Gabor Marth

Gabor Marth, DSc

Languages spoken: Hungarian, English

Academic Information

Departments Primary - Human Genetics

Academic Office Information

gmarth@genetics.utah.edu

Lab

Dr. Marth is Professor of Human Genetics and Co-Director of the Utah 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.

Education History

Fellowship Washington University School of Medicine
 Postdoctoral Research Associate
Doctoral Training Washington University
 DSc
Postdoctoral Fellowship Hungarian Academy of Science
 Postdoctoral Fellow
Undergraduate Technical University of Budapest
 BS, MS

Selected Publications

Journal Article

  1. Black GS, Huang X, Qiao Y, Tarapcsak S, Rogers KA, Misra S, Byrd JC, Marth GT, Stephens DM, Woyach JA (2022). Subclonal evolution of CLL driver mutations is associated with relapse in ibrutinib and acalabrutinib treated patients. Blood, 140, 401-405. (Read full article)
  2. Nicholas TJ, Al-Sweel N, Farrell A, Mao R, Bayrak-Toydemir P, Miller CE, Bentley D, Palmquist R, Moore B, Hernandez EJ, Cormier MJ, Fredrickson E, Noble K, Rynearson S, Holt C, Karren MA, Bonkowsky JL, Tristani-Firouzi M, Yandell M, Marth G, Quinlan AR, Brunelli L, Toydemir RM, Shayota BJ, Carey JC, Boyden SE, Malone Jenkins S (2022). Comprehensive variant calling from whole-genome sequencing identifies a complex inversion that disrupts ZFPM2 in familial congenital diaphragmatic hernia. Mol Genet Genomic Med, 10(4), e1888. (Read full article)
  3. Ward A, Velinder M, Di Sera T, Ekawade A, Malone Jenkins S, Moore B, Mao R, Bayrak-Toydemir P, Marth G (2022). Clin.iobio: A Collaborative Diagnostic Workflow to Enable Team-Based Precision Genomics. J Pers Med, 12(1). (Read full article)
  4. Huang X, Qiao Y, Brady SW, Factor RE, Downs-Kelly E, Farrell A, McQuerry JA, Shrestha G, Jenkins D, Johnson WE, Cohen AL, Bild AH, Marth GT (2021). Novel temporal and spatial patterns of metastatic colonization from breast cancer rapid-autopsy tumor biopsies. Genome Med, 13(1), 170. (Read full article)
  5. Di Sera T, Velinder M, Ward A, Qiao Y, Georges S, Miller C, Pitman A, Richards W, Ekawade A, Viskochil D, Carey JC, Pace L, Bale J, Clardy SL, Andrews A, Botto L, Marth G (2021). Gene.iobio: an interactive web tool for versatile, clinically-driven variant interrogation and prioritization. Sci Rep, 11(1), 20307. (Read full article)
  6. Steely CJ, Russell KL, Feusier JE, Qiao Y, Tavtigian SV, Marth G, Jorde LB (2021). Mobile element insertions and associated structural variants in longitudinal breast cancer samples. Sci Rep, 11(1), 13020. (Read full article)
  7. Nicholas TJ, Cormier MJ, Huang X, Qiao Y, Marth GT, Quinlan AR (2021). OncoGEMINI: software for investigating tumor variants from multiple biopsies with integrated cancer annotations. Genome Med, 13(1), 46. (Read full article)
  8. Velinder M, Lee D, Marth G (2020). ped_draw: pedigree drawing with ease. BMC Bioinformatics, 21(1), 569. (Read full article)
  9. Bogenschutz EL, Fox ZD, Farrell A, Wynn J, Moore B, Yu L, Aspelund G, Marth G, Yandell M, Shen Y, Chung WK, Kardon G (2020). Deep whole-genome sequencing of multiple proband tissues and parental blood reveals the complex genetic etiology of congenital diaphragmatic hernias. HGG Adv, 1(1). (Read full article)
  10. Richter F, Morton SU, Kim SW, Kitaygorodsky A, Wasson LK, Chen KM, Zhou J, Qi H, Patel N, DePalma SR, Parfenov M, Homsy J, Gorham JM, Manheimer KB, Velinder M, Farrell A, Marth G, Schadt EE, Kaltman JR, Newburger JW, Giardini A, Goldmuntz E, Brueckner M, Kim R, Porter GA Jr, Bernstein D, Chung WK, Srivastava D, Tristani-Firouzi M, Troyanskaya OG, Dickel DE, Shen Y, Seidman JG, Seidman CE, Gelb BD (2020). Genomic analyses implicate noncoding de novo variants in congenital heart disease. Nat Genet, 52(8), 769-777. (Read full article)
  11. Pedersen BS, Bhetariya PJ, Brown J, Kravitz SN, Marth G, Jensen RL, Bronner MP, Underhill HR, Quinlan AR (2020). Somalier: rapid relatedness estimation for cancer and germline studies using efficient genome sketches. Genome Med, 12(1), 62. (Read full article)
  12. Ireland AS, Micinski AM, Kastner DW, Guo B, Wait SJ, Spainhower KB, Conley CC, Chen OS, Guthrie MR, Soltero D, Qiao Y, Huang X, Tarapcsk S, Devarakonda S, Chalishazar MD, Gertz J, Moser JC, Marth G, Puri S, Witt BL, Spike BT, Oliver TG (2020). MYC Drives Temporal Evolution of Small Cell Lung Cancer Subtypes by Reprogramming Neuroendocrine Fate. Cancer Cell, 38(1), 60-78.e12. (Read full article)
  13. Nix DA, Hellwig S, Conley C, Thomas A, Fuertes CL, Hamil CL, Bhetariya PJ, Garrido-Laguna I, Marth GT, Bronner MP, Underhill HR (2020). The stochastic nature of errors in next-generation sequencing of circulating cell-free DNA. PLoS One, 15(2), e0229063. (Read full article)
  14. Ekawade A, Velinder M, Ward A, DiSera T, Miller C, Qiao Y, Marth G (2019). Genepanel.iobio - an easy to use web tool for generating disease- and phenotype-associated gene lists. BMC Med Genomics, 12(1), 190. (Read full article)
  15. Wooderchak-Donahue WL, Akay G, Whitehead K, Briggs E, Stevenson DA, OFallon B, Velinder M, Farrell A, Shen W, Bedoukian E, Skrabann CM, Antaya RJ, Henderson K, Pollak J, Treat J, Day R, Jacher JE, Hannibal M, Bontempo K, Marth G, Bayrak-Toydemir P, McDonald J (2019). Phenotype of CM-AVM2 caused by variants in EPHB4: how much overlap with hereditary hemorrhagic telangiectasia (HHT)? Genet Med, 21(9), 2007-2014. (Read full article)
  16. Chaisson MJP, Sanders AD, Zhao X, Malhotra A, Porubsky D, Rausch T, Gardner EJ, Rodriguez OL, Guo L, Collins RL, Fan X, Wen J, Handsaker RE, Fairley S, Kronenberg ZN, Kong X, Hormozdiari F, Lee D, Wenger AM, Hastie AR, Antaki D, Anantharaman T, Audano PA, Brand H, Cantsilieris S, Cao H, Cerveira E, Chen C, Chen X, Chin CS, Chong Z, Chuang NT, Lambert CC, Church DM, Clarke L, Farrell A, Flores J, Galeev T, Gorkin DU, Gujral M, Guryev V, Heaton WH, Korlach J, Kumar S, Kwon JY, Lam ET, Lee JE, Lee J, Lee WP, Lee SP, Li S, Marks P, Viaud-Martinez K, Meiers S, Munson KM, Navarro FCP, Nelson BJ, Nodzak C, Noor A, Kyriazopoulou-Panagiotopoulou S, Pang AWC, Qiu Y, Rosanio G, Ryan M, Sttz A, Spierings DCJ, Ward A, Welch AE, Xiao M, Xu W, Zhang C, Zhu Q, Zheng-Bradley X, Lowy E, Yakneen S, McCarroll S, Jun G, Ding L, Koh CL, Ren B, Flicek P, Chen K, Gerstein MB, Kwok PY, Lansdorp PM, Marth GT, Sebat J, Shi X, Bashir A, Ye K, Devine SE, Talkowski ME, Mills RE, Marschall T, Korbel JO, Eichler EE, Lee C (2019). Multi-platform discovery of haplotype-resolved structural variation in human genomes. Nat Commun, 10(1), 1784. (Read full article)
  17. An JY, Lin K, Zhu L, Werling DM, Dong S, Brand H, Wang HZ, Zhao X, Schwartz GB, Collins RL, Currall BB, Dastmalchi C, Dea J, Duhn C, Gilson MC, Klei L, Liang L, Markenscoff-Papadimitriou E, Pochareddy S, Ahituv N, Buxbaum JD, Coon H, Daly MJ, Kim YS, Marth GT, Neale BM, Quinlan AR, Rubenstein JL, Sestan N, State MW, Willsey AJ, Talkowski ME, Devlin B, Roeder K, Sanders SJ (2018). Genome-wide de novo risk score implicates promoter variation in autism spectrum disorder. Science, 362(6420). (Read full article)
  18. Wooderchak-Donahue WL, McDonald J, Farrell A, Akay G, Velinder M, Johnson P, VanSant-Webb C, Margraf R, Briggs E, Whitehead KJ, Thomson J, Lin AE, Pyeritz RE, Marth G, Bayrak-Toydemir P (2018). Genome sequencing reveals a deep intronic splicing ACVRL1 mutation hotspot in Hereditary Haemorrhagic Telangiectasia. J Med Genet, 55(12), 824-830. (Read full article)
  19. Than H, Qiao Y, Huang X, Yan D, Khorashad JS, Pomicter AD, Kovacsovics TJ, Marth GT, OHare T, Deininger MW (2018). Ongoing clonal evolution in chronic myelomonocytic leukemia on hypomethylating agents: a computational perspective. Leukemia, 32(9), 2049-2054. (Read full article)
  20. 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 (2018). Whole-genome analysis for effective clinical diagnosis and gene discovery in early infantile epileptic encephalopathy. NPJ Genom Med, 3, 22. (Read full article)
  21. Hellwig S, Nix DA, Gligorich KM, OShea JM, Thomas A, Fuertes CL, Bhetariya PJ, Marth GT, Bronner MP, Underhill HR (2018). Automated size selection for short cell-free DNA fragments enriches for circulating tumor DNA and improves error correction during next generation sequencing. PLoS One, 13(7), e0197333. (Read full article)
  22. Werling DM, Brand H, An JY, Stone MR, Zhu L, Glessner JT, Collins RL, Dong S, Layer RM, Markenscoff-Papadimitriou E, Farrell A, Schwartz GB, Wang HZ, Currall BB, Zhao X, Dea J, Duhn C, Erdman CA, Gilson MC, Yadav R, Handsaker RE, Kashin S, Klei L, Mandell JD, Nowakowski TJ, Liu Y, Pochareddy S, Smith L, Walker MF, Waterman MJ, He X, Kriegstein AR, Rubenstein JL, Sestan N, McCarroll SA, Neale BM, Coon H, Willsey AJ, Buxbaum JD, Daly MJ, State MW, Quinlan AR, Marth GT, Roeder K, Devlin B, Talkowski ME, Sanders SJ (2018). An analytical framework for whole-genome sequence association studies and its implications for autism spectrum disorder. Nat Genet, 50(5), 727-736. (Read full article)
  23. Brady SW, McQuerry JA, Qiao Y, 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 (2018). Publisher Correction: Combating subclonal evolution of resistant cancer phenotypes. Nat Commun, 9(1), 572. (Read full article)
  24. Layer RM, Pedersen BS, DiSera T, Marth GT, Gertz J, Quinlan AR (2018). GIGGLE: a search engine for large-scale integrated genome analysis. Nat Methods, 15(2), 123-126. (Read full article)
  25. Ward A, Karren MA, Di Sera T, Miller C, Velinder M, Qiao Y, Filloux FM, Ostrander B, Butterfield R, Bonkowsky JL, Dere W, Marth GT (2017). Rapid clinical diagnostic variant investigation of genomic patient sequencing data with iobio web tools. J Clin Transl Sci, 1(6), 381-386. (Read full article)
  26. Brady SW, McQuerry JA, Qiao Y, 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 (2017). Combating subclonal evolution of resistant cancer phenotypes. Nat Commun, 8(1), 1231. (Read full article)
  27. Lubin IM, Aziz N, Babb LJ, Ballinger D, Bisht H, Church DM, Cordes S, Eilbeck K, Hyland F, Kalman L, Landrum M, Lockhart ER, Maglott D, Marth G, Pfeifer JD, Rehm HL, Roy S, Tezak Z, Truty R, Ullman-Cullere M, Voelkerding KV, Worthey EA, Zaranek AW, Zook JM (2017). Principles and Recommendations for Standardizing the Use of the Next-Generation Sequencing Variant File in Clinical Settings. J Mol Diagn, 19(3), 417-426. (Read full article)
  28. Runge CL, Indap A, Zhou Y, Kent JW Jr, King E, Erbe CB, Cole R, Littrell J, Merath K, James R, Rschendorf F, Kerschner JE, Marth G, Hbner N, Gring HH, Friedland DR, Kwok WM, Olivier M (2016). Association of TMTC2 With Human Nonsyndromic Sensorineural Hearing Loss. JAMA Otolaryngol Head Neck Surg, 142(9), 866-72. (Read full article)
  29. Flygare S, Simmon K, Miller C, Qiao Y, Kennedy B, Di Sera T, Graf EH, Tardif KD, Kapusta A, Rynearson S, Stockmann C, Queen K, Tong S, Voelkerding KV, Blaschke A, Byington CL, Jain S, Pavia A, Ampofo K, Eilbeck K, Marth G, Yandell M, Schlaberg R (2016). Taxonomer: an interactive metagenomics analysis portal for universal pathogen detection and host mRNA expression profiling. Genome Biol, 17(1), 111. (Read full article)
  30. Sudmant PH, Rausch T, Gardner EJ, Handsaker RE, Abyzov A, Huddleston J, Zhang Y, Ye K, Jun G, Fritz MH, Konkel MK, Malhotra A, Sttz AM, Shi X, Casale FP, Chen J, Hormozdiari F, Dayama G, Chen K, Malig M, Chaisson MJP, Walter K, Meiers S, Kashin S, Garrison E, Auton A, Lam HYK, Mu XJ, Alkan C, Antaki D, Bae T, Cerveira E, Chines P, Chong Z, Clarke L, Dal E, Ding L, Emery S, Fan X, Gujral M, Kahveci F, Kidd JM, Kong Y, Lameijer EW, McCarthy S, Flicek P, Gibbs RA, Marth G, Mason CE, Menelaou A, Muzny DM, Nelson BJ, Noor A, Parrish NF, Pendleton M, Quitadamo A, Raeder B, Schadt EE, Romanovitch M, Schlattl A, Sebra R, Shabalin AA, Untergasser A, Walker JA, Wang M, Yu F, Zhang C, Zhang J, Zheng-Bradley X, Zhou W, Zichner T, Sebat J, Batzer MA, McCarroll SA, 1000 Genomes Project Consortium, Mills RE, Gerstein MB, Bashir A, Stegle O, Devine SE, Lee C, Eichler EE, Korbel JO (2015). An integrated map of structural variation in 2,504 human genomes. Nature, 526(7571), 75-81. (Read full article)
  31. Chiang C, Layer RM, Faust GG, Lindberg MR, Rose DB, Garrison EP, Marth GT, Quinlan AR, Hall IM (2015). SpeedSeq: ultra-fast personal genome analysis and interpretation. Nat Methods, 12(10), 966-8. (Read full article)
  32. Konkel MK, Walker JA, Hotard AB, Ranck MC, Fontenot CC, Storer J, Stewart C, Marth GT, 1000 Genomes Consortium, Batzer MA (2015). Sequence Analysis and Characterization of Active Human Alu Subfamilies Based on the 1000 Genomes Pilot Project. Genome Biol Evol, 7(9), 2608-22. (Read full article)
  33. Challis D, Antunes L, Garrison E, Banks E, Evani US, Muzny D, Poplin R, Gibbs RA, Marth G, Yu F (2015). The distribution and mutagenesis of short coding INDELs from 1,128 whole exomes. BMC Genomics, 16, 143. (Read full article)
  34. Lee WP, Wu J, Marth GT (2015). Toolbox for mobile-element insertion detection on cancer genomes. Cancer Inform, 14(Suppl 1), 37-44. (Read full article)
  35. 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 (2015). Extending reference assembly models. Genome Biol, 16, 13. (Read full article)
  36. Lee WP, Wu J, Marth GT (2014). Toolbox for mobile-element insertion detection on cancer genomes. Cancer Inform, 13(Suppl 4), 45-52. (Read full article)
  37. Wu J, Lee WP, Ward A, Walker JA, Konkel MK, Batzer MA, Marth GT (2014). Tangram: a comprehensive toolbox for mobile element insertion detection. BMC Genomics, 15, 795. (Read full article)
  38. Qiao Y, Quinlan AR, Jazaeri AA, Verhaak RG, Wheeler DA, Marth GT (2014). SubcloneSeeker: a computational framework for reconstructing tumor clone structure for cancer variant interpretation and prioritization. Genome Biol, 15(8), 443. (Read full article)
  39. 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 (2014). Novel somatic and germline mutations in intracranial germ cell tumours. Nature, 511(7508), 241-5. (Read full article)
  40. 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 (2014). Human genomic regions with exceptionally high levels of population differentiation identified from 911 whole-genome sequences. Genome Biol, 15(6), R88. (Read full article)
  41. Brown KM, Suvorova E, Farrell A, McLain A, Dittmar A, Wiley GB, Marth G, Gaffney PM, Gubbels MJ, White M, Blader IJ (2014). Forward genetic screening identifies a small molecule that blocks Toxoplasma gondii growth by inhibiting both host- and parasite-encoded kinases. PLoS Pathog, 10(6), e1004180. (Read full article)
  42. Farrell A, Coleman BI, Benenati B, Brown KM, Blader IJ, Marth GT, Gubbels MJ (2014). Whole genome profiling of spontaneous and chemically induced mutations in Toxoplasma gondii. BMC Genomics, 15, 354. (Read full article)
  43. Lee WP, Stromberg MP, Ward A, Stewart C, Garrison EP, Marth GT (2014). MOSAIK: a hash-based algorithm for accurate next-generation sequencing short-read mapping. PLoS One, 9(3), e90581. (Read full article)
  44. Zhao M, Lee WP, Garrison EP, Marth GT (2013). SSW library: an SIMD Smith-Waterman C/C++ library for use in genomic applications. PLoS One, 8(12), e82138. (Read full article)
  45. Khurana E, Fu Y, Colonna V, Mu XJ, Kang HM, Lappalainen T, Sboner A, Lochovsky L, Chen J, Harmanci A, Das J, Abyzov A, Balasubramanian S, Beal K, Chakravarty D, Challis D, Chen Y, Clarke D, Clarke L, Cunningham F, Evani US, Flicek P, Fragoza R, Garrison E, Gibbs R, Gm ZH, Herrero J, Kitabayashi N, Kong Y, Lage K, Liluashvili V, Lipkin SM, MacArthur DG, Marth G, Muzny D, Pers TH, Ritchie GRS, Rosenfeld JA, Sisu C, Wei X, Wilson M, Xue Y, Yu F, 1000 Genomes Project Consortium, Dermitzakis ET, Yu H, Rubin MA, Tyler-Smith C, Gerstein M (2013). Integrative annotation of variants from 1092 humans: application to cancer genomics. Science, 342(6154), 1235587. (Read full article)
  46. Indap AR, Cole R, Runge CL, Marth GT, Olivier M (2013). Variant discovery in targeted resequencing using whole genome amplified DNA. BMC Genomics, 14, 468. (Read full article)
  47. Yang N, Farrell A, Niedelman W, Melo M, Lu D, Julien L, Marth GT, Gubbels MJ, Saeij JP (2013). Genetic basis for phenotypic differences between different Toxoplasma gondii type I strains. BMC Genomics, 14, 467. (Read full article)
  48. Busby MA, Stewart C, Miller CA, Grzeda KR, Marth GT (2013). Scotty: a web tool for designing RNA-Seq experiments to measure differential gene expression. Bioinformatics, 29(5), 656-7. (Read full article)
  49. Miller CA, Anthony J, Meyer MM, Marth G (2013). Scribl: an HTML5 Canvas-based graphics library for visualizing genomic data over the web. Bioinformatics, 29(3), 381-3. (Read full article)
  50. Lorestani A, Ivey FD, Thirugnanam S, Busby MA, Marth GT, Cheeseman IM, Gubbels MJ (2012). Targeted proteomic dissection of Toxoplasma cytoskeleton sub-compartments using MORN1. Cytoskeleton (Hoboken), 69(12), 1069-85. (Read full article)
  51. Wu J, Grzeda KR, Stewart C, Grubert F, Urban AE, Snyder MP, Marth GT (2012). Copy Number Variation detection from 1000 Genomes Project exon capture sequencing data. BMC Bioinformatics, 13, 305. (Read full article)
  52. 1000 Genomes Project Consortium, Abecasis GR, Auton A, Brooks LD, DePristo MA, Durbin RM, Handsaker RE, Kang HM, Marth GT, McVean GA (2012). An integrated map of genetic variation from 1,092 human genomes. Nature, 491(7422), 56-65. (Read full article)
  53. Huang W, Li L, Myers JR, Marth GT (2012). ART: a next-generation sequencing read simulator. Bioinformatics, 28(4), 593-4. (Read full article)
  54. Farrell A, Thirugnanam S, Lorestani A, Dvorin JD, Eidell KP, Ferguson DJ, Anderson-White BR, Duraisingh MT, Marth GT, Gubbels MJ (2012). A DOC2 protein identified by mutational profiling is essential for apicomplexan parasite exocytosis. Science, 335(6065), 218-21. (Read full article)
  55. Busby MA, Gray JM, Costa AM, Stewart C, Stromberg MP, Barnett D, Chuang JH, Springer M, Marth GT (2011). Expression divergence measured by transcriptome sequencing of four yeast species. BMC Genomics, 12, 635. (Read full article)
  56. 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, 1000 Genomes Project (2011). The functional spectrum of low-frequency coding variation. Genome Biol, 12(9), R84. (Read full article)
  57. Stewart C, Kural D, Strmberg MP, Walker JA, Konkel MK, Sttz AM, Urban AE, Grubert F, Lam HY, Lee WP, Busby M, Indap AR, Garrison E, Huff C, Xing J, Snyder MP, Jorde LB, Batzer MA, Korbel JO, Marth GT, 1000 Genomes Project (2011). A comprehensive map of mobile element insertion polymorphisms in humans. PLoS Genet, 7(8), e1002236. (Read full article)
  58. 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 (2011). The variant call format and VCFtools. Bioinformatics, 27(15), 2156-8. (Read full article)
  59. Gravel S, Henn BM, Gutenkunst RN, Indap AR, Marth GT, Clark AG, Yu F, Gibbs RA, 1000 Genomes Project, Bustamante CD (2011). Demographic history and rare allele sharing among human populations. Proc Natl Acad Sci U S A, 108(29), 11983-8. (Read full article)
  60. Barnett DW, Garrison EK, Quinlan AR, Strmberg MP, Marth GT (2011). BamTools: a C++ API and toolkit for analyzing and managing BAM files. Bioinformatics, 27(12), 1691-2. (Read full article)
  61. Mills RE, Walter K, Stewart C, Handsaker RE, Chen K, Alkan C, Abyzov A, Yoon SC, Ye K, Cheetham RK, Chinwalla A, Conrad DF, Fu Y, Grubert F, Hajirasouliha I, Hormozdiari F, Iakoucheva LM, Iqbal Z, Kang S, Kidd JM, Konkel MK, Korn J, Khurana E, Kural D, Lam HY, Leng J, Li R, Li Y, Lin CY, Luo R, Mu XJ, Nemesh J, Peckham HE, Rausch T, Scally A, Shi X, Stromberg MP, Sttz AM, Urban AE, Walker JA, Wu J, Zhang Y, Zhang ZD, Batzer MA, Ding L, Marth GT, McVean G, Sebat J, Snyder M, Wang J, Ye K, Eichler EE, Gerstein MB, Hurles ME, Lee C, McCarroll SA, Korbel JO, 1000 Genomes Project (2011). Mapping copy number variation by population-scale genome sequencing. Nature, 470(7332), 59-65. (Read full article)
  62. 1000 Genomes Project Consortium, Abecasis GR, Altshuler D, Auton A, Brooks LD, Durbin RM, Gibbs RA, Hurles ME, McVean GA (2010). A map of human genome variation from population scale sequencing. Nature, 467(7319), 1061-73.
  63. Reese MG, Moore B, Batchelor C, Salas F, Cunningham F, Marth GT, Stein L, Flicek P, Yandell M, Eilbeck K (2010). A standard variation file format for human genome sequences. Genome Biol, 11(8), R88. (Read full article)
  64. Sackton TB, Kulathinal RJ, Bergman CM, Quinlan AR, Dopman EB, Carneiro M, Marth GT, Hartl DL, Clark AG (2009). Population genomic inferences from sparse high-throughput sequencing of two populations of Drosophila melanogaster. Genome Biol Evol, 1, 449-65. (Read full article)
  65. Li H, Handsaker B, Wysoker A, Fennell T, Ruan J, Homer N, Marth G, Abecasis G, Durbin R, 1000 Genome Project Data Processing Subgroup (2009). The Sequence Alignment/Map format and SAMtools. Bioinformatics, 25(16), 2078-9. (Read full article)
  66. Smith DR, Quinlan AR, Peckham HE, Makowsky K, Tao W, Woolf B, Shen L, Donahue WF, Tusneem N, Stromberg MP, Stewart DA, Zhang L, Ranade SS, Warner JB, Lee CC, Coleman BE, Zhang Z, McLaughlin SF, Malek JA, Sorenson JM, Blanchard AP, Chapman J, Hillman D, Chen F, Rokhsar DS, McKernan KJ, Jeffries TW, Marth GT, Richardson PM (2008). Rapid whole-genome mutational profiling using next-generation sequencing technologies. Genome Res, 18(10), 1638-42. (Read full article)
  67. Huang W, Marth G (2008). EagleView: a genome assembly viewer for next-generation sequencing technologies. Genome Res, 18(9), 1538-43. (Read full article)
  68. Hillier LW, Marth GT, Quinlan AR, Dooling D, Fewell G, Barnett D, Fox P, Glasscock JI, Hickenbotham M, Huang W, Magrini VJ, Richt RJ, Sander SN, Stewart DA, Stromberg M, Tsung EF, Wylie T, Schedl T, Wilson RK, Mardis ER (2008). Whole-genome sequencing and variant discovery in C. elegans. Nat Methods, 5(2), 183-8. (Read full article)
  69. Quinlan AR, Stewart DA, Stromberg MP, Marth GT (2008). Pyrobayes: an improved base caller for SNP discovery in pyrosequences. Nat Methods, 5(2), 179-81. (Read full article)
  70. Indap AR, Marth GT, Struble CA, Tonellato P, Olivier M (2005). Analysis of concordance of different haplotype block partitioning algorithms. BMC Bioinformatics, 6, 303. (Read full article)
  71. Marth GT, Czabarka E, Murvai J, Sherry ST (2004). The allele frequency spectrum in genome-wide human variation data reveals signals of differential demographic history in three large world populations. Genetics, 166(1), 351-72. (Read full article)
  72. Ghebranious N, Vaske D, Yu A, Zhao C, Marth G, Weber JL (2003). STRP screening sets for the human genome at 5 cM density. BMC Genomics, 4(1), 6. (Read full article)
  73. 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 (2003). Sequence variations in the public human genome data reflect a bottlenecked population history. Proc Natl Acad Sci U S A, 100(1), 376-81. (Read full article)
  74. Marth GT (2003). Computational SNP discovery in DNA sequence data. Methods Mol Biol, 212, 85-110. (Read full article)
  75. Weber JL, David D, Heil J, Fan Y, Zhao C, Marth G (2002). Human diallelic insertion/deletion polymorphisms. Am J Hum Genet, 71(4), 854-62. (Read full article)
  76. Marth G, Yeh R, Minton M, Donaldson R, Li Q, Duan S, Davenport R, Miller RD, Kwok PY (2001). Single-nucleotide polymorphisms in the public domain: how useful are they? Nat Genet, 27(4), 371-2. (Read full article)
  77. Sachidanandam R, Weissman D, Schmidt SC, Kakol JM, Stein LD, Marth G, Sherry S, Mullikin JC, Mortimore BJ, Willey DL, Hunt SE, Cole CG, Coggill PC, Rice CM, Ning Z, Rogers J, Bentley DR, Kwok PY, Mardis ER, Yeh RT, Schultz B, Cook L, Davenport R, Dante M, Fulton L, Hillier L, Waterston RH, McPherson JD, Gilman B, Schaffner S, Van Etten WJ, Reich D, Higgins J, Daly MJ, Blumenstiel B, Baldwin J, Stange-Thomann N, Zody MC, Linton L, Lander ES, Altshuler D (2001). A map of human genome sequence variation containing 1.42 million single nucleotide polymorphisms. Nature, 409(6822), 928-33. (Read full article)
  78. Marth GT, Korf I, Yandell MD, Yeh RT, Gu Z, Zakeri H, Stitziel NO, Hillier L, Kwok PY, Gish WR (1999). A general approach to single-nucleotide polymorphism discovery. Nat Genet, 23(4), 452-6. (Read full article)
  79. Dear S, Durbin R, Hillier L, Marth G, Thierry-Mieg J, Mott R (1998). Sequence assembly with CAFTOOLS. Genome Res, 8(3), 260-7. (Read full article)

Book Chapter

  1. Vieux E, Marth GT, Kwok PY (2003). SNP Discovery in DNA Sequence Data. In Barnes M, Gray IC (Eds.), Bioinformatics for Geneticists (pp. 203-15). Wiley and Sons.

Case Report

  1. Guillen KP, Fujita M, Butterfield AJ, Scherer SD, Bailey MH, Chu Z, DeRose YS, Zhao L, Cortes-Sanchez E, Yang CH, Toner J, Wang G, Qiao Y, Huang X, Greenland JA, Vahrenkamp JM, Lum DH, Factor RE, Nelson EW, Matsen CB, Poretta JM, Rosenthal R, Beck AC, Buys SS, Vaklavas C, Ward JH, Jensen RL, Jones KB, Li Z, Oesterreich S, Dobrolecki LE, Pathi SS, Woo XY, Berrett KC, Wadsworth ME, Chuang JH, Lewis MT, Marth GT, Gertz J, Varley KE, Welm BE, Welm AL (2022). A human breast cancer-derived xenograft and organoid platform for drug discovery and precision oncology. Nat Cancer, 3(2), 232-250. (Read full article)

Letter

  1. Khorashad JS, Tantravahi SK, Yan D, Mason CC, Qiao Y, Eiring AM, Gligorich K, Hein T, Pomicter AD, Reid AG, Kelley TW, Marth GT, OHare T, Deininger MW (2016). Rapid conversion of chronic myeloid leukemia to chronic myelomonocytic leukemia in a patient on imatinib therapy. [Letter to the editor]. Leukemia, 30(11), 2275-2279. (Read full article)
  2. Miller CA, Qiao Y, DiSera T, DAstous B, Marth GT (2014). bam.iobio: a web-based, real-time, sequence alignment file inspector. [Letter to the editor]. Nat Methods, 11(12), 1189. (Read full article)
  3. Quinlan AR, Marth GT (2007). Primer-site SNPs mask mutations. [Letter to the editor]. Nat Methods, 4(3), 192. (Read full article)