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Items: 45

1.

Genome-wide de novo risk score implicates promoter variation in autism spectrum disorder.

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.

Science. 2018 Dec 14;362(6420). pii: eaat6576. doi: 10.1126/science.aat6576.

PMID:
30545852
2.

Whole-genome analysis for effective clinical diagnosis and gene discovery in early infantile epileptic encephalopathy.

Ostrander BEP, Butterfield RJ, Pedersen BS, Farrell AJ, Layer RM, Ward A, Miller C, DiSera T, Filloux FM, Candee MS, Newcomb T, Bonkowsky JL, Marth GT, Quinlan AR.

NPJ Genom Med. 2018 Aug 13;3:22. doi: 10.1038/s41525-018-0061-8. eCollection 2018.

3.

Automated size selection for short cell-free DNA fragments enriches for circulating tumor DNA and improves error correction during next generation sequencing.

Hellwig S, Nix DA, Gligorich KM, O'Shea JM, Thomas A, Fuertes CL, Bhetariya PJ, Marth GT, Bronner MP, Underhill HR.

PLoS One. 2018 Jul 25;13(7):e0197333. doi: 10.1371/journal.pone.0197333. eCollection 2018.

4.

Rapid clinical diagnostic variant investigation of genomic patient sequencing data with iobio web tools.

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.

J Clin Transl Sci. 2017 Dec;1(6):381-386. doi: 10.1017/cts.2017.311.

5.

An analytical framework for whole-genome sequence association studies and its implications for autism spectrum disorder.

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.

Nat Genet. 2018 May;50(5):727-736. doi: 10.1038/s41588-018-0107-y. Epub 2018 Apr 26.

6.

Ongoing clonal evolution in chronic myelomonocytic leukemia on hypomethylating agents: a computational perspective.

Than H, Qiao Y, Huang X, Yan D, Khorashad JS, Pomicter AD, Kovacsovics TJ, Marth GT, O'Hare T, Deininger MW.

Leukemia. 2018 Sep;32(9):2049-2054. doi: 10.1038/s41375-018-0050-z. Epub 2018 Mar 27. No abstract available.

7.

GIGGLE: a search engine for large-scale integrated genome analysis.

Layer RM, Pedersen BS, DiSera T, Marth GT, Gertz J, Quinlan AR.

Nat Methods. 2018 Feb;15(2):123-126. doi: 10.1038/nmeth.4556. Epub 2018 Jan 8.

8.

Rapid conversion of chronic myeloid leukemia to chronic myelomonocytic leukemia in a patient on imatinib therapy.

Khorashad JS, Tantravahi SK, Yan D, Mason CC, Qiao Y, Eiring AM, Gligorich K, Hein T, Pomicter AD, Reid AG, Kelley TW, Marth GT, O'Hare T, Deininger MW.

Leukemia. 2016 Nov;30(11):2275-2279. doi: 10.1038/leu.2016.218. Epub 2016 Aug 2. No abstract available.

9.

Sequence Analysis and Characterization of Active Human Alu Subfamilies Based on the 1000 Genomes Pilot Project.

Konkel MK, Walker JA, Hotard AB, Ranck MC, Fontenot CC, Storer J, Stewart C, Marth GT; 1000 Genomes Consortium, Batzer MA.

Genome Biol Evol. 2015 Aug 29;7(9):2608-22. doi: 10.1093/gbe/evv167.

10.

SpeedSeq: ultra-fast personal genome analysis and interpretation.

Chiang C, Layer RM, Faust GG, Lindberg MR, Rose DB, Garrison EP, Marth GT, Quinlan AR, Hall IM.

Nat Methods. 2015 Oct;12(10):966-8. doi: 10.1038/nmeth.3505. Epub 2015 Aug 10.

11.

Toolbox for mobile-element insertion detection on cancer genomes.

Lee WP, Wu J, Marth GT.

Cancer Inform. 2015 Feb 12;14(Suppl 1):37-44. doi: 10.4137/CIN.S24657. eCollection 2015.

12.

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. doi: 10.1186/s13059-015-0587-3.

13.

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. doi: 10.4137/CIN.S13979. eCollection 2014.

14.

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. doi: 10.1038/nmeth.3174. No abstract available.

15.

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. doi: 10.1186/1471-2164-15-795.

16.

SubcloneSeeker: a computational framework for reconstructing tumor clone structure for cancer variant interpretation and prioritization.

Qiao Y, Quinlan AR, Jazaeri AA, Verhaak RG, Wheeler DA, Marth GT.

Genome Biol. 2014 Aug 26;15(8):443. doi: 10.1186/s13059-014-0443-x.

17.

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. doi: 10.1186/gb-2014-15-6-r88.

18.

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. doi: 10.1186/1471-2164-15-354.

19.

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. doi: 10.1371/journal.pone.0090581. eCollection 2014.

20.

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. doi: 10.1371/journal.pone.0082138. eCollection 2013.

21.

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. doi: 10.1186/1471-2164-14-468.

22.

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. doi: 10.1186/1471-2164-14-467.

23.

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. doi: 10.1093/bioinformatics/btt015. Epub 2013 Jan 12.

24.

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. doi: 10.1186/1471-2105-13-305.

25.

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. doi: 10.1038/nature11632.

26.

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. doi: 10.1002/cm.21077. Epub 2012 Oct 11.

27.

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. doi: 10.1126/science.1210829. Erratum in: Science. 2012 Apr 13;336(6078):155.

28.

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. doi: 10.1186/1471-2164-12-635.

29.

ART: a next-generation sequencing read simulator.

Huang W, Li L, Myers JR, Marth GT.

Bioinformatics. 2012 Feb 15;28(4):593-4. doi: 10.1093/bioinformatics/btr708. Epub 2011 Dec 23.

30.

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. doi: 10.1186/gb-2011-12-9-r84.

31.

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. doi: 10.1371/journal.pgen.1002236. Epub 2011 Aug 18.

32.

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. doi: 10.1073/pnas.1019276108. Epub 2011 Jul 5.

33.

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. doi: 10.1093/bioinformatics/btr330. Epub 2011 Jun 7.

34.

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. doi: 10.1093/bioinformatics/btr174. Epub 2011 Apr 14.

35.

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. doi: 10.1038/nature09708.

36.

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. doi: 10.1186/gb-2010-11-8-r88. Epub 2010 Aug 26.

37.

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. doi: 10.1093/gbe/evp048.

38.

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. doi: 10.1101/gr.077776.108. Epub 2008 Sep 4.

39.

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. doi: 10.1038/nmeth.1179. Epub 2008 Jan 20.

PMID:
18204455
40.

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. doi: 10.1038/nmeth.1172. Epub 2008 Jan 13.

PMID:
18193056
41.

Primer-site SNPs mask mutations.

Quinlan AR, Marth GT.

Nat Methods. 2007 Mar;4(3):192. No abstract available.

PMID:
17327845
42.

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.

44.

Computational SNP discovery in DNA sequence data.

Marth GT.

Methods Mol Biol. 2003;212:85-110. No abstract available.

PMID:
12491905
45.

A general approach to single-nucleotide polymorphism discovery.

Marth GT, Korf I, Yandell MD, Yeh RT, Gu Z, Zakeri H, Stitziel NO, Hillier L, Kwok PY, Gish WR.

Nat Genet. 1999 Dec;23(4):452-6.

PMID:
10581034

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