Main

My research focuses on development of DNA sequence analysis software. Over the past 15 years, my group has developed software to aid genome sequence completion (finishing), for single-nucleotide polymorphism discovery, for population genetic analysis of genomic variation data. We have developed software packages for base calling, read mapping, variant discovery, and data visualization in high-throughput, next-generation sequencing data. My current research is aimed at developing complete, automated pipelines for sequence processing, variant detection, and variant interpretation; adapt and extend our tools for cancer sequence analysis, and at developing informatics technologies to support population, medical, and personal genome sequencing of very large numbers of samples.

Research

Dr. Marth is Professor of Human Genetics and Director of the USTAR 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.

People

Principal Investigator

Gabor Marth, Ph.D.

Lab

Alistair Ward, Ph.D.

Director of Research and Science

Chase Miller, Ph.D.

Director of Research and Science

Matt Velinder

Lab Manager

Yi Qiao

Director of Research and Science

Dillon Lee, BS

Senior Software Developer

Tonya Di Sera, BS

Senior Web Software Developer

Andrew Farrell, Ph.D.

Research Associate

Xiaomeng Huang

Assoc. Director of Research and Science

Nancy Benson

Administrative Manager

Stephanie Georges

Software Developer

Aditya Ekawade

Software Developer

Anders Pitman

Software and Backend Developer

Matt Bailey

Postdoctoral Fellow

Will Richards

Software Developer

Preetida Bhetariya

Postdoctoral Research Associate

Szabolcs Tarapcsak

Postdoctoral Fellow

Chris Fahim

Project Lead

Corin Thummel

Software Developer

Contact

Address

Department of Human Genetics
University of Utah
Human Genetics
15 N 2030 E RM 7410
Salt Lake City, Utah 84112-5330

Phone

801-581-6158

Fax

801-581-7796

Publications

Links:

Publications in PubMed

References to Publications:

 

Journal Article

  1. 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.
  2. 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)?LID – 10.1038/s41436-019-0443-z [doi]. (Epub ahead of print) Genet Med.
  3. 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).
  4. 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.
  5. 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.
  6. 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.
  7. 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.
  8. 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.
  9. 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.
  10. 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.
  11. 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.
  12. 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.
  13. 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.
  14. 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.
  15. 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 Biology, 17(1), 111.
  16. 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.
  17. 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.
  18. 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.
  19. 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.
  20. Lee WP, Wu J, Marth GT (2015). Toolbox for mobile-element insertion detection on cancer genomes. Cancer Inform, 14(Suppl 1), 37-44.
  21. 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 Biology, 16, 13.
  22. Lee WP, Wu J, Marth GT (2014). Toolbox for mobile-element insertion detection on cancer genomes. Cancer Inform, 13(Suppl 4), 45-52.
  23. 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.
  24. 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 Biology, 15(8), 443.
  25. 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.
  26. 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 Biology, 15(6), R88.
  27. 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.
  28. 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.
  29. 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.
  30. 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.
  31. 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.
  32. 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.
  33. 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.
  34. 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.
  35. 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.
  36. 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.
  37. 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.
  38. 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.
  39. Huang W, Li L, Myers JR, Marth GT (2012). ART: a next-generation sequencing read simulator. Bioinformatics, 28(4), 593-4.
  40. 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.
  41. 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.
  42. 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.
  43. 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.
  44. 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.
  45. 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.
  46. 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.
  47. 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.
  48. 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.
  49. 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.
  50. 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.
  51. 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.
  52. 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.
  53. Huang W, Marth G (2008). EagleView: a genome assembly viewer for next-generation sequencing technologies. Genome Res, 18(9), 1538-43.
  54. 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.
  55. 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.
  56. Quinlan AR, Marth GT (2007). Primer-site SNPs mask mutations. Nat Methods, 4(3), 192.
  57. Indap AR, Marth GT, Struble CA, Tonellato P, Olivier M (2005). Analysis of concordance of different haplotype block partitioning algorithms. BMC Bioinformatics, 6, 303.
  58. 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.
  59. 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.
  60. 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.
  61. Marth GT (2003). Computational SNP discovery in DNA sequence data. Methods Mol Biol, 212, 85-110.
  62. 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.
  63. 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.
  64. 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.
  65. 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.
  66. Dear S, Durbin R, Hillier L, Marth G, Thierry-Mieg J, Mott R (1998). Sequence assembly with CAFTOOLS. Genome Res, 8(3), 260-7.

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.

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.
  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.