Gabor Marth, D.Sc.

Dr. Marth is Professor of Human Genetics and Director of the UCGD Center for Genetic Discovery at University of Utah Health Sciences Center. He is an internationally recognized expert in the analysis of DNA sequence variations. 

Dr. Marth and his group played a key role in the development of methods and software that support the use of high-throughput sequencing technologies to study DNA variation on large scale, and led the design of standardized formats (SAM/BAM, VCF) that have now been widely adopted by the genomics community as the common currency for storing genomic sequencing data. Dr. Marth and his laboratory are currently at the forefront of developing computational algorithms for precision oncology: tracking cancer patients’ tumors as they progress across chemo-resistance, relapse, and metastasis; and using advanced genomic, tumor modeling, and drug screening approaches for personalized cancer treatment. As part of NHGRI’s Undiagnosed Disease Network, Dr. Marth and his team develop computational algorithms for discovering the genetic causes of common and rare diseases, and a comprehensive web tool system for rare disease diagnostics. He serves as Principal Investigator on academic and small-business research projects funded by the National Human Genome Research Institute, the National Cancer Institute, the National Center for Advancing Translational Sciences, the Simons Foundation, the Margolis Family Foundation, and the Utah Science Technology and Research Initiative. Dr. Marth is leading the Genomics of Advanced and Complex Cancers Initiative, and organizes the Single Cell Genomics working group at the University of Utah and Huntsman Cancer Institute. He serves on the Scientific Advisory Boards of the Ontario Institute of Cancer Research Adaptive Oncology Program, Canada’s Genomic Enterprise, and the Galaxy Project. Dr. Marth is co-founder and Chief Scientific Officer of Frameshift Genomics, Inc., a technology startup company building web tools for genomic data management and visual analytics.

A general approach to single-nucleotide polymorphism discovery. Marth GT, Korf I, Yandell MD, Yeh RT, Gu Z, Zakeri H, et al. Nature Genetics 1999;23:452-456. PMID: 10581034

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; the 1000 Genomes Project. Genome Biol. 2011 Sep 14;12(9). PMID: 21917140 PMCID: PMC3308047

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.  PMID: 23128226 PMCID: PMC3498066

Whole-genome analysis for effective clinical diagnosis and gene discovery in early infantile epileptic encephalopathy. Ostrander BEP, Butterfield RJ, Pedersen BS, Farrell AJ, Layer RM, Ward A, Miller C, DiSera T, Filloux FM, Candee MS, Newcomb T, Bonkowsky JL, Marth GT, Quinlan AR. NPJ Genomic Medicine. 2018 Aug 13;3:22. PMID: 30109124 PMCID: PMC6089881

The Sequence Alignment/Map format and SAMtools. Li H, Handsaker B, Wysoker A, Fennell T, Ruan J, Homer N, Marth G, Abecasis G, Durbin R; 1000 Genome Project Data Processing Subgroup. Bioinformatics. 2009 Aug 15;25(16):2078-9. Epub 2009 Jun 8. PMID: 19505943

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. Epub 2011 Jun 7. PMID: 21653522 PMCID: PMC3137218

A standard variation file format for human genome sequences. Reese MG, Moore B, Batchelor C, Salas F, Cunningham F, Marth GT, Stein L, Flicek P, Yandell M, Eilbeck K. Genome Biol. 2010;11(8). PMID: 20796305 PMCID: PMC2945790

Extending reference assembly models. Church DM, Schneider VA, Steinberg KM, Schatz MC, Quinlan AR, Chin CS, Kitts PA, Aken B, Marth GT, Hoffman MM, Herrero J, Mendoza ML, Durbin R, Flicek P. Genome Biol. 2015 Jan 24;16:13. PMID: 25651527

Sequence variations in the public human genome data reflect a bottlenecked population history. Marth G, Schuler G, Yeh R, Davenport R, Agarwala R, Church D, Wheelan S, Baker J, Ward M, Kholodov M, Phan L, Czabarka E, Murvai J, Cutler D, Wooding S, Rogers A, Chakravarti A, Harpending HC, Kwok PY, Sherry ST. Proc Natl Acad Sci U S A. 2003 Jan 7;100(1):376-81. Epub 2002 Dec 26. PMID: 12502794 PMCID: PMC140982

The allele frequency spectrum in genome-wide human variation data reveals signals of differential demographic history in three large world populations. Marth GT, Czabarka E, Murvai J, Sherry ST. Genetics. 2004 Jan;166(1):351-72. PMID: 15020430 PMCID: PMC1470693

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. Epub 2011 Jul 5. PMC3142009

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). PMID: 24980144 PMCID: PMC4197830

Novel somatic and germline mutations in intracranial germ cell tumours. Wang L, Yamaguchi S, Burstein MD, Terashima K, Chang K, Ng HK, Nakamura H, He Z, Doddapaneni H, Lewis L, Wang M, Suzuki T, Nishikawa R, Natsume A, Terasaka S, Dauser R, Whitehead W, Adekunle A, Sun J, Qiao Y, Marth G, Muzny DM, Gibbs RA, Leal SM, Wheeler DA, Lau CC. Nature. 2014 Jul 10;511(7508):241-5. PMID: 24896186

SubcloneSeeker: a computational framework for reconstructing tumor clone structure for cancer variant interpretation and prioritization. Qiao Y, Quinlan AR, Jazaeri AA, Verhaak R, Wheeler DA, Marth GT. Genome Biol. 2014 Aug 26;15(8):443. PMID: 25160522 PMCID: PMC4180956

Combating subclonal evolution of resistant cancer phenotypes. Brady SW, McQuerry, Qiao, Piccolo SR, Shrestha G, Jenkins DF, Layer RM, Pedersen BS, Miller RH, Esch A, Selitsky SR, Parker JS, Anderson LA, Dalley BK, Factor RE, Reddy CB, Boltax JP, Li DY, Moos PJ, Gray JW, Heiser LM, Buys SS, Cohen AL, Johnson WE, Quinlan AR, Marth G, Werner TL, Bild AH. Nature Communications. 2017 Nov 1;8(1):1231. doi: 10.1038/s41467-017-01174-3. PMID: 29093439

Ongoing clonal evolution in chronic myelomonocytic leukemia on hypomethylating agents: a computational perspective. Than H, Qiao Y, Huang X, Yan D, Khorashad JS, Pomicter AD, Kovacsovics TJ, Marth GT, O'Hare T, Deininger MW. Leukemia. 2018 Sep;32(9):2049-2054. PMID: 29588547 PMCID: PMC6128729

bam.iobio: a web-based, real-time, sequence alignment file inspector. Miller CA, Qiao Y, DiSera T, D'Astous B, Marth GT. Nature Methods. 2014 Dec;11(12):1189. PMID: 25423016 PMCID: PMC4282680

Rapid clinical diagnostic variant investigation of genomic patient sequencing data with iobio web tools. Alistair Ward, Mary A. Karren, Tonya Di Sera, Chase Miller, Matt Velinder, Yi Qiao, Francis M. Filloux, Betsy Ostrander, Russell Butterfield, Joshua L. Bonkowsky, Willard Dere, and Gabor T. Marth. Journal of Clinical and Translational Science. 2017 Dec;1(6):381-386. PMID: 29707261 PMCID: PMC5915807

Genepanel.iobio - an easy to use web tool for generating disease- and phenotype-associated gene lists. Ekawade A, Velinder M, Ward A, DiSera T, Miller C, Qiao Y, Marth G. BMC Med Genomics. 2019 Dec 11;12(1):190. doi: 10.1186/s12920-019-0641-1. PMID: 31829207 PMCID: PMC6907284

gene.iobio: an interactive web tool for versatile, clinically-driven variant interrogation and prioritization. Tonya Di Sera, Matt Velinder, Alistair Ward, Yi Qiao, Stephanie Georges, Chase Miller, Anders Pitman, Will Richards, Aditya Ekawade, David Viskochil, John C Carey, Laura Pace, Jim Bale, Stacey L Clardy, Ashley Andrews, Lorenzo Botto, Gabor Marth