Gabor T Marth

Gabor T Marth

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Gabor T Marth

Gabor T Marth

Publications by authors named "Gabor T Marth"

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Multi-platform discovery of haplotype-resolved structural variation in human genomes.

Nat Commun 2019 04 16;10(1):1784. Epub 2019 Apr 16.

The Jackson Laboratory for Genomic Medicine, Farmington, CT, 06032, USA.

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http://www.nature.com/articles/s41467-018-08148-z
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http://dx.doi.org/10.1038/s41467-018-08148-zDOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC6467913PMC
April 2019

GIGGLE: a search engine for large-scale integrated genome analysis.

Nat Methods 2018 02 8;15(2):123-126. Epub 2018 Jan 8.

Department of Human Genetics, University of Utah, Salt Lake City, Utah, USA.

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http://dx.doi.org/10.1038/nmeth.4556DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC5872823PMC
February 2018

Rapid clinical diagnostic variant investigation of genomic patient sequencing data with web tools.

J Clin Transl Sci 2017 Dec;1(6):381-386

Department of Human Genetics, USTAR Center for Genetic Discovery, University of Utah School of Medicine, Salt Lake City, UT 84112, USA.

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http://dx.doi.org/10.1017/cts.2017.311DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC5915807PMC
December 2017

SpeedSeq: ultra-fast personal genome analysis and interpretation.

Nat Methods 2015 Oct 10;12(10):966-8. Epub 2015 Aug 10.

McDonnell Genome Institute, Washington University School of Medicine, St. Louis, Missouri, USA.

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http://dx.doi.org/10.1038/nmeth.3505DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4589466PMC
October 2015

Toolbox for mobile-element insertion detection on cancer genomes.

Cancer Inform 2015 12;14(Suppl 1):37-44. Epub 2015 Feb 12.

Department of Biology, Boston College, Chestnut Hill, MA, USA. ; Currently at the Department of Human Genetics and Utah Center for Genetic Discovery, University of Utah, Salt Lake City, UT, USA.

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http://dx.doi.org/10.4137/CIN.S24657DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4338948PMC
May 2015

MOSAIK: a hash-based algorithm for accurate next-generation sequencing short-read mapping.

PLoS One 2014 5;9(3):e90581. Epub 2014 Mar 5.

Department of Biology, Boston College, Chestnut Hill, Massachusetts, United States of America.

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http://journals.plos.org/plosone/article?id=10.1371/journal.pone.0090581PLOS
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3944147PMC
January 2015

bam.iobio: a web-based, real-time, sequence alignment file inspector.

Nat Methods 2014 Dec;11(12):1189

1] Department of Biology, Boston College, Chestnut Hill, Massachusetts, USA. [2] Department of Human Genetics, University of Utah, Salt Lake City, Utah, USA. [3] Utah Science Technology and Research Center for Genetic Discovery, University of Utah, Salt Lake City, Utah, USA.

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http://dx.doi.org/10.1038/nmeth.3174DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4282680PMC
December 2014

Toolbox for mobile-element insertion detection on cancer genomes.

Cancer Inform 2014 15;13(Suppl 4):45-52. Epub 2014 Oct 15.

Department of Biology, Boston College, Chestnut Hill, MA, USA. ; Currently at the Department of Human Genetics and Utah Center for Genetic Discovery, University of Utah, Salt Lake City, UT, USA.

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http://dx.doi.org/10.4137/CIN.S13979DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4218655PMC
December 2014

SSW library: an SIMD Smith-Waterman C/C++ library for use in genomic applications.

PLoS One 2013 4;8(12):e82138. Epub 2013 Dec 4.

Department of Biology, Boston College, Chestnut Hill, Massachusetts, United States of America.

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http://journals.plos.org/plosone/article?id=10.1371/journal.pone.0082138PLOS
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3852983PMC
September 2014

Tangram: a comprehensive toolbox for mobile element insertion detection.

BMC Genomics 2014 Sep 16;15:795. Epub 2014 Sep 16.

Department of Human Genetics and USTAR Center for Genetic Discovery, University of Utah, Salt Lake City, Utah, USA.

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http://dx.doi.org/10.1186/1471-2164-15-795DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4180832PMC
September 2014

Whole genome profiling of spontaneous and chemically induced mutations in Toxoplasma gondii.

BMC Genomics 2014 May 10;15:354. Epub 2014 May 10.

Department of Biology, Boston College, Higgins Hall 355, 140 Commonwealth Avenue, Chestnut Hill, MA 02467, USA.

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http://dx.doi.org/10.1186/1471-2164-15-354DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4035079PMC
May 2014

Genetic basis for phenotypic differences between different Toxoplasma gondii type I strains.

BMC Genomics 2013 Jul 10;14:467. Epub 2013 Jul 10.

Biology Department, Massachusetts Institute of Technology, 77 Massachusetts Ave, building 68-270, Cambridge, MA 02139, USA.

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http://dx.doi.org/10.1186/1471-2164-14-467DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3710486PMC
July 2013

Variant discovery in targeted resequencing using whole genome amplified DNA.

BMC Genomics 2013 Jul 10;14:468. Epub 2013 Jul 10.

Department of Biology, Boston College, Chestnut Hill, MA, USA.

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http://dx.doi.org/10.1186/1471-2164-14-468DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3716764PMC
July 2013

Scotty: a web tool for designing RNA-Seq experiments to measure differential gene expression.

Bioinformatics 2013 Mar 12;29(5):656-7. Epub 2013 Jan 12.

Department of Biology, Boston College, Chestnut Hill, MA 02467, USA.

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http://dx.doi.org/10.1093/bioinformatics/btt015DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3582267PMC
March 2013

Targeted proteomic dissection of Toxoplasma cytoskeleton sub-compartments using MORN1.

Cytoskeleton (Hoboken) 2012 Dec 11;69(12):1069-85. Epub 2012 Oct 11.

Department of Biology, Boston College, Chestnut Hill, MA 02467, USA.

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http://doi.wiley.com/10.1002/cm.21077
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http://dx.doi.org/10.1002/cm.21077DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3566231PMC
December 2012

ART: a next-generation sequencing read simulator.

Bioinformatics 2012 Feb 23;28(4):593-4. Epub 2011 Dec 23.

Biostatistics Branch, National Institute of Environmental Health Sciences, Research Triangle Park, NC 27709, USA.

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http://dx.doi.org/10.1093/bioinformatics/btr708DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3278762PMC
February 2012

Expression divergence measured by transcriptome sequencing of four yeast species.

BMC Genomics 2011 Dec 29;12:635. Epub 2011 Dec 29.

Department of Biology, Boston College, 140 Commonwealth Avenue, Chestnut Hill, MA 02467-3961, USA.

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http://dx.doi.org/10.1186/1471-2164-12-635DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3296765PMC
December 2011

Demographic history and rare allele sharing among human populations.

Proc Natl Acad Sci U S A 2011 Jul 5;108(29):11983-8. Epub 2011 Jul 5.

Department of Genetics, Stanford University School of Medicine, Stanford, CA 94305-5120, USA.

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http://dx.doi.org/10.1073/pnas.1019276108DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3142009PMC
July 2011

BamTools: a C++ API and toolkit for analyzing and managing BAM files.

Bioinformatics 2011 Jun 14;27(12):1691-2. Epub 2011 Apr 14.

Department of Biology, Boston College, Chestnut Hill, MA 02467, USA.

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http://dx.doi.org/10.1093/bioinformatics/btr174DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3106182PMC
June 2011

Pyrobayes: an improved base caller for SNP discovery in pyrosequences.

Nat Methods 2008 Feb 13;5(2):179-81. Epub 2008 Jan 13.

Department of Biology, Boston College, 140 Commonwealth Avenue, Chestnut Hill, Massachusetts 02467, USA.

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http://lysine.umiacs.umd.edu/files/teaching/quinlan_et_al_su
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http://www.nature.com/doifinder/10.1038/nmeth.1172
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http://dx.doi.org/10.1038/nmeth.1172DOI Listing
February 2008

Whole-genome sequencing and variant discovery in C. elegans.

Nat Methods 2008 Feb 20;5(2):183-8. Epub 2008 Jan 20.

Washington University School of Medicine, Department of Genetics and Genome Sequencing Center, 4444 Forest Park Blvd., St. Louis, Missouri 63108, USA.

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http://dx.doi.org/10.1038/nmeth.1179DOI Listing
February 2008

Primer-site SNPs mask mutations.

Nat Methods 2007 Mar;4(3):192

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http://dx.doi.org/10.1038/nmeth0307-192DOI Listing
March 2007

Analysis of concordance of different haplotype block partitioning algorithms.

BMC Bioinformatics 2005 Dec 15;6:303. Epub 2005 Dec 15.

Human and Molecular Genetics Center, Medical College of Wisconsin, Milwaukee, USA.

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http://dx.doi.org/10.1186/1471-2105-6-303DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC1343594PMC
December 2005

The allele frequency spectrum in genome-wide human variation data reveals signals of differential demographic history in three large world populations.

Genetics 2004 Jan;166(1):351-72

National Center for Biotechnology Information, National Library of Medicine, National Institutes of Health, Bethesda, Maryland 20894, USA.

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http://www.ncbi.nlm.nih.gov/pmc/articles/PMC1470693PMC
January 2004

Computational SNP discovery in DNA sequence data.

Authors:
Gabor T Marth

Methods Mol Biol 2003 ;212:85-110

National Center for Biotechnology Information, National Library of Medicine, National Institutes of Health, Bethesda, MD, USA.

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http://dx.doi.org/10.1385/1-59259-327-5:085DOI Listing
May 2003