Publications

This list includes publications about TVAP tools or publications that have used TVAP tools.

All Publications
article is about TVAP
article used TVAP

  • Advances for studying clonal evolution in cancer.

    Ding L, Raphael BJ, Chen F, Wendl MC.

    Cancer Lett. 2013 Jan 23. pii: S0304-3835(13)00034-7. doi: 10.1016/j.canlet.2012.12.028. [Epub ahead of print]

  • BreakDancer: an algorithm for high-resolution mapping of genomic structural variation.

    Chen K, Wallis JW, McLellan MD, Larson DE, Kalicki JM, Pohl CS, McGrath SD, Wendl MC, Zhang Q, Locke DP, Shi X, Fulton RS, Ley TJ, Wilson RK, Ding L, Mardis ER.

    Nat Methods. 2009 Sep;6(9):677-81. doi: 10.1038/nmeth.1363. Epub 2009 Aug 9.

  • BreakFusion: Targeted Assembly-based Identification of Gene Fusions in Whole Transcriptome Paired-end Sequencing Data.

    Chen K, Wallis JW, Kandoth C, Kalicki-Veizer JM, Mungall KL, Mungall AJ, Jones SJ, Marra MA, Ley TJ, Mardis ER, Wilson RK, Weinstein JN, Ding L.

    Bioinformatics. 2012 Jul 15;28(14):1923-4. doi: 10.1093/bioinformatics/bts272. Epub 2012 May 4.

  • BreakTrans: uncovering the genomic architecture of gene fusions

    Ken Chen, Nicholas E Navin, Yong Wang, Heather K Schmidt, John W Wallis, Beifang Niu, Xian Fan, Hao Zhao, Michael D McLellan, Katherine A Hoadley, Elaine R Mardis, Timothy J Ley, Charles M Perou, Richard K Wilson, Li Ding

    Genome Biology 2013, 14:R87

  • CMDS: a population-based method for identifying recurrent DNA copy number aberrations in cancer from high-resolution data.

    Zhang Q, Ding L, Larson DE, Koboldt DC, McLellan MD, Chen K, Shi X, Kraja A, Mardis ER, Wilson RK, Borecki IB, Province MA.

    Bioinformatics. 2010 Feb 15;26(4):464-9. doi: 10.1093/bioinformatics/btp708. Epub 2009 Dec 23.

  • CREST maps somatic structural variation in cancer genomes with base-pair resolution.

    Wang J, Mullighan CG, Easton J, Roberts S, Heatley SL, Ma J, Rusch MC, Chen K, Harris CC, Ding L, Holmfeldt L, Payne-Turner D, Fan X, Wei L, Zhao D, Obenauer JC, Naeve C, Mardis ER, Wilson RK, Downing JR, Zhang J.

    Nat Methods. 2011 Jun 12;8(8):652-4. doi: 10.1038/nmeth.1628.

  • Clonal diversity of recurrently mutated genes in myelodysplastic syndromes

    M J Walter, D Shen, J Shao, L Ding, B S White, C Kandoth, C A Miller, B Niu, M D McLellan, N D Dees, R Fulton, K Elliot, S Heath, M Grillot, P Westervelt, D C Link, J F DiPersio, E Mardis, T J Ley, R K Wilson and T A Graubert

    Leukemia advance online publication 26 March 2013; doi: 10.1038/leu.2013.58

  • Comprehensive genomic characterization defines human glioblastoma genes and core pathways.

    McLendon R, Friedman A, Bigner D, Van Meir EG, Brat DJ, Mastrogianakis GM, Olson JJ, Mikkelsen T, Lehman N, Aldape K, Yung WK, Bogler O, Weinstein JN, VandenBerg S, Berger M, Prados M, Muzny D, Morgan M, Scherer S, Sabo A, Nazareth L, Lewis L, Hall O, Zhu Y, Ren Y, Alvi O, Yao J, Hawes A, Jhangiani S, Fowler G, San Lucas A, Kovar C, Cree A, Dinh H, Santibanez J, Joshi V, Gonzalez-Garay ML, Miller CA, Milosavljevic A, Donehower L, Wheeler DA, Gibbs RA, Cibulskis K, Sougnez C, Fennell T, Mahan S, Wilkinson J, Ziaugra L, Onofrio R, Bloom T, Nicol R, Ardlie K, Baldwin J, Gabriel S, Lander ES, Ding L, Fulton RS, McLellan MD, Wallis J, Larson DE, Shi X, Abbott R, Fulton L, Chen K, Koboldt DC, Wendl MC, Meyer R, Tang Y, Lin L, Osborne JR, Dunford-Shore BH, Miner TL, Delehaunty K, Markovic C, Swift G, Courtney W, Pohl C, Abbott S, Hawkins A, Leong S, Haipek C, Schmidt H, Wiechert M, Vickery T, Scott S, Dooling DJ, Chinwalla A, Weinstock GM, Mardis ER, Wilson RK, Getz G, Winckler W, Verhaak RG, Lawrence MS, O'Kelly M, Robinson J, Alexe G, Beroukhim R, Carter S, Chiang D, Gould J, Gupta S, Korn J, Mermel C, Mesirov J, Monti S, Nguyen H, Parkin M, Reich M, Stransky N, Weir BA, Garraway L, Golub T, Meyerson M, Chin L, Protopopov A, Zhang J, Perna I, Aronson S, Sathiamoorthy N, Ren G, Yao J, Wiedemeyer WR, Kim H, Kong SW, Xiao Y, Kohane IS, Seidman J, Park PJ, Kucherlapati R, Laird PW, Cope L, Herman JG, Weisenberger DJ, Pan F, Van den Berg D, Van Neste L, Yi JM, Schuebel KE, Baylin SB, Absher DM, Li JZ, Southwick A, Brady S, Aggarwal A, Chung T, Sherlock G, Brooks JD, Myers RM, Spellman PT, Purdom E, Jakkula LR, Lapuk AV, Marr H, Dorton S, Choi YG, Han J, Ray A, Wang V, Durinck S, Robinson M, Wang NJ, Vranizan K, Peng V, Van Name E, Fontenay GV, Ngai J, Conboy JG, Parvin B, Feiler HS, Speed TP, Gray JW, Brennan C, Socci ND, Olshen A, Taylor BS, Lash A, Schultz N, Reva B, Antipin Y, Stukalov A, Gross B, Cerami E, Wang WQ, Qin LX, Seshan VE, Villafania L, Cavatore M, Borsu L, Viale A, Gerald W, Sander C, Ladanyi M, Perou CM, Hayes DN, Topal MD, Hoadley KA, Qi Y, Balu S, Shi Y, Wu J, Penny R, Bittner M, Shelton T, Lenkiewicz E, Morris S, Beasley D, Sanders S, Kahn A, Sfeir R, Chen J, Nassau D, Feng L, Hickey E, Barker A, Gerhard DS, Vockley J, Compton C, Vaught J, Fielding P, Ferguson ML, Schaefer C, Zhang J, Madhavan S, Buetow KH, Collins F, Good P, Guyer M, Ozenberger B, Peterson J, Thomson E.

    Nature. 2008 Oct 23;455(7216):1061-8. doi: 10.1038/nature07385. Epub 2008 Sep 4.

  • DNA sequencing of a cytogenetically normal acute myeloid leukaemia genome.

    Ley TJ, Mardis ER, Ding L, Fulton B, McLellan MD, Chen K, Dooling D, Dunford-Shore BH, McGrath S, Hickenbotham M, Cook L, Abbott R, Larson DE, Koboldt DC, Pohl C, Smith S, Hawkins A, Abbott S, Locke D, Hillier LW, Miner T, Fulton L, Magrini V, Wylie T, Glasscock J, Conyers J, Sander N, Shi X, Osborne JR, Minx P, Gordon D, Chinwalla A, Zhao Y, Ries RE, Payton JE, Westervelt P, Tomasson MH, Watson M, Baty J, Ivanovich J, Heath S, Shannon WD, Nagarajan R, Walter MJ, Link DC, Graubert TA, DiPersio JF, Wilson RK.

    Nature. 2008 Nov 6;456(7218):66-72. doi: 10.1038/nature07485.

  • DNMT3A mutations in acute myeloid leukemia.

    Ley TJ, Ding L, Walter MJ, McLellan MD, Lamprecht T, Larson DE, Kandoth C, Payton JE, Baty J, Welch J, Harris CC, Lichti CF, Townsend RR, Fulton RS, Dooling DJ, Koboldt DC, Schmidt H, Zhang Q, Osborne JR, Lin L, O'Laughlin M, McMichael JF, Delehaunty KD, McGrath SD, Fulton LA, Magrini VJ, Vickery TL, Hundal J, Cook LL, Conyers JJ, Swift GW, Reed JP, Alldredge PA, Wylie T, Walker J, Kalicki J, Watson MA, Heath S, Shannon WD, Varghese N, Nagarajan R, Westervelt P, Tomasson MH, Link DC, Graubert TA, DiPersio JF, Mardis ER, Wilson RK.

    N Engl J Med. 2010 Dec 16;363(25):2424-33. doi: 10.1056/NEJMoa1005143. Epub 2010 Nov 10.

  • Design and implementation of a generalized laboratory data model.

    Wendl MC, Smith S, Pohl CS, Dooling DJ, Chinwalla AT, Crouse K, Hepler T, Leong S, Carmichael L, Nhan M, Oberkfell BJ, Mardis ER, Hillier LW, Wilson RK.

    BMC Bioinformatics. 2007 Sep 26;8:362.

  • Integrated analysis of germline and somatic variants in ovarian cancer

    Krishna L. Kanchi, Kimberly J. Johnson, Charles Lu, Michael D. McLellan, Mark D. M. Leiserson, Michael C. Wendl, Qunyuan Zhang, Daniel C. Koboldt, Mingchao Xie, Cyriac Kandoth, Joshua F. McMichael, Matthew A. Wyczalkowski, David E. Larson, Heather K. Schmidt, Christopher A. Miller, Robert S. Fulton, Paul T. Spellman, Elaine R. Mardis, Todd E. Druley, Timothy A. Graubert, Paul J. Goodfellow, Benjamin J. Raphael, Richard K. Wilson & Li Ding

    Nature Communications 5, Article number: 3156 (January 2014), doi:10.1038/ncomms4156

  • MSIsensor: microsatellite instability detection using paired tumor-normal sequence data

    Beifang Niu, Kai Ye, Qunyuan Zhang, Charles Lu, Mingchao Xie, Michael D McLellan, Michael C Wendl, Li Ding

    Bioinformatics (2013) doi: 10.1093/bioinformatics/btt755

  • 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.

  • MuSiC: Identifying mutational significance in cancer genomes.

    Dees ND, Zhang Q, Kandoth C, Wendl MC, Schierding W, Koboldt DC, Mooney TB, Callaway MB, Dooling D, Mardis ER, Wilson RK, Ding L.

    Genome Res. 2012 Aug;22(8):1589-98. doi: 10.1101/gr.134635.111. Epub 2012 Jul 3.

  • Mutational landscape and significance across 12 major cancer types

    Cyriac Kandoth, Michael D McLellan, Fabio Vandin, Kai Ye, Beifang Niu, Charles Lu, Mingchao Xie, Qunyuan Zhang, Joshua F McMichael, Matthew A Wyczalkowski, Mark DM Leiserson, Christopher A Miller, John S Welch, Matthew J Walter, Michael C Wendl, Timothy J Ley, Richard K Wilson, Benjamin J Raphael, Li Ding

    Nature 502 (7471), 333-339 (17 October 2013) doi:10.1038/nature12634

  • PASSion: a pattern growth algorithm-based pipeline for splice junction detection in paired-end RNA-Seq data.

    Zhang Y, Lameijer EW, 't Hoen PA, Ning Z, Slagboom PE, Ye K.

    Bioinformatics. 2012 Feb 15;28(4):479-86. doi: 10.1093/bioinformatics/btr712. Epub 2012 Jan 4.

  • PathScan: a tool for discerning mutational significance in groups of putative cancer genes.

    Wendl MC, Wallis JW, Lin L, Kandoth C, Mardis ER, Wilson RK, Ding L.

    Bioinformatics. 2011 Jun 15;27(12):1595-602. doi: 10.1093/bioinformatics/btr193. Epub 2011 Apr 14.

  • Pindel: a pattern growth approach to detect break points of large deletions and medium sized insertions from paired-end short reads.

    Ye K, Schulz MH, Long Q, Apweiler R, Ning Z.

    Bioinformatics. 2009 Nov 1;25(21):2865-71. doi: 10.1093/bioinformatics/btp394. Epub 2009 Jun 26.

  • Recurring mutations found by sequencing an acute myeloid leukemia genome.

    Mardis ER, Ding L, Dooling DJ, Larson DE, McLellan MD, Chen K, Koboldt DC, Fulton RS, Delehaunty KD, McGrath SD, Fulton LA, Locke DP, Magrini VJ, Abbott RM, Vickery TL, Reed JS, Robinson JS, Wylie T, Smith SM, Carmichael L, Eldred JM, Harris CC, Walker J, Peck JB, Du F, Dukes AF, Sanderson GE, Brummett AM, Clark E, McMichael JF, Meyer RJ, Schindler JK, Pohl CS, Wallis JW, Shi X, Lin L, Schmidt H, Tang Y, Haipek C, Wiechert ME, Ivy JV, Kalicki J, Elliott G, Ries RE, Payton JE, Westervelt P, Tomasson MH, Watson MA, Baty J, Heath S, Shannon WD, Nagarajan R, Link DC, Walter MJ, Graubert TA, DiPersio JF, Wilson RK, Ley TJ.

    N Engl J Med. 2009 Sep 10;361(11):1058-66. doi: 10.1056/NEJMoa0903840. Epub 2009 Aug 5.

  • SciClone: Inferring clonal architecture and tracking the spatial and temporal patterns of tumor evolution.

    Christopher A. Miller*, Brian S. White*, Nathan D. Dees, John S. Welch, Malachi Griffith, Obi Griffith, Ravi Vij, Michael H. Tomasson, Timothy A. Graubert, Matthew J. Walter, William Schierding, Timothy J. Ley, John F. DiPersio, Elaine R. Mardis, Richard K. Wilson, and Li Ding

    Submitted to PLoS Computational Biology

  • Somatic mutations affect key pathways in lung adenocarcinoma.

    Ding L, Getz G, Wheeler DA, Mardis ER, McLellan MD, Cibulskis K, Sougnez C, Greulich H, Muzny DM, Morgan MB, Fulton L, Fulton RS, Zhang Q, Wendl MC, Lawrence MS, Larson DE, Chen K, Dooling DJ, Sabo A, Hawes AC, Shen H, Jhangiani SN, Lewis LR, Hall O, Zhu Y, Mathew T, Ren Y, Yao J, Scherer SE, Clerc K, Metcalf GA, Ng B, Milosavljevic A, Gonzalez-Garay ML, Osborne JR, Meyer R, Shi X, Tang Y, Koboldt DC, Lin L, Abbott R, Miner TL, Pohl C, Fewell G, Haipek C, Schmidt H, Dunford-Shore BH, Kraja A, Crosby SD, Sawyer CS, Vickery T, Sander S, Robinson J, Winckler W, Baldwin J, Chirieac LR, Dutt A, Fennell T, Hanna M, Johnson BE, Onofrio RC, Thomas RK, Tonon G, Weir BA, Zhao X, Ziaugra L, Zody MC, Giordano T, Orringer MB, Roth JA, Spitz MR, Wistuba II, Ozenberger B, Good PJ, Chang AC, Beer DG, Watson MA, Ladanyi M, Broderick S, Yoshizawa A, Travis WD, Pao W, Province MA, Weinstock GM, Varmus HE, Gabriel SB, Lander ES, Gibbs RA, Meyerson M, Wilson RK.

    Nature. 2008 Oct 23;455(7216):1069-75. doi: 10.1038/nature07423.

  • SomaticSniper: identification of somatic point mutations in whole genome sequencing data.

    Larson DE, Harris CC, Chen K, Koboldt DC, Abbott TE, Dooling DJ, Ley TJ, Mardis ER, Wilson RK, Ding L.

    Bioinformatics. 2012 Feb 1;28(3):311-7. doi: 10.1093/bioinformatics/btr665. Epub 2011 Dec 6.

  • TIGRA: A Targeted Iterative Graph Routing Assembler for Breakpoint Assembly

    Ken Chen, Lei Chen, Xian Fan, John Wallis, Li Ding, George Weinstock

    Genome Res. published online December 4, 2013 (DOI: 10.1101/gr.162883.113)

  • VarScan 2: Somatic mutation and copy number alteration discovery in cancer by exome sequencing.

    Koboldt DC, Zhang Q, Larson DE, Shen D, McLellan MD, Lin L, Miller CA, Mardis ER, Ding L, Wilson RK.

    Genome Res. 2012 Mar;22(3):568-76. doi: 10.1101/gr.129684.111. Epub 2012 Feb 2.

  • VarScan: variant detection in massively parallel sequencing of individual and pooled samples.

    Koboldt DC, Chen K, Wylie T, Larson DE, McLellan MD, Mardis ER, Weinstock GM, Wilson RK, Ding L.

    Bioinformatics. 2009 Sep 1;25(17):2283-5. doi: 10.1093/bioinformatics/btp373. Epub 2009 Jun 19.