Pre-2006 | 2007 | 2008 | 2009 | 2010 | 2011 | 2012 | 20132014 | 2015 | 2016 | 2017

*  These authors contributed equally to this work


2017

Comprehensive and Integrated Genomic Characterization of Adult Soft Tissue Sarcomas
Cancer Genome Atlas Network (Corresponding author Ding L. Contributors include: Bailey MH, Gao Q, Wong W, Wyczalkowski M, Yellapantula V)
Cell. 2017 Nov 2;171(4):950-965

MIRMMR: binary classification of microsatellite instability using methylation and mutations
Foltz S, Liang W, Xie M, and Ding L
Bioinformatics 7 (August 17, 2017): 153–62

Breast tumors educate the proteome of stromal tissue in an individualized but coordinated manner
Wang X, Mooradian AD, Erdmann-Gilmore P, Zhang Q, Viner R, Davies SR, Huang KL, Bomgarden R, Van Tine BA, Shao J, Ding L, Li S, Ellis MJ, Rogers JC, Townsend RR, Fenyo D, Held JM
Sci Signal 2017 Aug 8;10(491)

DNA defects, epigenetics, and gene expression in cancer-adjacent breast: a study from The Cancer Genome Atlas
Troester MA, Hoadley KA, D'Arcy M, Cherniack AD, Stewart C, Koboldt DC, Robertson AG, Mahurkar S, Shen H, Wilkerson MD, Sandhu R, Johnson NB, Allison KH, Beck AH, Yau C, Bowen J, Sheth M, Hwang ES, Perou CM, Laird PW, Ding L, Benz CC
NPJ Breast Cancer 2016 May 4;2:16007

Integrative genomic analysis of cholangiocarcinoma identifies distinct IDH-mutant molecular profiles
Farshidfar F, Zheng S, Gingras MC, Newton Y, Shih J, Robertson AG, Hinoue T, Hoadley KA, Gibb EA, Roszik J, Covington KR, Wu CC, Shinbrot E, Stransky N, Hegde A, Yang JD, Reznik E, Sadeghi S, Pedamallu CS, Ojesina AI, Hess JM, Auman JT, Rhie SK, Bowlby R, Borad MJ, Zhu AX, Stuart JM, Sander C, Akbani R, Cherniack AD, Deshpande V, Mounajjed T, Foo WC, Torbenson MS, Kleiner DE, Laird PW, Wheeler DA, McRee AJ, Bathe OF, Andersen JB, Bardeesy N, Roberts LR, Kwong LN
Cancer Genome Atlas Network (Contributors include: Ding L)
Cell Rep 2017 Jun 27;19(13):2878-2880

BreakPoint Surveyor: a pipeline for structural variant visualization
Wyczalkowski MA, Wylie KM, Cao S, McLellan MD, Flynn J, Huang M, Ye K, Fan X, Chen K, Wendl MC, Ding L
Bioinformatics 2017 Jun 5; [Epub ahead of print]

GenomeVIP: a cloud platform for genomic variant discovery and interpretation
Mashl RJ, Scott AS, Huang KL, Wyczalkowski MA, Yoon CJ, Niu B, DeNardo E, Yellapantula VD, Handsaker RE, Chen K, Koboldt DC, Ye K, Fenyö D, Raphael B, Wendl MC, Ding L
Genome Res 2017 May 18; [Epub ahead of print]

Proteogenomic integration reveals therapeutic targets in breast cancer xenografts
Huang KL, Li S, Mertins P, Cao S, Gunawardena HP, Ruggles KV, Mani DR, Clauser KR, Tanioka M, Usary J, Kavuri SM, Xie L, Yoon C, Qiao JW, Wrobel J, Wyczalkowski MA, Erdmann-Gilmore P, Snider JE, Hoog J, Singh P, Niu B, Guo Z, Sun SQ, Sanati S, Kawaler E, Wang X, Scott A, Ye K, McLellan MD, Wendl MC, Malovannaya A, Held JM, Gillette MA, Fenyo D, Kinsinger CR, Mesri M, Rodriguez H, Davies SR, Perou CM, Ma C, Reid Townsend R, Chen X, Carr SA, Ellis MJ, Ding L
Nat Commun 2017 Mar 28;8:14864

CTCF genetic alterations in endometrial carcinoma are pro-tumorigenic
Marshall AD, Bailey CG, Champ K, Vellozzi M, O'Young P, Metierre C, Feng Y, Thoeng A, Richards AM, Schmitz U, Biro M, Jayasinghe R, Ding L, Anderson L, Mardis ER, Rasko JE
Oncogene 2017 Mar 20; [Epub ahead of print]

Integrated genomic and molecular characterization of cervical cancer
Cancer Genome Atlas Research Network (Contributors include: Ding L, Bailey M, Wyczalkowski M)
Nature 2017 Mar 16;543(7645):378-384

Precancerous clonal expansion: a new therapeutic target?
Ding L, Chen F
J Clin Oncol 2017 Mar 14:JCO2017722868; [Epub ahead of print]

Integrated genomic characterization of oesophageal carcinoma
Cancer Genome Atlas Research Network (Contributors include: Ding L)
Nature 2017 Jan 12;541(7636):169-175


Tumor evolution in two patients with basal-like breast cancer: a retrospective genomics study of multiple metastases
Hoadley KA, Siegel MB, Kanchi KL, Miller CA, Ding L, Zhao W, He X, Parker JS, Wendl MC, Fulton RS, Demeter RT, Wilson RK, Carey LA, Perou CM, Mardis ER
PLoS Med 2016 Dec 6;13(12):e1002174

novoBreak: local assembly for breakpoint detection in cancer genomes
Chong Z, Ruan J, Gao M, Zhou W, Chen T, Fan X, Ding L, Lee AY, Boutros P, Chen J, Chen K
Nat Methods 2016 Nov 28; [Epub ahead of print]

Visualizing tumor evolution with the fishplot package for R
Miller CA, McMichael J, Dang HX, Maher CA, Ding L, Ley TJ, Mardis ER, Wilson RK
BMC Genomics 2016 Nov 7;17(1):880

The genomic landscape of core-binding factor acute myeloid leukemias
Faber ZJ, Chen X, Gedman AL, Boggs K, Cheng J, Ma J, Radtke I, Chao JR, Walsh MP, Song G, Andersson AK, Dang J, Dong L, Liu Y, Huether R, Cai Z, Mulder H, Wu G, Edmonson M, Rusch M, Qu C, Li Y, Vadodaria B, Wang J, Hedlund E, Cao X, Yergeau D, Nakitandwe J, Pounds SB, Shurtleff S, Fulton RS, Fulton LL, Easton J, Parganas E, Pui CH, Rubnitz JE, Ding L, Mardis ER, Wilson RK, Gruber TA, Mullighan CG, Schlenk RF, Paschka P, Dohner K, Dohner H, Bullinger L, Zhang J, Klco JM, Downing JR
Nat Genet 2016 Oct 31; [Epub ahead of print]

Deregulation of DUX4 and ERG in acute lymphoblastic leukemia
Zhang J, McCastlain K, Yoshihara H, Xu B, Chang Y, Churchman ML, Wu G, Li Y, Wei L, Iacobucci I, Liu Y, Qu C, Wen J, Edmonson M, Payne-Turner D, Kaufmann KB, Takayanagi SI, Wienholds E, Waanders E, Ntziachristos P, Bakogianni S, Wang J, Aifantis I, Roberts KG, Ma J, Song G, Easton J, Mulder HL, Chen X, Newman S, Ma X, Rusch M, Gupta P, Boggs K, Vadodaria B, Dalton J, Liu Y, Valentine ML, Ding L, Lu C, Fulton RS, Fulton L, Tabib Y, Ochoa K, Devidas M, Pei D, Cheng C, Yang J, Evans WE, Relling MV, Pui CH, Jeha S, Harvey RC, Chen IL, Willman CL, Marcucci G, Bloomfield CD, Kohlschmidt J, Mrozek K, Paietta E, Tallman MS, Stock W, Foster MC, Racevskis J, Rowe JM, Luger S, Kornblau SM, Shurtleff SA, Raimondi SC, Mardis ER, Wilson RK, Dick JE, Hunger SP, Loh ML, Downing JR, Mullighan CG
St. Jude Children's Research Hospital-Washington University Pediatric Cancer Genome Project
Nat Genet 2016 Oct 24; [Epub ahead of print]

The impact of chromosomal translocation locus and fusion oncogene coding sequence in synovial sarcomagenesis
Jones KB, Barrott JJ, Xie M, Haldar M, Jin H, Zhu JF, Monument MJ, Mosbruger TL, Langer EM, Randall RL, Wilson RK, Cairns BR, Ding L, Capecchi MR
Oncogene 2016 Sep 22;35(38):5021-32

Integrated proteogenomic characterization of human high-grade serous ovarian cancer
Zhang H, Liu T, Zhang Z, Payne SH, Zhang B, McDermott JE, Zhou JY, Petyuk VA, Chen L, Ray D, Sun S, Yang F, Chen L, Wang J, Shah P, Cha SW, Aiyetan P, Woo S, Tian Y, Gritsenko MA, Clauss TR, Choi C, Monroe ME, Thomas S, Nie S, Wu C, Moore RJ, Yu KH, Tabb DL, Fenyo D, Bafna V, Wang Y, Rodriguez H, Boja ES, Hiltke T, Rivers RC, Sokoll L, Zhu H, Shih IM, Cope L, Pandey A, Zhang B, Snyder MP, Levine DA, Smith RD, Chan DW, Rodland KD
CPTAC Investigators (Contributors include: Ding L)
Cell 2016 Jul 28;166(3):755-765

Protein-structure-guided discovery of functional mutations across 19 cancer types
Niu B, Scott AD, Sengupta S, Bailey MH, Batra P, Ning J, Wyczalkowski MA, Liang WW, Zhang Q, McLellan MD, Sun SQ, Tripathi P, Lou C, Ye K, Mashl RJ, Wallis J, Wendl MC, Chen F, Ding L
Nat Genet 2016 Aug;48(8):827-37

Divergent viral presentation among human tumors and adjacent normal tissues
Cao S, Wendl MC, Wyczalkowski MA, Wylie K, Ye K, Jayasinghe R, Xie M, Wu S, Niu B, Grubb R 3rd, Johnson KJ, Gay H, Chen K, Rader JS, DiPersio JF, Chen F, Ding L
Sci Rep 2016 Jun 24;6:28294

NFATc1 promotes prostate tumorigenesis and overcomes PTEN loss-induced senescence
Manda KR, Tripathi P, Hsi AC, Ning J, Ruzinova MB, Liapis H, Bailey M, Zhang H, Maher CA, Humphrey PA, Andriole GL, Ding L, You Z, Chen F
Oncogene 2016 Jun 23;35(25):3282-92

Proteogenomics connects somatic mutations to signalling in breast cancer
Mertins P*, Mani DR*, Ruggles KV*, Gillette MA*, Clauser KR, Wang P, Wang X, Qiao JW, Cao S, Petralia F, Kawaler E, Mundt F, Krug K, Tu Z, Lei JT, Gatza ML, Wilkerson M, Perou CM, Yellapantula V, Huang KL, Lin C, McLellan MD, Yan P, Davies SR, Townsend RR, Skates SJ, Wang J, Zhang B, Kinsinger CR, Mesri M, Rodriguez H, Ding L, Paulovich AG, Fenyo D, Ellis MJ, Carr SA
NCI CPTAC
Nature 2016 May 25;534(7605):55-62

An analysis of the sensitivity of proteogenomic mapping of somatic mutations and novel splicing events in cancer
Ruggles KV, Tang Z, Wang X, Grover H, Askenazi M, Teubl J, Cao S, McLellan MD, Clauser KR, Tabb DL, Mertins P, Slebos R, Erdmann-Gilmore P, Li S, Gunawardena HP, Xie L, Liu T, Zhou JY, Sun S, Hoadley KA, Perou CM, Chen X, Davies SR, Maher CA, Kinsinger CR, Rodland KD, Zhang H, Zhang Z, Ding L, Townsend RR, Rodriguez H, Chan D, Smith RD, Liebler DC, Carr SA, Payne S, Ellis MJ, Fenyo D
Mol Cell Proteomics 2016 Mar;15(3):1060-71

Systematic discovery of complex insertions and deletions in human cancers
Ye K, Wang J, Jayasinghe R, Lameijer EW, McMichael JF, Ning J, McLellan MD, Xie M, Cao S, Yellapantula V, Huang KL, Scott A, Foltz S, Niu B, Johnson KJ, Moed M, Slagboom PE, Chen F, Wendl MC, Ding L
Nat Med 2016 Jan;22(1):97-104


Patterns and functional implications of rare germline variants across 12 cancer types
Lu C*, Xie M*, Wendl MC*, Wang J*, McLellan MD*, Leiserson MD*, Huang KL, Wyczalkowski MA, Jayasinghe R, Banerjee T, Ning J, Tripathi P, Zhang Q, Niu B, Ye K, Schmidt HK, Fulton RS, McMichael JF, Batra P, Kandoth C, Bharadwaj M, Koboldt DC, Miller CA, Kanchi KL, Eldred JM, Larson DE, Welch JS, You M, Ozenberger BA, Govindan R, Walter MJ, Ellis MJ, Mardis ER, Graubert TA, DiPersio JF, Ley TJ, Wilson RK, Goodfellow PJ, Raphael BJ, Chen F, Johnson KJ, Parvin JD, Ding L
Nat Commun 2015 Dec 22;6:10086

Germline mutations in predisposition genes in pediatric cancer
Zhang J*, Walsh MF*, Wu G*, Edmonson MN, Gruber TA, Easton J, Hedges D, Ma X, Zhou X, Yergeau DA, Wilkinson MR, Vadodaria B, Chen X, McGee RB, Hines-Dowell S, Nuccio R, Quinn E, Shurtleff SA, Rusch M, Patel A, Becksfort JB, Wang S, Weaver MS, Ding L, Mardis ER, Wilson RK, Gajjar A, Ellison DW, Pappo AS, Pui CH, Nichols KE, Downing JR
N Engl J Med 2015 Dec 10;373(24):2336-2346

Optimizing cancer genome sequencing and analysis
Griffith M*, Miller CA*, Griffith OL, Krysiak K, Skidmore ZL, Ramu A, Walker JR, Dang HX, Trani L, Larson DE, Demeter RT, Wendl MC, McMichael JF, Austin RE, Magrini V, McGrath SD, Ly A, Kulkarni S, Cordes MG, Fronick CC, Fulton RS, Maher CA, Ding L, Klco JM, Mardis ER, Ley TJ, Wilson RK
Cell Syst 2015 Sep 23;1(3):210-223

Comprehensive molecular portraits of invasive lobular breast cancer
Ciriello G*, Gatza ML*, Beck AH, Wilkerson MD, Rhie SK, Pastore A, Zhang H, McLellan M, Yau C, Kandoth C, Bowlby R, Shen H, Hayat S, Fieldhouse R, Lester SC, Tse GM, Factor RE, Collins LC, Allison KH, Chen YY, Jensen K, Johnson NB, Oesterreich S, Mills GB, Cherniack AD, Robertson G, Benz C, Sander C, Laird PW, Hoadley KA, King TA, Perou CM
TCGA Research Network (Contributors include: Ding L)
Cell 2015 Oct 8;163(2):506-519

The dynamic genome and transcriptome of the human fungal pathogen Blastomyces and close relative Emmonsia
Muñoz JF*, Gauthier GM*, Desjardins CA*, Gallo JE, Holder J, Sullivan TD, Marty AJ, Carmen JC, Chen Z, Ding L, Gujja S, Magrini V, Misas E, Mitreva M, Priest M, Saif S, Whiston EA, Young S, Zeng Q, Goldman WE, Mardis ER, Taylor JW, McEwen JG, Clay OK, Klein BS, Cuomo CA
PLoS Genet 2015 Oct 6;11(10):e1005493

An integrated map of structural variation in 2,504 human genomes
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, Stutz AM, Shi X, Paolo Casale F, Chen J, Hormozdiari F, Dayama G, Chen K, Malig M, Chaisson MJ, Walter K, Meiers S, Kashin S, Garrison E, Auton A, Lam HY, Jasmine Mu X, 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, Mills RE, Gerstein MB, Bashir A, Stegle O, Devine SE, Lee C, Eichler EE, Korbel JO
1000 Genomes Project Consortium
Nature 2015 Sep 30;526(7571):75-81

A global reference for human genetic variation
1000 Genomes Project Consortium (Contributors include: Ding L)
Nature 2015 Sep 30;526(7571):68-74

Association of somatic mutations of ADAMTS genes with chemotherapy sensitivity and survival in high-grade serous ovarian carcinoma
Liu Y, Yasukawa M, Chen K, Hu L, Broaddus RR, Ding L, Mardis ER, Spellman P, Levine DA, Mills GB, Shmulevich I, Sood AK, Zhang W
JAMA Oncol 2015 Jul 1;1(4):486-494

Genome Modeling System: a knowledge management platform for genomics
Griffith M*, Griffith OL*, Smith SM*, Ramu A, Callaway MB, Brummett AM, Kiwala MJ, Coffman AC, Regier AA, Oberkfell BJ, Sanderson GE, Mooney TP, Nutter NG, Belter EA, Du F, Long RL, Abbott TE, Ferguson IT, Morton DL, Burnett MM, Weible JV, Peck JB, Dukes A, McMichael JF, Lolofie JT, Derickson BR, Hundal J, Skidmore ZL, Ainscough BJ, Dees ND, Schierding WS, Kandoth C, Kim KH, Lu C, Harris CC, Maher N, Maher CA, Magrini VJ, Abbott BS, Chen K, Clark E, Das I, Fan X, Hawkins AE, Hepler TG, Wylie TN, Leonard SM, Schroeder WE, Shi X, Carmichael LK, Weil MR, Wohlstadter RW, Stiehr G, McLellan MD, Pohl CS, Miller CA, Koboldt DC, Walker JR, Eldred JM, Larson DE, Dooling DJ, Ding L, Mardis ER, Wilson RK
PLoS Comput Biol 2015 Jul 9;11(7):e1004274

U2AF1 mutations alter sequence specificity of pre-mRNA binding and splicing
Okeyo-Owuor T, White BS, Chatrikhi R, Mohan DR, Kim S, Griffith M, Ding L, Ketkar-Kulkarni S, Hundal J, Laird KM, Kielkopf CL, Ley TJ, Walter MJ, Graubert TA
Leukemia 2015 Apr;29(4):909-917

The landscape of somatic mutations in infant MLL-rearranged acute lymphoblastic leukemias
Andersson AK*, Ma J*, Wang J, Chen X, Gedman AL, Dang J, Nakitandwe J, Holmfeldt L, Parker M, Easton J, Huether R, Kriwacki R, Rusch M, Wu G, Li Y, Mulder H, Raimondi S, Pounds S, Kang G, Shi L, Becksfort J, Gupta P, Payne-Turner D, Vadodaria B, Boggs K, Yergeau D, Manne J, Song G, Edmonson M, Nagahawatte P, Wei L, Cheng C, Pei D, Sutton R, Venn NC, Chetcuti A, Rush A, Catchpoole D, Heldrup J, Fioretos T, Lu C, Ding L, Pui CH, Shurtleff S, Mullighan CG, Mardis ER, Wilson RK, Gruber TA, Zhang J, Downing JR
St. Jude Children's Research Hospital-Washington University Pediatric Cancer Genome Project
Nat Genet 2015 Apr;47(4):330-337

The genomic landscape of childhood and adolescent melanoma
Lu C*, Zhang J*, Nagahawatte P, Easton J, Lee S, Liu Z, Ding L, Wyczalkowski MA, Valentine M, Navid F, Mulder H, Tatevossian RG, Dalton J, Davenport J, Yin Z, Edmonson M, Rusch M, Wu G, Li Y, Parker M, Hedlund E, Shurtleff S, Raimondi S, Bhavin V, Donald Y, Mardis ER, Wilson RK, Evans WE, Ellison DW, Pounds S, Dyer M, Downing JR, Pappo A, Bahrami A
J Invest Dermatol 2015 Mar;135(3):816-23

Role of TP53 mutations in the origin and evolution of therapy-related acute myeloid leukaemia
Wong TN*, Ramsingh G*, Young AL*, Miller CA, Touma W, Welch JS, Lamprecht TL, Shen D, Hundal J, Fulton RS, Heath S, Baty JD, Klco JM, Ding L, Mardis ER, Westervelt P, DiPersio JF, Walter MJ, Graubert TA, Ley TJ, Druley TE, Link DC, Wilson RK
Nature 2015 Feb 26;518(7540):552-555


Integrating sequence and array data to create an improved 1000 Genomes Project haplotype reference panel
Delaneau O, Marchini J
1000 Genomes Project Consortium (Contributors include: Ding L)
Nat Commun 2014 Jun 13;5:3934

Pan-cancer network analysis identifies combinations of rare somatic mutations across pathways and protein complexes
Leiserson MD*, Vandin F*, Wu HT, Dobson JR, Eldridge JV, Thomas JL, Papoutsaki A, Kim Y, Niu B, McLellan M, Lawrence MS, Gonzalez-Perez A, Tamborero D, Cheng Y, Ryslik GA, Lopez-Bigas N, Getz G, Ding L, Raphael BJ
Nat Genet 2015 Feb;47(2):106-14

Age-related mutations associated with clonal hematopoietic expansion and malignancies
Xie M*, Lu C*, Wang J*, McLellan MD, Johnson KJ, Wendl MC, McMichael JF, Schmidt HK, Yellapantula V, Miller CA, Ozenberger BA, Welch JS, Link DC, Walter MJ, Mardis ER, DiPersio JF, Chen F, Wilson RK, Ley TJ, Ding L
Nat Med 2014 Dec;20(12):1472-1478

Clonal architectures and driver mutations in metastatic melanomas
Ding L*, Kim M*, Kanchi KL*, Dees ND, Lu C, Griffith M, Fenstermacher D, Sung H, Miller CA, Goetz B, Wendl MC, Griffith O, Cornelius LA, Linette GP, McMichael JF, Sondak VK, Fields RC, Ley TJ, Mule JJ, Wilson RK, Weber JS
PLoS One 2014 Nov 13;9(11):e111153

Genomic landscape of Ewing sarcoma defines an aggressive subtype with co-association of STAG2 and TP53 mutations
Tirode F*, Surdez D*, Ma X, Parker M, Le Deley MC, Bahrami A, Zhang Z, Lapouble E, Grossetete-Lalami S, Rusch M, Reynaud S, Rio-Frio T, Hedlund E, Wu G, Chen X, Pierron G, Oberlin O, Zaidi S, Lemmon G, Gupta P, Vadodaria B, Easton J, Gut M, Ding L, Mardis ER, Wilson RK, Shurtleff S, Laurence V, Michon J, Marec-Berard P, Gut I, Downing J, Dyer M, Zhang J, Delattre O
St. Jude Children's Research Hospital-Washington University Pediatric Cancer Genome Project and the International Cancer Genome Consortium
Cancer Discov 2014 Nov;4(11):1342-53

Proteogenomic characterization of human colon and rectal cancer
Zhang B, Wang J, Wang X, Zhu J, Liu Q, Shi Z, Chambers MC, Zimmerman LJ, Shaddox KF, Kim S, Davies SR, Wang S, Wang P, Kinsinger CR, Rivers RC, Rodriguez H, Townsend RR, Ellis MJ, Carr SA, Tabb DL, Coffey RJ, Slebos RJ, Liebler DC
NCI CPTAC (Contributors include: Ding L)
Nature 2014 Sep 18;513(7518):382-7

Comprehensive molecular characterization of gastric adenocarcinoma
Cancer Genome Atlas Research Network (Contributors include: Ding L)
Nature 2014 Sep 11;513(7517):202-9

Targetable kinase-activating lesions in Ph-like acute lymphoblastic leukemia
Roberts KG*, Li Y*, Payne-Turner D, Harvey RC, Yang YL, Pei D, McCastlain K, Ding L, Lu C, Song G, Ma J, Becksfort J, Rusch M, Chen SC, Easton J, Cheng J, Boggs K, Santiago-Morales N, Iacobucci I, Fulton RS, Wen J, Valentine M, Cheng C, Paugh SW, Devidas M, Chen IM, Reshmi S, Smith A, Hedlund E, Gupta P, Nagahawatte P, Wu G, Chen X, Yergeau D, Vadodaria B, Mulder H, Winick NJ, Larsen EC, Carroll WL, Heerema NA, Carroll AJ, Grayson G, Tasian SK, Moore AS, Keller F, Frei-Jones M, Whitlock JA, Raetz EA, White DL, Hughes TP, Guidry Auvil JM, Smith MA, Marcucci G, Bloomfield CD, Mrozek K, Kohlschmidt J, Stock W, Kornblau SM, Konopleva M, Paietta E, Pui CH, Jeha S, Relling MV, Evans WE, Gerhard DS, Gastier-Foster JM, Mardis E, Wilson RK, Loh ML, Downing JR, Hunger SP, Willman CL, Zhang J, Mullighan CG
N Engl J Med 2014 Sep 11;371(11):1005-1015

Multiplatform analysis of 12 cancer types reveals molecular classification within and across tissues of origin
Hoadley KA*, Yau C*, Wolf DM*, Cherniack AD*, Tamborero D, Ng S, Leiserson MD, Niu B, McLellan MD, Uzunangelov V, Zhang J, Kandoth C, Akbani R, Shen H, Omberg L, Chu A, Margolin AA, Van't Veer LJ, Lopez-Bigas N, Laird PW, Raphael BJ, Ding L, Robertson AG, Byers LA, Mills GB, Weinstein JN, Van Waes C, Chen Z, Collisson EA, Benz CC, Perou CM, Stuart JM
The Cancer Genome Atlas Research Network
Cell 2014 Aug 14;158(4):929-944

SciClone: inferring clonal architecture and tracking the spatial and temporal patterns of tumor evolution
Miller CA*, White BS*, Dees ND, Griffith M, Welch JS, Griffith OL, Vij R, Tomasson MH, Graubert TA, Walter MJ, Ellis MJ, Schierding W, DiPersio JF, Ley TJ, Mardis ER, Wilson RK, Ding L
PLoS Comput Biol 2014 Aug 7;10(8):e1003665

Comprehensive molecular profiling of lung adenocarcinoma
The Cancer Genome Atlas Research Network (Contributors include: Ding L)
Nature 2014 Jul 31;511(7511):543-550

Clonal architecture of secondary acute myeloid leukemia defined by single-cell sequencing
Hughes AE, Magrini V, Demeter R, Miller CA, Fulton R, Fulton LL, Eades WC, Elliott K, Heath S, Westervelt P, Ding L, Conrad DF, White BS, Shao J, Link DC, DiPersio JF, Mardis ER, Wilson RK, Ley TJ, Walter MJ, Graubert TA
PLoS Genet 2014 Jul 10;10(7):e1004462

The genomic landscape of diffuse intrinsic pontine glioma and pediatric non-brainstem high-grade glioma
Wu G*, Diaz AK*, Paugh BS, Rankin SL, Ju B, Li Y, Zhu X, Qu C, Chen X, Zhang J, Easton J, Edmonson M, Ma X, Lu C, Nagahawatte P, Hedlund E, Rusch M, Pounds S, Lin T, Onar-Thomas A, Huether R, Kriwacki R, Parker M, Gupta P, Becksfort J, Wei L, Mulder HL, Boggs K, Vadodaria B, Yergeau D, Russell JC, Ochoa K, Fulton RS, Fulton LL, Jones C, Boop FA, Broniscer A, Wetmore C, Gajjar A, Ding L, Mardis ER, Wilson RK, Taylor MR, Downing JR, Ellison DW, Zhang J, Baker SJ
Nat Genet 2014 May;46(5):444-50

Activation of NFAT signaling establishes a tumorigenic microenvironment through cell autonomous and non-cell autonomous mechanisms
Tripathi P, Wang Y, Coussens M, Manda KR, Casey AM, Lin C, Poyo E, Pfeifer JD, Basappa N, Bates CM, Ma L, Zhang H, Pan M, Ding L, Chen F
Oncogene 2014 Apr 3;33(14):1840-9

The landscape of somatic mutations in epigenetic regulators across 1,000 paediatric cancer genomes
Huether R*, Dong L*, Chen X, Wu G, Parker M, Wei L, Ma J, Edmonson MN, Hedlund EK, Rusch MC, Shurtleff SA, Mulder HL, Boggs K, Vadordaria B, Cheng J, Yergeau D, Song G, Becksfort J, Lemmon G, Weber C, Cai Z, Dang J, Walsh M, Gedman AL, Faber Z, Easton J, Gruber T, Kriwacki RW, Partridge JF, Ding L, Wilson RK, Mardis ER, Mullighan CG, Gilbertson RJ, Baker SJ, Zambetti G, Ellison DW, Zhang J, Downing JR
Nat Commun 2014 Apr 8;5:3630

MSIsensor: microsatellite instability detection using paired tumor-normal sequence data
Niu B*, Ye K*, Zhang Q, Lu C, Xie M, McLellan MD, Wendl MC, Ding L
Bioinformatics 2014 Apr 1;30(7):1015-6

C11orf95-RELA fusions drive oncogenic NF-kappaB signalling in ependymoma
Parker M*, Mohankumar KM*, Punchihewa C*, Weinlich R*, Dalton JD, Li Y, Lee R, Tatevossian RG, Phoenix TN, Thiruvenkatam R, White E, Tang B, Orisme W, Gupta K, Rusch M, Chen X, Li Y, Nagahawhatte P, Hedlund E, Finkelstein D, Wu G, Shurtleff S, Easton J, Boggs K, Yergeau D, Vadodaria B, Mulder HL, Becksford J, Gupta P, Huether R, Ma J, Song G, Gajjar A, Merchant T, Boop F, Smith AA, Ding L, Lu C, Ochoa K, Zhao D, Fulton RS, Fulton LL, Mardis ER, Wilson RK, Downing JR, Green DR, Zhang J, Ellison DW, Gilbertson RJ
Nature 2014 Feb 27;506(7489):451-5

High frequency strand slippage mutations in CTCF in MSI-positive endometrial cancers
Zighelboim I, Mutch DG, Knapp A, Ding L, Xie M, Cohn DE, Goodfellow PJ
Hum Mutat 2014 Jan;35(1):63-5

TIGRA: A targeted iterative graph routing assembler for breakpoint assembly
Chen K*, Chen L*, Fan X*, Wallis J, Ding L, Weinstock G
Genome Res 2014 Feb;24(2):310-7

Integrated analysis of germline and somatic variants in ovarian cancer
Kanchi KL*, Johnson KJ*, Lu C*, McLellan MD, Leiserson MD, Wendl MC, Zhang Q, Koboldt DC, Xie M, Kandoth C, McMichael JF, Wyczalkowski MA, Larson DE, Schmidt HK, Miller CA, Fulton RS, Spellman PT, Mardis ER, Druley TE, Graubert TA, Goodfellow PJ, Raphael BJ, Wilson RK, Ding L
Nat Commun 2014 Jan 22;5:3156


DGIdb: mining the druggable genome
Griffith M*, Griffith OL*, Coffman AC, Weible JV, McMichael JF, Spies NC, Koval J, Das I, Callaway MB, Eldred JM, Miller CA, Subramanian J, Govindan R, Kumar RD, Bose R, Ding L, Walker JR, Larson DE, Dooling DJ, Smith SM, Ley TJ, Mardis ER, Wilson RK
Nat Methods 2013 Dec;10(12):1209-10

Identification of a pan-cancer oncogenic microRNA superfamily anchored by a central core seed motif
Hamilton MP, Rajapakshe K, Hartig SM, Reva B, McLellan MD, Kandoth C, Ding L, Zack TI, Gunaratne PH, Wheeler DA, Coarfa C, McGuire SE
Nat Commun 2013;4:2730

Mutational landscape and significance across 12 major cancer types
Kandoth C*, McLellan MD*, Vandin F, Ye K, Niu B, Lu C, Xie M, Zhang Q, McMichael JF, Wyczalkowski MA, Leiserson MD, Miller CA, Welch JS, Walter MJ, Wendl MC, Ley TJ, Wilson RK, Raphael BJ, Ding L
Nature 2013 Oct 17;502(7471):333-9

The somatic genomic landscape of glioblastoma
Brennan CW*, Verhaak RG*, McKenna A*, Campos B, Noushmehr H, Salama SR, Zheng S, Chakravarty D, Sanborn JZ, Berman SH, Beroukhim R, Bernard B, Wu CJ, Genovese G, Shmulevich I, Barnholtz-Sloan J, Zou L, Vegesna R, Shukla SA, Ciriello G, Yung WK, Zhang W, Sougnez C, Mikkelsen T, Aldape K, Bigner DD, Van Meir EG, Prados M, Sloan A, Black KL, Eschbacher J, Finocchiaro G, Friedman W, Andrews DW, Guha A, Iacocca M, O'Neill BP, Foltz G, Myers J, Weisenberger DJ, Penny R, Kucherlapati R, Perou CM, Hayes DN, Gibbs R, Marra M, Mills GB, Lander E, Spellman P, Wilson R, Sander C, Weinstein J, Meyerson M, Gabriel S, Laird PW, Haussler D, Getz G, Chin L; The Cancer Genome Atlas Research Network
Cell 2013 Oct 10;155(2):462-77

Comprehensive identification of mutational cancer driver genes across 12 tumor types
Tamborero D*, Gonzalez-Perez A*, Perez-Llamas C, Deu-Pons J, Kandoth C, Reimand J, Lawrence MS, Getz G, Bader GD, Ding L, Lopez-Bigas N
Sci Rep 2013 Oct 2;3:2650

Endocrine-therapy-resistant ESR1 variants revealed by genomic characterization of breast-cancer-derived xenografts
Li S*, Shen D*, Shao J, Crowder R, Liu W, Prat A, He X, Liu S, Hoog J, Lu C, Ding L, Griffith OL, Miller C, Larson D, Fulton RS, Harrison M, Mooney T, McMichael JF, Luo J, Tao Y, Goncalves R, Schlosberg C, Hiken JF, Saied L, Sanchez C, Giuntoli T, Bumb C, Cooper C, Kitchens RT, Lin A, Phommaly C, Davies SR, Zhang J, Kavuri MS, McEachern D, Dong YY, Ma C, Pluard T, Naughton M, Bose R, Suresh R, McDowell R, Michel L, Aft R, Gillanders W, DeSchryver K, Wilson RK, Wang S, Mills GB, Gonzalez-Angulo A, Edwards JR, Maher C, Perou CM, Mardis ER, Ellis MJ
Cell Rep 2013 Sep 26;4(6):1116-30

The Cancer Genome Atlas Pan-Cancer analysis project
Weinstein JN, Collisson EA, Mills GB, Shaw KR, Ozenberger BA, Ellrott K, Shmulevich I, Sander C, Stuart JM; The Cancer Genome Atlas Research Network
Nat Genet 2013 Oct;45(10):1113-20

BreakTrans: uncovering the genomic architecture of gene fusions
Chen K, Navin NE, Wang Y, Schmidt HK, Wallis JW, Niu B, Fan X, Zhao H, McLellan MD, Hoadley KA, Mardis ER, Ley TJ, Perou CM, Wilson RK, Ding L
Genome Biol 2013 Aug 23;14(8):R87

Computational approaches to identify functional genetic variants in cancer genomes
Gonzalez-Perez A*, Mustonen V*, Reva B*, Ritchie GR*, Creixell P, Karchin R, Vazquez M, Fink JL, Kassahn KS, Pearson JV, Bader GD, Boutros PC, Muthuswamy L, Ouellette BF, Reimand J, Linding R, Shibata T, Valencia A, Butler A, Dronov S, Flicek P, Shannon NB, Carter H, Ding L, Sander C, Stuart JM, Stein LD, Lopez-Bigas N
Nat Methods 2013 Aug;10(8):723-9

Clonal diversity of recurrently mutated genes in myelodysplastic syndromes
Walter MJ*, Shen D*, Shao J*, Ding L, White BS, Kandoth C, Miller CA, Niu B, McLellan MD, Dees ND, Fulton R, Elliot K, Heath S, Grillot M, Westervelt P, Link DC, DiPersio JF, Mardis E, Ley TJ, Wilson RK, Graubert TA
Leukemia 2013 Jun;27(6):1275-82

Genomic and epigenomic landscapes of adult de novo acute myeloid leukemia
Ley TJ, Miller C, Ding L, Raphael BJ, Mungall AJ, Robertson A, Hoadley K, Triche TJ Jr, Laird PW, Baty JD, Fulton LL, Fulton R, Heath SE, Kalicki-Veizer J, Kandoth C, Klco JM, Koboldt DC, Kanchi KL, Kulkarni S, Lamprecht TL, Larson DE, Lin L, Lu C, McLellan MD, McMichael JF, Payton J, Schmidt H, Spencer DH, Tomasson MH, Wallis JW, Wartman LD, Watson MA, Welch J, Wendl MC, Ally A, Balasundaram M, Birol I, Butterfield Y, Chiu R, Chu A, Chuah E, Chun HJ, Corbett R, Dhalla N, Guin R, He A, Hirst C, Hirst M, Holt RA, Jones S, Karsan A, Lee D, Li HI, Marra MA, Mayo M, Moore RA, Mungall K, Parker J, Pleasance E, Plettner P, Schein J, Stoll D, Swanson L, Tam A, Thiessen N, Varhol R, Wye N, Zhao Y, Gabriel S, Getz G, Sougnez C, Zou L, Leiserson MD, Vandin F, Wu HT, Applebaum F, Baylin SB, Akbani R, Broom BM, Chen K, Motter TC, Nguyen K, Weinstein JN, Zhang N, Ferguson ML, Adams C, Black A, Bowen J, Gastier-Foster J, Grossman T, Lichtenberg T, Wise L, Davidsen T, Demchok JA, Shaw KR, Sheth M, Sofia HJ, Yang L, Downing JR, Eley G, Alonso S, Ayala B, Baboud J, Backus M, Barletta SP, Berton DL, Chu AL, Girshik S, Jensen MA, Kahn A, Kothiyal P, Nicholls MC, Pihl TD, Pot DA, Raman R, Sanbhadti RN, Snyder EE, Srinivasan D, Walton J, Wan Y, Wang Z, Issa JP, Le Beau M, Carroll M, Kantarjian H, Kornblau S, Bootwalla MS, Lai PH, Shen H, Van Den Berg DJ, Weisenberger DJ, Link DC, Walter MJ, Ozenberger BA, Mardis ER, Westervelt P, Graubert TA, DiPersio JF, Wilson RK
N Engl J Med 2013 May 30;368(22):2059-74

Whole-genome sequencing identifies genetic alterations in pediatric low-grade gliomas
Zhang J, Wu G, Miller CP, Tatevossian RG, Dalton JD, Tang B, Orisme W, Punchihewa C, Parker M, Qaddoumi I, Boop FA, Lu C, Kandoth C, Ding L, Lee R, Huether R, Chen X, Hedlund E, Nagahawatte P, Rusch M, Boggs K, Cheng J, Becksfort J, Ma J, Song G, Li Y, Wei L, Wang J, Shurtleff S, Easton J, Zhao D, Fulton RS, Fulton LL, Dooling DJ, Vadodaria B, Mulder HL, Tang C, Ochoa K, Mullighan CG, Gajjar A, Kriwacki R, Sheer D, Gilbertson RJ, Mardis ER, Wilson RK, Downing JR, Baker SJ, Ellison DW
Nat Genet 2013 Apr 14;45(6):602-12

Integrated genomic characterization of endometrial carcinoma
Kandoth C, Schultz N, Cherniack AD, Akbani R, Liu Y, Shen H, Robertson AG, Pashtan I, Shen R, Benz CC, Yau C, Laird PW, Ding L, Zhang W, Mills GB, Kucherlapati R, Mardis ER, Levine DA
Nature 2013 May 2;497(7447):67-73

Retrotransposition of gene transcripts leads to structural variation in mammalian genomes
Ewing AD, Ballinger TJ, Earl D, Harris CC, Ding L, Wilson RK, Haussler D
Broad Institute Genome Sequencing and Analysis Program and Platform
Genome Biol 2013 Mar 13;14(3):R22

Somatic neurofibromatosis type 1 (NF1) inactivation characterizes NF1-associated pilocytic astrocytoma
Gutmann DH, McLellan MD, Hussain I, Wallis JW, Fulton LL, Fulton RS, Magrini V, Demeter R, Wylie T, Kandoth C, Leonard JR, Guha A, Miller CA, Ding L, Mardis ER
Genome Res 2013 Mar;23(3):431-9

The genomic landscape of hypodiploid acute lymphoblastic leukemia
Holmfeldt L*, Wei L*, Diaz-Flores E, Walsh M, Zhang J, Ding L, Payne-Turner D, Churchman M, Andersson A, Chen SC, McCastlain K, Becksfort J, Ma J, Wu G, Patel SN, Heatley SL, Phillips LA, Song G, Easton J, Parker M, Chen X, Rusch M, Boggs K, Vadodaria B, Hedlund E, Drenberg C, Baker S, Pei D, Cheng C, Huether R, Lu C, Fulton RS, Fulton LL, Tabib Y, Dooling DJ, Ochoa K, Minden M, Lewis ID, To LB, Marlton P, Roberts AW, Raca G, Stock W, Neale G, Drexler HG, Dickins RA, Ellison DW, Shurtleff SA, Pui CH, Ribeiro RC, Devidas M, Carroll AJ, Heerema NA, Wood B, Borowitz MJ, Gastier-Foster JM, Raimondi SC, Mardis ER, Wilson RK, Downing JR, Hunger SP, Loh ML, Mullighan CG
Nat Genet 2013 Mar;45(3):242-52

Activating HER2 mutations in HER2 gene amplification negative breast cancer
Bose R*, Kavuri SM*, Searleman AC, Shen W, Shen D, Koboldt DC, Monsey J, Goel N, Aronson AB, Li S, Ma CX, Ding L, Mardis ER, Ellis MJ
Cancer Discov 2013 Feb;3(2):224-37


Genomic landscape of non-small cell lung cancer in smokers and never-smokers
Govindan R*, Ding L*, Griffith M, Subramanian J, Dees ND, Kanchi KL, Maher CA, Fulton R, Fulton L, Wallis J, Chen K, Walker J, McDonald S, Bose R, Ornitz D, Xiong D, You M, Dooling DJ, Watson M, Mardis ER, Wilson RK
Cell 2012 Sep 14;150(6):1121-34

The origin and evolution of mutations in acute myeloid leukemia
Welch JS*, Ley TJ*, Link DC*, Miller CA, Larson DE, Koboldt DC, Wartman LD, Lamprecht TL, Liu F, Xia J, Kandoth C, Fulton RS, McLellan MD, Dooling DJ, Wallis JW, Chen K, Harris CC, Schmidt HK, Kalicki-Veizer JM, Lu C, Zhang Q, Lin L, O'Laughlin MD, McMichael JF, Delehaunty KD, Fulton LA, Magrini VJ, McGrath SD, Demeter RT, Vickery TL, Hundal J, Cook LL, Swift GW, Reed JP, Alldredge PA, Wylie TN, Walker JR, Watson MA, Heath SE, Shannon WD, Varghese N, Nagarajan R, Payton JE, Baty JD, Kulkarni S, Klco JM, Tomasson MH, Westervelt P, Walter MJ, Graubert TA, DiPersio JF, Ding L, Mardis ER, Wilson RK
Cell 2012 Jul 20;150(2):264-78

Landscape of somatic retrotransposition in human cancers
Lee E, Iskow R, Yang L, Gokcumen O, Haseley P, Luquette LJ 3rd, Lohr JG, Harris CC, Ding L, Wilson RK, Wheeler DA, Gibbs RA, Kucherlapati R, Lee C, Kharchenko PV, Park PJ
Science 2012 Aug 24;337(6097):967-71

Novel mutations target distinct subgroups of medulloblastoma
Robinson G*, Parker M*, Kranenburg TA*, Lu C, Chen X, Ding L, Phoenix TN, Hedlund E, Wei L, Zhu X, Chalhoub N, Baker SJ, Huether R, Kriwacki R, Curley N, Thiruvenkatam R, Wang J, Wu G, Rusch M, Hong X, Becksfort J, Gupta P, Ma J, Easton J, Vadodaria B, Onar-Thomas A, Lin T, Li S, Pounds S, Paugh S, Zhao D, Kawauchi D, Roussel MF, Finkelstein D, Ellison DW, Lau CC, Bouffet E, Hassall T, Gururangan S, Cohn R, Fulton RS, Fulton LL, Dooling DJ, Ochoa K, Gajjar A, Mardis ER, Wilson RK, Downing JR, Zhang J, Gilbertson RJ
Nature 2012 Aug 2;488(7409):43-8

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

Background mutations in parental cells account for most of the genetic heterogeneity of induced pluripotent stem cells
Young MA, Larson DE, Sun CW, George DR, Ding L, Miller CA, Lin L, Pawlik KM, Chen K, Fan X, Schmidt H, Kalicki-Veizer J, Cook LL, Swift GW, Demeter RT, Wendl MC, Sands MS, Mardis ER, Wilson RK, Townes TM, Ley TJ
Cell Stem Cell 2012 May 4;10(5):570-82

The Pediatric Cancer Genome Project
Downing JR, Wilson RK, Zhang J, Mardis ER, Pui CH, Ding L, Ley TJ, Evans WE
Nat Genet 2012 May 29;44(6):619-22

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

Whole-genome analysis informs breast cancer response to aromatase inhibition
Ellis MJ*, Ding L*, Shen D*, Luo J, Suman VJ, Wallis JW, Van Tine BA, Hoog J, Goiffon RJ, Goldstein TC, Ng S, Lin L, Crowder R, Snider J, Ballman K, Weber J, Chen K, Koboldt DC, Kandoth C, Schierding WS, McMichael JF, Miller CA, Lu C, Harris CC, McLellan MD, Wendl MC, DeSchryver K, Allred DC, Esserman L, Unzeitig G, Margenthaler J, Babiera GV, Marcom PK, Guenther JM, Leitch M, Hunt K, Olson J, Tao Y, Maher CA, Fulton LL, Fulton RS, Harrison M, Oberkfell B, Du F, Demeter R, Vickery TL, Elhammali A, Piwnica-Worms H, McDonald S, Watson M, Dooling DJ, Ota D, Chang LW, Bose R, Ley TJ, Piwnica-Worms D, Stuart JM, Wilson RK, Mardis ER
Nature 2012 Jun 10;486(7403):353-60

Association of age at diagnosis and genetic mutations in patients with neuroblastoma
Cheung NK*, Zhang J*, Lu C*, Parker M, Bahrami A, Tickoo SK, Heguy A, Pappo AS, Federico S, Dalton J, Cheung IY, Ding L, Fulton R, Wang J, Chen X, Becksfort J, Wu J, Billups CA, Ellison D, Mardis ER, Wilson RK, Downing JR, Dyer MA
JAMA 2012 Mar 14;307(10):1062-71

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

Clonal architecture of secondary acute myeloid leukemia
Walter MJ*, Shen D*, Ding L*, Shao J, Koboldt DC, Chen K, Larson DE, McLellan MD, Dooling D, Abbott R, Fulton R, Magrini V, Schmidt H, Kalicki-Veizer J, O'Laughlin M, Fan X, Grillot M, Witowski S, Heath S, Frater JL, Eades W, Tomasson M, Westervelt P, DiPersio JF, Link DC, Mardis ER, Ley TJ, Wilson RK, Graubert TA
N Engl J Med 2012 Mar 22;366(12):1090-8

Somatic histone H3 alterations in pediatric diffuse intrinsic pontine gliomas and non-brainstem glioblastomas
Wu G*, Broniscer A*, McEachron TA*, Lu C, Paugh BS, Becksfort J, Qu C, Ding L, Huether R, Parker M, Zhang J, Gajjar A, Dyer MA, Mullighan CG, Gilbertson RJ, Mardis ER, Wilson RK, Downing JR, Ellison DW, Zhang J, Baker SJ
Nat Genet 2012 Jan 29;44(3):251-3

A novel retinoblastoma therapy from genomic and epigenetic analyses
Zhang J*, Benavente CA*, McEvoy J*, Flores-Otero J*, Ding L, Chen X, Ulyanov A, Wu G, Wilson M, Wang J, Brennan R, Rusch M, Manning AL, Ma J, Easton J, Shurtleff S, Mullighan C, Pounds S, Mukatira S, Gupta P, Neale G, Zhao D, Lu C, Fulton RS, Fulton LL, Hong X, Dooling DJ, Ochoa K, Naeve C, Dyson NJ, Mardis ER, Bahrami A, Ellison D, Wilson RK, Downing JR, Dyer MA
Nature 2012 Jan 11;481(7381):329-34

Clonal evolution in relapsed acute myeloid leukaemia revealed by whole-genome sequencing
Ding L*, Ley TJ*, Larson DE, Miller CA, Koboldt DC, Welch JS, Ritchey JK, Young MA, Lamprecht T, McLellan MD, McMichael JF, Wallis JW, Lu C, Shen D, Harris CC, Dooling DJ, Fulton RS, Fulton LL, Chen K, Schmidt H, Kalicki-Veizer J, Magrini VJ, Cook L, McGrath SD, Vickery TL, Wendl MC, Heath S, Watson MA, Link DC, Tomasson MH, Shannon WD, Payton JE, Kulkarni S, Westervelt P, Walter MJ, Graubert TA, Mardis ER, Wilson RK, DiPersio JF
Nature 2012 Jan 11;481(7382):506-10

The genetic basis of early T-cell precursor acute lymphoblastic leukaemia
Zhang J*, Ding L*, Holmfeldt L*, Wu G, Heatley SL, Payne-Turner D, Easton J, Chen X, Wang J, Rusch M, Lu C, Chen SC, Wei L, Collins-Underwood JR, Ma J, Roberts KG, Pounds SB, Ulyanov A, Becksfort J, Gupta P, Huether R, Kriwacki RW, Parker M, McGoldrick DJ, Zhao D, Alford D, Espy S, Bobba KC, Song G, Pei D, Cheng C, Roberts S, Barbato MI, Campana D, Coustan-Smith E, Shurtleff SA, Raimondi SC, Kleppe M, Cools J, Shimano KA, Hermiston ML, Doulatov S, Eppert K, Laurenti E, Notta F, Dick JE, Basso G, Hunger SP, Loh ML, Devidas M, Wood B, Winter S, Dunsmore KP, Fulton RS, Fulton LL, Hong X, Harris CC, Dooling DJ, Ochoa K, Johnson KJ, Obenauer JC, Evans WE, Pui CH, Naeve CW, Ley TJ, Mardis ER, Wilson RK, Downing JR, Mullighan CG
Nature 2012 Jan 11;481(7380):157-63


Recurrent mutations in the U2AF1 splicing factor in myelodysplastic syndromes
Graubert TA*, Shen D*, Ding L*, Okeyo-Owuor T, Lunn CL, Shao J, Krysiak K, Harris CC, Koboldt DC, Larson DE, McLellan MD, Dooling DJ, Abbott RM, Fulton RS, Schmidt H, Kalicki-Veizer J, O'Laughlin M, Grillot M, Baty J, Heath S, Frater JL, Nasim T, Link DC, Tomasson MH, Westervelt P, DiPersio JF, Mardis ER, Ley TJ, Wilson RK, Walter MJ
Nat Genet 2011 Dec 11;44(1):53-7

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

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

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

Identification of a novel TP53 cancer susceptibility mutation through whole-genome sequencing of a patient with therapy-related AML
Link DC*, Schuettpelz LG*, Shen D*, Wang J, Walter MJ, Kulkarni S, Payton JE, Ivanovich J, Goodfellow PJ, Le Beau M, Koboldt DC, Dooling DJ, Fulton RS, Bender RH, Fulton LL, Delehaunty KD, Fronick CC, Appelbaum EL, Schmidt H, Abbott R, O'Laughlin M, Chen K, McLellan MD, Varghese N, Nagarajan R, Heath S, Graubert TA, Ding L, Ley TJ, Zambetti GP, Wilson RK, Mardis ER
JAMA 2011 Apr 20;305(15):1568-76

Use of whole-genome sequencing to diagnose a cryptic fusion oncogene
Welch JS*, Westervelt P*, Ding L, Larson DE, Klco JM, Kulkarni S, Wallis J, Chen K, Payton JE, Fulton RS, Veizer J, Schmidt H, Vickery TL, Heath S, Watson MA, Tomasson MH, Link DC, Graubert TA, DiPersio JF, Mardis ER, Ley TJ, Wilson RK
JAMA 2011 Apr 20;305(15):1577-84

Sequencing a mouse acute promyelocytic leukemia genome reveals genetic events relevant for disease progression
Wartman LD, Larson DE, Xiang Z, Ding L, Chen K, Lin L, Cahan P, Klco JM, Welch JS, Li C, Payton JE, Uy GL, Varghese N, Ries RE, Hoock M, Koboldt DC, McLellan MD, Schmidt H, Fulton RS, Abbott RM, Cook L, McGrath SD, Fan X, Dukes AF, Vickery T, Kalicki J, Lamprecht TL, Graubert TA, Tomasson MH, Mardis ER, Wilson RK, Ley TJ
J Clin Invest 2011 Apr;121(4):1445-55

Integrated genomic analyses of ovarian carcinoma
Cancer Genome Atlas Research Network
Nature 2011 Jun 29;474(7353):609-15

Recurrent DNMT3A mutations in patients with myelodysplastic syndromes
Walter M*J, Ding L*, Shen D*, Shao J, Grillot M, McLellan M, Fulton R, Schmidt H, Kalicki-Veizer J, O'Laughlin M, Kandoth C, Baty J, Westervelt P, DiPersio JF, Mardis ER, Wilson RK, Ley TJ, Graubert TA
Leukemia 2011 Jul;25(7):1153-8

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, Stutz 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
Nature 2011 Feb 3;470(7332):59-65

Identification of disease-causing mutations in autosomal dominant retinitis pigmentosa (adRP) using next-generation DNA sequencing
Bowne SJ*, Sullivan LS*, Koboldt DC*, Ding L, Fulton R, Abbott RM, Sodergren EJ, Birch DG, Wheaton DH, Heckenlively JR, Liu Q, Pierce EA, Weinstock GM, Daiger SP
Invest Ophthalmol Vis Sci 2011 Jan 25;52(1):494-503


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

A map of human genome variation from population-scale sequencing
1000 Genomes Project Consortium
Nature 2010 Oct 28;467(7319):1061-73

Complete characterization of the microRNAome in a patient with acute myeloid leukemia
Ramsingh G*, Koboldt DC*, Trissal M, Chiappinelli KB, Wylie T, Koul S, Chang LW, Nagarajan R, Fehniger TA, Goodfellow P, Magrini V, Wilson RK, Ding L, Ley TJ, Mardis ER, Link DC
Blood 2010 Dec 9;116(24):5316-26

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

Genome remodelling in a basal-like breast cancer metastasis and xenograft
Ding L*, Ellis MJ*, Li S, Larson DE, Chen K, Wallis JW, Harris CC, McLellan MD, Fulton RS, Fulton LL, Abbott RM, Hoog J, Dooling DJ, Koboldt DC, Schmidt H, Kalicki J, Zhang Q, Chen L, Lin L, Wendl MC, McMichael JF, Magrini VJ, Cook L, McGrath SD, Vickery TL, Appelbaum E, Deschryver K, Davies S, Guintoli T, Lin L, Crowder R, Tao Y, Snider JE, Smith SM, Dukes AF, Sanderson GE, Pohl CS, Delehaunty KD, Fronick CC, Pape KA, Reed JS, Robinson JS, Hodges JS, Schierding W, Dees ND, Shen D, Locke DP, Wiechert ME, Eldred JM, Peck JB, Oberkfell BJ, Lolofie JT, Du F, Hawkins AE, O'Laughlin MD, Bernard KE, Cunningham M, Elliott G, Mason MD, Thompson DM Jr, Ivanovich JL, Goodfellow PJ, Perou CM, Weinstock GM, Aft R, Watson M, Ley TJ, Wilson RK, Mardis ER
Nature 2010 Apr 15;464(7291):999-1005

Identification of a CpG island methylator phenotype that defines a distinct subgroup of glioma
Noushmehr H*, Weisenberger DJ*, Diefes K*, Phillips HS, Pujara K, Berman BP, Pan F, Pelloski CE, Sulman EP, Bhat KP, Verhaak RG, Hoadley KA, Hayes DN, Perou CM, Schmidt HK, Ding L, Wilson RK, Van Den Berg D, Shen H, Bengtsson H, Neuvial P, Cope LM, Buckley J, Herman JG, Baylin SB, Laird PW, Aldape K
Cancer Cell 2010 May 18;17(5):510-22

Integrated genomic analysis identifies clinically relevant subtypes of glioblastoma characterized by abnormalities in PDGFRA, IDH1, EGFR, and NF1
Verhaak RG*, Hoadley KA*, Purdom E, Wang V, Qi Y, Wilkerson MD, Miller CR, Ding L, Golub T, Mesirov JP, Alexe G, Lawrence M, O'Kelly M, Tamayo P, Weir BA, Gabriel S, Winckler W, Gupta S, Jakkula L, Feiler HS, Hodgson JG, James CD, Sarkaria JN, Brennan C, Kahn A, Spellman PT, Wilson RK, Speed TP, Gray JW, Meyerson M, Getz G, Perou CM, Hayes DN
Cancer Cell 2010 Jan 19;17(1):98-110


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

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

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


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

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

Novel MEK1 mutation identified by mutational analysis of epidermal growth factor receptor signaling pathway genes in lung adenocarcinoma
Marks JL, Gong Y, Chitale D, Golas B, McLellan MD, Kasai Y, Ding L, Mardis ER, Wilson RK, Solit D, Levine R, Michel K, Thomas RK, Rusch VW, Ladanyi M, Pao W
Cancer Res 2008 Jul 15;68(14):5524-8

The chromosome 3p21.3-encoded gene, LIMD1, is a critical tumor suppressor involved in human lung cancer development
Sharp TV, Al-Attar A, Foxler DE, Ding L, de A Vallim TQ, Zhang Y, Nijmeh HS, Webb TM, Nicholson AG, Zhang Q, Kraja A, Spendlove I, Osborne J, Mardis E, Longmore GD
Proc Natl Acad Sci U S A 2008 Dec 16;105(50):19932-7


Calcineurin-NFATc signaling pathway regulates AQP2 expression in response to calcium signals and osmotic stress
Li SZ, McDill BW, Kovach PA, Ding L, Go WY, Ho SN, Chen F
Am J Physiol Cell Physiol 2007 May;292(5):C1606-16

PolyScan: an automatic indel and SNP detection approach to the analysis of human resequencing data
Chen K, McLellan MD, Ding L, Wendl MC, Kasai Y, Wilson RK, Mardis ER
Genome Res 2007 May;17(5):659-66

Characterizing the cancer genome in lung adenocarcinoma
Weir BA*, Woo MS*, Getz G*, Perner S, Ding L, Beroukhim R, Lin WM, Province MA, Kraja A, Johnson LA, Shah K, Sato M, Thomas RK, Barletta JA, Borecki IB, Broderick S, Chang AC, Chiang DY, Chirieac LR, Cho J, Fujii Y, Gazdar AF, Giordano T, Greulich H, Hanna M, Johnson BE, Kris MG, Lash A, Lin L, Lindeman N, Mardis ER, McPherson JD, Minna JD, Morgan MB, Nadel M, Orringer MB, Osborne JR, Ozenberger B, Ramos AH, Robinson J, Roth JA, Rusch V, Sasaki H, Shepherd F, Sougnez C, Spitz MR, Tsao MS, Twomey D, Verhaak RG, Weinstock GM, Wheeler DA, Winckler W, Yoshizawa A, Yu S, Zakowski MF, Zhang Q, Beer DG, Wistuba II, Watson MA, Garraway LA, Ladanyi M, Travis WD, Pao W, Rubin MA, Gabriel SB, Gibbs RA, Varmus HE, Wilson RK, Lander ES, Meyerson M
Nature 2007 Dec 6;450(7171):893-8


Congenital progressive hydronephrosis (cph) is caused by an S256L mutation in aquaporin-2 that affects its phosphorylation and apical membrane accumulation
McDill BW, Li SZ, Kovach PA, Ding L, Chen F
Proc Natl Acad Sci U S A 2006 May 2;103(18):6952-7

Generation and annotation of the DNA sequences of human chromosomes 2 and 4
Hillier LW, Graves TA, Fulton RS, Fulton LA, Pepin KH, Minx P, Wagner-McPherson C, Layman D, Wylie K, Sekhon M, Becker MC, Fewell GA, Delehaunty KD, Miner TL, Nash WE, Kremitzki C, Oddy L, Du H, Sun H, Bradshaw-Cordum H, Ali J, Carter J, Cordes M, Harris A, Isak A, van Brunt A, Nguyen C, Du F, Courtney L, Kalicki J, Ozersky P, Abbott S, Armstrong J, Belter EA, Caruso L, Cedroni M, Cotton M, Davidson T, Desai A, Elliott G, Erb T, Fronick C, Gaige T, Haakenson W, Haglund K, Holmes A, Harkins R, Kim K, Kruchowski SS, Strong CM, Grewal N, Goyea E, Hou S, Levy A, Martinka S, Mead K, McLellan MD, Meyer R, Randall-Maher J, Tomlinson C, Dauphin-Kohlberg S, Kozlowicz-Reilly A, Shah N, Swearengen-Shahid S, Snider J, Strong JT, Thompson J, Yoakum M, Leonard S, Pearman C, Trani L, Radionenko M, Waligorski JE, Wang C, Rock SM, Tin-Wollam AM, Maupin R, Latreille P, Wendl MC, Yang SP, Pohl C, Wallis JW, Spieth J, Bieri TA, Berkowicz N, Nelson JO, Osborne J, Ding L, Meyer R, Sabo A, Shotland Y, Sinha P, Wohldmann PE, Cook LL, Hickenbotham MT, Eldred J, Williams D, Jones TA, She X, Ciccarelli FD, Izaurralde E, Taylor J, Schmutz J, Myers RM, Cox DR, Huang X, McPherson JD, Mardis ER, Clifton SW, Warren WC, Chinwalla AT, Eddy SR, Marra MA, Ovcharenko I, Furey TS, Miller W, Eichler EE, Bork P, Suyama M, Torrents D, Waterston RH, Wilson RK
Nature 2005 Apr 7;434(7034):724-31

EAnnot: a genome annotation tool using experimental evidence
Ding L, Sabo A, Berkowicz N, Meyer RR, Shotland Y, Johnson MR, Pepin KH, Wilson RK, Spieth J
Genome Res 2004 Dec;14(12):2503-9

Finishing the euchromatic sequence of the human genome
International Human Genome Sequencing Consortium
Nature 2004 Oct 21;431(7011):931-45

Evaluation of human diacylglycerol kinase(iota), DGKI, a homolog of Drosophila rdgA, in inherited retinopathy mapping to 7q
Bowne SJ, Sullivan LS, Ding L, Traer E, Prescott SM, Birch DG, Kennan A, Humphries P, Daiger SP
Mol Vis 2000 Feb 22;6:6-9

The cloning and characterization of a novel human diacylglycerol kinase, DGKiota
Ding L, Traer E, McIntyre TM, Zimmerman GA, Prescott SM
J Biol Chem 1998 Dec 4;273(49):32746-52

The cloning and developmental regulation of murine diacylglycerol kinase zeta
Ding L, McIntyre TM, Zimmerman GA, Prescott SM
FEBS Lett 1998 Jun 5;429(1):109-14

Alternative splicing of the human diacylglycerol kinase zeta gene in muscle
Ding L, Bunting M, Topham MK, McIntyre TM, Zimmerman GA, Prescott SM
Proc Natl Acad Sci U S A 1997 May 27;94(11):5519-24