.

4.

Human genomic regions with exceptionally high levels of population differentiation identified from 911 whole-genome sequences.

Colonna V, Ayub Q, Chen Y, Pagani L, Luisi P, Pybus M, Garrison E, Xue Y, Tyler-Smith C; 1000 Genomes Project Consortium, Abecasis GR, Auton A, Brooks LD, DePristo MA, Durbin RM, Handsaker RE, Kang HM, Marth GT, McVean GA.

Genome Biol. 2014 Jun 30;15(6):R88. doi: 10.1186/gb-2014-15-6-r88.

5.

An integrated map of genetic variation from 1,092 human genomes.

1000 Genomes Project Consortium, Abecasis GR, Auton A, Brooks LD, DePristo MA, Durbin RM, Handsaker RE, Kang HM, Marth GT, McVean GA.

Nature. 2012 Nov 1;491(7422):56-65. doi: 10.1038/nature11632.

6.

Pacific biosciences sequencing technology for genotyping and variation discovery in human data.

Carneiro MO, Russ C, Ross MG, Gabriel SB, Nusbaum C, DePristo MA.

BMC Genomics. 2012 Aug 5;13:375. doi: 10.1186/1471-2164-13-375.

7.

Efficiency and power as a function of sequence coverage, SNP array density, and imputation.

Flannick J, Korn JM, Fontanillas P, Grant GB, Banks E, Depristo MA, Altshuler D.

PLoS Comput Biol. 2012;8(7):e1002604. doi: 10.1371/journal.pcbi.1002604. Epub 2012 Jul 12.

8.

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.

9.

Variation in genome-wide mutation rates within and between human families.

Conrad DF, Keebler JE, DePristo MA, Lindsay SJ, Zhang Y, Casals F, Idaghdour Y, Hartl CL, Torroja C, Garimella KV, Zilversmit M, Cartwright R, Rouleau GA, Daly M, Stone EA, Hurles ME, Awadalla P; 1000 Genomes Project.

Nat Genet. 2011 Jun 12;43(7):712-4. doi: 10.1038/ng.862.

10.

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. Epub 2011 Jun 7.

11.

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.

12.

Next-generation sequencing for HLA typing of class I loci.

Erlich RL, Jia X, Anderson S, Banks E, Gao X, Carrington M, Gupta N, DePristo MA, Henn MR, Lennon NJ, de Bakker PI.

BMC Genomics. 2011 Jan 18;12:42. doi: 10.1186/1471-2164-12-42.

13.

Exome sequencing reveals a novel mutation for autosomal recessive non-syndromic mental retardation in the TECR gene on chromosome 19p13.

Çalışkan M, Chong JX, Uricchio L, Anderson R, Chen P, Sougnez C, Garimella K, Gabriel SB, dePristo MA, Shakir K, Matern D, Das S, Waggoner D, Nicolae DL, Ober C.

Hum Mol Genet. 2011 Apr 1;20(7):1285-9. doi: 10.1093/hmg/ddq569. Epub 2011 Jan 6.

14.

Exome sequencing, ANGPTL3 mutations, and familial combined hypolipidemia.

Musunuru K, Pirruccello JP, Do R, Peloso GM, Guiducci C, Sougnez C, Garimella KV, Fisher S, Abreu J, Barry AJ, Fennell T, Banks E, Ambrogio L, Cibulskis K, Kernytsky A, Gonzalez E, Rudzicz N, Engert JC, DePristo MA, Daly MJ, Cohen JC, Hobbs HH, Altshuler D, Schonfeld G, Gabriel SB, Yue P, Kathiresan S.

N Engl J Med. 2010 Dec 2;363(23):2220-7. doi: 10.1056/NEJMoa1002926. Epub 2010 Oct 13.

15.

The Genome Analysis Toolkit: a MapReduce framework for analyzing next-generation DNA sequencing data.

McKenna A, Hanna M, Banks E, Sivachenko A, Cibulskis K, Kernytsky A, Garimella K, Altshuler D, Gabriel S, Daly M, DePristo MA.

Genome Res. 2010 Sep;20(9):1297-303. doi: 10.1101/gr.107524.110. Epub 2010 Jul 19.

16.

Low-complexity regions in Plasmodium falciparum: missing links in the evolution of an extreme genome.

Zilversmit MM, Volkman SK, DePristo MA, Wirth DF, Awadalla P, Hartl DL.

Mol Biol Evol. 2010 Sep;27(9):2198-209. doi: 10.1093/molbev/msq108. Epub 2010 Apr 28.

17.

Sublethal antibiotic treatment leads to multidrug resistance via radical-induced mutagenesis.

Kohanski MA, DePristo MA, Collins JJ.

Mol Cell. 2010 Feb 12;37(3):311-20. doi: 10.1016/j.molcel.2010.01.003.

18.

Introducing simulated cellular architecture to the quantitative analysis of fluorescent microscopy.

DePristo MA, Chang L, Vale RD, Khan SM, Lipkow K.

Prog Biophys Mol Biol. 2009 Sep-Oct;100(1-3):25-32. doi: 10.1016/j.pbiomolbio.2009.07.002. Epub 2009 Jul 21.

19.

Temporal constraints on the incorporation of regulatory mutants in evolutionary pathways.

Brown KM, Depristo MA, Weinreich DM, Hartl DL.

Mol Biol Evol. 2009 Nov;26(11):2455-62. doi: 10.1093/molbev/msp151. Epub 2009 Jul 14.

20.

The subtle benefits of being promiscuous: adaptive evolution potentiated by enzyme promiscuity.

Depristo MA.

HFSP J. 2007 Jul;1(2):94-8. doi: 10.2976/1.2754665. Epub 2007 Jul 10.

21.

Mutational reversions during adaptive protein evolution.

DePristo MA, Hartl DL, Weinreich DM.

Mol Biol Evol. 2007 Aug;24(8):1608-10. Epub 2007 Jun 7.

PMID:
17556755
22.

Knowledge-based real-space explorations for low-resolution structure determination.

Furnham N, Doré AS, Chirgadze DY, de Bakker PI, Depristo MA, Blundell TL.

Structure. 2006 Aug;14(8):1313-20.

23.

Relation between native ensembles and experimental structures of proteins.

Best RB, Lindorff-Larsen K, DePristo MA, Vendruscolo M.

Proc Natl Acad Sci U S A. 2006 Jul 18;103(29):10901-6. Epub 2006 Jul 7.

24.

On the abundance, amino acid composition, and evolutionary dynamics of low-complexity regions in proteins.

DePristo MA, Zilversmit MM, Hartl DL.

Gene. 2006 Aug 15;378:19-30. Epub 2006 May 11.

PMID:
16806741
25.

The RNA degradosome: life in the fast lane of adaptive molecular evolution.

Marcaida MJ, DePristo MA, Chandran V, Carpousis AJ, Luisi BF.

Trends Biochem Sci. 2006 Jul;31(7):359-65.

PMID:
16766188
26.

Darwinian evolution can follow only very few mutational paths to fitter proteins.

Weinreich DM, Delaney NF, Depristo MA, Hartl DL.

Science. 2006 Apr 7;312(5770):111-4.

27.

Is one solution good enough?

Furnham N, Blundell TL, DePristo MA, Terwilliger TC.

Nat Struct Mol Biol. 2006 Mar;13(3):184-5; discussion 185. No abstract available.

PMID:
16518382
28.

Conformer generation under restraints.

de Bakker PI, Furnham N, Blundell TL, DePristo MA.

Curr Opin Struct Biol. 2006 Apr;16(2):160-5. Epub 2006 Feb 17. Review.

PMID:
16483766
29.

Crystallographic refinement by knowledge-based exploration of complex energy landscapes.

Depristo MA, de Bakker PI, Johnson RJ, Blundell TL.

Structure. 2005 Sep;13(9):1311-9.

30.

Missense meanderings in sequence space: a biophysical view of protein evolution.

DePristo MA, Weinreich DM, Hartl DL.

Nat Rev Genet. 2005 Sep;6(9):678-87. Review.

PMID:
16074985
31.

Simultaneous determination of protein structure and dynamics.

Lindorff-Larsen K, Best RB, Depristo MA, Dobson CM, Vendruscolo M.

Nature. 2005 Jan 13;433(7022):128-32.

PMID:
15650731
32.

Heterogeneity and inaccuracy in protein structures solved by X-ray crystallography.

DePristo MA, de Bakker PI, Blundell TL.

Structure. 2004 May;12(5):831-8.

33.

Advantages of fine-grained side chain conformer libraries.

Shetty RP, De Bakker PI, DePristo MA, Blundell TL.

Protein Eng. 2003 Dec;16(12):963-9.

PMID:
14983076
34.

Discrete restraint-based protein modeling and the Calpha-trace problem.

DePristo MA, De Bakker PI, Shetty RP, Blundell TL.

Protein Sci. 2003 Sep;12(9):2032-46.

35.

Ab initio construction of polypeptide fragments: efficient generation of accurate, representative ensembles.

DePristo MA, de Bakker PI, Lovell SC, Blundell TL.

Proteins. 2003 Apr 1;51(1):41-55.

PMID:
12596262

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