• * co-first author
  • # co-corresponding author
  • Bold names: members of the Yang Lab

  • 2024


    • Yang Y, Badura M, O'Leary P, Delavan HM, Robison TM, Egusa EA, Zhong X, Swinderman JT, Li H, Zhang M, Kim M, Ashworth A, Feng FY, Chou J#, Yang L#. (2024) Transcription and DNA replication collisions lead to large tandem duplications and expose targetable therapeutic vulnerabilities in cancer. Nat Cancer, online. Pubmed [UChicago Medicine Forefront news]

    Chou J, Robinson TM, Egusa EA, Lodha R, Zhang M, Badura M, Mikayelyan M, Delavan H, Swinderman J, Wilson C, Zhu J, Das R, Nguyen M, Loehr A, Golsorkhi T, Simmons A, Abida W, Chinnaiyan AM, Arkin MR, Small EJ, Quigley DA, Yang L, Kim M, Ashworth A, Feng FY. (2024) Synthetic Lethal Targeting of Cyclin Dependent Kinase-12-Deficient Prostate Cancer with PARP Inhibitors. Clin Cancer Res, online. Pubmed

    Yu A*, Yesilkanal AE*, Thakur A, Wang F, Yang Y, Phillips W, Wu X, Muir A, He X, Spitz F, Yang L. (2024) HYENA detects oncogenes activated by distal enhancers in cancer. Nucleic Acids Res, 52:e77. Pubmed [NCI CBIIT news]

  • 2023


    • Yang Y, Yang L. (2023) Somatic structural variation signatures in pediatric brain cancer. Cell Reports, 42:113276. Pubmed

    Zhong X*, Luan J*, Yu A*, Lee-Hasset A, Miao Y#, Yang L#. (2023) SFyNCS detects oncogenic fusions involving non-coding sequences in cancer. Nucleic Acids Res, 51:e96. Pubmed

    Yang X, Xu X, Breuss MW, Antaki D, Ball LL, Chung C, Shen J, Li C, George RD, Wang Y, Bae T, Cheng Y, Abyzov A, Wei L, Alexandrov LB, Sebat JL; NIMH Brain Somatic Mosaicism Network; Gleeson JG. (2023) Control-independent mosaic single nucleotide variant detection with DeepMosaic. Nat Biotechnol, 41:870-877. Pubmed

    Chung C, Yang X, Bae T, Vong KI, Mittal S, Donkels C, Westley Phillips H, Li Z, Marsh APL, Breuss MW, Ball LL, Garcia CAB, George RD, Gu J, Xu M, Barrows C, James KN, Stanley V, Nidhiry AS, Khoury S, Howe G, Riley E, Xu X, Copeland B, Wang Y, Kim SH, Kang HC, Schulze-Bonhage A, Haas CA, Urbach H, Prinz M, Limbrick DD Jr, Gurnett CA, Smyth MD, Sattar S, Nespeca M, Gonda DD, Imai K, Takahashi Y, Chen HH, Tsai JW, Conti V, Guerrini R, Devinsky O, Silva WA Jr, Machado HR, Mathern GW, Abyzov A, Baldassari S, Baulac S; Focal Cortical Dysplasia Neurogenetics Consortium; Brain Somatic Mosaicism Network; Gleeson JG. (2023) Comprehensive multi-omic profiling of somatic mutations in malformations of cortical development. Nat Genet, 55:209-220. Pubmed

  • 2022


    • Bao L, Zhong X, Yang Y, Yang L. (2022) Starfish infers signatures of complex genomic rearrangements across human cancers. Nat Cancer, 3:1247-1259. Pubmed [Nature Cancer News & Views]

    Breuss MW, Yang X, Schlachetzki JCM, Antaki D, Lana AJ, Xu X, Chung C, Chai G, Stanley V, Song Q, Newmeyer TF, Nguyen A, O'Brien S, Hoeksema MA, Cao B, Nott A, McEvoy-Venneri J, Pasillas MP, Barton ST, Copeland BR, Nahas S, Van Der Kraan L, Ding Y; NIMH Brain Somatic Mosaicism Network. (2022) Somatic mosaicism reveals clonal distributions of neocortical development. Nature, 604:689-696. Pubmed

    Yang L. (2022) Meerkat: An Algorithm to Reliably Identify Structural Variations and Predict Their Forming Mechanisms. Methods Mol Biol, 107-135. Pubmed

    Li J, Lu H, Ng PK, Pantazi A, Ip CKM, Jeong KJ, Amador B, Tran R, Tsang YH, Yang L, Song X, Dogruluk T, Ren X, Hadjipanayis A, Bristow CA, Lee S, Kucherlapati M, Parfenov M, Tang J, Seth S, Mahadeshwar HS, Mojumdar K, Zeng D, Zhang J, Protopopov A, Seidman JG, Creighton CJ, Lu Y, Sahni N, Shaw KR, Meric-Bernstam F, Futreal A, Chin L, Scott KL, Kucherlapati R, Mills GB, Liang H. (2022) A functional genomic approach to actionable gene fusions for precision oncology. Sci Adv, 8:eabm2382. Pubmed

  • 2021


    • Carrot-Zhang J, Yao X, Devarakonda S, Deshpande A, Damrauer JS, Silva TC, Wong CK, Choi HY, Felau I, Robertson AG, Castro MAA, Bao L, Rheinbay E, Liu EM, Trieu T, Haan D, Yau C, Hinoue T, Liu Y, Shapira O, Kumar K, Mungall KL, Zhang H, Lee JJ, Berger A, Gao GF, Zhitomirsky B, Liang WW, Zhou M, Moorthi S, Berger AH, Collisson EA, Zody MC, Ding L, Cherniack AD, Getz G, Elemento O, Benz CC, Stuart J, Zenklusen JC, Beroukhim R, Chang JC, Campbell JD, Hayes DN, Yang L, Laird PW, Weinstein JN, Kwiatkowski DJ, Tsao MS, Travis WD, Khurana E, Berman BP, Hoadley KA, Robine N; TCGA Research Network, Meyerson M, Govindan R, Imielinski M. (2021) Whole-genome characterization of lung adenocarcinomas lacking alterations in the RTK/RAS/RAF pathway. Cell Rep, 34:108707. Pubmed

  • 2020


    • Yang L. (2020) A practical guide for structural variation detection in the human genome. Curr Protoc Hum Genet, 107:e103. Pubmed

    Bailey MH, Meyerson WU, Dursi LJ, Wang LB, Dong G, Liang WW, Weerasinghe A, Li S, Li Y, Kelso S; MC3 Working Group; PCAWG novel somatic mutation calling methods working group, Saksena G, Ellrott K, Wendl MC, Wheeler DA, Getz G, Simpson JT, Gerstein MB, Ding L; PCAWG Consortium. (2020) Retrospective evaluation of whole exome and genome mutation calls in 746 cancer samples. Nat Commun, 11:4748. Pubmed

    Li CH, Prokopec SD, Sun RX, Yousif F, Schmitz N; PCAWG Tumour Subtypes and Clinical Translation, Boutros PC; PCAWG Consortium. (2020) Sex differences in oncogenic mutational processes. Nat Commun, 11:4330. Pubmed

    Yun JW, Yang L, Park HY, Lee CW, Cha H, Shin HT, Noh KW, Choi YL, Park WY, Park PJ. (2020) Dysregulation of cancer genes by recurrent intergenic fusions. Genome Biol, 21:166. Pubmed

    PCAWG Transcriptome Core Group; Calabrese C, Davidson NR, Demircioğlu D, Fonseca NA, He Y, Kahles A, Lehmann KV, Liu F, Shiraishi Y, Soulette CM, Urban L, Greger L, Li S, Liu D, Perry MD, Xiang Q, Zhang F, Zhang J, Bailey P, Erkek S, Hoadley KA, Hou Y, Huska MR, Kilpinen H, Korbel JO, Marin MG, Markowski J, Nandi T, Pan-Hammarström Q, Pedamallu CS, Siebert R, Stark SG, Su H, Tan P, Waszak SM, Yung C, Zhu S, Awadalla P, Creighton CJ, Meyerson M, Ouellette BFF, Wu K, Yang H; PCAWG Transcriptome Working Group; Brazma A, Brooks AN, Göke J, Rätsch G, Schwarz RF, Stegle O, Zhang Z; PCAWG Consortium. (2020) Genomic basis for RNA alterations in cancer. Nature, 578:129-136. Pubmed

    Alexandrov LB, Kim J, Haradhvala NJ, Huang MN, Tian Ng AW, Wu Y, Boot A, Covington KR, Gordenin DA, Bergstrom EN, Islam SMA, Lopez-Bigas N, Klimczak LJ, McPherson JR, Morganella S, Sabarinathan R, Wheeler DA, Mustonen V; PCAWG Mutational Signatures Working Group; Getz G, Rozen SG, Stratton MR; PCAWG Consortium. (2020) The repertoire of mutational signatures in human cancer. Nature, 578:94-101. Pubmed

    Rheinbay E, Nielsen MM, Abascal F, Wala JA, Shapira O, Tiao G, Hornshøj H, Hess JM, Juul RI, Lin Z, Feuerbach L, Sabarinathan R, Madsen T, Kim J, Mularoni L, Shuai S, Lanzós A, Herrmann C, Maruvka YE, Shen C, Amin SB, Bandopadhayay P, Bertl J, Boroevich KA, Busanovich J, Carlevaro-Fita J, Chakravarty D, Chan CWY, Craft D, Dhingra P, Diamanti K, Fonseca NA, Gonzalez-Perez A, Guo Q, Hamilton MP, Haradhvala NJ, Hong C, Isaev K, Johnson TA, Juul M, Kahles A, Kahraman A, Kim Y, Komorowski J, Kumar K, Kumar S, Lee D, Lehmann KV, Li Y, Liu EM, Lochovsky L, Park K, Pich O, Roberts ND, Saksena G, Schumacher SE, Sidiropoulos N, Sieverling L, Sinnott-Armstrong N, Stewart C, Tamborero D, Tubio JMC, Umer HM, Uusküla-Reimand L, Wadelius C, Wadi L, Yao X, Zhang CZ, Zhang J, Haber JE, Hobolth A, Imielinski M, Kellis M, Lawrence MS, von Mering C, Nakagawa H, Raphael BJ, Rubin MA, Sander C, Stein LD, Stuart JM, Tsunoda T, Wheeler DA, Johnson R, Reimand J, Gerstein M, Khurana E, Campbell PJ, López-Bigas N; PCAWG Drivers and Functional Interpretation Working Group; PCAWG Structural Variation Working Group, Weischenfeldt J, Beroukhim R, Martincorena I, Pedersen JS, Getz G; PCAWG Consortium. (2020) Analyses of non-coding somatic drivers in 2,658 cancer whole genomes. Nature, 578:102-111. Pubmed

    Gerstung M, Jolly C, Leshchiner I, Dentro SC, Gonzalez S, Rosebrock D, Mitchell TJ, Rubanova Y, Anur P, Yu K, Tarabichi M, Deshwar A, Wintersinger J, Kleinheinz K, Vázquez-García I, Haase K, Jerman L, Sengupta S, Macintyre G, Malikic S, Donmez N, Livitz DG, Cmero M, Demeulemeester J, Schumacher S, Fan Y, Yao X, Lee J, Schlesner M, Boutros PC, Bowtell DD, Zhu H, Getz G, Imielinski M, Beroukhim R, Sahinalp SC, Ji Y, Peifer M, Markowetz F, Mustonen V, Yuan K, Wang W, Morris QD; PCAWG Evolution & Heterogeneity Working Group; Spellman PT, Wedge DC, Van Loo P; PCAWG Consortium. (2020) The evolutionary history of 2,658 cancers. Nature, 578:122-128. Pubmed

    Li Y, Roberts ND, Wala JA, Shapira O, Schumacher SE, Kumar K, Khurana E, Waszak S, Korbel JO, Haber JE, Imielinski M; PCAWG Structural Variation Working Group, Weischenfeldt J, Beroukhim R, Campbell PJ; PCAWG Consortium. (2020) Patterns of somatic structural variation in human cancer genomes. Nature, 578:112-121. Pubmed

    ICGC/TCGA Pan-Cancer Analysis of Whole Genomes Consortium. (2020) Pan-cancer analysis of whole genomes. Nature, 578:82-93. Pubmed

    Cortés-Ciriano I, Lee JJ, Xi R, Jain D, Jung YL, Yang L, Gordenin D, Klimczak LJ, Zhang CZ, Pellman DS; PCAWG Structural Variation Working Group, Park PJ; PCAWG Consortium. Comprehensive analysis of chromothripsis in 2,658 human cancers using whole-genome sequencing. Nat Genet, 52:331-341. Pubmed

    Zapatka M, Borozan I, Brewer DS, Iskar M, Grundhoff A, Alawi M, Desai N, Sültmann H, Moch H; PCAWG Pathogens; Cooper CS, Eils R, Ferretti V, Lichter P; PCAWG Consortium. (2020) The landscape of viral associations in human cancers. Nat Genet, 52:320-330. Pubmed

    Akdemir KC, Le VT, Chandran S, Li Y, Verhaak RG, Beroukhim R, Campbell PJ, Chin L, Dixon JR, Futreal PA; PCAWG Structural Variation Working Group; PCAWG Consortium. (2020) Disruption of chromatin folding domains by somatic genomic rearrangements in human cancer. Nat Genet, 52:294-305. Pubmed

    Rodriguez-Martin B, Alvarez EG, Baez-Ortega A, Zamora J, Supek F, Demeulemeester J, Santamarina M, Ju YS, Temes J, Garcia-Souto D, Detering H, Li Y, Rodriguez-Castro J, Dueso-Barroso A, Bruzos AL, Dentro SC, Blanco MG, Contino G, Ardeljan D, Tojo M, Roberts ND, Zumalave S, Edwards PAW, Weischenfeldt J, Puiggròs M, Chong Z, Chen K, Lee EA, Wala JA, Raine K, Butler A, Waszak SM, Navarro FCP, Schumacher SE, Monlong J, Maura F, Bolli N, Bourque G, Gerstein M, Park PJ, Wedge DC, Beroukhim R, Torrents D, Korbel JO, Martincorena I, Fitzgerald RC, Van Loo P, Kazazian HH, Burns KH; PCAWG Structural Variation Working Group, Campbell PJ, Tubio JMC; PCAWG Consortium. (2020) Pan-cancer analysis of whole genomes identifies driver rearrangements promoted by LINE-1 retrotransposition. Nat Genet, 52:306-319. Pubmed

    Yuan Y, Ju YS, Kim Y, Li J, Wang Y, Yoon CJ, Yang Y, Martincorena I, Creighton CJ, Weinstein JN, Xu Y, Han L, Kim HL, Nakagawa H, Park K, Campbell PJ, Liang H; PCAWG Consortium. (2020) Comprehensive molecular characterization of mitochondrial genomes in human cancers. Nat Genet, 52:342-352. Pubmed

    Carlevaro-Fita J, Lanzós A, Feuerbach L, Hong C, Mas-Ponte D, Pedersen JS; PCAWG Drivers and Functional Interpretation Group; Johnson R; PCAWG Consortium. (2020) Cancer LncRNA Census reveals evidence for deep functional conservation of long noncoding RNAs in tumorigenesis. Commun Biol, 3:56. Pubmed

    Yakneen S, Waszak SM; PCAWG Technical Working Group; Gertz M, Korbel JO; PCAWG Consortium. (2020) Butler enables rapid cloud-based analysis of thousands of human genomes. Nat Biotechnol, 38:288-292. Pubmed

    Reyna MA, Haan D, Paczkowska M, Verbeke LPC, Vazquez M, Kahraman A, Pulido-Tamayo S, Barenboim J, Wadi L, Dhingra P, Shrestha R, Getz G, Lawrence MS, Pedersen JS, Rubin MA, Wheeler DA, Brunak S, Izarzugaza JMG, Khurana E, Marchal K, von Mering C, Sahinalp SC, Valencia A; PCAWG Drivers and Functional Interpretation Working Group; Reimand J, Stuart JM, Raphael BJ; PCAWG Consortium. (2020) Pathway and network analysis of more than 2500 whole cancer genomes. Nat Commun, 11:729. Pubmed

    Jiao W, Atwal G, Polak P, Karlic R, Cuppen E; PCAWG Tumor Subtypes and Clinical Translation Working Group; Danyi A, de Ridder J, van Herpen C, Lolkema MP, Steeghs N, Getz G, Morris QD, Stein LD; PCAWG Consortium. (2020) A deep learning system accurately classifies primary and metastatic cancers using passenger mutation patterns. Nat Commun, 11:728. Pubmed

    Paczkowska M, Barenboim J, Sintupisut N, Fox NS, Zhu H, Abd-Rabbo D, Mee MW, Boutros PC; PCAWG Drivers and Functional Interpretation Working Group; Reimand J; PCAWG Consortium. (2020) Integrative pathway enrichment analysis of multivariate omics data. Nat Commun, 11:735. Pubmed

    Cmero M, Yuan K, Ong CS, Schröder J; PCAWG Evolution and Heterogeneity Working Group; Corcoran NM, Papenfuss T, Hovens CM, Markowetz F, Macintyre G; PCAWG Consortium. (2020) Inferring structural variant cancer cell fraction. Nat Commun, 11:730. Pubmed

    Rubanova Y, Shi R, Harrigan CF, Li R, Wintersinger J, Sahin N, Deshwar AG; PCAWG Evolution and Heterogeneity Working Group; Morris QD; PCAWG Consortium. (2020) Reconstructing evolutionary trajectories of mutation signature activities in cancer using TrackSig. Nat Commun, 11:731. Pubmed

    Zhang Y, Chen F, Fonseca NA, He Y, Fujita M, Nakagawa H, Zhang Z, Brazma A; PCAWG Transcriptome Working Group; PCAWG Structural Variation Working Group, Creighton CJ; PCAWG Consortium. (2020) High-coverage whole-genome analysis of 1220 cancers reveals hundreds of genes deregulated by rearrangement-mediated cis-regulatory alterations. Nat Commun, 11:736. Pubmed

    Bhandari V, Li CH, Bristow RG, Boutros PC; PCAWG Consortium. (2020) Divergent mutational processes distinguish hypoxic and normoxic tumours. Nat Commun, 11:737. Pubmed

    Shuai S; PCAWG Drivers and Functional Interpretation Working Group; Gallinger S, Stein LD; PCAWG Consortium. (2020) Combined burden and functional impact tests for cancer driver discovery using DriverPower. Nat Commun, 11:734. Pubmed

    Sieverling L, Hong C, Koser SD, Ginsbach P, Kleinheinz K, Hutter B, Braun DM, Cortés-Ciriano I, Xi R, Kabbe R, Park PJ, Eils R, Schlesner M; PCAWG-Structural Variation Working Group, Brors B, Rippe K, Jones DTW, Feuerbach L; PCAWG Consortium. (2020) Genomic footprints of activated telomere maintenance mechanisms in cancer. Nat Commun, 11:733. Pubmed

  • 2019


    • Zhang Y, Yang L, Kucherlapati M, Hadjipanayis A, Pantazi A, Bristow CA, Lee EA, Mahadeshwar HS, Tang J, Zhang J, Seth S, Lee S, Ren X, Song X, Sun H, Seidman J, Luquette LJ, Xi R, Chin L, Protopopov A, Park PJ, Kucherlapati R, Creighton CJ. (2019) Global impact of somatic structural variation on the DNA methylome of human cancers. Genome Biol, 20:209. Pubmed

    Yang L#, Wang S, Lee JJ, Lee S, Lee E, Shinbrot E, Wheeler DA, Kucherlapati R, Park PJ#. (2019) An enhanced genetic model of colorectal cancer progression history. Genome Biol, 20:168. Pubmed

  • 2018


    • Zhang Y*, Yang L*, Kucherlapati M*, Chen F, Hadjipanayis A, Pantazi A, Bristow CA, Lee EA, Mahadeshwar HS, Tang J, Zhang J, Seth S, Lee S, Ren X, Song X, Sun H, Seidman J, Luquette LJ, Xi R, Chin L, Protopopov A, Li W, Park PJ, Kucherlapati R, Creighton CJ. (2018) A Pan-Cancer Compendium of Genes Deregulated by Somatic Genomic Rearrangement across More Than 1,400 Cases. Cell Rep, 24:515-527. Pubmed

    Ricketts CJ, De Cubas AA, Fan H, Smith CC, Lang M, Reznik E, Bowlby R, Gibb EA, Akbani R, Beroukhim R, Bottaro DP, Choueiri TK, Gibbs RA, Godwin AK, Haake S, Hakimi AA, Henske EP, Hsieh JJ, Ho TH, Kanchi RS, Krishnan B, Kwaitkowski DJ, Lui W, Merino MJ, Mills GB, Myers J, Nickerson ML, Reuter VE, Schmidt LS, Shelley CS, Shen H, Shuch B, Signoretti S, Srinivasan R, Tamboli P, Thomas G, Vincent BG, Vocke CD, Wheeler DA, Yang L, Kim WT, Robertson AG; Cancer Genome Atlas Research Network, Spellman PT, Rathmell WK, Linehan WM. (2018) The Cancer Genome Atlas Comprehensive Molecular Characterization of Renal Cell Carcinoma. Cell Rep, 23:313-326. Pubmed

  • 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. Pubmed

    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. Pubmed

    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. Pubmed

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

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

  • 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. Pubmed

    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. Pubmed

    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. Pubmed

  • 2015


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

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

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

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

  • 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. Pubmed

    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. Pubmed

    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. Pubmed

    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. Pubmed

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

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

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

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

    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. Pubmed

  • 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. Pubmed

    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. Pubmed

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

  • 2012


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

    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. Pubmed

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

    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. Pubmed

  • 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. Pubmed

  • 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. Pubmed

    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. Pubmed

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

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

    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. Pubmed

    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. Pubmed