Melissa Gymrek

Melissa Gymrek

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Melissa Gymrek

Melissa Gymrek

Publications by authors named "Melissa Gymrek"

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34Publications

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The impact of short tandem repeat variation on gene expression.

Nat Genet 2019 11 1;51(11):1652-1659. Epub 2019 Nov 1.

Department of Computer Science and Engineering, University of California San Diego, La Jolla, CA, USA.

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http://dx.doi.org/10.1038/s41588-019-0521-9DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC6917484PMC
November 2019

Profiling the genome-wide landscape of tandem repeat expansions.

Nucleic Acids Res 2019 09;47(15):e90

Department of Medicine, University of California San Diego, 9500 Gilman Drive, MC 0639, La Jolla, CA 92093, USA.

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http://dx.doi.org/10.1093/nar/gkz501DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC6735967PMC
September 2019

Targeted genotyping of variable number tandem repeats with adVNTR.

Genome Res 2018 11 23;28(11):1709-1719. Epub 2018 Oct 23.

Department of Computer Science and Engineering, University of California, San Diego, La Jolla, California 92093, USA.

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http://genome.cshlp.org/lookup/doi/10.1101/gr.235119.118
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http://dx.doi.org/10.1101/gr.235119.118DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC6211647PMC
November 2018

A reference haplotype panel for genome-wide imputation of short tandem repeats.

Nat Commun 2018 10 23;9(1):4397. Epub 2018 Oct 23.

Department of Computer Science and Engineering, University of California San Diego, 9500 Gilman Drive, La Jolla, CA, 92093, USA.

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http://dx.doi.org/10.1038/s41467-018-06694-0DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC6199332PMC
October 2018

Recommendations for open data science.

Gigascience 2016 18;5:22. Epub 2016 May 18.

Data Science and Data Engineering, Broad Institute of MIT and Harvard, Cambridge, MA USA.

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http://dx.doi.org/10.1186/s13742-016-0127-4DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4870738PMC
October 2017

Interpreting short tandem repeat variations in humans using mutational constraint.

Nat Genet 2017 Oct 11;49(10):1495-1501. Epub 2017 Sep 11.

New York Genome Center, New York, New York, USA.

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http://dx.doi.org/10.1038/ng.3952DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC5679271PMC
October 2017

A genomic view of short tandem repeats.

Authors:
Melissa Gymrek

Curr Opin Genet Dev 2017 Jun 16;44:9-16. Epub 2017 Feb 16.

Department of Medicine, University of California San Diego, La Jolla, CA 92093, USA; Department of Computer Science and Engineering, University of California San Diego, La Jolla, CA 92093, USA. Electronic address:

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http://dx.doi.org/10.1016/j.gde.2017.01.012DOI Listing
June 2017

Genome-wide profiling of heritable and de novo STR variations.

Nat Methods 2017 Jun 24;14(6):590-592. Epub 2017 Apr 24.

New York Genome Center, New York, New York, USA.

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http://dx.doi.org/10.1038/nmeth.4267DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC5482724PMC
June 2017

The Simons Genome Diversity Project: 300 genomes from 142 diverse populations.

Nature 2016 Oct 21;538(7624):201-206. Epub 2016 Sep 21.

Department of Genetics, Harvard Medical School, Boston, Massachusetts 02115, USA.

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http://dx.doi.org/10.1038/nature18964DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC5161557PMC
October 2016

Polymorphic tandem repeats within gene promoters act as modifiers of gene expression and DNA methylation in humans.

Nucleic Acids Res 2016 05 7;44(8):3750-62. Epub 2016 Apr 7.

Department of Genetics and Genomic Sciences, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA

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http://dx.doi.org/10.1093/nar/gkw219DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4857002PMC
May 2016

Population-Scale Sequencing Data Enable Precise Estimates of Y-STR Mutation Rates.

Am J Hum Genet 2016 05 25;98(5):919-933. Epub 2016 Apr 25.

New York Genome Center, New York, NY 10013, USA; Whitehead Institute for Biomedical Research, 9 Cambridge Center, Cambridge, MA 02139, USA; Department of Computer Science, Fu Foundation School of Engineering, Columbia University, New York, NY 10027, USA; Center for Computational Biology and Bioinformatics, Columbia University, New York, NY 10032, USA. Electronic address:

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http://dx.doi.org/10.1016/j.ajhg.2016.04.001DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4863667PMC
May 2016

PyBamView: a browser-based application for viewing short read alignments.

Authors:
Melissa Gymrek

Bioinformatics 2014 Dec 21;30(23):3405-7. Epub 2014 Aug 21.

Whitehead Institute for Biomedical Research, 9 Cambridge Center, Cambridge, MA 02142, Harvard-MIT Division of Health Sciences and Technology, MIT, Cambridge, MA 02139 and Program in Medical and Population Genetics, Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA Whitehead Institute for Biomedical Research, 9 Cambridge Center, Cambridge, MA 02142, Harvard-MIT Division of Health Sciences and Technology, MIT, Cambridge, MA 02139 and Program in Medical and Population Genetics, Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA Whitehead Institute for Biomedical Research, 9 Cambridge Center, Cambridge, MA 02142, Harvard-MIT Division of Health Sciences and Technology, MIT, Cambridge, MA 02139 and Program in Medical and Population Genetics, Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA.

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http://dx.doi.org/10.1093/bioinformatics/btu565DOI Listing
December 2014

The landscape of human STR variation.

Genome Res 2014 Nov 18;24(11):1894-904. Epub 2014 Aug 18.

Whitehead Institute for Biomedical Research, Cambridge, Massachusetts 02142, USA;

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http://dx.doi.org/10.1101/gr.177774.114DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4216929PMC
November 2014

Back to the family: a renewed approach to rare variant studies.

Genome Med 2012 19;4(12):97. Epub 2012 Dec 19.

Whitehead Institute for Biomedical Research, 9 Cambridge Center, Cambridge, MA 02142, USA.

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http://dx.doi.org/10.1186/gm398DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3580437PMC
August 2014

Profiling short tandem repeats from short reads.

Methods Mol Biol 2013 ;1038:113-35

Harvard-MIT Division of Health Sciences and Technology, MIT, Cambridge, MA, USA.

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http://dx.doi.org/10.1007/978-1-62703-514-9_7DOI Listing
February 2014

LoQAtE--Localization and Quantitation ATlas of the yeast proteomE. A new tool for multiparametric dissection of single-protein behavior in response to biological perturbations in yeast.

Nucleic Acids Res 2014 Jan 22;42(Database issue):D726-30. Epub 2013 Oct 22.

Department of Molecular Genetics, Weizmann Institute of Science, Rehovot 7610001, Israel and Whitehead Institute for Biomedical Research, Nine Cambridge Center, Cambridge, MA 02142, USA.

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https://academic.oup.com/nar/article-lookup/doi/10.1093/nar/
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http://dx.doi.org/10.1093/nar/gkt933DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3965041PMC
January 2014

A novel single-cell screening platform reveals proteome plasticity during yeast stress responses.

J Cell Biol 2013 Mar;200(6):839-50

Department of Molecular Genetics, Weizmann Institute of Science, Rehovot, Israel.

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http://dx.doi.org/10.1083/jcb.201301120DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3601363PMC
March 2013

Identifying personal genomes by surname inference.

Science 2013 Jan;339(6117):321-4

Whitehead Institute for Biomedical Research, 9 Cambridge Center, Cambridge, MA 02142, USA.

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http://dx.doi.org/10.1126/science.1229566DOI Listing
January 2013

lobSTR: A short tandem repeat profiler for personal genomes.

Genome Res 2012 Jun 20;22(6):1154-62. Epub 2012 Apr 20.

Harvard-MIT Division of Health Sciences and Technology, Massachusetts Institute of Technology, Cambridge, MA 02139, USA.

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http://dx.doi.org/10.1101/gr.135780.111DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3371701PMC
June 2012

Using DNA sequencers as stethoscopes.

Genome Med 2011 Nov 21;3(11):73. Epub 2011 Nov 21.

Whitehead Institute for Biomedical Research, 9 Cambridge Center, Cambridge, MA 02142, USA.

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http://dx.doi.org/10.1186/gm289DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3308028PMC
November 2011

PTMScout, a Web resource for analysis of high throughput post-translational proteomics studies.

Mol Cell Proteomics 2010 Nov 14;9(11):2558-70. Epub 2010 Jul 14.

Department of Biological Engineering, Massachusetts Institute of Technology, Cambridge, Massachusetts 02139, USA.

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http://dx.doi.org/10.1074/mcp.M110.001206DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC2984232PMC
November 2010

Digital transcriptome profiling from attomole-level RNA samples.

Genome Res 2010 Apr 4;20(4):519-25. Epub 2010 Feb 4.

Helicos BioSciences Corporation, Cambridge, MA 02139, USA.

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http://dx.doi.org/10.1101/gr.102129.109DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC2847755PMC
April 2010

Chromatin profiling by directly sequencing small quantities of immunoprecipitated DNA.

Nat Methods 2010 Jan 29;7(1):47-9. Epub 2009 Nov 29.

Broad Institute of Harvard and Massachusetts Institute of Technology, Cambridge, Massachusetts, USA.

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http://www.nature.com/doifinder/10.1038/nmeth.1404
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http://dx.doi.org/10.1038/nmeth.1404DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC2862482PMC
January 2010