• * co-first author
  • & co-corresponding author

2017


Robertson AG, Shih J, Yau C, Gibb EA, Oba J, Mungall KL, Hess JM, Uzunangelov V, Walter V, Danilova L, Lichtenberg TM, Kucherlapati M, Kimes PK, Tang M, Penson A, Babur O, Akbani R, Bristow CA, Hoadley KA, Iype L, Chang MT; TCGA Research Network, Cherniack AD, Benz C, Mills GB, Verhaak RGW, Griewank KG, Felau I, Zenklusen JC, Gershenwald JE, Schoenfield L, Lazar AJ, Abdel-Rahman MH, Roman-Roman S, Stern MH, Cebulla CM, Williams MD, Jager MJ, Coupland SE, Esmaeli B, Kandoth C, Woodman SE. (2017) Integrative analysis identifies four molecular and clinical subsets in uveal melanoma. Cancer Cell, 32:204-220.

Zhang Y, Kwok-Shing Ng P, Kucherlapati M, Chen F, Liu Y, Tsang YH, de Velasco G, Jeong KJ, Akbani R, Hadjipanayis A, Pantazi A, Bristow CA, Lee E, Mahadeshwar HS, Tang J, Zhang J, Yang L, Seth S, Lee S, Ren X, Song X, Sun H, Seidman J, Luquette LJ, Xi R, Chin L, Protopopov A, Westbrook TF, Shelley CS, Choueiri TK, Ittmann M, Van Waes C, Weinstein JN, Liang H, Henske EP, Godwin AK, Park PJ, Kucherlapati R, Scott KL, Mills GB, Kwiatkowski DJ, Creighton CJ. (2017) A Pan-cancer proteogenomic atlas of PI3K/AKT/mTOR pathway alterations. Cancer Cell, 31:820-832.

Lu H, Villafane N, Dogruluk T, Grzeskowiak CL, Kong K, Tsang YH, Zagorodna O, Pantazi A, Yang L, Neill NJ, Kim YW, Creighton CJ, Verhaak RG, Mills GB, Park P, Kucherlapati RS, Scott KL. (2017) Engineering and functional characterization of fusion genes identifies novel oncogenic drivers of cancer. Cancer Res, 77:3502-3512.

Cancer Genome Atlas Research Network. (2017) Integrated genomic and molecular characterization of cervical cancer. Nature, 543:378-384.

Cancer Genome Atlas Research Network. (2017) Integrated genomic characterization of oesophageal carcinoma. Nature, 541:169-175.


2016


Yang L*, Lee M*, Lu H*, Oh D, Kim YJ, Park D, Park G, Ren X, Bristow CA, Haseley PS, Lee S, Pantazi A, Kucherlapati R, Park W, Scott K, Choi Y, Park PJ. (2016) Analyzing somatic genome rearrangements in human cancers by using whole-exome sequencing. Am J Hum Genet, 98:843-856.

Chen F, Zhang Y, Senbabaoglu Y, Ciriello G, Yang L, Reznik E, Shuch B, Micevic G, De Velasco G, Shinbrot E, Noble MS, Lu Y, Covington KR, Xi L, Drummond JA, Muzny D, Kang H, Lee J, Tamboli P, Reuter V, Shelley CS, Kaipparettu BA, Bottaro DP, Godwin AK, Gibbs RA, Getz G, Kucherlapati R, Park PJ, Sander C, Henske EP, Zhou JH, Kwiatkowski DJ, Ho TH, Choueiri TK, Hsieh JJ, Akbani R, Mills GB, Hakimi AA, Wheeler DA, Creighton CJ. (2016) Multilevel genomics-based taxonomy of renal cell carcinoma. Cell Rep, 14:2476-2489.

Ceccarelli M, Barthel FP, Malta TM, Sabedot TS, Salama SR, Murray BA, Morozova O, Newton Y, Radenbaugh A, Pagnotta SM, Anjum S, Wang J, Manyam G, Zoppoli P, Ling S, Rao AA, Grifford M, Cherniack AD, Zhang H, Poisson L, Carlotti CG Jr, Tirapelli DP, Rao A, Mikkelsen T, Lau CC, Yung WK, Rabadan R, Huse J, Brat DJ, Lehman NL, Barnholtz-Sloan JS, Zheng S, Hess K, Rao G, Meyerson M, Beroukhim R, Cooper L, Akbani R, Wrensch M, Haussler D, Aldape KD, Laird PW, Gutmann DH; TCGA Research Network, Noushmehr H, Iavarone A, Verhaak RG. (2016) Molecular profiling reveals biologically discrete subsets and pathways of progression in diffuse glioma. Cell, 164:550-563.


2015


Cancer Genome Atlas Research Network. (2015) The molecular taxonomy of primary prostate cancer. Cell, 163:1011-1025.

Cancer Genome Atlas Research Network. (2015) Comprehensive, integrative genomic analysis of diffuse lower-grade gliomas. N Engl J Med, 372:2481-2498.

Cancer Genome Atlas Research Network. (2015) Genomic classification of cutaneous melanoma. Cell, 161:1681-1696.

Cancer Genome Atlas Research Network. (2015) Comprehensive genomic characterization of head and neck squamous cell carcinomas. Nature, 517:576-582.


2014


Evrony GD, Lee E, Mehta BK, Benjamini Y, Johnson RM, Cai X, Yang L, Haseley P, Lehmann HS, Park PJ, Walsh CA. (2014) Cell lineage analysis in human brain using endogenous retroelements. Neuron, 85:49-59.

Parfenov M, Pedamallu CS, Gehlenborg N, Freeman SS, Danilova L, Bristow C, Lee S, Hadjipanayis AG, Ivanova EV, Wilkerson MD, Protopopov A, Yang L, Seth S, Song X, Tang J, Ren X, Zhang J, Pantazi A, Santoso N, Xu AW, Mahadeshwar H, Wheeler DA, Haddad RI, Jong J, Ojesina A, Isaeva N, Yarbrough WG, Hayes DN, Grandis JR,El-Naggar AK, Meyerson M,Park PJ, Chin L, Seidman JG, Hammerman PS, Kucherlapati R, TCGA Network. (2014) Characterization of HPV and host genome interactions in primary head and neck cancers. Proc Natl Acad Sci USA, 111:15544-15549.

Cancer Genome Atlas Research Network. (2014) Integrated genomic characterization of papillary thyroid carcinoma. Cell, 159:676-690.

Cancer Genome Atlas Research Network. (2014) Comprehensive molecular characterization of gastric adenocarcinoma. Nature, 513:202-209.

Davis CF*, Ricketts C*, Wang M*, Yang L*, Cherniack AD, Shen H, Buhay C, Kim SC, Fahey CC, Hacker KE, Bhanot G, Gordenin DA, Chu A, Gunaratne PH, Biehl M, Seth S, Kaipparettu BA, Bristow CA, Donehower LA, Wallen EM, Smith AB, Tickoo SK, Tamboli P, Reuter V, Schmidt LS, Hsieh JJ, Choueiri TK, Hakimi AA, The Cancer Genome Atlas Research Network, Chin L, Meyerson ML, Kucherlapati R, Park WY, Robertson AG, Laird PW, Henske EP, Kwiatkowski DJ, Park PJ, Morgan M, Shuch B, Muzny D, Wheeler DA, Linehan WM, Gibbs RA, Rathmell WK, Creighton CJ. (2014) The somatic genomic landscape of chromophobe renal cell carcinoma. Cancer Cell, 26:319-330.

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; Cancer Genome Atlas Research Network, Benz CC, Perou CM, Stuart JM. (2014) Multiplatform analysis of 12 cancer types reveals molecular classification within and across tissues of origin. Cell. 158:929-944.

Cancer Genome Atlas Research Network. (2014) Comprehensive molecular profiling of lung adenocarcinoma. Nature, 511:543-550.

Cancer Genome Atlas Research Network. (2014) Comprehensive molecular characterization of urothelial bladder carcinoma. Nature, 507:315-322.

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, TCGA Research Network. (2014) The somatic genomic landscape of glioblastoma. Cell, 155:462-477.


2013


Cancer Genome Atlas Research Network, Weinstein JN, Collisson EA, Mills GB, Shaw KRM, Ozenberger BA, Ellrott K, Shmulevich I, Sander C, Stuart JM. (2013) The Cancer Genome Atlas Pan-Cancer analysis project. Nat Genet, 45:1113-1120.

Yang L, Luquette LJ, Gehlenborg N, Xi R, Haseley PS, Hsieh C, Zhang C, Ren X, Protopopov A, Chin L, Kucherlapati R, Lee C, Park PJ. (2013) Diverse mechanisms of somatic structural variations in human cancer genomes. Cell, 153:919-929.

Cancer Genome Atlas Research Network. (2013) Integrated genomic characterization of endometrial carcinoma. Nature, 497:67-73.


2012


Cancer Genome Atlas Research Network. (2012) Comprehensive genomic characterization of squamous cell lung cancers. Nature, 489:519-525.

Zhu Q, Smith SM, Ayele M, Yang L, Jogi A, Chaluvadi SR, Bennetzen JL. (2012) High throughput discovery of mutations in tef semi-dwarfing genes by next generation sequencing analysis. Genetics, 192:819-829.

Cancer Genome Atlas Research Network. (2012) Comprehensive molecular characterization of human colon and rectal cancer. Nature, 487:330-337.

Lee E, Iskow R, Yang L, Gokcumen O, Haseley P, Luquette LJ, Lohr JG, Harris CC, Ding L, Wilson RK, Wheeler DA, Gibbs RA, Kucherlapati R, Lee C, Kharchenko PV, Park PJ, Cancer Genome Atlas Research Network. (2012) Landscape of somatic retrotransposition in human cancers. Science, 337:967-971.


2011


Banks JA, Nishiyama T, Hasebe M, Bowman JL, Gribskov M, dePamphilis C, Albert VA, Aono N, Aoyama T, Ambrose BA, Ashton NW, Axtell MJ, Barker E, Barker MS, Bennetzen JL, Bonawitz ND, Chapple C, Cheng C, Correa LGG, Dacre M, DeBarry J, Dreyer I, Elias M, Engstrom EM, Estelle M, Feng L, Finet C, Floyd SK, Frommer WB, Fujita T, Gramzow L, Gutensohn M, Harholt J, Hattori M, Heyl A, Hirai T, Hiwatashi Y, Ishikawa M, Iwata M, Karol KG, Koehler B, Kolukisaoglu U, Kubo M, Kurata T, Lalonde S, Li K, Li Y, Litt A, Lyons E, Manning G, Maruyama T, Michael TP, Mikami K, Miyazaki S, Morinaga S, Murata T, Mueller-Roeber B, Nelson DR, Obara M, Oguri Y, Olmstead RG, Onodera N, Petersen BL, Pils B, Prigge M, Rensing SA, Riao-Pachón DM, Roberts AW, Sato Y, Scheller HV, Schulz B, Schulz C, Shakirov EV, Shibagaki N, Shinohara N, Shippen DE, Srensen I, Sotooka R, Sugimoto N, Sugita M, Sumikawa N, Tanurdzic M, Theien G, Ulvskov P, Wakazuki S, Weng J, Willats WWGT, Wipf D, Wolf PG, Yang L, Zimmer AD, Zhu Q, Mitros T, Hellsten U, Loqué D, Otillar R, Salamov A, Schmutz J, Shapiro H, Lindquist E, Lucas S, Rokhsar D, Grigoriev IV. (2011) The Selaginella genome identifies genetic changes associated with the evolution of vascular plants. Science, 332:960-963.


2010 and before


Schnable PS, Ware D, Fulton RS, Stein JC, Wei F, Pasternak S, Liang C, Zhang J, Fulton L, Graves TA, Minx P, Reily AD, Courtney L, Kruchowski SS, Tomlinson C, Strong C, Delehaunty K, Fronick C, Courtney B, Rock SM, Belter E, Du F, Kim K, Abbott RM, Cotton M, Levy A, Marchetto P, Ochoa K, Jackson SM, Gillam B, Chen W, Yan L, Higginbotham J, Cardenas M, Waligorski J, Applebaum E, Phelps L, Falcone J, Kanchi K, Thane T, Scimone A, Thane N, Henke J, Wang T, Ruppert J, Shah N, Rotter K, Hodges J, Ingenthron E, Cordes M, Kohlberg S, Sgro J, Delgado B, Mead K, Chinwalla A, Leonard S, Crouse K, Collura K, Kudrna D, Currie J, He R, Angelova A, Rajasekar S, Mueller T, Lomeli R, Scara G, Ko A, Delaney K, Wissotski M, Lopez G, Campos D, Braidotti M, Ashley E, Golser W, Kim H, Lee S, Lin J, Dujmic Z, Kim W, Talag J, Zuccolo A, Fan C, Sebastian A, Kramer M, Spiegel L, Nascimento L, Zutavern T, Miller B, Ambroise C, Muller S, Spooner W, Narechania A, Ren L, Wei S, Kumari S, Faga B, Levy MJ, McMahan L, Van Buren P, Vaughn MW, Ying K, Yeh C, Emrich SJ, Jia Y, Kalyanaraman A, Hsia A, Barbazuk WB, Baucom RS, Brutnell TP, Carpita NC, Chaparro C, Chia J, Deragon J, Estill JC, Fu Y, Jeddeloh JA, Han Y, Lee H, Li P, Lisch DR, Liu S, Liu Z, Nagel DH, McCann MC, SanMiguel P, Myers AM, Nettleton D, Nguyen J, Penning BW, Ponnala L, Schneider KL, Schwartz DC, Sharma A, Soderlund C, Springer NM, Sun Q, Wang H, Waterman M, Westerman R, Wolfgruber TK, Yang L, Yu Y, Zhang L, Zhou S, Zhu Q, Bennetzen JL, Dawe RK, Jiang J, Jiang N, Presting GG, Wessler SR, Aluru S, Martienssen RA, Clifton SW, McCombie WR, Wing RA, Wilson RK. (2009) The B73 maize genome: complexity, diversity, and dynamics. Science, 326:1112-1115.

Wei F, Stein JC, Liang C, Zhang J, Fulton RS, Baucom RS, De Paoli E, Zhou S, Yang L, Han Y, Pasternak S, Narechania A, Zhang L, Yeh C, Ying K, Nagel DH, Collura K, Kudrna D, Currie J, Lin J, Kim H, Angelova A, Scara G, Wissotski M, Golser W, Courtney L, Kruchowski S, Graves TA, Rock SM, Adams S, Fulton LA, Fronick C, Courtney W, Kramer M, Spiegel L, Nascimento L, Kalyanaraman A, Chaparro C , Deragon J , San Miguel P , Jiang N , Wessler SR, Green PJ, Yu Y, Schwartz DC, Meyers BC, Bennetzen JL, Martienssen RA, McCombie WR, Aluru S , Clifton SW, Schnable PS, Ware D, Wilson RK, Wing RA. (2009) Detailed analysis of a contiguous 22-Mb region of the maize genome. PLoS Genet, 5:e1000728.

Yang L, Bennetzen JL. (2009) Distribution, diversity, evolution, and survival of Helitrons in the maize genome. Proc Natl Acad Sci USA, 106:19922-19927.

Yang L, Bennetzen JL. (2009) Structure-based discovery and description of plant and animal Helitrons. Proc Natl Acad Sci USA, 106:12832-12837.

Conner JA, Goel S, Gunawan G, Cordonnier-Pratt MM, Johnson VE, Liang C, Wang H, Pratt LH, Mullet JE, DeBarry J, Yang L, Bennetzen JL, Klein PE, Ozias-Akins P. (2008) Sequence analysis of Bacterial Artificial Chromosome clones from the Apospory-specific genomic region of Pennisetum and Cenchrus. Plant Physiol, 147:1396-1411.

Rensing SA, Lang D, Zimmer AD, Terry A, Salamov A, Shapiro H, Nishiyama T, Perroud P, Lindquist EA, Kamisugi Y, Tanahashi T, Sakakibara K, Fujita T, Oishi K, Shin-I K, Kuroki Y, Toyoda A, Suzuki Y, Hashimoto S, Yamaguchi K, Sugano S, Kohara Y, Fujiyama A, Anterola A, Aoki S, Ashton N, Barbazuk WB, Barker E, Bennetzen JL, Blankenship R, Cho SY, Dutcher SK, Estelle M, Fawcett JA, Gundlach H, Hanada K, Heyl A, Hicks KA, Hughes J, Lohr M, Mayer K, Melkozernov A, Murata T, Nelson DR, Pils B, Prigge M, Reiss B, Renner T, Rombauts S, Rushton PJ, Sanderfoot A, Schween G, Shiu S, Stueber K, Theodoulou FL, Tu H,Van de Peer Y, Verrier PJ, Waters E, Wood A, Yang L, Cove D, Cuming AC, Hasebe M, Lucas S, Mishler BD, Reski R, Grigoriev IV, Quatrano RS, Boore JL. (2008) The Physcomitrella genome reveals evolutionary insights into the conquest of land by plants. Science, 319:64-69.