Gabor Marth

Professor of Human Genetics

Gabor Marth

B.S., M.S. Technical University of Budapest

D.Sc. Washington University

Research

References

gmarth@genetics.utah.edu

Gabor Marth's Lab Page

Garbor Marth's USTAR Center

Gabor Marth's PubMed Literature Search

 

Molecular Biology Program

DNA sequence analysis software

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.

References

  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. Preetida J Bhetariya, David Nix, Sabine Hellwig, Gabor Marth, Mary Bronner, Hunter Underhill. Larger family sizes improve stochastic error correction during untargeted searches of very-low frequency variant alleles in circulating cell-free DNA (ccfDNA). (2018). American Association for Cancer Research. Vol. 78, Issue 13 Supplement, Page 4590.

  12. Xiaomeng Huang, Yi Qiao, Samuel W Brady, Adam Cohen, Andrea H Bild, Gabor T Marth. Temporal and spatial dynamics of metastatic colonization revealed by 26 rapid-autopsy tumor biopsies from a TNBC patient. (2018). American Association for Cancer Research. Vol. 78, Issue 13 Supplement, Pages 2195-2195.

  13. Dillon Lee, Yi Qiao, Gabor Marth. A graph remapping framework for in silico adjudication of SNVs, INDELs, and structural variants from genetic sequencing data. (2018). American Association for Cancer Research. Vol. 78, 13 Supplement, Page 3272.

  14. Yi Qiao, Xiaomeng Huang, Dillon Lee, Andrew Farrell, Thomas Nicholas, Brent Pederson, Aaron Quinlan, Gabor Marth. Utah somatic variant calling pipeline featuring multi-sample joint calling, variant-graph based accurate allele frequency estimation and subclone analysis. (2018), American Association for Cancer Research. Vol 78, Issue 13 Supplement, Page 3280.

  15. Katrin P Guillen, Sandra D Scherer, Yi Qiao, Satya S Pathi, James M Graham, Maihi Fujita, Yoko S DeRose, Jason Gertz, Gabor T Marth, Katherine E Varley, Alana L Welm, Bryan E Welm. Abstract LB-038: Predicting breast cancer therapy response using a patient-derived xenograft organoid screening platform. (2018).  Cancer Research. American Association for Cancer Research.  Vol. 78, Issue 13 Supplement, Pages LB-038-LB-038.

  16. Hein Than, Yi Qiao, Xiaomeng Huang, Dongqing Yan, Jamshid S Khorashad, Anthony D Pomicter, Tibor J Kovacsovics, Gabor T Marth, Thomas O’Hare, Michael W Deininger. Ongoing clonal evolution in chronic myelomonocytic leukemia on hypomethylating agents: a computational perspective. (2018). Leukemia. Nature Publishing Group. Page 1.

  17. Samuel W Brady, Jasmine A McQuerry, Yi Qiao, Stephen R Piccolo, Gajendra Shrestha, David F Jenkins, Ryan M Layer, Brent S Pedersen, Ryan H Miller, Amanda Esch, Sara R Selitsky, Joel S Parker, Layla A Anderson, Brian K Dalley, Rachel E Factor, Chakravarthy B Reddy, Jonathan P Boltax, Dean Y Li, Philip J Moos, Joe W Gray, Laura M Heiser, Saundra S Buys, Adam L Cohen, W Evan Johnson, Aaron R Quinlan, Gabor Marth, Theresa L Werner, Andrea H Bild. Publisher Correction: Combating subclonal evolution of resistant cancer phenotypes. (2018). Nature communications. Nature Publishing Group. Vol. 9, Issue 1, Page 572.

  18. Whitney Wooderchak-Donahue, Andrew Farrell, Peter Johnson, Jamie McDonald, Jennifer Thompson, Matt Velinder, Alistair Ward, Gabor Marth, Pinar Bayrak-Toydemir. Unraveling the mystery: analysis of the human genome with refus highlights the genetic complexity of HHT. (2018). ANGIOGENESIS. SPRINGER. Vol. 21, Issue 1, Pages 151-152.

  19. Ryan M Layer, Brent S Pedersen, Tonya DiSera, Gabor T Marth, Jason Gertz, Aaron R Quinlan. GIGGLE: a search engine for large-scale integrated genome analysis. (2018). Nature methods. Nature Publishing Group. Vol. 15, Issue 2, Page 123.

  20. Mark JP Chaisson, Ashley D Sanders, Xuefang Zhao, Ankit Malhotra, David Porubsky, Tobias Rausch, Eugene J Gardner, Oscar Rodriguez, Li Guo, Ryan L Collins, Xian Fan, Jia Wen, Robert E Handsaker, Susan Fairley, Zev N Kronenberg, Xiangmeng Kong, Fereydoun Hormozdiari, Dillon Lee, Aaron M Wenger, Alex Hastie, Danny Antaki, Peter Audano, Harrison Brand, Stuart Cantsilieris, Han Cao, Eliza Cerveira, Chong Chen, Xintong Chen, Chen-Shan Chin, Zechen Chong, Nelson T Chuang, Christine C Lambert, Deanna M Church, Laura Clarke, Andrew Farrell, Joey Flores, Timur Galeev, David Gorkin, Madhusudan Gujral, Victor Guryev, William Haynes Heaton, Jonas Korlach, Sushant Kumar, Jee Young Kwon, Jong Eun Lee, Joyce Lee, Wan-Ping Lee, Sau Peng Lee, Shantao Li, Patrick Marks, Karine Viaud-Martinez, Sascha Meiers, Katherine M Munson, Fabio Navarro, Bradley J Nelson, Conor Nodzak, Amina Noor, Sofia Kyriazopoulou-Panagiotopoulou, Andy Pang, Yunjiang Qiu, Gabriel Rosanio, Mallory Ryan, Adrian Stutz, Diana CJ Spierings, Alistair Ward, AnneMarie E Welch, Ming Xiao, Wei Xu, Chengsheng Zhang, Qihui Zhu, Xiangqun Zheng-Bradley, Ernesto Lowy, Sergei Yakneen, Steven McCarroll, Goo Jun, Li Ding, Chong Lek Koh, Bing Ren, Paul Flicek, Ken Chen, Mark B Gerstein, Pui-Yan Kwok, Peter M Lansdorp, Gabor Marth, Jonathan Sebat, Xinghua Shi, Ali Bashir, Kai Ye, Scott E Devine, Michael Talkowski, Ryan E Mills, Tobias Marschall, Jan O Korbel, Evan E Eichler, Charles Lee. Multi-platform discovery of haplotype-resolved structural variation in human genomes. (2018). bioRxiv. Cold Spring Harbor Laboratory Page 193144.

  21. Hein Than, Yi Qiao, Xiaomeng Huang, Dongqing Yan, Jamshid Sorouri Khorashad, Anthony D Pomicter, Anca Franzini, Tibor Kovacsovics, Thomas O'Hare, Gabor T Marth, Michael W Deininger. Persistence of Somatic Mutation Spectrum and Clonal Architecture in Chronic Myelomonocytic Leukemia Treated with Hypomethylating Agents. (2017). American Society of Hematology. Vol. 130, Suppl 1, Page 2527

  22. 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, Gabor T Marth. Rapid clinical diagnostic variant investigation of genomic patient sequencing data with iobio web tools. (2017). Journal of clinical and translational science. Cambridge University Press. Vol. 1, Issue 6, Pages 381-386

  23. Samuel W Brady, Jasmine A McQuerry, Yi Qiao, Stephen R Piccolo, Gajendra Shrestha, David F Jenkins, Ryan M Layer, Brent S Pedersen, Ryan H Miller, Amanda Esch, Sara R Selitsky, Joel S Parker, Layla A Anderson, Brian K Dalley, Rachel E Factor, Chakravarthy B Reddy, Jonathan P Boltax, Dean Y Li, Philip J Moos, Joe W Gray, Laura M Heiser, Saundra S Buys, Adam L Cohen, W Evan Johnson, Aaron R Quinlan, Gabor Marth, Theresa L Werner, Andrea H Bild. Combating subclonal evolution of resistant cancer phenotypes. (2017). Nature communications. Nature Publishing Group. Vol. 8, Issue 1, Page 1231.
  24. J Bonkowsky, B Ostrander, R Butterfield, R Layer, B Pedersen, T Stevenson, A Farrell, A Ward, C Miller, T DiSera, M Candee, F Filloux, T Newcomb, G Marth, A Quinlan. Deep Whole Genome Analysis (DWGA) for Effective Diagnosis and Gene Discovery in Early Infantile Epileptic Encephalopathy. (2017). ANNALS OF NEUROLOGY. WILEY. Vol. 82. Page S 283.

  25. Alistair N Ward, Chase Miller, Gabor Marth. 2254: iobio: From academic project to commercial enterprise. (2017). Journal of Clinical and Translational Science. Cambridge University Press. Vol. 1, Issue S1, Page 38.

  26. Alistair N Ward, Matt Velinder, Chase Miller, Tony Di Sera, Yi Qiao, Dave Viskochil, Gabor Marth. 2278: Identifying causative mutations in Treacher Collins syndrome using iobio. (2017). Journal of Clinical and Translational Science. Cambridge University Press. Vol. 1, Issue S1, Pages 13-14.

  27. Ira M Lubin, Nazneen Aziz, Lawrence J Babb, Dennis Ballinger, Himani Bisht, Deanna M Church, Shaun Cordes, Karen Eilbeck, Fiona Hyland, Lisa Kalman, Melissa Landrum, Edward R Lockhart, Donna Maglott, Gabor Marth, John D Pfeifer, Heidi L Rehm, Somak Roy, Zivana Tezak, Rebecca Truty, Mollie Ullman-Cullere, Karl V Voelkerding, Elizabeth A Worthey, Alexander W Zaranek, Justin M Zook. Principles and recommendations for standardizing the use of the next-generation sequencing variant file in clinical settings. (2017). The Journal of Molecular Diagnostics. Elsevier. Vol. 19, Issue 3, Pages 471-426.

  28. Alistair N Ward, Chase Miller, Gabor Marth. Journal of Clinical and Translational Science. (2017) Journal of Clinical and Translational Science. Vol. 1 Page 381-386.

  29. Donna M Werling, Harrison Brand, Joon-Yong An, Matthew R Stone, Joseph T Glessner, Lingxue Zhu, Ryan L Collins, Shan Dong, Ryan M Layer, Eiriene-Chloe Markenscoff-Papadimitriou, Andrew Farrell, Grace B Schwartz, Benjamin B Currall, Jeanselle Dea, Clif Duhn, Carolyn Erdman, Michael Gilson, Robert E Handsaker, Seva Kashin, Lambertus Klei, Jeffrey D Mandell, Tomasz J Nowakowski, Yuwen Liu, Sirisha Pochareddy, Louw Smith, Michael F Walker, Harold Z Wang, Mathew J Waterman, Xin He, Arnold R Kriegstein, John L Rubenstein, Nenad Sestan, Steven A McCarroll, Ben M Neale, Hilary Coon, A Jeremy Willsey, Joseph D Buxbaum, Mark J Daly, Aaron Quinlan, Gabor T Marth, Kathryn Roeder, Bernie Devlin, Michael E Talkowski, Stephan J Sanders. Limited contribution of rare, noncoding variation to autism spectrum disorder from sequencing of 2,076 genomes in quartet families. (2017). bioRxiv. Cold Spring Harbor Laboratory. Page 127043.

  30. Steven Flygare, Keith Simmon, Chase Miller, Yi Qiao, Brett Kennedy, Tonya Di Sera, Erin H Graf, Keith D Tardif, Aurélie Kapusta, Shawn Rynearson, Chris Stockmann, Krista Queen, Suxiang Tong, Karl V Voelkerding, Anne Blaschke, Carrie L Byington, Seema Jain, Andrew Pavia, Krow Ampofo, Karen Eilbeck, Gabor Marth, Mark Yandell, Robert Schlaberg. Taxonomer: an interactive metagenomics analysis portal for universal pathogen detection and host mRNA expression profiling. (2016). Genome biology. BioMed Central. Vol. 17, Issue 1, Page 111.

  31. Jamshid S Khorashad, Srinivas K Tantravahi, Dongqing Yan, Clinton C Mason, Yi Qiao, Anna M Eiring, Keith Gligorich, Than Hein, Anthony D Pomicter, Alistair G Reid, Todd W Kelley, Gabor T Marth, Thomas O'Hare, Michael W Deininger. Rapid conversion of chronic myeloid leukemia to chronic myelomonocytic leukemia in a patient on imatinib therapy. (2016). Leukemia. Nature Publishing Group. Vol. 30. Issue 11. Page 2275.

  32. Christina L Runge, Amit Indap, Yifan Zhou, Jack W Kent, Ericka King, Christy B Erbe, Regina Cole, Jack Littrell, Kate Merath, Roland James, Franz Rüschendorf, Joseph E Kerschner, Gabor Marth, Norbert Hübner, Harald HH Göring, David R Friedland, Wai-Meng Kwok, Michael Olivier. Association of TMTC2 with human nonsyndromic sensorineural hearing loss. (2016). JAMA Otolaryngology–Head & Neck Surgery. American Medical Association. Vol. 142, Issue 9, Page 866-872

  33. 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.
  34. Toolbox for mobile-element insertion detection on cancer genomes. Lee WP, Wu J, Marth GT. Cancer Inform. 2014 Oct 15;13(Suppl 4):45-52.
  35. bam.iobio: a web-based, real-time, sequence alignment file inspector. Miller CA, Qiao Y, DiSera T, D'Astous B, Marth GT. Nat Methods. 2014 Dec;11(12):1189.
  36. Tangram: a comprehensive toolbox for mobile element insertion detection. Wu J, Lee WP, Ward A, Walker JA, Konkel MK, Batzer MA, Marth GT. BMC Genomics. 2014 Sep 16;15:795.
  37. 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.
  38. 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):R88.
  39. Whole genome profiling of spontaneous and chemically induced mutations in Toxoplasma gondii. Farrell A, Coleman BI, Benenati B, Brown KM, Blader IJ, Marth GT, Gubbels MJ. BMC Genomics. 2014 May 10;15:354.
  40. MOSAIK: a hash-based algorithm for accurate next-generation sequencing short-read mapping. Lee WP, Stromberg MP, Ward A, Stewart C, Garrison EP, Marth GT. PLoS One. 2014 Mar 5;9(3):e90581.
  41. SSW library: an SIMD Smith-Waterman C/C++ library for use in genomic applications. Zhao M, Lee WP, Garrison EP, Marth GT. PLoS One. 2013 Dec 4;8(12):e82138.
  42. Integrative annotation of variants from 1092 humans: application to cancer genomics. 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, Gümüs ZH, Herrero J, Kitabayashi N, Kong Y, Lage K, Liluashvili V, Lipkin SM, MacArthur DG, Marth G, Muzny D, Pers TH, Ritchie GR, 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. Science. 2013 Oct 4;342(6154):1235587.
  43. Variant discovery in targeted resequencing using whole genome amplified DNA. Indap AR, Cole R, Runge CL, Marth GT, Olivier M. BMC Genomics. 2013 Jul 10;14:468.
  44. Genetic basis for phenotypic differences between different Toxoplasma gondii type I strains. Yang N, Farrell A, Niedelman W, Melo M, Lu D, Julien L, Marth GT, Gubbels MJ, Saeij JP. BMC Genomics. 2013 Jul 10;14:467.
  45. Scotty: a web tool for designing RNA-Seq experiments to measure differential gene expression. Busby MA, Stewart C, Miller CA, Grzeda KR, Marth GT. Bioinformatics. 2013 Mar 1;29(5):656-7.
  46. Copy Number Variation detection from 1000 Genomes Project exon capture sequencing data. Wu J, Grzeda KR, Stewart C, Grubert F, Urban AE, Snyder MP, Marth GT. BMC Bioinformatics. 2012 Nov 17;13:305.
  47. 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.
  48. Targeted proteomic dissection of Toxoplasma cytoskeleton sub-compartments using MORN1. Lorestani A, Ivey FD, Thirugnanam S, Busby MA, Marth GT, Cheeseman IM, Gubbels MJ. Cytoskeleton (Hoboken). 2012 Dec;69(12):1069-85.
  49. The 1000 Genomes Project: data management and community access. Clarke L, Zheng-Bradley X, Smith R, Kulesha E, Xiao C, Toneva I, Vaughan B, Preuss D, Leinonen R, Shumway M, Sherry S, Flicek P; 1000 Genomes Project Consortium. Nat Methods. 2012 Apr 27;9(5):459-62.
  50. A DOC2 protein identified by mutational profiling is essential for apicomplexan parasite exocytosis. Farrell A, Thirugnanam S, Lorestani A, Dvorin JD, Eidell KP, Ferguson DJ, Anderson-White BR, Duraisingh MT, Marth GT, Gubbels MJ. Science. 2012 Jan 13;335(6065):218-21.
  51. Expression divergence measured by transcriptome sequencing of four yeast species. Busby MA, Gray JM, Costa AM, Stewart C, Stromberg MP, Barnett D, Chuang JH, Springer M, Marth GT. BMC Genomics. 2011 Dec 29;12:635.
  52. ART: a next-generation sequencing read simulator. Huang W, Li L, Myers JR, Marth GT. Bioinformatics. 2012 Feb 15;28(4):593-4.
  53. 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; 1000 Genomes Project. Genome Biol. 2011 Sep 14;12(9):R84.
  54. A comprehensive map of mobile element insertion polymorphisms in humans. Stewart C, Kural D, Strömberg MP, Walker JA, Konkel MK, Stütz 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. PLoS Genet. 2011 Aug;7(8):e1002236.
  55. 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.
  56. Variation in genome-wide mutation rates within and between human families. Conrad DF, Keebler JE, DePristo MA, Lindsay SJ, Zhang Y, Casals F, Idaghdour Y, Hartl CL, Torroja C, Garimella KV, Zilversmit M, Cartwright R, Rouleau GA, Daly M, Stone EA, Hurles ME, Awadalla P; 1000 Genomes Project. Nat Genet. 2011 Jun 12;43(7):712-4.
  57. 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.
  58. BamTools: a C++ API and toolkit for analyzing and managing BAM files. Barnett DW, Garrison EK, Quinlan AR, Strömberg MP, Marth GT. Bioinformatics. 2011 Jun 15;27(12):1691-2.
  59. Mapping copy number variation by population-scale genome sequencing. 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, Stütz 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. Nature. 2011 Feb 3;470(7332):59-65.
  60. Diversity of human copy number variation and multicopy genes. Sudmant PH, Kitzman JO, Antonacci F, Alkan C, Malig M, Tsalenko A, Sampas N, Bruhn L, Shendure J; 1000 Genomes Project, Eichler EE. Science. 2010 Oct 29;330(6004):641-6.
  61. A map of human genome variation from population-scale sequencing. 1000 Genomes Project Consortium, Abecasis GR, Altshuler D, Auton A, Brooks LD, Durbin RM, Gibbs RA, Hurles ME, McVean GA. Nature. 2010 Oct 28;467(7319):1061-73.
  62. 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):R88.
  63. Population genomic inferences from sparse high-throughput sequencing of two populations of Drosophila melanogaster. Sackton TB, Kulathinal RJ, Bergman CM, Quinlan AR, Dopman EB, Carneiro M, Marth GT, Hartl DL, Clark AG. Genome Biol Evol. 2009 Nov 18;1:449-65.
  64. Rapid whole-genome mutational profiling using next-generation sequencing technologies. 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. Genome Res. 2008 Oct;18(10):1638-42.
  65. Whole-genome sequencing and variant discovery in C. elegans. 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. Nat Methods. 2008 Feb;5(2):183-8.
  66. Pyrobayes: an improved base caller for SNP discovery in pyrosequences. Quinlan AR, Stewart DA, Strömberg MP, Marth GT. Nat Methods. 2008 Feb;5(2):179-81.
  67. Primer-site SNPs mask mutations. Quinlan AR, Marth GT. Nat Methods. 2007 Mar;4(3):192.
  68. Analysis of concordance of different haplotype block partitioning algorithms. Indap AR, Marth GT, Struble CA, Tonellato P, Olivier M. BMC Bioinformatics. 2005 Dec 15;6:303.
  69. 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.
  70. Computational SNP discovery in DNA sequence data. Marth GT. Methods Mol Biol. 2003;212:85-110.

to page top

Last Updated: 8/21/19