Mark A DePristo

Mark A DePristo

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Mark A DePristo

Mark A DePristo

Publications by authors named "Mark A DePristo"

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39Publications

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GenomeWarp: an alignment-based variant coordinate transformation.

Bioinformatics 2019 Mar 27. Epub 2019 Mar 27.

Verily Life Sciences, 1600 Amphitheatre Pkwy, Mountain View, CA, USA.

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http://dx.doi.org/10.1093/bioinformatics/btz218DOI Listing
March 2019

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

Eur J Hum Genet 2017 02 23;25(2):227-233. Epub 2016 Nov 23.

Department of Medical Genetics, Center for Molecular Medicine, University Medical Center Utrecht, Utrecht, The Netherlands.

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http://dx.doi.org/10.1038/ejhg.2016.147DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC5255947PMC
February 2017

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

Nature 2015 Feb 10;518(7537):102-6. Epub 2014 Dec 10.

1] Center for Human Genetic Research, Massachusetts General Hospital, Boston, Massachusetts 02114, USA. [2] Cardiovascular Research Center, Massachusetts General Hospital, Boston, Massachusetts 02114, USA. [3] Department of Medicine, Harvard Medical School, Boston, Massachusetts 02114, USA. [4] Program in Medical and Population Genetics, Broad Institute, 7 Cambridge Center, Cambridge, Massachusetts 02142, USA.

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http://kooperberg.fhcrc.org/papers/2015do.pdf
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http://www.nature.com/doifinder/10.1038/nature13917
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http://dx.doi.org/10.1038/nature13917DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4319990PMC
February 2015

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

PLoS Comput Biol 2012 12;8(7):e1002604. Epub 2012 Jul 12.

Broad Institute of Harvard and MIT, Cambridge, Massachusetts, United States of America.

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http://dx.doi.org/10.1371/journal.pcbi.1002604DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3395607PMC
January 2013

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

BMC Genomics 2012 Aug 5;13:375. Epub 2012 Aug 5.

Broad Institute of MIT and Harvard, Medical and Population Genetics Program, Cambridge, MA 02141, USA.

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http://dx.doi.org/10.1186/1471-2164-13-375DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3443046PMC
August 2012

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

Mol Biol Evol 2010 Sep 28;27(9):2198-209. Epub 2010 Apr 28.

Department of Organismic and Evolutionary Biology, Harvard University, Boston, MA, USA.

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http://dx.doi.org/10.1093/molbev/msq108DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC2922621PMC
September 2010

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

Genome Res 2010 Sep 19;20(9):1297-303. Epub 2010 Jul 19.

Program in Medical and Population Genetics, The Broad Institute of Harvard and MIT, Cambridge, Massachusetts 02142, USA.

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http://dx.doi.org/10.1101/gr.107524.110DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC2928508PMC
September 2010

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

Prog Biophys Mol Biol 2009 Sep-Oct;100(1-3):25-32. Epub 2009 Jul 21.

The Physiology Course, Marine Biological Laboratory, Woods Hole, MA 02543, USA.

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http://dx.doi.org/10.1016/j.pbiomolbio.2009.07.002DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC2805826PMC
April 2010

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

Mol Biol Evol 2009 Nov 14;26(11):2455-62. Epub 2009 Jul 14.

Department of Organismic and Evolutionary Biology, Harvard University, Cambridge, MA, USA.

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http://dx.doi.org/10.1093/molbev/msp151DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC2912465PMC
November 2009

Mutational reversions during adaptive protein evolution.

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

Department of Organismic and Evolutionary Biology, Harvard University, MA, USA.

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http://dx.doi.org/10.1093/molbev/msm118DOI Listing
August 2007

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

Authors:
Mark A Depristo

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

Department of Organismic and Evolutionary Biology, Harvard University, 16 Divinity Avenue, Cambridge, Massachusetts 02138.

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https://www.tandfonline.com/doi/full/10.2976/1.2754665
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http://dx.doi.org/10.2976/1.2754665DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC2639842PMC
July 2007

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

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

Department of Organismic and Evolutionary Biology, Hartl Lab, 16 Divinity Street, Harvard University, Cambridge, MA 02138, USA.

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http://dx.doi.org/10.1016/j.gene.2006.03.023DOI Listing
August 2006

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

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

Sanger Building, Department of Biochemistry, University of Cambridge, Tennis Court Road, Cambridge, CB2 1GA, United Kingdom.

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http://linkinghub.elsevier.com/retrieve/pii/S096921260600297
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http://dx.doi.org/10.1016/j.str.2006.06.014DOI Listing
August 2006

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

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

Department of Biochemistry, University of Cambridge, 80 Tennis Court Road, Cambridge CB2 1GA, UK.

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http://dx.doi.org/10.1016/j.tibs.2006.05.005DOI Listing
July 2006

Relation between native ensembles and experimental structures of proteins.

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

Department of Chemistry, Cambridge University, Lensfield Road, Cambridge CB2 1EW, United Kingdom.

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http://www.pnas.org/cgi/doi/10.1073/pnas.0511156103
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http://dx.doi.org/10.1073/pnas.0511156103DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC1544146PMC
July 2006

Conformer generation under restraints.

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

Department of Molecular Biology and Center for Human Genetic Research, Massachusetts General Hospital, and Department of Genetics, Harvard Medical School, Boston, MA 02114-2790, USA.

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http://dx.doi.org/10.1016/j.sbi.2006.02.001DOI Listing
April 2006

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

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

Department of Organismic and Evolutionary Biology, Harvard University, 16 Divinity Avenue, Cambridge, MA 02138, USA.

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http://www.sciencemag.org/cgi/doi/10.1126/science.1123539
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http://dx.doi.org/10.1126/science.1123539DOI Listing
April 2006

Is one solution good enough?

Nat Struct Mol Biol 2006 Mar;13(3):184-5; discussion 185

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http://dx.doi.org/10.1038/nsmb0306-184DOI Listing
March 2006

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

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

Department of Organismic and Evolutionary Biology, Harvard University, Cambridge, Massachusetts 02138, USA.

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http://dx.doi.org/10.1038/nrg1672DOI Listing
September 2005

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

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

Department of Biochemistry, University of Cambridge, 80 Tennis Court Road, Cambridge, CB2 1GA, United Kingdom.

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http://dx.doi.org/10.1016/j.str.2005.06.008DOI Listing
September 2005

Simultaneous determination of protein structure and dynamics.

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

Department of Chemistry, University of Cambridge, Lensfield Road, Cambridge CB2 1EW, UK.

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http://dx.doi.org/10.1038/nature03199DOI Listing
January 2005

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

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

Department of Biochemistry, University of Cambridge, 80 Tennis Court Road, Cambridge CB2 1GA, United Kingdom.

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http://linkinghub.elsevier.com/retrieve/pii/S096921260400114
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http://dx.doi.org/10.1016/j.str.2004.02.031DOI Listing
May 2004

Advantages of fine-grained side chain conformer libraries.

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

Department of Biochemistry, University of Cambridge, 80 Tennis Court Road, Cambridge CB2 1GA, UK.

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http://dx.doi.org/10.1093/protein/gzg143DOI Listing
December 2003

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

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

Department of Biochemistry, University of Cambridge, Cambridge CB2 1GA, England.

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http://www.ncbi.nlm.nih.gov/pmc/articles/PMC2323999PMC
http://dx.doi.org/10.1110/ps.0386903DOI Listing
September 2003

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

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

Department of Biochemistry, University of Cambridge, Cambridge, United Kingdom.

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http://dx.doi.org/10.1002/prot.10285DOI Listing
April 2003