2024
Nature Collection: The Human Tumor Atlas Network (HTAN): exploring tumor evolution in time and space
The Human Tumor Atlas Network (HTAN)
Nature. Oct. 30, 2024; Spotlighted in Nature HTAN Collection
Tumor evolution and microenvironment interactions in 2D and 3D space
Mo CK*, Liu J*, Chen Sˉ , Storrs Eˉ , Targino da Costa ALˉ , Houston Aˉ , Wendl MC, Jayasinghe RG, Iglesia MD, Ma C, Herndon JM, Southard-Smith AN, Liu X, Mudd J, Karpova A, Shinkle A, Goedegebuure SP, Abdelsaher ATMA, Bo P, Fulghum L, Livingston S, Balaban M, Hill A, Ippolito JE, Thorsson V, Held JM, Hagemann IS, Kim EH, Bayguinov PO, Kim AH, Mullen MM, Shoghi KI, Ju T, Reimers MA, Weimholt C, Kang L, Puram SV, Veis DJ, Pachynski R, Fuh KC, Chheda MG, Gillanders WE^, Fields RC^, Raphael BJ^, Chen F^, Ding L^
Nature. Oct. 30, 2024; Spotlighted in Nature Cover and Research Briefings by NCI directors
Differential chromatin accessibility and transcriptional dynamics define breast cancer subtypes and their lineages
Iglesia MD*, Jayasinghe RG*, Chen S*, Terekhanova NV*, Herndon JM*, Storrs E, Karpova A, Zhou DC, Naser Al Deen N, Shinkle AT, Lu RJH, Caravan W, Houston A, Zhao Y, Sato K, Lal P, Street C, Rodrigues FM, Southard-Smith AN, Targino da Costa ALN, Zhu H, Mo CK, Crowson L, Fulton RS, Wyczalkowski MA, Fronick CC, Fulton LA, Sun H, Davies SR, Appelbaum EL, Chasnoff SE, Carmody M, Brooks C, Liu R, Wendl MC, Oh C, Bender D, Cruchaga C, Harari O, Bredemeyer A, Lavine K, Bose R, Margenthaler J, Held JM, Achilefu S, Ademuyiwa F, Aft R, Ma C, Colditz GA, Ju T, Oh ST, Fitzpatrick J, Hwang ES, Shoghi KI, Chheda MG, Veis DJ, Chen F, Fields RC, Gillanders WE^, Ding L^
Nature Cancer. Oct. 30, 2024
Inferring allele-specific copy number aberrations and tumor phylogeography from spatially resolved transcriptomics Ma C, Balaban M, Liu J, Chen S, Wilson MJ, Sun CH, Ding L^, Raphael BJ^
Nature Methods. Oct. 30, 2024
Defining precancer: a grand challenge for the cancer community
Faupel-Badger J, Kohaar I, Bahl M, Chan AT, Campbell JD, Ding L, De Marzo AM, Maitra A, Merrick DT, Hawk ET, Wistuba II, Ghobrial IM, Lippman SM, Lu KH, Lawler M, Kay NE, Tlsty TD, Rebbeck TR, Srivastava S^
The Precancer Think Tank Team
Nature Reviews Cancer, 24, 792–809 (2024).
SenNet recommendations for detecting senescent cells in different tissues
Suryadevara V, Hudgins AD, Rajesh A, Pappalardo A, Karpova A, Dey AK, Hertzel A, Agudelo A, Rocha A, Soygur B, Schilling B, Carver CM, Aguayo-Mazzucato C, Baker DJ, Bernlohr DA, Jurk D, Mangarova DB, Quardokus EM, Enninga EAL, Schmidt EL, Chen F, Duncan FE, Cambuli F, Kaur G, Kuchel GA, Lee G, Daldrup-Link HE, Martini H, Phatnani H, Al-Naggar IM, Rahman I, Nie J, Passos JF, Silverstein JC, Campisi J, Wang J, Iwasaki K, Barbosa K, Metis K, Nernekli K, Niedernhofer LJ, Ding L, Wang L, Adams LC, Liu R, Doolittle ML, Teneche MG, Schafer MJ, Xu M, Hajipour M, Boroumand M, Basisty N, Sloan N, Slavov N, Kuksenko O, Robson P, Gomez PT, Vasilikos P, Adams PD, Carapeto P, Zhu Q, Ramasamy R, Perez-Lorenzo R, Fan R, Dong R, Montgomery RR, Shaikh S, Vickovic S, Yin S, Kang S, Suvakov S, Khosla S, Garovic VD, Menon V, Xu Y, Song Y, Suh Y, Dou Z, Neretti N
Nature Reviews Molecular Cell Biology . 2024 Jun 3:1-23
Traversing the Bench to Bedside Journey for iNKT Cell Therapies
O'Neal J*, Mavers M*, Jayasinghe RG, DiPersio JF
Frontiers in Immunology.;15:1436968
Multi-scale signaling and tumor evolution in high-grade gliomas
Liu J*, Cao S*, Imbach KJ* , Gritsenko MA* , Lih TM* , Kyle JEˉ, Yaron-Barir TMˉ, Binder ZAˉ, Li Yˉ, Strunilin Iˉ, Wang YTˉ, Tsai CFˉ, Ma Wˉ, Chen Lˉ, Clark NM, Shinkle A, Naser Al Deen N, Caravan W, Houston A, Simin FA, Wyczalkowski MA, Wang LB, Storrs E, Chen S, Illindala R, Li YD, Jayasinghe RG, Rykunov D, Cottingham SL, Chu RK, Weitz KK, Moore RJ, Sagendorf T, Petyuk VA, Nestor M, Bramer LM, Stratton KG, Schepmoes AA, Couvillion SP, Eder J, Kim YM, Gao Y, Fillmore TL, Zhao R, Monroe ME, Southard-Smith AN, Li YE, Lu RJ, Johnson JL, Wiznerowicz M, Hostetter G, Newton CJ, Ketchum KA, Thangudu RR, Barnholtz-Sloan JS, Wang P, Fenyö D, An E, Thiagarajan M, Robles AI, Mani DR, Smith RD, Porta-Pardo E, Cantley LC, Iavarone A, Chen F, Mesri M, Nasrallah MP, Zhang H, Resnick AC, Chheda MG^, Rodland KD^, Liu T^ , Ding L^ Philadelphia Coalition for a Cure, Clinical Proteomic Tumor Analysis Consortium
Cancer Cell (2024): 1217-1238
Comprehensive proteogenomic characterization of rare kidney tumors
Li GX*, Chen L*, Hsiao Y*, Mannan R, Zhang Y, Luo J, Petralia F, Cho H, Hosseini N, Leprevost FV, Calinawan A, Li Y, Anand S, Dagar A, Geffen Y, Kumar-Sinha C, Chugh S, Le A, Ponce S, Guo S, Zhang C, Schnaubelt M, Naser Al Deen N, Chen F, Caravan W, Houston A, Hopkins A, Newton CJ, Wang X, Polasky DA, Haynes S, Yu F, Jing X, Chen S, Robles AI, Mesri M, Thiagarajan M, An E, Getz GA, Linehan WM, Hostetter G, Jewell SD, Chan DW, Wang P, Omenn GS, Mehra R, Ricketts CJ, Ding L, Chinnaiyan AM, Cieslik MP, Dhanasekaran SM^, Zhang H^, Nesvizhskii AI ^ Clinical Proteomic Tumor Analysis Consortium
Cell Reports Medicine. 2024 May 21;5(5)
A Pan-Cancer Patient-Derived Xenograft Histology Image Repository with Genomic and Pathologic Annotations Enables Deep Learning Analysis
White BS, Woo XY, Koc S, Sheridan T, Neuhauser SB, Wang S, Evrard YA, Chen L, Foroughi Pour A, Landua JD, Mashl RJ, Davies SR, Fang B, Rosa MG, Evans KW, Bailey MH, Chen Y, Xiao M, Rubinstein JC, Sanderson BJ, Lloyd MW, Domanskyi S, Dobrolecki LE, Fujita M, Fujimoto J, Xiao G, Fields RC, Mudd JL, Xu X, Hollingshead MG, Jiwani S, Acevedo S, Davis-Dusenbery BN, Robinson PN, Moscow JA, Doroshow JH, Mitsiades N, Kaochar S, Pan CX, Carvajal-Carmona LG, Welm AL, Welm BE, Govindan R, Li S, Davies MA, Roth JA, Meric-Bernstam F, Xie Y, Herlyn M, Ding L, Lewis MT, Bult CJ, Dean DA II, Chuang JH
Cancer Research 84.13 (2024): 2060-2072
Combined KRAS-MAPK pathway inhibitors and HER2-directed drug conjugate is efficacious in pancreatic cancer
Bulle A*, Liu P*, Seehra K, Bansod S, Chen Y, Zahra K, Somani V, Khawar IA, Chen H-P, Dodhiawala PB, Li L, Geng Y, Mo C-K, Mahsl J, Ding L, Govindan R, Davies S, Mudd J, Hawkins WG, Fields RC, DeNardo DG, Knoerzer D, Held JM, Grierson PM, Wang-Gillam A, Ruzinova MB, Lim K-H^
Nature Communications 15.1 (2024): 2503
Pan-cancer proteogenomics characterization of tumor immunity
Petralia F*^, Ma W*, Yaron TM*, Caruso FP*, Tignor N*, Wang JM*, Charytonowicz D, Johnson JL, Huntsman EM, Marino GB, Calinawan A, Evangelista JE, Selvan ME, Chowdhury S, Rykunov D, Krek A, Song X, Turhan B, Christianson KE, Lewis DA, Deng EZ, Clarke DJB, Whiteaker JR, Kennedy JJ, Zhao L, Segura RL, Batra H, Raso MGR, Parra ER, Soundararajan R, Tang X, Li Y, Yi X, Satpathy S, Wang Y, Wiznerowicz M, González-Robles TJ, Iavarone A, Gosline SJC, Reva B, Robles AI, Nesvizhskii AI, Mani DR, Gillette MA, Klein RJ, Cieslik M, Zhang B, Paulovich AG, Sebra R, Gümüş ZH, Hostetter G, Fenyö D, Omenn GS, Cantley LC, Ma'ayan A, Lazar AJ, Ceccarelli M, Wang P^ Clinical Proteomic Tumor Analysis Consortium (Contributors include: Ding L, Cao S, Zhou DC, RodriguesFM, Song Y, Storrs EP, Wang LB, Terekhanova NV, Wu Y, Wyczalkowski MA, Yao L). Cell (2024). https://doi.org/10.1016/j.cell.2024.01.027
Proteogenomic characterization of small cell lung cancer identifies biological insights and subtype-specific therapeutic strategies
Liu Q*, Zhang J*, Guo C*, Wang M,* Wang C*, Yan Y*, Sun L*, Wang D*, Zhang L, Yu H, Hou L, Wu C, Zhu Y, Jiang G, Zhu H, Zhou Y, Fang S, Zhang T, Hu L, Li J, Liu Y, Zhang H, Zhang B, Ding L, Robles A I, Rodriguez H, Gao D^, Ji H^, Zhou H^, Zhang P^.
Cell (2024). https://doi.org/10.1016/j.cell.2023.12.004
2023
Combining the Tyrosine Kinase Inhibitor Cabozantinib and the mTORC1/2 Inhibitor Sapanisertib Blocks ERK Pathway Activity and Suppresses Tumor Growth in Renal Cell Carcinoma
Wu Y*, Chen S*, Yang X*, Sato K*, Lal P*, Wang Y, Shinkle A, Wendl M, Primeau T, Zhao Y, Gould A, Sun H, Mudd J, Hoog J, Mashl RJ, Wyczalkowski M, Mo C, Liu R, Herndon J, Davies R, Liu D, Ding X, Evrard Y, Welm B, Lum D, Koh M, Welm A, Chuang J, Moscow J, Meric-Bernstam F, Govindan R, Li S, Hsieh J, Fields RC, Lim K, Ma C, Zhang H, Ding L^, Chen F^
Cancer Res (2023). https://doi.org/10.1158/0008-5472.CAN-23-0604
Epigenetic regulation during cancer transitions across 11 tumour types
Terekhanova NV*, Karpova A*, Liang WW*, Strzalkowski A, Chen S, Li Y, Southard-Smith AN, Iglesia MD, Wendl MC, Jayasinghe RG, Liu J, Song Y, Cao S, Houston A, X L, Wyczalkowski MA, Lu RJ, Caravan W, Shinkle A, Naser Al Deen N, Herndon JM, Mudd J, Ma C, Sarkar H, Sato K, Ibrahim OM, Mo C, Chasnoff SE, Porta-Pardo E, Held JM, Pachynski R, Schwarz JK, Gillanders WE, Kim AH, Vij R, DiPersio JF, Puram SV, Chheda MG, Fuh KC, DeNardo DG, Fields RC^, Chen F^, Raphael BJ^, Ding L^
Nature 623, 432–441 (2023) Spotlighted in Nature Genetics Research Highlight: A single-nucleus pan-cancer epigenetic and transcriptomic landscape Fletcher M^ Nature Genetics, 55(12), 2019-2019
Immune Cell Deconvolution Reveals Possible Association of γδ T Cells with Poor Survival in Head and Neck Squamous Cell Carcinoma
Parikh AS^, Li Y, Mazul A, Yu VX, Thorstad W, Rich J, Paniello R, Caruana SM, Troob SH, Jackson RS, Pipkorn P, Zolkind P, Qi Z, Adkins D, Ding L, Puram SV^.
Cancers. 2023; 15(19):4855. https://doi.org/10.3390/cancers15194855
Single-Nucleotide Variant Calling in Single-Cell Sequencing Data With Monopogen
Dou J, Tan Y, Kock KH, Wang J, Cheng X, Tan LM, Han KY, Hon CC, Park WY, Shin JW, Jin H, Wang Y, Chen H, Ding L, Prabhakar S, Navin N, Chen R, Chen K
Nat Biotechnol 2023 Aug 17; [ahead of print]
Pan-cancer proteogenomics connects oncogenic drivers to functional states
Li Y*, Porta-Pardo E*, Tokheim C*, Bailey MH*, Yaron TM*, Stathias Vˉ , Geffen Yˉ , Imbach KJˉ , Cao Sˉ , Anand S, Akiyama Y, Liu W, Wyczalkowski MA, Song Y, Storrs EP, Wendl MC, Zhang W, Sibai M, Ruiz-Serra V, Liang WW, Terekhanova NV, Rodrigues FM, Clauser KR, Heiman DI, Zhang Q, Aguet F, Calinawan AP, Dhanasekaran SM, Birger C, Satpathy S, Zhou DC, Wang LB, Baral J, Johnson JL, Huntsman EM, Pugliese P, Colaprico A, Iavarone A, Chheda MG, Ricketts CJ, Fenyö D, Payne SH, Rodriguez H, Robles AI, Gillette MA, Kumar-Sinha C, Lazar AJ, Cantley LC^, Getz G^, Ding L^
Clinical Proteomic Tumor Analysis Consortium
Cell 2023; DOI: 10.1016/j.cell.2023.07.014
Pan-cancer analysis of post-translational modifications reveals shared patterns of protein regulation
Geffen Y*, Anand S*, Akiyama Y*, Yaron TM*, Song Y*, Johnson JLˉ , Govindan Aˉ , Babur Öˉ , Li Yˉ , Huntsman E, Wang LB, Birger C, Heiman DI, Zhang Q, Miller M, Maruvka YE, Haradhvala NJ, Calinawan A, Belkin S, Kerelsky A, Clauser KR, Krug K, Satpathy S, Payne SH, Mani DR, Gillette MA, Dhanasekaran SM, Thiagarajan M, Mesri M, Rodriguez H, Robles AI, Carr SA, Lazar AJ, Aguet F^, Cantley LC^, Ding L^, Getz G^
Clinical Proteomic Tumor Analysis Consortium
Cell 2023 Aug 31;186(18):3945-3967; DOI: 10.1016/j.cell.2023.07.013
Integrative multi-omic cancer profiling reveals DNA methylation patterns associated with therapeutic vulnerability and cell-of-origin
Liang WW, Lu RJH, Jayasinghe RG, Foltz SM, Porta-Pardo E, Geffen Y, Wendl MC, Lazcano R, Kolodziejczak I, Song Y, Govindan A, Demicco EG, Li X, Li Y, Sethuraman S, Payne SH, Fenyö D, Rodriguez H, Wiznerowicz M, Shen H, Mani DR, Rodland KD, Lazar AJ, Robles AI, Ding L
Clinical Proteomic Tumor Analysis Consortium
Cancer Cell 2023 Sep 11;41(9):1567-1585; DOI: 10.1016/j.ccell.2023.07.013
Proteogenomic data and resources for pan-cancer analysis
Li Y*, Dou Y*, Da Veiga Leprevost F*, Geffen Y*, Calinawan AP*, Aguet F, Akiyama Y, Anand S, Birger C, Cao S, Chaudhary R, Chilappagari P, Cieslik M, Colaprico A, Zhou DC, Day C, Domagalski MJ, Esai Selvan M, Fenyö D, Foltz SM, Francis A, Gonzalez-Robles T, Gümüş ZH, Heiman D, Holck M, Hong R, Hu Y, Jaehnig EJ, Ji J, Jiang W, Katsnelson L, Ketchum KA, Klein RJ, Lei JT, Liang WW, Liao Y, Lindgren CM, Ma W, Ma L, MacCoss MJ, Martins Rodrigues F, McKerrow W, Nguyen N, Oldroyd R, Pilozzi A, Pugliese P, Reva B, Rudnick P, Ruggles KV, Rykunov D, Savage SR, Schnaubelt M, Schraink T, Shi Z, Singhal D, Song X, Storrs E, Terekhanova NV, Thangudu RR, Thiagarajan M, Wang LB, Wang JM, Wang Y, Wen B, Wu Y, Wyczalkowski MA, Xin Y, Yao L, Yi X, Zhang H, Zhang Q, Zuhl M, Getz G, Ding L, Nesvizhskii AI, Wang P, Robles AI^, Zhang B^, Payne SH^
Clinical Proteomic Tumor Analysis Consortium
Cancer Cell 41 (8), 1397-1406
Deep learning integrates histopathology and proteogenomics at a pan-cancer level
Wang JM*, Hong R*, Demicco EG, Tan J, Lazcano R, Moreira AL, Li Y, Calinawan A, Razavian N, Schraink T, Gillette MA, Omenn GS, An E, Rodriguez H, Tsirigos A, Ruggles KV, Ding L, Robles AI, Mani DR, Rodland KD, Lazar AJ^, Liu W^, Fenyö D^
Clinical Proteomic Tumor Analysis Consortium
Cell Reports Medicine 2023; DOI: 10.1016/j.xcrm.2023.101173
Pharmaco-proteogenomic characterization of liver cancer organoids for precision oncology
Ji S, Feng L, Fu Z, Wu G, Wu Y, Lin Y, Lu D, Song Y, Cui P, Yang Z, Sang C, Song G, Cai S, Li Y, Lin H, Zhang S, Wang X, Qiu S, Zhang X, Hua G, Li J, Zhou J, Dai Z, Wang X, Ding L, Wang P, Gao D, Zhang B, Rodriguez H, Fan J, Clevers H, Zhou H, Sun Y, Gao Q
Science translational medicine 15.706 (2023): eadg3358
Proteomics of Adjacent-To-Tumor Samples Uncovers Clinically Relevant Biological Events in Hepatocellular Carcinoma
Zhu H^, Lin Y, Lu D, Wang S, Liu Y, Dong L, Meng Q, Gao J, Wang Y, Song N, Suo Y, Ding L, Wang P, Zhang B, Gao D, Fan J, Gao Q^, Zhou H^
Natl Sci Rev 2023 Jun 2;10(8):nwad167
Proteogenomic Insights Suggest Druggable Pathways in Endometrial Carcinoma
Dou Y*, Katsnelson L*, Gritsenko MA*, Hu Y, Reva B, Hong R, Wang YT, Kolodziejczak I, Lu RJ, Tsai CF, Bu W, Liu W, Guo X, An E, Arend RC, Bavarva J, Chen L, Chu RK, Czekanski A, Davoli T, Demicco EG, DeLair D, Devereaux K, Dhanasekaran SM, Dottino P, Dover B, Fillmore TL, Foxall M, Hermann CE, Hiltke T, Hostetter G, Jedryka M, Jewell SD, Johnson I, Kahn AG, Ku AT, Kumar-Sinha C, Kurzawa P, Lazar AJ, Lazcano R, Lei JT, Li Y, Liao Y, Lih TM, Lin TT, Martignetti JA, Masand RP, Matkowski R, McKerrow W, Mesri M, Monroe ME, Moon J, Moore RJ, Nestor MD, Newton C, Omelchenko T, Omenn GS, Payne SH, Petyuk VA, Robles AI, Rodriguez H, Ruggles KV, Rykunov D, Savage SR, Schepmoes AA, Shi T, Shi Z, Tan J, Taylor M, Thiagarajan M, Wang JM, Weitz KK, Wen B, Williams CM, Wu Y, Wyczalkowski MA, Yi X, Zhang X, Zhao R, Mutch D, Chinnaiyan AM, Smith RD, Nesvizhskii AI, Wang P, Wiznerowicz M, Ding L, Mani DR, Zhang H, Anderson ML, Rodland KD, Zhang B^, Liu T^, Fenyo D^
Clinical Proteomic Tumor Analysis Consortium
Cancer Cell 2023 Aug 2:S1535-6108(23)00247-7; [ahead of print]
Fibrosis Induced by Resident Macrophages Has Divergent Roles in Pancreas Inflammatory Injury and PDAC
Baer JM, Zuo C, Kang LI, de la Lastra AA, Borcherding NC, Knolhoff BL, Bogner SJ, Zhu Y, Yang L, Laurent J, Lewis MA, Zhang N, Kim KW, Fields RC, Yokoyama WM, Mills JC, Ding L, Randolph GJ, DeNardo DG
Nat Immunol 2023 Sep;24(9):1443-1457
Pharmaco-Proteogenomic Characterization of Liver Cancer Organoids for Precision Oncology
Ji S*, Feng L*, Fu Z*, Wu G*, Wu Y*, Lin Y, Lu D, Song Y, Cui P, Yang Z, Sang C, Song G, Cai S, Li Y, Lin H, Zhang S, Wang X, Qiu S, Zhang X, Hua G, Li J, Zhou J, Dai Z, Wang X, Ding L, Wang P, Gao D, Zhang B, Rodriguez H, Fan J, Clevers H, Zhou H^, Sun Y^, Gao Q^
Sci Transl Med 2023 Jul 26;15(706):eadg3358
Cellular States Are Coupled to Genomic and Viral Heterogeneity in HPV-Related Oropharyngeal Carcinoma
Puram SV*^, Mints M*, Pal A, Qi Z, Reeb A, Gelev K, Barrett TF, Gerndt S, Liu P, Parikh AS, Ramadan S, Law T, Mroz EA, Rocco JW, Adkins D, Thorstad WL, Gay HA, Ding L, Paniello RC, Pipkorn P, Jackson RS, Wang X, Mazul A, Chernock R, Zevallos JP, Silva-Fisher J, Tirosh I^
Nat Genet 2023 Apr;55(4):640-650
Epigenetic and Transcriptomic Characterization Reveals Progression Markers and Essential Pathways in Clear Cell Renal Cell Carcinoma
Wu Y*, Terekhanova NV*, Caravan W*, Naser Al Deen N*, Lal P*, Chen S, Mo CK, Cao S, Li Y, Karpova A, Liu R, Zhao Y, Shinkle A, Strunilin I, Weimholt C, Sato K, Yao L, Serasanambati M, Yang X, Wyczalkowski M, Zhu H, Zhou DC, Jayasinghe RG, Mendez D, Wendl MC, Clark D, Newton C, Ruan Y, Reimers MA, Pachynski RK, Kinsinger C, Jewell S, Chan DW, Zhang H, Chaudhuri AA, Chheda MG, Humphreys BD, Mesri M, Rodriguez H, Hsieh JJ, Ding L^, Chen F^
Nat Commun 2023 Mar 27;14(1):1681
Single-Cell Discovery and Multi-Omic Characterization of Therapeutic Targets in Multiple Myeloma
Yao L*, Wang JT*, Jayasinghe RG*, O'Neal J, Tsai CF, Rettig MP, Song Y, Liu R, Zhao Y, Ibrahim OM, Fiala MA, Fortier JM, Chen S, Gehrs L, Martins Rodrigues F, Wendl MC, Kohnen D, Shinkle A, Cao S, Foltz SM, Zhou DC, Storrs E, Wyczalkowski MA, Mani S, Goldsmith SR, Zhu Y, Hamilton M, Liu T, Chen F, Vij R^, Ding L^, DiPersio JF^
Cancer Res 2023 Feb 13:CAN-22-1769; [ahead of print]
Cross Center Single-Cell RNA Sequencing Study of the Immune Microenvironment in Rapid Progressing Multiple Myeloma
Pilcher W, Thomas BE, Bhasin SS, Jayasinghe RG, Yao L, Gonzalez-Kozlova E, Dasari S, Kim-Schulze S, Rahman A, Patton J, Fiala M, Cheloni G, Kourelis T, Dhodapkar MV, Vij R, Mehr S, Hamilton M, Cho HJ, Auclair D, Avigan DE^, Kumar SK^, Gnjatic S^, Ding L^, Bhasin M^
NPJ Genom Med 2023 Jan 26;8(1):3
2022
Histopathologic and Proteogenomic Heterogeneity Reveals Features of Clear Cell Renal Cell Carcinoma Aggressiveness
Li Y*, Lih TM*, Dhanasekaran SM*^, Mannan R*, Chen L*, Cieslik M, Wu Y, Lu RJ, Clark DJ, Kolodziejczak I, Hong R, Chen S, Zhao Y, Chugh S, Caravan W, Naser Al Deen N, Hosseini N, Newton CJ, Krug K, Xu Y, Cho KC, Hu Y, Zhang Y, Kumar-Sinha C, Ma W, Calinawan A, Wyczalkowski MA, Wendl MC, Wang Y, Guo S, Zhang C, Le A, Dagar A, Hopkins A, Cho H, Leprevost FDV, Jing X, Teo GC, Liu W, Reimers MA, Pachynski R, Lazar AJ, Chinnaiyan AM, Van Tine BA, Zhang B, Rodland KD, Getz G, Mani DR, Wang P, Chen F, Hostetter G, Thiagarajan M, Linehan WM, Fenyo D, Jewell SD, Omenn GS, Mehra R, Wiznerowicz M, Robles AI, Mesri M, Hiltke T, An E, Rodriguez H, Chan DWˇ, Ricketts CJ^ˇ, Nesvizhskii AIˇ, Zhang H^ˇ, Ding L^ˇ
Clinical Proteomic Tumor Analysis Consortium
Cancer Cell 2022 Dec 20:S1535-6108(22)00565-7;
Clonal Hematopoiesis and Risk of Incident Lung Cancer
Tian R*, Wiley B*, Liu J*, Zong X*, Truong B*, Zhao S, Uddin MM, Niroula A, Miller CA, Mukherjee S, Heiden BT, Luo J, Puri V, Kozower BD, Walter MJ, Ding L, Link DC, Amos CI, Ebert BL, Govindan Rˇ, Natarajan Pˇ, Bolton KLˇ, Cao Yˇ^
J Clin Oncol 2022 Dec 8:JCO2200857; [ahead of print]
NIH SenNet Consortium to map senescent cells throughout the human lifespan to understand physiological health
SenNet Consortium (Contributors include: Ding L, Wendl MC, Wyczalkowski MA)
Nature Aging; 20 December 2022
Neoplastic Cell Enrichment of Tumor Tissues Using Coring and Laser Microdissection for Proteomic and Genomic Analyses of Pancreatic Ductal Adenocarcinoma
Li QK^, Hu Y, Chen L, Schnaubelt M, Cui Zhou D, Li Y, Lu RJ, Thiagarajan M, Hostetter G, Newton CJ, Jewell SD, Omenn G, Robles AI, Mesri M, Bathe OF, Zhang B, Ding L, Hruban RH, Chan DW, Zhang H^
Clin Proteomics 2022 Oct 20;19(1):36
Comprehensive Characterization of the Multiple Myeloma Immune Microenvironment Using Integrated scRNA-seq, CyTOF, and CITE-seq Analysis
Yao L, Jayasinghe RG, Lee BH, Bhasin SS, Pilcher W, Doxie DB, Gonzalez-Kozlova E, Dasari S, Fiala MA, Pita-Juarez Y, Strausbauch M, Kelly G, Thomas BD, Kumar SK, Cho HJ, Anderson E, Wendl MC, Dawson T, D’souza D, Oh ST, Cheloni G, Li Y, DiPersio JF, Rahman AH, Dhodapkar KM, Kim-Schulze S, Vij R, Vlachos IS, Mehr S, Hamilton M, Auclair D, Kourelis T^, Avigan D^, Dhodapkar MV^, Gnjatic S^, Bhasin MK^, and Ding L^
Cancer Res Commun; 2(10) October 2022
Transitioning cancer cells and the surrounding tumor environment in pancreatic cancer
Jayasinghe RG, Ding L
Nature Genetics; 05 September 2022
Spatially Restricted Drivers and Transitional Cell Populations Cooperate With the Microenvironment in Untreated and Chemo-Resistant Pancreatic Cancer
Cui Zhou D*, Jayasinghe RG*, Chen S, Herndon JM, Iglesia MD, Navale P, Wendl MC, Caravan W, Sato K, Storrs E, Mo CK, Liu J, Southard-Smith AN, Wu Y, Naser Al Deen N, Baer JM, Fulton RS, Wyczalkowski MA, Liu R, Fronick CC, Fulton LA, Shinkle A, Thammavong L, Zhu H, Sun H, Wang LB, Li Y, Zuo C, McMichael JF, Davies SR, Appelbaum EL, Robbins KJ, Chasnoff SE, Yang X, Reeb AN, Oh C, Serasanambati M, Lal P, Varghese R, Mashl JR, Ponce J, Terekhanova NV, Yao L, Wang F, Chen L, Schnaubelt M, Lu RJ, Schwarz JK, Puram SV, Kim AH, Song SK, Shoghi KI, Lau KS, Ju T, Chen K, Chatterjee D, Hawkins WG, Zhang H, Achilefu S, Chheda MG, Oh ST, Gillanders WE, Chen F, DeNardo DG^, Fields RC^, Ding L^
Nature genetics, 2022 Aug 22
CS1 CAR-T Targeting the Distal Domain of CS1 (SLAMF7) Shows Efficacy in High Tumor Burden Myeloma Model Despite Fratricide of CD8+CS1 Expressing CAR-T Cells
O'Neal J^, Ritchey JK, Cooper ML, Niswonger J, Sofia Gonzalez L, Street E, Rettig MP, Gladney SW, Gehrs L, Abboud R, Prior JL, Haas GJ, Jayasinghe RG, Ding L, Ghobadi A, Vij R, DiPersio JF^
Leukemia 2022 Jun;36(6):1625-1634
Pollock: Fishing for Cell States
Storrs EP, Zhou DC, Wendl MC, Wyczalkowski MA, Karpova A, Wang LB, Li Y, Southard-Smith A, Jayasinghe RG, Yao L, Liu R, Wu Y, Terekhanova NV, Zhu H, Herndon JM, Puram S, Chen F, Gillanders WE, Fields RC, Ding L
Bioinform Adv 2022 May 13;2(1):vbac028
Cancer Proteogenomics: Current Impact and Future Prospects
Mani DR^, Krug K, Zhang B, Satpathy S, Clauser KR, Ding L, Ellis M, Gillette MA, Carr SA^
Nat Rev Cancer 2022 May;22(5):298-313
PDXNet Portal: Patient-Derived Xenograft Model, Data, Workflow and Tool Discovery
Koc S*, Lloyd MW*, Grover JW, Xiao N, Seepo S, Subramanian SL, Ray M, Frech C, DiGiovanna J, Webster P, Neuhauser S, Srivastava A, Woo XY, Sanderson BJ, White B, Lott P, Dobrolecki LE, Dowst H, Evrard YA, Wallace TA, Moscow JA, Doroshow JH, Mitsiades N, Kaochar S, Pan CX, Chen MS, Carvajal-Carmona L, Welm AL, Welm BE, Lewis MT, Govindan R, Ding L, Li S, Herlyn M, Davies MA, Roth J, Meric-Bernstam F, Robinson PN, Bult CJ, Davis-Dusenbery B, Dean DA 2nd^, Chuang JH^
PDXNet Consortium
NAR Cancer 2022 Apr 22;4(2):zcac014
LINC00355 Regulates p27(KIP) Expression by Binding to MENIN to Induce Proliferation in Late-Stage Relapse Breast Cancer
Eteleeb AM, Thunuguntla PK, Gelev KZ, Tang CY, Rozycki EB, Miller A, Lei JT, Jayasinghe RG, Dang HX, White NM, Reis-Filho JS, Mardis ER, Ellis MJ, Ding L, Silva-Fisher JM^, Maher CA^
NPJ Breast Cancer 2022 Apr 13;8(1):49
MITI Minimum Information Guidelines for Highly Multiplexed Tissue Images
Schapiro D, Yapp C, Sokolov A, Reynolds SM, Chen YA, Sudar D, Xie Y, Muhlich J, Arias-Camison R, Arena S, Taylor AJ, Nikolov M, Tyler M, Lin JR, Burlingame EA, Chang YH, Farhi SL, Thorsson V, Venkatamohan N, Drewes JL, Pe'er D, Gutman DA, Herrmann MD, Gehlenborg N, Bankhead P, Roland JT, Herndon JM, Snyder MP, Angelo M, Nolan G, Swedlow JR, Schultz N, Merrick DT, Mazzili SA, Cerami E, Rodig SJ, Santagata S, Sorger PK
Human Tumor Atlas Network (Contributors include: Ding L)
Nat Methods 2022 Mar;19(3):262-267
LINE-1 Expression in Cancer Correlates With p53 Mutation, Copy Number Alteration, and S Phase Checkpoint
McKerrow W, Wang X, Mendez-Dorantes C, Mita P, Cao S, Grivainis M, Ding L, LaCava J, Burns KH, Boeke JD^, Fenyö D^
Proc Natl Acad Sci U S A 2022 Feb 22;119(8):e2115999119
Proteogenomic Characterization Identifies Clinically Relevant Subgroups of Intrahepatic Cholangiocarcinoma
Dong L*, Lu D*, Chen R*, Lin Y*, Zhu H*, Zhang Z*, Cai S*, Cui P, Song G, Rao D, Yi X, Wu Y, Song N, Liu F, Zou Y, Zhang S, Zhang X, Wang X, Qiu S, Zhou J, Wang S, Zhang X, Shi Y, Figeys D, Ding L, Wang P, Zhang B, Rodriguez H, Gao Q^, Gao D^, Zhou H^, Fan J^
Cancer Cell 40, 70–87, January 10, 2022
2021
RNA Splicing and Immune-Checkpoint Inhibition
Ding L, Odunsi K
N Engl J Med 2021 Nov 4;385(19):1807-1809
Genomic Profiling of Lung Adenocarcinoma in Never-Smokers
Devarakonda S*, Li Y*, Martins Rodrigues F*, Sankararaman S, Kadara H, Goparaju C, Lanc I, Pepin K, Waqar SN, Morgensztern D, Ward J, Masood A, Fulton R, Fulton L, Gillette MA, Satpathy S, Carr SA, Wistuba I, Pass H, Wilson RKˇ, Ding Lˇ, Govindan Rˇ^
J Clin Oncol 2021 Sep 30:JCO2101691;
Moving pan-cancer studies from basic research toward the clinic
Chen F, Wendl MC, Wyczalkowski MA, Bailey MH, Li Y, Ding L^
Nature Cancer, 2021 Sep 16
Proteogenomic characterization of pancreatic ductal adenocarcinoma
Cao L*, Huang C*, Zhou DC*, Hu Yˉ, Lih TMˉ, Savage SRˉ, Krug Kˉ, Clark DJˉ, Schnaubelt M, Chen L, Leprevost F, Eguez RV, Yang W, Pan J, Wen B, Dou Y, Jiang W, Liao Y, Shi Z, Terekhanova NV, Cao S, Lu RJ, Li Y, Liu R, Zhu H, Ronning P, Wu Y, Wyczalkowski MA, Easwaran H, Danilova L, Mer AS, Yoo S, Wang JM, Liu W, Haibe-Kains B, Thiagarajan M, Jewell SD, Hostetter G, Newton CJ, Li QK, Roehrl MH, Fenyö D, Wang P, Nesvizhskii AI, Mani DR, Omenn GS, Boja ES, Mesri M, Robles AI, Rodriguez H, Bathe OFˇ, Chan DWˇ, Hruban RHˇ, Ding Lˇ^, Zhang Bˇ^, Zhang Hˇ^
Clinical Proteomic Tumor Analysis Consortium
Cell184, 5031–5052, September 16, 2021
Cell-Free DNA Ultra-Low-Pass Whole Genome Sequencing to Distinguish Malignant Peripheral Nerve Sheath Tumor (MPNST) From Its Benign Precursor Lesion: A Cross-Sectional Study
Szymanski JJ, Sundby RT, Jones PA, Srihari D, Earland N, Harris PK, Feng W, Qaium F, Lei H, Roberts D, Landeau M, Bell J, Huang Y, Hoffman L, Spencer M, Spraker MB, Ding L, Widemann BC, Shern JF, Hirbe AC, Chaudhuri AA
PLoS Med 2021 Aug 31;18(8):e1003734
Urine Tumor DNA Detection of Minimal Residual Disease in Muscle-Invasive Bladder Cancer Treated With Curative-Intent Radical Cystectomy: A Cohort Study
Chauhan PS*, Chen K*, Babbra RK, Feng W, Pejovic N, Nallicheri A, Harris PK, Dienstbach K, Atkocius A, Maguire L, Qaium F, Szymanski JJ, Baumann BC, Ding L, Cao D, Reimers MA, Kim EH, Smith ZL^, Arora VK^, Chaudhuri AA^
PLoS Med 2021 Aug 31;18(8):e1003732
Comprehensive Characterization of 536 Patient-Derived Xenograft Models Prioritizes Candidates For Targeted Treatment
Sun H*, Cao S*, Mashl RJ*, Mo CK*, Zaccaria S*, Wendl MC, Davies SR, Bailey MH, Primeau TM, Hoog J, Mudd JL, Dean DA 2nd, Patidar R, Chen L, Wyczalkowski MA, Jayasinghe RG, Rodrigues FM, Terekhanova NV, Li Y, Lim KH, Wang-Gillam A, Van Tine BA, Ma CX, Aft R, Fuh KC, Schwarz JK, Zevallos JP, Puram SV, DiPersio JF, Davis-Dusenbery B, Ellis MJ, Lewis MT, Davies MA, Herlyn M, Fang B, Roth JA, Welm AL, Welm BE, Meric-Bernstam F, Chen F, Fields RC, Li S, Govindan R, Doroshow JH, Moscow JA, Evrard YA, Chuang JH, Raphael BJ, Ding L^
NCI PDXNet Consortium
Nat Commun 2021 Aug 24;12(1):5086
A Proteogenomic Portrait of Lung Squamous Cell Carcinoma
Satpathy S*^, Krug K*, Jean Beltran PM*, Savage SR*, Petralia Fˉ, Kumar-Sinha Cˉ, Dou Yˉ, Reva Bˉ, Kane MHˉ, Avanessian SCˉ, Vasaikar SVˉ, Krek A, Lei JT, Jaehnig EJ, Omelchenko T, Geffen Y, Bergstrom EJ, Stathias V, Christianson KE, Heiman DI, Cieslik MP, Cao S, Song X, Ji J, Liu W, Li K, Wen B, Li Y, Gumus ZH, Selvan ME, Soundararajan R, Visal TH, Raso MG, Parra ER, Babur O, Vats P, Anand S, Schraink T, Cornwell M, Rodrigues FM, Zhu H, Mo CK, Zhang Y, da Veiga Leprevost F, Huang C, Chinnaiyan AM, Wyczalkowski MA, Omenn GS, Newton CJ, Schurer S, Ruggles KV, Fenyo D, Jewell SD, Thiagarajan M, Mesri M, Rodriguez H, Mani SA, Udeshi ND, Getz G, Suh J, Li QK, Hostetter G, Paik PK, Dhanasekaran SM, Govindan R, Ding L, Robles AI, Clauser KR, Nesvizhskii AI, Wang P, Carr SA^, Zhang B^, Mani DR^, Gillette MA^
Clinical Proteomic Tumor Analysis Consortium
Cell 2021 Aug 5;184(16):4348-4371
The Clear Cell Sarcoma Functional Genomic Landscape
Panza E*, Ozenberger BB*, Straessler KM*, Barrott JJ, Li L, Wang Y, Xie M, Boulet A, Titen SW, Mason CC, Lazar AJ, Ding L, Capecchi MR, Jones KB
J Clin Invest 2021 Aug 2;131(15):e146301
Co-Evolution of Tumor and Immune Cells During Progression of Multiple Myeloma
Liu R*, Gao Q*, Foltz SM*, Fowles JS, Yao L, Wang JT, Cao S, Sun H, Wendl MC, Sethuraman S, Weerasinghe A, Rettig MP, Storrs EP, Yoon CJ, Wyczalkowski MA, McMichael JF, Kohnen DR, King J, Goldsmith SR, O'Neal J, Fulton RS, Fronick CC, Ley TJ, Jayasinghe RG, Fiala MA, Oh ST, DiPersio JF, Vij R^, Ding L^
Nat Commun 2021 May 7;12(1):2559
Spatially interacting phosphorylation sites and mutations in cancer
Huang KL^, Scott AD, Zhou DC, Wang LB, Weerasinghe A, Elmas A, Liu R, Wu Y, Wendl MC, Wyczalkowski MA, Baral J, Sengupta S, Lai CW, Ruggles K, Payne SH, Raphael B, Fenyö D, Chen K, Mills G, Ding L^
Nature Communications volume 12, Article number: 2313 (2021)
Proteogenomic and metabolomic characterization of human glioblastoma
Wang LB*, Karpova A*, Gritsenko MA*, Kyle JE*, Cao S*, Li Y*, Rykunov Dˉ, Colaprico Aˉ, Rothstein JHˉ, Hong Rˉ, Stathias Vˉ, Cornwell Mˉ, Petralia Fˉ, Wu Y, Reva B, Krug K, Pugliese P, Kawaler E, Olsen LK, Liang WW, Song X, Dou Y, Wendl MC, Caravan W, Liu W, Zhou DC, Ji J, Tsai CF, Petyuk VA, Moon J, Ma W, Chu RK, Weitz KK, Moore RJ, Monroe ME, Zhao R, Yang X, Yoo S, Krek A, Demopoulos A, Zhu H, Wyczalkowski MA, McMichael JF, Henderson BL, Lindgren CM, Boekweg H, Lu S, Baral J, Yao L, Stratton KG, Bramer LM, Zink E, Couvillion SP, Bloodsworth KJ, Satpathy S, Sieh W, Boca SM, Schürer S, Chen F, Wiznerowicz M, Ketchum KA, Boja ES, Kinsinger CR, Robles AI, Hiltke T, Thiagarajan M, Nesvizhskii AI, Zhang B, Mani DR, Ceccarelli M, Chen XS, Cottingham SL, Li QK, Kim AH, Fenyö D, Ruggles KV, Rodriguez H, Mesri M, Payne SH, Resnick AC, Wang P, Smith RD, Iavarone A, Chheda MG, Barnholtz-Sloan JS, Rodland KD^, Liu T^, Ding L^
Clinical Proteomic Tumor Analysis Consortium
Cancer Cell 39, 1–20 April 12, 2021
MSIsensor-Ct: Microsatellite Instability Detection Using CfDNA Sequencing Data
Han X*, Zhang S*, Zhou DC, Wang D, He X, Yuan D, Li R, He J, Duan X, Wendl MC, Ding L^, Niu B^
Brief Bioinform 2021 Jan 18;
Proteogenomic Insights Into the Biology and Treatment of HPV-Negative Head and Neck Squamous Cell Carcinoma
Huang C*, Chen L*, Savage SR*, Eguez RV, Dou Y, Li Y, da Veiga Leprevost F, Jaehnig EJ, Lei JT, Wen B, Schnaubelt M, Krug K, Song X, Cieslik M, Chang HY, Wyczalkowski MA, Li K, Colaprico A, Li QK, Clark DJ, Hu Y, Cao L, Pan J, Wang Y, Cho KC, Shi Z, Liao Y, Jiang W, Anurag M, Ji J, Yoo S, Zhou DC, Liang WW, Wendl M, Vats P, Carr SA, Mani DR, Zhang Z, Qian J, Chen XS, Pico AR, Wang P, Chinnaiyan AM, Ketchum KA, Kinsinger CR, Robles AI, An E, Hiltke T, Mesri M, Thiagarajan M, Weaver AM, Sikora AG, Lubinski J, Wierzbicka M, Wiznerowicz M, Satpathy S, Gillette MA, Miles G, Ellis MJ, Omenn GS, Rodriguez H, Boja ES, Dhanasekaran SM, Ding L, Nesvizhskii AI, El-Naggar AK, Chan DW^, Zhang H^, Zhang B^
Clinical Proteomic Tumor Analysis Consortium
Cancer Cell 2021 Jan 5;
Conservation of Copy Number Profiles During Engraftment and Passaging of Patient-Derived Cancer Xenografts
Woo XY*, Giordano J*, Srivastava A, Zhao ZM, Lloyd MW, de Bruijn R, Suh YS, Patidar R, Chen L, Scherer S, Bailey MH, Yang CH, Cortes-Sanchez E, Xi Y, Wang J, Wickramasinghe J, Kossenkov AV, Rebecca VW, Sun H, Mashl RJ, Davies SR, Jeon R, Frech C, Randjelovic J, Rosains J, Galimi F, Bertotti A, Lafferty A, O'Farrell AC, Modave E, Lambrechts D, Ter Brugge P, Serra V, Marangoni E, El Botty R, Kim H, Kim JI, Yang HK, Lee C, Dean DA 2nd, Davis-Dusenbery B, Evrard YA, Doroshow JH, Welm AL, Welm BE, Lewis MT, Fang B, Roth JA, Meric-Bernstam F, Herlyn M, Davies MA, Ding L, Li S, Govindan R, Isella C, Moscow JA, Trusolino L, Byrne AT, Jonkers J, Bult CJ, Medico E, Chuang JH
PDXNET Consortium
Nat Genet 2021 Jan;53(1):86-99
2020
Proteogenomic Landscape of Breast Cancer Tumorigenesis and Targeted Therapy
Krug K*, Jaehnig EJ*, Satpathy S*, Blumenberg L*, Karpova A*, Anurag M*, Miles G, Mertins P, Geffen Y, Tang L, Heiman D, Cao S, Maruvka Y, Lei J, Huang C, Kothadia R, Colaprico A, Birger C, Wang J, Dou Y, Wen B, Shi Z, Liao Y, Wiznerowicz M, Wyczalkowski MA, Chen XS, Kennedy JJ, Paulovich AG, Thiagarajan M, Kinsinger CR, Hiltke T, Boja ES, Mesri M, Robles AI, Rodriguez H, Westbrook TF, Ding L, Getz G, Clauser KRF, Fenyö D, Ruggles KV, Zhang B, Mani DR^, Carr SA^, Ellis MJ^, Gillette MA^
Cell 183, 1–21, November 25, 2020
Discovery of driver non-coding splice-site-creating mutations in cancer
Cao S, Cui Zhou D, Oh C, Jayasinghe RG, Zhao Y, Yoon C, Wyczalkowski MA, Bailey MH, Tsou T, Gao Q, Malone A, Reynolds S, Shmulevich I, Wendl MC, Chen F^ & Ding L^
Nat Commun 11, 5573 (2020)
Retrospective evaluation of whole exome and genome mutation calls in 746 cancer samples
Bailey MH, Meyerson WU, Dursi LJ, Wang LB, Dong G, Liang WW, Weerasinghe A, Li S, 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
Nat Commun 11, 4748 (2020)
Proteogenomic Characterization Reveals Therapeutic Vulnerabilities in Lung Adenocarcinoma
Gillette MA*^, Satpathy S*^, Cao Sˉ, Dhanasekaran Sˉ, Vasaikar Sˉ, Krug Kˉ, Petralia Fˉ, Li Y, Liang WW, Reva B, Hong R,…, Yao L, …, Wendl MC, …, Wyczalkowski MA, …, Ding Lˇ, Mani DRˇ, Carr SAˇ^
Clinical Proteomic Tumor Analysis Consortium
Cell 2020 July 9; 182(1): 200–225.e35
Evolution and structure of clinically relevant gene fusions in multiple myeloma
Foltz SM, Gao Q, Yoon C, Sun H, Yao L, Li Y, Jayasinghe RG, Cao S, King J, Kohnen DR, Fiala MA, Ding L^, Vij R^
Nat Commun 2020 May 29; 11: 2666
Comprehensive Analysis of Genetic Ancestry and Its Molecular Correlates in Cancer
Carrot-Zhang J*, Chambwe N*, Damrauer JS*, Knijnenburg TA*, Robertson AG*, Yau C*, Zhou W*, Berger AC*, Huang KL*, Newberg JY*, Mashl RJˉ, Romanel Aˉ, Sayaman RWˉ, Demichelis F, Felau I, Frampton GM, Han S, Hoadley KA, Kemal A, Laird PW, Lazar AJ, Le X, Oak N, Shen H, Wong CK, Zenklusen JC, Ziv E; Cancer Genome Atlas Analysis Network, Cherniack AD^, Beroukhim R^
Cancer Cell. 2020 May 11;37(5):639-654.e6
The Human Tumor Atlas Network: Charting Tumor Transitions across Space and Time at Single-Cell Resolution
Rozenblatt-Rosen O*, Regev A*, Oberdoerffer P*, Nawy T*, Hupalowska A, Rood J, Ashenberg O, Cerami E, Coffey R, Demir E, Ding L, Esplin E, Ford J, Goecks J, Ghosh S, Gray J, Guinney J, Hanlon S, Hughes S, Hwang S, A. Iacobuzio-Donahue C, Jane-Valbuena J, …, Tan K, West RB, Williams EH
Human Tumor Atlas Network
Cell 2020 Apr 16; 181(2): 236-249
Proteogenomic Characterization of Endometrial Carcinoma Dou Y*, Kawaler EA*, Cui Zhou D*, Gritsenko MA*, Huang C, Blumenberg L, Karpova A, Petyuk VA, Savage SR, Satpathy S, Liu W, Wu Y, Tsai C, Wen B, Li Z, Cao S, Moon J, Shi Z, Wyczalkowski MA, …, Gao Q, …, Sethuraman S, Rodland KD^, Ding L^, Zhang B^, Liu T^, Fenyö D^
Clinical Proteomic Tumor Analysis Consortium Cell 2020 Feb 20; 180(4): 729–748.e26
Pan-cancer analysis of whole genomes ICGC/TCGA Pan-Cancer Analysis of Whole Genomes Consortium (Contributors include: Bailey MH, Ding L, Mashl RJ, Huang K, McLellan MD, Wendl MC)
Nature 2020 Feb 5; 578(7793): 82-93
2019
Integrated Proteogenomic Characterization of Clear Cell Renal Cell Carcinoma
Clark DJ*, Dhanasekaran SM*, Petralia F*, Pan J*, Song X*, Hu Y*, da Veiga Leprevost F*, Reva B*, Lih TM*, Chang HY, Ma W, Huang C, Ricketts CJ, Chen L, Krek A, Li Y, Rykunov D, Li QK, Chen LS, Ozbek U, Vasaikar S, Wu Y, Yoo S, Chowdhury S, Wyczalkowski MA, Ji J, Schnaubelt M, Kong A, Sethuraman S, Avtonomov DM, Ao M, Colaprico A, Cao S, Cho KC, Kalayci S, Ma S, Liu W, Ruggles K, Calinawan A, Gumus ZH, Geizler D, Kawaler E, Teo GC, Wen B, Zhang Y, Keegan S, Li K, Chen F, Edwards N, Pierorazio PM, Chen XS, Pavlovich CP, Hakimi AA, Brominski G, Hsieh JJ, Antczak A, Omelchenko T, Lubinski J, Wiznerowicz M, Linehan WM, Kinsinger CR, Thiagarajan M, Boja ES, Mesri M, Hiltke T, Robles AI, Rodriguez H, Qian J, Fenyo D, Zhang B, Ding L, Schadt E, Chinnaiyan AM, Zhang Z, Omenn GS, Cieslik M^, Chan DW^, Nesvizhskii AI^, Wang P^, Zhang H^
Clinical Proteomic Tumor Analysis Consortium
Cell 2019 Oct 31; 179(4): 964-983.e31
Integrated Proteogenomic Characterization of HBV-Related Hepatocellular Carcinoma Gao Q*, Zhu H*, Dong L*, Shi W*, Chen R*, Song Z, Huang C, Li J, Dong X, Zhou Y, Liu Q, L Ma, Wang X, Zhou J ,Liu Y, Boja E, Robles A, Ma W, Wang P, Li Y, Ding L, Wen B, Zhang B, Rodriguez H, Gao D^, Zhou H^, Fan J^
Cell 2019 Oct 3; 179(2): 561-577.e22
Predicting Tumor Response to PD-1 Blockade Ding L, Chen F N Engl J Med 2019 Aug 1; 381(5): 477-479
Before and After: Comparison of Legacy and Harmonized TCGA Genomic Data Commons' Data
Gao GF*, Parker JS*, Reynolds SM*, Silva TC*, Wang LB*, Zhou W*, Akbani R, Bailey M, Balu S, Berman BP, Brooks D, Chen H, Cherniack AD, Demchok JA, Ding L, Felau I, Gaheen S, Gerhard DS, Heiman DI, Hernandez KM, Hoadley KA, Jayasinghe R, Kemal A, Knijnenburg TA, Laird PW, Mensah MKA, Mungall AJ, Robertson AG, Shen H, Tarnuzzer R, Wang Z, Wyczalkowski M, Yang L, Zenklusen JC, Zhang Z, Liang H^, Noble MS^
Genomic Data Analysis Network
Cell Syst 2019 Jul 24; 9(1): 24-34.e10
Regulated Phosphosignaling Associated With Breast Cancer Subtypes and Druggability
Huang KL*^, Wu Y, Primeau T, Wang YT, Gao Y, McMichael JF, Scott AD, Cao S, Wendl MC, Johnson KJ, Ruggles K, Held J, Payne SH, Davies SR, Dar A, Kinsinger CR, Mesri M, Rodriguez H, Ellis MJ, Townsend RR, Chen F, Fenyo D, Li S, Liu T, Carr SA, Ding L^
Mol Cell Proteomics 2019 Aug; 18(8): 1630-1650
Proteogenomic Analysis of Human Colon Cancer Reveals New Therapeutic Opportunities Vasaikar S*, Huang C*, Wang X*, Petyuk VA*, Savage SR*, Wen B, Dou Y, Zhang Y, Shi Z, Arshad OA, Gritsenko MA, Zimmerman LJ, McDermott JE, Clauss TR, Moore RJ, Zhao R, Monroe ME, Wang YT, Chambers MC, Slebos RJC, Lau KS, Mo Q, Ding L, Ellis M, Thiagarajan M, Kinsinger CR, Rodriguez H, Smith RD, Rodland KD^, Liebler DC^, Liu T^, Zhang B^
Clinical Proteomic Tumor Analysis Consortium. Cell 2019 May 2; 177(4): 1035-1049.e19
Dynamic host immune response in virus-associated cancers
Cao S, Wylie KM, Wyczalkowski MA, Karpova A, Ley J, Sun S, Mashl RJ, Liang W, Wang X, Johnson K, DiPersio JF, Gay H, Ratner L, Chen F, Adkins DR, Ding L
Commun Biol 2019 Mar 22; 2: 109
Functional analysis of BARD1 missense variants in homology-directed repair and damage sensitivity
Adamovich AI, Banerjee T, Wingo M, Duncan K, Ning J, Rodrigues FM, Huang KL, Lee C, Chen F, Ding L, Parvin JD
PLoS Genet 2019 Mar 29; 15(3): e1008049
CharGer: Clinical Characterization of Germline Variants
Scott AD^, Huang KL, Weerasinghe A, Mashl RJ, Gao Q, Martins Rodrigues F, Wyczalkowski MA, Ding L^
Bioinformatics 2019 Mar 1; 35(5): 865-867
Framework for MicroRNA Variant Annotation and Prioritization Using Human Population and Disease Datasets
Oak N, Ghosh R, Huang KL, Wheeler DA, Ding L, Plon SE
Hum Mutat 2019 Jan; 40(1): 73-89
2018
Database of Evidence for Precision Oncology Portal
Sun SQ, Mashl RJ, Sengupta S, Scott AD, Wang W, Batra P, Wang LB, Wyczalkowski MA, Ding L
Bioinformatics 2018 Dec 15; 34(24): 4315-4317
Discriminating a Common Somatic ASXL1 Mutation (C.1934dup; P.G646Wfs*12) From Artifact in Myeloid Malignancies Using NGS
Alberti MO, Srivatsan SN, Shao J, McNulty SN, Chang GS, Miller CA, Dunlap JB, Yang F, Press RD, Gao Q, Ding L, Heusel JW, Duncavage EJ, Walter MJ
Leukemia 2018 Aug; 32(8): 1874-1878
Integrative Omics Analyses Broaden Treatment Targets in Human Cancer
Sengupta S*, Sun SQ*, Huang KL, Oh C, Bailey MH, Varghese R, Wyczalkowski MA, Ning J, Tripathi P, McMichael JF, Johnson KJ, Kandoth C, Welch J, Ma C, Wendl MC, Payne SH, Fenyo D, Townsend RR, DiPersio JF, Chen F^, Ding L^
Genome Med 2018 Jul 27; 10(1): 60
The Cancer Genome Atlas Comprehensive Molecular Characterization of Renal Cell Carcinoma
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, Kwiatkowski 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 WY, Robertson AG, Spellman PT, Rathmell WK, Linehan WM
Cancer Genome Atlas Research Network (Contributors include: Ding L)
Cell Rep 2018 Jun 19; 23(12): 3698
Pan-Cancer Analysis of Somatic Mutations Across 21 Neuroendocrine Tumor Types
Cao Y*, Zhou W*, Li L*, Wang J*, Gao Z*, Jiang Y, Jiang X, Shan A, Bailey MH, Huang KL, Sun SQ, McLellan MD, Niu B, Wang W^, Ding L^, Ning G^
Cell Res 2018 May; 28(5): 601-604
Mass Spectrometry-Based Proteomics Reveals Potential Roles of NEK9 and MAP2K4 in Resistance to PI3K Inhibition in Triple-Negative Breast Cancers
Mundt F, Rajput S, Li S, Ruggles KV, Mooradian AD, Mertins P, Gillette MA, Krug K, Guo Z, Hoog J, Erdmann-Gilmore P, Primeau T, Huang S, Edwards DP, Wang X, Wang X, Kawaler E, Mani DR, Clauser KR, Gao F, Luo J, Davies SR, Johnson GL, Huang KL, Yoon CJ, Ding L, Fenyo D, Ellis MJ, Townsend RR, Held JM, Carr SA, Ma CX
Cancer Res 2018 May 15; 78(10): 2732-2746
Perspective on Oncogenic Processes at the End of the Beginning of Cancer Genomics
Ding L*, Bailey MH*, Porta-Pardo E*, Thorsson V, Colaprico A, Bertrand D, Gibbs DL, Weerasinghe A, Huang KL, Tokheim C, Cortés-Ciriano I, Jayasinghe R, Chen F, Yu L, Sun S, Olsen C, Kim J, Taylor AM, Cherniack AD, Akbani R, Suphavilai C, Nagarajan N, Stuart JM, Mills GB, Wyczalkowski MA, Vincent BG, Hutter CM, Zenklusen JC, Hoadley KA, Wendl MC, Shmulevich I, Lazar AJ, Wheeler DA, Getz G, The Cancer Genome Atlas Research Network
Cell 2018 Apr 5; 173(2): 305-320.e10
Pathogenic Germline Variants in 10,389 Adult Cancers
Huang KL, Mashl RJ, Wu Y, Ritter DI, Wang J, Oh C, Paczkowska M, Reynolds S, Wyczalkowski MA, Oak N, Scott AD, Krassowski M, Cherniack AD, Houlahan KE, Jayasinghe R, Wang L, Zhou DC, Liu D, Cao S, Kim YW, Koire A, McMichael JF, Hucthagowder V, Kim T, Hahn A, Wang C, McLellan MD, Al-Mulla F, Johnson KJ, The Cancer Genome Atlas Research Network , Lichtarge O, Boutros PC, Raphael B, Lazar AJ, Zhang W, Wendl MC, Govindan R, Jain S, Wheeler D, Kulkarni S, Dipersio JF, Reimand J, Meric-Bernstam F, Chen K, Shmulevich I, Plon SE, Chen F^, Ding L^
Cell 2018 Apr 5; 173(2): 355-370.e14
Comprehensive Characterization of Cancer Driver Genes and Mutations
Bailey MH*, Tokheim C*, Porta-Pardo E*, Sengupta S, Bertrand D, Weerasinghe A, Colaprico A, Wendl MC, Kim J, Reardon B, Ng PK, Jeong KJ, Cao S, Wang Z, Gao J, Gao Q, Wang F, Liu EM, Mularoni L, Rubio-Perez C, Nagarajan N, Cortés-Ciriano I, Zhou DC, Liang W, Hess JM, Yellapantula VD, Tamborero D, Gonzalez-Perez A, Suphavilai C, Ko JY, Khurana E, Park PJ, Van Allen EM, Liang H, The MC3 Working Group, The Cancer Genome Atlas Research Network, Lawrence MS, Godzik A, Lopez-Bigas A, Stuart J, Wheeler D, Getz G, Chen K, Lazar AJ, Mills GB, Karchin R^, Ding L^
Cell 2018 Apr 5; 173(2): 371-385.e18
Driver Fusions and Their Implications in the Development and Treatment of Human Cancers
Gao Q*, Liang W*, Foltz SM*, Mutharasu G, Jayasinghe RG, Cao S, Liao W, Reynolds SM, Wyczalkowski MA, Yao L, Yu L, Sun SQ, The Fusion Analysis Working Group, The Cancer Genome Atlas Research Network , Chen K, Lazar AJ, Fields RC, Wendl MC, Van Tine BA, Vij R, Chen F, Nykter N, Shmulevich I, Ding L
Cell Rep 2018 Apr 3; 23(1): 227-238
Systematic Analysis of Splice-Site-Creating Mutations in Cancer
Jayasinghe RG*, Cao S*, Gao Q, Wendl MC, Vo NS, Reynolds SM, Zhao Y, Climente-González H, Chai S, Wang F, Varghese R, Huang M, Liang W, Wyczalkowski MA, Sengupta S, Li Z, Payne SH, Fenyö D, Miner JH, Walter MJ, The Cancer Genome Atlas Research Network, Vincent B, Eyras E, Chen K, Shmulevich I^, Chen F^, Ding L^
Cell Rep 2018 Apr 3; 23(1): 270-281
Scalable Open Science Approach for Mutation Calling of Tumor Exomes Using Multiple Genomic Pipelines
Ellrott K, Bailey MH, Saksena G, Covington KR, Kandoth C, Stewart C, Hess J, Ma S, Chiotti KE, McLellan M, Sofia HJ, Hutter C, Getz G, Wheeler D, Ding L, the MC3 Working Group, The Cancer Genome Atlas Research Network
Cell Syst 2018 Mar 28; 6(3): 271-281
Systematic Functional Annotation of Somatic Mutations in Cancer
Ng PK, Li J, Jeong KJ, Shao S, Chen H, Tsang YH, Sengupta S, Wang Z, Bhavana VH, Tran R, Soewito S, Minussi DC, Moreno D, Kong K, Dogruluk T, Lu H, Gao J, Tokheim C, Zhou DC, Johnson AM, Zeng J, Ip CKM, Ju Z, Wester M, Yu S, Li Y, Vellano CP, Schultz N, Karchin R, Ding L, Lu Y, Cheung LWT, Chen K, Shaw KR, Meric-Bernstam F, Scott KL, Yi S, Sahni N, Liang H, Mills GB
Cancer Cell 2018 Mar 12; 33(3): 450-462.e10
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 MA, Yellapantula V)
Cell 2017 Nov 2; 171(4): 950-965
MIRMMR: binary classification of microsatellite instability using methylation and mutations
Foltz SM, Liang WW, Xie M, and Ding L
Bioinformatics 2017 Dec 1; 33(23): 3799–3801
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): eaam8065
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 Oct 1; 33(19): 3121-3122
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 Aug; 27(8): 1450-1459
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 July 20; 36(29): 4100-4110
Integrated genomic and molecular characterization of cervical cancer
Cancer Genome Atlas Research Network (Contributors include: Ding L, Bailey M, Wyczalkowski MA)
Nature 2017 Mar 16; 543(7645): 378-384
Precancerous clonal expansion: a new therapeutic target?
Ding L, Chen F
J Clin Oncol 2017 May 10; 35(14):1503-1505
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 Jan; 14(1): 65-67
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 Dec; 48(12): 1551-1556
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 Dec; 48(12): 1481-1489
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): 5021-5032
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): 827-837
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): 3282-3292
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): 1060-1071
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
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
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 Oct 19;20(12):1472-1478
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
Expanding the computational toolbox for mining cancer genomes Ding L, Wendl MC, McMichael JF, Raphael BJ Nature Reviews Genetics. 2014 Aug;15(8):556-70
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
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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
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A panoramic view of cancer
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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
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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
2012
Comprehensive molecular characterization of human colon and rectal cancer
The Cancer Genome Atlas Network (Ding L is the contributor)
Nature 487.7407 (2012): 330
An integrated map of genetic variation from 1,092 human genomes
The 1000 Genomes Project Consortium (Ding L is the contributor)
Nature 491.7422 (2012): 56
Comprehensive molecular portraits of human breast tumours
The Cancer Genome Atlas Network (Ding L is the contributor)
Nature 490.7418 (2012): 61-70
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
2011
Integrated genomic analyses of ovarian carcinoma
The Cancer Genome Atlas Network (Ding L is the contributor)
Nature 474.7353 (2011): 609
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
2010
Integrated Genomic Analysis Identifies Clinically Relevant Subtypes of Glioblastoma Characterized by Abnormalities in PDGFRA, IDH1, EGFR, and NF1
Verhaak RGW, 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, The Cancer Genome Atlas Research Network
Cancer cell 17.1 (2010): 98-110
A map of human genome variation from population-scale sequencing
The 1000 Genomes Project Consortium (Ding L is the contributor)
Nature 467.7319 (2010): 1061
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
2008
Comprehensive genomic characterization defines human glioblastoma genes and core pathways
The Cancer Genome Atlas Network (Ding L is the contributor)
Nature 455.7216 (2008): 1061-1068
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
PRe 2006
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