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Gabor T. Marth - Publications

Affiliations: 
Boston College, Newton, MA, United States 
 Human Genetics University of Utah, Salt Lake City, UT 
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54 high-probability publications. We are testing a new system for linking publications to authors. You can help! If you notice any inaccuracies, please sign in and mark papers as correct or incorrect matches. If you identify any major omissions or other inaccuracies in the publication list, please let us know.

Year Citation  Score
2024 Chamberlin JT, Lee Y, Marth G, Quinlan AR. Differences in molecular sampling and data processing explain variation among single-cell and single-nucleus RNA-seq experiments. Genome Research. PMID 38355308 DOI: 10.1101/gr.278253.123  0.525
2024 Qiao Y, Huang X, Moos PJ, Ahmann JM, Pomicter AD, Deininger MW, Byrd JC, Woyach JA, Stephens DM, Marth GT. A Bayesian framework to study tumor subclone-specific expression by combining bulk DNA and single-cell RNA sequencing data. Genome Research. PMID 38195207 DOI: 10.1101/gr.278234.123  0.379
2023 Pitman A, Huang X, Marth GT, Qiao Y. quickBAM: a parallelized BAM file access API for high-throughput sequence analysis informatics. Bioinformatics (Oxford, England). 39. PMID 37498562 DOI: 10.1093/bioinformatics/btad463  0.372
2022 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, ... ... Marth G, et al. Comprehensive variant calling from whole-genome sequencing identifies a complex inversion that disrupts ZFPM2 in familial congenital diaphragmatic hernia. Molecular Genetics & Genomic Medicine. e1888. PMID 35119225 DOI: 10.1002/mgg3.1888  0.67
2022 Ward A, Velinder M, Di Sera T, Ekawade A, Malone Jenkins S, Moore B, Mao R, Bayrak-Toydemir P, Marth G. : A Collaborative Diagnostic Workflow to Enable Team-Based Precision Genomics. Journal of Personalized Medicine. 12. PMID 35055388 DOI: 10.3390/jpm12010073  0.454
2021 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, ... ... Marth G, et al. Gene.iobio: an interactive web tool for versatile, clinically-driven variant interrogation and prioritization. Scientific Reports. 11: 20307. PMID 34645894 DOI: 10.1038/s41598-021-99752-5  0.339
2021 Nicholas TJ, Cormier MJ, Huang X, Qiao Y, Marth GT, Quinlan AR. OncoGEMINI: software for investigating tumor variants from multiple biopsies with integrated cancer annotations. Genome Medicine. 13: 46. PMID 33771218 DOI: 10.1186/s13073-021-00854-6  0.588
2020 Bogenschutz EL, Fox ZD, Farrell A, Wynn J, Moore B, Yu L, Aspelund G, Marth G, Yandell M, Shen Y, Chung WK, Kardon G. Deep whole-genome sequencing of multiple proband tissues and parental blood reveals the complex genetic etiology of congenital diaphragmatic hernias. Hgg Advances. 1. PMID 33263113 DOI: 10.1016/j.xhgg.2020.100008  0.388
2020 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, ... ... Marth G, et al. gene.iobio: an interactive web tool for versatile, clinically-driven variant interrogation and prioritization. Medrxiv : the Preprint Server For Health Sciences. PMID 33173897 DOI: 10.1101/2020.11.05.20224865  0.359
2020 Pedersen BS, Bhetariya PJ, Brown J, Kravitz SN, Marth G, Jensen RL, Bronner MP, Underhill HR, Quinlan AR. Somalier: rapid relatedness estimation for cancer and germline studies using efficient genome sketches. Genome Medicine. 12: 62. PMID 32664994 DOI: 10.1186/S13073-020-00761-2  0.629
2019 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, ... ... Marth GT, et al. Multi-platform discovery of haplotype-resolved structural variation in human genomes. Nature Communications. 10: 1784. PMID 30992455 DOI: 10.1038/S41467-018-08148-Z  0.475
2018 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, ... ... Marth GT, et al. Genome-wide de novo risk score implicates promoter variation in autism spectrum disorder. Science (New York, N.Y.). 362. PMID 30545852 DOI: 10.1126/Science.Aat6576  0.643
2018 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. Genome sequencing reveals a deep intronic splicing mutation hotspot in Hereditary Haemorrhagic Telangiectasia. Journal of Medical Genetics. PMID 30244195 DOI: 10.1136/jmedgenet-2018-105561  0.366
2018 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. Whole-genome analysis for effective clinical diagnosis and gene discovery in early infantile epileptic encephalopathy. Npj Genomic Medicine. 3: 22. PMID 30109124 DOI: 10.1038/S41525-018-0061-8  0.668
2018 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, ... ... Marth GT, et al. An analytical framework for whole-genome sequence association studies and its implications for autism spectrum disorder. Nature Genetics. PMID 29700473 DOI: 10.1038/S41588-018-0107-Y  0.673
2018 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, ... ... Marth G, et al. Publisher Correction: Combating subclonal evolution of resistant cancer phenotypes. Nature Communications. 9: 572. PMID 29402882 DOI: 10.1038/S41467-017-02383-6  0.524
2018 Layer RM, Pedersen BS, DiSera T, Marth GT, Gertz J, Quinlan AR. GIGGLE: a search engine for large-scale integrated genome analysis. Nature Methods. PMID 29309061 DOI: 10.1038/Nmeth.4556  0.642
2017 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. Rapid clinical diagnostic variant investigation of genomic patient sequencing data with web tools. Journal of Clinical and Translational Science. 1: 381-386. PMID 29707261 DOI: 10.1017/cts.2017.311  0.433
2017 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, ... ... Marth G, et al. Combating subclonal evolution of resistant cancer phenotypes. Nature Communications. 8: 1231. PMID 29093439 DOI: 10.1038/S41467-017-01174-3  0.543
2017 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, et al. Principles and Recommendations for Standardizing the Use of the Next-Generation Sequencing Variant File in Clinical Settings. The Journal of Molecular Diagnostics : Jmd. PMID 28315672 DOI: 10.1016/J.Jmoldx.2016.12.001  0.394
2015 Sudmant PH, Rausch T, Gardner EJ, Handsaker RE, Abyzov A, Huddleston J, Zhang Y, Ye K, Jun G, Hsi-Yang Fritz M, Konkel MK, Malhotra A, Stütz AM, Shi X, Paolo Casale F, ... ... Marth G, et al. An integrated map of structural variation in 2,504 human genomes. Nature. 526: 75-81. PMID 26432246 DOI: 10.1038/Nature15394  0.376
2015 Konkel MK, Walker JA, Hotard AB, Ranck MC, Fontenot CC, Storer J, Stewart C, Marth GT, Batzer MA. Sequence Analysis and Characterization of Active Human Alu Subfamilies Based on the 1000 Genomes Pilot Project. Genome Biology and Evolution. 7: 2608-22. PMID 26319576 DOI: 10.1093/Gbe/Evv167  0.418
2015 Chiang C, Layer RM, Faust GG, Lindberg MR, Rose DB, Garrison EP, Marth GT, Quinlan AR, Hall IM. SpeedSeq: ultra-fast personal genome analysis and interpretation. Nature Methods. 12: 966-8. PMID 26258291 DOI: 10.1038/nmeth.3505  0.722
2015 Challis D, Antunes L, Garrison E, Banks E, Evani US, Muzny D, Poplin R, Gibbs RA, Marth G, Yu F. The distribution and mutagenesis of short coding INDELs from 1,128 whole exomes. Bmc Genomics. 16: 143. PMID 25765891 DOI: 10.1186/S12864-015-1333-7  0.333
2015 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. Extending reference assembly models. Genome Biology. 16: 13. PMID 25651527 DOI: 10.1186/S13059-015-0587-3  0.654
2014 Lee WP, Wu J, Marth GT. Toolbox for mobile-element insertion detection on cancer genomes. Cancer Informatics. 13: 45-52. PMID 25452688 DOI: 10.4137/CIN.S13979  0.392
2014 Wu J, Lee WP, Ward A, Walker JA, Konkel MK, Batzer MA, Marth GT. Tangram: a comprehensive toolbox for mobile element insertion detection. Bmc Genomics. 15: 795. PMID 25228379 DOI: 10.1186/1471-2164-15-795  0.349
2014 Qiao Y, Quinlan AR, Jazaeri AA, Verhaak RG, Wheeler DA, Marth GT. SubcloneSeeker: a computational framework for reconstructing tumor clone structure for cancer variant interpretation and prioritization. Genome Biology. 15: 443. PMID 25160522 DOI: 10.1186/s13059-014-0443-x  0.594
2014 Colonna V, Ayub Q, Chen Y, Pagani L, Luisi P, Pybus M, Garrison E, Xue Y, Tyler-Smith C, Abecasis GR, Auton A, Brooks LD, DePristo MA, Durbin RM, ... ... Marth GT, et al. Human genomic regions with exceptionally high levels of population differentiation identified from 911 whole-genome sequences. Genome Biology. 15: R88. PMID 24980144 DOI: 10.1186/Gb-2014-15-6-R88  0.351
2014 Farrell A, Coleman BI, Benenati B, Brown KM, Blader IJ, Marth GT, Gubbels MJ. Whole genome profiling of spontaneous and chemically induced mutations in Toxoplasma gondii. Bmc Genomics. 15: 354. PMID 24885922 DOI: 10.1186/1471-2164-15-354  0.385
2014 Lee WP, Stromberg MP, Ward A, Stewart C, Garrison EP, Marth GT. MOSAIK: a hash-based algorithm for accurate next-generation sequencing short-read mapping. Plos One. 9: e90581. PMID 24599324 DOI: 10.1371/journal.pone.0090581  0.344
2013 Zhao M, Lee WP, Garrison EP, Marth GT. SSW library: an SIMD Smith-Waterman C/C++ library for use in genomic applications. Plos One. 8: e82138. PMID 24324759 DOI: 10.1371/journal.pone.0082138  0.311
2013 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, ... ... Marth G, et al. Integrative annotation of variants from 1092 humans: application to cancer genomics. Science (New York, N.Y.). 342: 1235587. PMID 24092746 DOI: 10.1126/Science.1235587  0.412
2013 Indap AR, Cole R, Runge CL, Marth GT, Olivier M. Variant discovery in targeted resequencing using whole genome amplified DNA. Bmc Genomics. 14: 468. PMID 23837845 DOI: 10.1186/1471-2164-14-468  0.413
2013 Miller CA, Anthony J, Meyer MM, Marth G. Scribl: an HTML5 Canvas-based graphics library for visualizing genomic data over the web. Bioinformatics (Oxford, England). 29: 381-3. PMID 23172864 DOI: 10.1093/Bioinformatics/Bts677  0.368
2012 Wu J, Grzeda KR, Stewart C, Grubert F, Urban AE, Snyder MP, Marth GT. Copy Number Variation detection from 1000 Genomes Project exon capture sequencing data. Bmc Bioinformatics. 13: 305. PMID 23157288 DOI: 10.1186/1471-2105-13-305  0.421
2012 Abecasis GR, Auton A, Brooks LD, DePristo MA, Durbin RM, Handsaker RE, Kang HM, Marth GT, McVean GA. An integrated map of genetic variation from 1,092 human genomes. Nature. 491: 56-65. PMID 23128226 DOI: 10.1038/Nature11632  0.389
2012 Huang W, Li L, Myers JR, Marth GT. ART: a next-generation sequencing read simulator. Bioinformatics (Oxford, England). 28: 593-4. PMID 22199392 DOI: 10.1093/Bioinformatics/Btr708  0.325
2011 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, et al. The functional spectrum of low-frequency coding variation. Genome Biology. 12: R84. PMID 21917140 DOI: 10.1186/Gb-2011-12-9-R84  0.321
2011 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, ... ... Marth GT, et al. A comprehensive map of mobile element insertion polymorphisms in humans. Plos Genetics. 7: e1002236. PMID 21876680 DOI: 10.1371/Journal.Pgen.1002236  0.384
2011 Gravel S, Henn BM, Gutenkunst RN, Indap AR, Marth GT, Clark AG, Yu F, Gibbs RA, Bustamante CD. Demographic history and rare allele sharing among human populations. Proceedings of the National Academy of Sciences of the United States of America. 108: 11983-8. PMID 21730125 DOI: 10.1073/Pnas.1019276108  0.324
2011 Danecek P, Auton A, Abecasis G, Albers CA, Banks E, DePristo MA, Handsaker RE, Lunter G, Marth GT, Sherry ST, McVean G, Durbin R. The variant call format and VCFtools. Bioinformatics (Oxford, England). 27: 2156-8. PMID 21653522 DOI: 10.1093/Bioinformatics/Btr330  0.338
2011 Barnett DW, Garrison EK, Quinlan AR, Strömberg MP, Marth GT. BamTools: a C++ API and toolkit for analyzing and managing BAM files. Bioinformatics (Oxford, England). 27: 1691-2. PMID 21493652 DOI: 10.1093/bioinformatics/btr174  0.614
2011 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, ... ... Marth GT, et al. Mapping copy number variation by population-scale genome sequencing. Nature. 470: 59-65. PMID 21293372 DOI: 10.1038/Nature09708  0.377
2010 Reese MG, Moore B, Batchelor C, Salas F, Cunningham F, Marth GT, Stein L, Flicek P, Yandell M, Eilbeck K. A standard variation file format for human genome sequences. Genome Biology. 11: R88. PMID 20796305 DOI: 10.1186/Gb-2010-11-8-R88  0.433
2009 Sackton TB, Kulathinal RJ, Bergman CM, Quinlan AR, Dopman EB, Carneiro M, Marth GT, Hartl DL, Clark AG. Population genomic inferences from sparse high-throughput sequencing of two populations of Drosophila melanogaster. Genome Biology and Evolution. 1: 449-65. PMID 20333214 DOI: 10.1093/Gbe/Evp048  0.686
2009 Li H, Handsaker B, Wysoker A, Fennell T, Ruan J, Homer N, Marth G, Abecasis G, Durbin R. The Sequence Alignment/Map format and SAMtools. Bioinformatics (Oxford, England). 25: 2078-9. PMID 19505943 DOI: 10.1093/Bioinformatics/Btp352  0.321
2008 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, ... ... Marth GT, et al. Rapid whole-genome mutational profiling using next-generation sequencing technologies. Genome Research. 18: 1638-42. PMID 18775913 DOI: 10.1101/Gr.077776.108  0.651
2008 Huang W, Marth G. EagleView: a genome assembly viewer for next-generation sequencing technologies. Genome Research. 18: 1538-43. PMID 18550804 DOI: 10.1101/gr.076067.108  0.442
2008 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, et al. Whole-genome sequencing and variant discovery in C. elegans. Nature Methods. 5: 183-8. PMID 18204455 DOI: 10.1038/Nmeth.1179  0.683
2008 Quinlan AR, Stewart DA, Strömberg MP, Marth GT. Pyrobayes: An improved base caller for SNP discovery in pyrosequences Nature Methods. 5: 179-181. PMID 18193056 DOI: 10.1038/nmeth.1172  0.593
2007 Quinlan AR, Marth GT. Primer-site SNPs mask mutations. Nature Methods. 4: 192. PMID 17327845 DOI: 10.1038/nmeth0307-192  0.562
2003 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, et al. Sequence variations in the public human genome data reflect a bottlenecked population history. Proceedings of the National Academy of Sciences of the United States of America. 100: 376-81. PMID 12502794 DOI: 10.1073/Pnas.222673099  0.432
2002 Weber JL, David D, Heil J, Fan Y, Zhao C, Marth G. Human diallelic insertion/deletion polymorphisms. American Journal of Human Genetics. 71: 854-62. PMID 12205564 DOI: 10.1086/342727  0.302
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