Ken Chen, Ph.D.

Peer-Reviewed Articles

1. Piha-Paul, SA, Tseng, C, Leung, CH, Yuan, Y, Karp, DD, Subbiah, V, Hong, DS, Fu, S, Naing, A, Rodon Ahnert, J, Javle, M, Ajani, JA, Raghav, KS, Somaiah, N, Mills, GB, Tsimberidou, AM, Zheng, X, Chen, K, Meric-Bernstam, F. Phase II study of talazoparib in advanced cancers with BRCA1/2, DNA repair, and PTEN alterations. npj Precision Oncology 8(1), 2024. e-Pub 2024. PMID: 39085400.
2. Piha-Paul, SA, Tseng, C, Leung, CH, Yuan, Y, Karp, DD, Subbiah, V, Hong, DS, Fu, S, Naing, A, Rodon Ahnert, J, Javle, M, Ajani, JA, Raghav, KS, Somaiah, N, Mills, GB, Tsimberidou, AM, Zheng, X, Chen, K, Meric-Bernstam, F. Phase II study of talazoparib in advanced cancers with BRCA1/2, DNA repair, and PTEN alterations. npj Precision Oncology 8(1), 2024. e-Pub 2024. PMID: 39085400.
3. Kumar B, Singh A, Basar R, Uprety N, Li Y, Fan H, Cortes AKN, Kaplan M, Acharya S, Shaim H, Xu AC, Wu M, Ensley E, Fang D, Banerjee PP, Garcia LM, Tiberti S, Lin P, Rafei H, Munir MN, Moore M, Shanley M, Mendt M, Kerbauy LN, Liu B, Biederstädt A, Gokdemir E, Ghosh S, Kundu K, Reyes-Silva F, Jiang XR, Wan X, Gilbert AL, Dede M, Mohanty V, Dou J, Zhang P, Liu E, Muniz-Feliciano L, Deyter GM, Jain AK, Rodriguez-Sevilla JJ, Colla S, Garcia-Manero G, Shpall EJ, Chen K, Abbas HA, Rai K, Rezvani K, Daher M. BATF is a major driver of NK cell epigenetic reprogramming and dysfunction in AML. Sci Transl Med 16(764):eadp0004, 2024. e-Pub 2024. PMID: 39259809.
4. Shanley M, Daher M, Dou J, Li S, Basar R, Rafei H, Dede M, Gumin J, Pantale?n Garc?a J, Nunez Cortes AK, He S, Jones CM, Acharya S, Fowlkes NW, Xiong D, Singh S, Shaim H, Hicks SC, Liu B, Jain A, Zaman MF, Miao Q, Li Y, Uprety N, Liu E, Muniz-Feliciano L, Deyter GM, Mohanty V, Zhang P, Evans SE, Shpall EJ, Lang FF, Chen K, Rezvani K. Interleukin-21 engineering enhances NK cell activity against glioblastoma via CEBPD. Cancer Cell 42(8):1450-1466.e11, 2024. e-Pub 2024. PMID: 39137729.
5. He, S, Gubin, M, Rafei, H, Basar, R, Dede, M, Jiang, XL, Liang, Q, Tan, Y, Kim, KH, Gillison, M, Rezvani, K, Peng, W, Haymaker, CL, Hernandez, S, Solis Soto, LM, Mohanty, V, Chen, K. Elucidating immune-related gene transcriptional programs via factorization of large-scale RNA-profiles. iScience 27(6), 2024. e-Pub 2024. PMID: 38957791.
6. Tan, Y, Dede, M, Mohanty, V, Dou, J, Hill, H, Bernstam, EV, Chen, K. Forecasting acute kidney injury and resource utilization in ICU patients using longitudinal, multimodal models. Journal of Biomedical Informatics 154, 2024. e-Pub 2024. PMID: 38692464.
7. Acharya S, Basar R, Daher M, Rafei H, Li P, Uprety N, Ensley E, Shanley M, Kumar B, Banerjee PP, Melo Garcia L, Lin P, Mohanty V, Kim KH, Jiang X, Pan Y, Li Y, Liu B, Nunez Cortes AK, Zhang C, Fathi M, Rezvan A, Montalvo MJ, Cha SL, Reyes-Silva F, Shrestha R, Guo X, Kundu K, Biederstadt A, Muniz-Feliciano L, Deyter GM, Kaplan M, Jiang XR, Liu E, Jain A, Roszik J, Fowlkes NW, Solis Soto LM, Raso MG, Khoury JD, Lin P, Vega F, Varadarajan N, Chen K, Marin D, Shpall EJ, Rezvani K. CD28 costimulation augments CAR signaling in NK cells via the LCK/CD3Z/ZAP70 signaling axis. Cancer Discov. e-Pub 2024. PMID: 38900051.
8. He S, Gubin MM, Rafei H, Basar R, Dede M, Jiang X, Liang Q, Tan Y, Kim K, Gillison ML, Rezvani K, Peng W, Haymaker C, Hernandez S, Solis LM, Mohanty V, Chen K. Elucidating immune-related gene transcriptional programs via factorization of large-scale RNA-profiles. iScience, 2024. e-Pub 2024. PMID: 38798470.
9. Tan Y, Dede M, Mohanty V, Dou J, Hill H, Bernstam E, Chen K. Forecasting Acute Kidney Injury and Resource Utilization in ICU patients using longitudinal, multimodal models. Journal of Biomedical Informatics, 2024. e-Pub 2024. PMID: 38559064.
10. Liang S, Dou J, Iqbal R, Chen K. Label-Aware Distance Mitigates Temporal and Spatial Variability for Clustering and Visualization of Single-Cell Gene Expression Data. Commun Biol 7(1):326, 2024. e-Pub 2024. PMID: 38486077.
11. Goldberg J, Qiao N, Guerriero JL, Gross B, Meneksedag Y, Lu YF, Philips AV, Rahman T, Meric-Bernstam F, Roszik J, Chen K, Jeselsohn R, Tolaney SM, Peoples GE, Alatrash G, Mittendorf EA. Estrogen Receptor Mutations as Novel Targets for Immunotherapy in Metastatic Estrogen Receptor-positive Breast Cancer. Cancer Res Commun 4(2):496-504, 2024. e-Pub 2024. PMID: 38335301.
12. Hou J, Wei Y, Zou J, Jaffery R, Sun L, Liang S, Zheng N, Guerrero AM, Egan NA, Bohat R, Chen S, Zheng C, Mao X, Yi SS, Chen K, McGrail DJ, Sahni N, Shi PY, Chen Y, Xie X, Peng W. Integrated multi-omics analyses identify anti-viral host factors and pathways controlling SARS-CoV-2 infection. Nat Commun 15(1):109, 2024. e-Pub 2024. PMID: 38168026.
13. Marin D, Li Y, Basar R, Rafei H, Daher M, Dou J, Mohanty V, Dede M, Nieto Y, Uprety N, Acharya S, Liu E, Wilson J, Banerjee P, Macapinlac HA, Ganesh C, Thall PF, Bassett R, Ammari M, Rao S, Cao K, Shanley M, Kaplan M, Hosing C, Kebriaei P, Nastoupil LJ, Flowers CR, Moseley SM, Lin P, Ang S, Popat UR, Qazilbash MH, Champlin RE, Chen K, Shpall EJ, Rezvani K. Safety, efficacy and determinants of response of Allogeneic CD19-specific CAR-NK cells in CD19+ B cell tumors: a phase 1/2 trial. Nat Med. e-Pub 2024. PMID: 38238616.
14. Liang Q, Huang Y, He S, Chen K. Pathway centric analysis for single-cell RNA-seq and spatial transcriptomics data with GSDensity. Nat Commun 14(1):8416, 2023. e-Pub 2023. PMID: 38110427.
15. Nieto Y, Banerjee P, Kaur I, Kim KH, Fang D, Thall PF, Griffin L, Barnett M, Basar R, Hosing C, Ramdial J, Srour S, Daher M, Marin D, Jiang X, Chen K, Champlin R, Shpall EJ, Rezvani K. Ex Vivo Expanded Cord Blood Natural Killer Cells Combined with Rituximab and High-Dose Chemotherapy and Autologous Stem Cell Transplantation for B Cell Non-Hodgkin Lymphoma. Transplant Cell Ther. e-Pub 2023. PMID: 38042257.
16. Huang Y, Mohanty V, Dede M, Tsai K, Daher M, Li L, Rezvani K, Chen K. Characterizing cancer metabolism from bulk and single-cell RNA-seq data using METAFlux. Nat Commun 14(1):4883, 2023. e-Pub 2023. PMID: 37573313.
17. 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. Single-nucleotide variant calling in single-cell sequencing data with Monopogen. Nat Biotechnol. e-Pub 2023. PMID: 37592035.
18. Hill HA, Jain P, Ok CY, Sasaki K, Chen H, Wang ML, Chen K. Integrative Prognostic Machine-Learning Models in Mantle Cell Lymphoma. Cancer Res Commun 3(8):1435-1446, 2023. e-Pub 2023. PMID: 37538987.
19. Fan H, Wang F, Zeng A, Murison A, Tomczak K, Hao D, Jelloul FZ, Wang B, Barrodia P, Liang S, Chen K, Wang L, Zhao Z, Rai K, Jain AK, Dick J, Daver N, Futreal A, Abbas HA. Single-cell chromatin accessibility profiling of acute myeloid leukemia reveals heterogeneous lineage composition upon therapy-resistance. Commun Biol 6(1):765, 2023. e-Pub 2023. PMID: 37479893.
20. Johnson A, Ng PK, Kahle M, Castillo J, Amador B, Wang Y, Zeng J, Holla V, Vu T, Su F, Kim SH, Conway T, Jiang X, Chen K, Shaw KRM, Yap TA, Rodon J, Mills GB, Meric-Bernstam F. Actionability Classification of Variants of Unknown Significance Correlates with Functional Effect. NPJ Precis Oncol 7(1):67, 2023. e-Pub 2023. PMID: 37454202.
21. Li L, Mohanty V, Dou J, Huang Y, Banerjee PP, Miao Q, Lohr JG, Vijaykumar T, Frede J, Knoechel B, Muniz-Feliciano L, Laskowski TJ, Liang S, Moyes JS, Nandivada V, Basar R, Kaplan M, Daher M, Liu E, Li Y, Acharya S, Lin P, Shanley M, Rafei H, Marin D, Mielke S, Champlin RE, Shpall EJ, Chen K, Rezvani K. Loss of metabolic fitness drives tumor resistance after CAR-NK cell therapy and can be overcome by cytokine engineering. Sci Adv 9(30):eadd6997, 2023. e-Pub 2023. PMID: 37494448.
22. Kumar T, Nee K, Wei R, He S, Nguyen QH, Bai S, Blake K, Pein M, Gong Y, Sei E, Hu M, Casasent AK, Thennavan A, Li J, Tran T, Chen K, Nilges B, Kashikar N, Braubach O, Ben Cheikh B, Nikulina N, Chen H, Teshome M, Menegaz B, Javaid H, Nagi C, Montalvan J, Lev T, Mallya S, Tifrea DF, Edwards R, Lin E, Parajuli R, Hanson S, Winocour S, Thompson A, Lim B, Lawson DA, Kessenbrock K, Navin N. A spatially resolved single-cell genomic atlas of the adult human breast. Nature. e-Pub 2023. PMID: 37380767.
23. Fathi M, Martinez-Paniagua M, Rezvan A, Montalvo MJ, Mohanty V, Chen K, Mani SA, Varadarajan N. Identifying signatures of EV secretion in metastatic breast cancer through functional single-cell profiling. iScience 26(4):106482, 2023. e-Pub 2023. PMID: 37091228.
24. Tan Y, Mohanty V, Liang S, Dou J, Ma J, Kim KH, Bonder MJ, Shi X, Lee C, Variation Consortium HGS, Chong Z, Chen AK. NovoRNAbreak: Local Assembly for Novel Splice Junction and Fusion Transcript Detection from RNA-Seq Data. J Bioinform Syst Biol, 2023. e-Pub 2023. PMID: None.
25. Hou J, Liang S, Xu C, Wei Y, Wang Y, Tan Y, Sahni N, McGrail DJ, Bernatchez C, Davies M, Li Y, Chen R, Yi SS, Chen Y, Yee C, Chen K, Peng W. Single-cell CRISPR immune screens reveal immunological roles of tumor intrinsic factors. NAR Cancer 4(4):zcac038, 2022. e-Pub 2022. PMID: 36518525.
26. Sconocchia G, Lanzilli G, Cesarini V, Silvestris DA, Rezvani K, Arriga R, Caratelli S, Chen K, Dou J, Cenciarelli C, Toietta G, Baldari S, Sconocchia T, De Paolis F, Aureli A, Iezzi G, Irno Consalvo M, Buccisano F, Del Principe MI, Maurillo L, Venditti A, Ottaviani A, Spagnoli GC. Direct CD32 T-cell cytotoxicity: implications for breast cancer prognosis and treatment. Life Sci Alliance 5(12), 2022. e-Pub 2022. PMID: 36241426.
27. Imahashi N, Basar R, Huang Y, Wang F, Baran N, Banerjee PP, Lu J, Nunez Cortes AK, Uprety N, Ensley E, Muniz-Feliciano L, Laskowski TJ, Moyes JS, Daher M, Mendt M, Kerbauy LN, Shanley M, Li L, FLWI L, Shaim H, Li Y, Konopleva M, Green M, Wargo J, Shpall EJ, Chen K, Rezvani K. Activated B cells suppress T cell function through metabolic competition. J Immunother Cancer 10(12), 2022. e-Pub 2022. PMID: 36543374.
28. Thompson PA, Jiang X, Banerjee P, Basar R, Garg N, Chen K, Kaplan M, Nandivada V, Cortes AKN, Ferrajoli A, Keating MJ, Peterson CB, Andreeff M, Rezvani K, Wierda WG. A phase two study of high dose blinatumomab in Richter's syndrome. Leukemia 36(9):2228-2232, 2022. e-Pub 2022. PMID: 35941212.
29. 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. Spatially restricted drivers and transitional cell populations cooperate with the microenvironment in untreated and chemo-resistant pancreatic cancer. Nat Genet 54(9):1390-1405, 2022. e-Pub 2022. PMID: 35995947.
30. Li Y, Basar R, Wang G, Liu E, Moyes JS, Li L, Kerbauy LN, Uprety N, Fathi M, Rezvan A, Banerjee PP, Muniz-Feliciano L, Laskowski TJ, Ensley E, Daher M, Shanley M, Mendt M, Acharya S, Liu B, Biederstädt A, Rafei H, Guo X, Melo Garcia L, Lin P, Ang S, Marin D, Chen K, Bover L, Champlin RE, Varadarajan N, Shpall EJ, Rezvani K. KIR-based inhibitory CARs overcome CAR-NK cell trogocytosis-mediated fratricide and tumor escape. Nat Med. e-Pub 2022. PMID: 36175679.
31. Lyu Y, Guan Y, Deliu L, Humphrey E, Frontera JK, Yang YJ, Zamler D, Kim KH, Mohanty V, Jin K, Mohanty V, Liu V, Dou J, Veillon LJ, Kumar SV, Lorenzi PL, Chen Y, McAndrews KM, Grivennikov S, Song X, Zhang J, Xi Y, Wang J, Chen K, Nagarajan P, Ge Y. KLF5 governs sphingolipid metabolism and barrier function of the skin. Genes Dev. e-Pub 2022. PMID: 36008138.
32. Wei R, He S, Bai S, Sei E, Hu M, Thompson A, Chen K, Krishnamurthy S, Navin NE. Spatial charting of single-cell transcriptomes in tissues. Nat Biotechnology 40(8):1190-1199, 2022. e-Pub 2022. PMID: 35314812.
33. Monberg ME, Geiger H, Lee JJ, Sharma R, Semaan A, Bernard V, Wong J, Wang F, Liang S, Swartzlander DB, Stephens BM, Katz MHG, Chen K, Robine N, Guerrero PA, Maitra A. Occult polyclonality of preclinical pancreatic cancer models drives in vitro evolution. Nat Commun 13(1):3652, 2022. e-Pub 2022. PMID: 35752636.
34. Dou J, Liang S, Mohanty V, Miao Q, Huang Y, Liang Q, Cheng X, Kim S, Choi J, Li Y, Li L, Daher M, Basar R, Rezvani K, Chen R, Chen K. Bi-order multimodal integration of single-cell data. Genome Biol 23(1):112, 2022. e-Pub 2022. PMID: 35534898.
35. Gaballa MR, Banerjee P, Milton DR, Jiang X, Ganesh C, Khazal S, Nandivada V, Islam S, Kaplan M, Daher M, Basar R, Alousi A, Mehta R, Alatrash G, Khouri I, Oran B, Marin D, Popat U, Olson A, Tewari P, Jain N, Jabbour E, Ravandi F, Kantarjian H, Chen K, Champlin R, Shpall E, Rezvani K, Kebriaei P. Blinatumomab maintenance after allogeneic hematopoietic cell transplantation for B-lineage acute lymphoblastic leukemia. Blood 139(12):1908-1919, 2022. e-Pub 2022. PMID: 34914826.
36. Stur E, Corvigno S, Xu M, Chen K, Tan Y, Lee S, Liu J, Ricco E, Kraushaar D, Castro P, Zhang J, Sood AK. Spatially resolved transcriptomics of high-grade serous ovarian carcinoma. iScience 25(3):103923, 2022. e-Pub 2022. PMID: 35252817.
37. Glassman D, Bateman NW, Lee S, Zhao L, Yao J, Tan Y, Ivan C, Rangel KM, Zhang J, Conrads KA, Hood BL, Abulez T, Futreal PA, Fleming ND, Afshar-Kharghan V, Maxwell GL, Conrads TP, Chen K, Sood AK. Molecular correlates of venous thromboembolism (VTE) in ovarian cancer. Cancers (Basel) 14(6), 2022. e-Pub 2022. PMID: 35326647.
38. Li L, Muftuoglu M, Liang S, Basyal M, Lv J, Akdogan ME, Chen K, Andreeff M, Parmar S. In-depth analysis of SARS-CoV-2-specific T cells reveals diverse differentiation hierarchies in vaccinated individuals. JCI Insight. e-Pub 2022. PMID: 35230977.
39. Garmezy B, Gheeya J, Lin HY, Huang Y, Kim T, Jiang X, Thein KZ, Pilié PG, Zeineddine F, Wang W, Shaw KR, Rodon J, Shen JP, Yuan Y, Meric-Bernstam F, Chen K, Yap TA. Clinical and Molecular Characterization of POLE Mutations as Predictive Biomarkers of Response to Immune Checkpoint Inhibitors in Advanced Cancers. JCO Precis Oncol 6:e2100267, 2022. e-Pub 2022. PMID: 35108036.
40. Salmon AJ, Shavkunov AS, Miao Q, Jarjour NN, Keshari S, Esaulova E, Williams CD, Ward JP, Highsmith AM, Pineda JE, Taneja R, Chen K, Edelson BT, Gubin MM. BHLHE40 Regulates the T-Cell Effector Function Required for Tumor Microenvironment Remodeling and Immune Checkpoint-Therapy Efficacy. Cancer Immunol Res. e-Pub 2022. PMID: 35181783.
41. Liang S, Willis J, Dou J, Mohanty V, Huang Y, Vilar E, Chen K. Sensei: how many samples to tell a change in cell type abundance?. BMC Bioinformatics 23(1):2, 2022. e-Pub 2022. PMID: 34983369.
42. Liang S, Liang Q, Chen R, Chen K. Stratified Test Accurately Identifies Differentially Expressed Genes Under Batch Effects in Single-Cell Data. IEEE/ACM Trans Comput Biol Bioinform PP(6):2072-2079, 2021. e-Pub 2021. PMID: 34232885.
43. Evans KW, Yuca E, Scott SS, Zhao M, Paez Arango N, Cruz Pico CX, Saridogan T, Shariati M, Class CA, Bristow CA, Vellano CP, Zheng X, Gonzalez-Angulo AM, Su X, Tapia C, Chen K, Akcakanat A, Lim B, Tripathy D, Yap TA, Di Francesco ME, Draetta GF, Jones P, Heffernan TP, Marszalek JR, Meric-Bernstam F. Oxidative Phosphorylation is a metabolic vulnerability in chemotherapy resistant triple negative breast cancer. Cancer Res. e-Pub 2021. PMID: 34518211.
44. Kerbauy LN, Marin ND, Kaplan M, Banerjee PP, Berrien-Elliott MM, Becker-Hapak M, Basar R, Foster M, Garcia Melo L, Neal CC, McClain E, Daher M, Nunez Cortes AK, Desai S, Inng Lim FW, Mendt MC, Schappe T, Li L, Shaim H, Shanley M, Ensley EL, Uprety N, Wong P, Liu E, Ang SO, Cai R, Nandivada V, Mohanty V, Miao Q, Shen Y, Baran N, Fowlkes NW, Chen K, Muniz-Feliciano L, Champlin RE, Nieto YL, Koch J, Treder M, Fischer W, Okamoto OK, Shpall EJ, Fehniger TA, Rezvani K. Combining AFM13, a bispecific CD30/CD16 antibody, with cytokine-activated cord blood-derived NK cells facilitates CAR-like responses against CD30+ malignancies. Clin Cancer Res 27(13):3744-3756, 2021. e-Pub 2021. PMID: 33986022.
45. Shaim H, Shanley M, Basar R, Daher M, Gumin J, Zamler DB, Uprety N, Wang F, Huang Y, Gabrusiewicz K, Miao Q, Dou J, Alsuliman A, Kerbauy LN, Acharya S, Mohanty V, Mendt M, Li S, Lu J, Wei J, Fowlkes NW, Gokdemir E, Ensley EL, Kaplan M, Kassab C, Li L, Ozcan G, Banerjee PP, Shen Y, Gilbert AL, Jones CM, Bdiwi M, Nunez-Cortes AK, Liu E, Yu J, Imahashi N, Muniz-Feliciano L, Li Y, Hu J, Draetta G, Marin D, Yu D, Mielke S, Eyrich M, Champlin RE, Chen K, Lang FF, Shpall EJ, Heimberger AB, Rezvani K. Targeting the αv integrin-TGF-β axis improves natural killer cell function against glioblastoma stem cells. J Clin Invest 131(14), 2021. e-Pub 2021. PMID: 34138753.
46. Basar R, Uprety N, Ensley E, Daher M, Klein K, Martinez F, Aung F, Shanley M, Hu B, Gokdemir E, Nunez Cortes AK, Mendt M, Reyes Silva F, Acharya S, Laskowski T, Muniz-Feliciano L, Banerjee PP, Li Y, Li S, Melo Garcia L, Lin P, Shaim H, Yates SG, Marin D, Kaur I, Rao S, Mak D, Lin A, Miao Q, Dou J, Chen K, Champlin RE, Shpall EJ, Rezvani K. Generation of glucocorticoid-resistant SARS-CoV-2 T cells for adoptive cell therapy. Cell Rep 36(3):109432, 2021. e-Pub 2021. PMID: 34270918.
47. Mohanty V, Wang F, Mills GB, Network CTD, Chen K. Uncoupling of gene expression from copy number presents therapeutic opportunities in aneuploid cancers. Cell Rep Med 2(7):100349, 2021. e-Pub 2021. PMID: 34337565.
48. Muftuoglu M, Li L, Liang S, Mak D, Lin AJ, Fang J, Burks JK, Chen K, Andreeff M. Extended Live-cell Barcoding Approach for Multiplexed Mass Cytometry. Sci Rep 11(1):12388, 2021. e-Pub 2021. PMID: 34117319.
49. Liang S, Mohanty V, Dou J, Miao Q, Huang Y, Müftüoglu M, Ding L, Peng W, Chen K. Single-cell manifold-preserving feature selection for detecting rare cell populations. Nat Comput Sci 1(5):374-384, 2021. e-Pub 2021. PMID: 36969355.
50. 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. Spatially Interacting Phosphorylation Sites and Mutations in Cancer. Nat Commun 12(1):2313, 2021. e-Pub 2021. PMID: 33875650.
51. Akcakanat A, Zheng X, Cruz Pico CX, Kim T, Chen K, Korkut A, Sahin AA, Holla VR, Tarco E, Singh G, Damodaran S, Mills GB, Gonzalez-Angulo AM, Meric-Bernstam F. Genomic, Transcriptomic and Proteomic Profiling of Metastatic Breast Cancer. Clin Cancer Res. e-Pub 2021. PMID: 33782032.
52. Zheng J, Ru W, Adolacion JR, Spurgat MS, Liu X, Yuan S, Liang RX, Dong J, Potter AS, Potter SS, Chen K, Chen R, Varadarajan N, Tang SJ. Single cell RNA-seq analysis reveals compartment-specific heterogeneity and plasticity of microglia. iScience 24(3):102186, 2021. e-Pub 2021. PMID: 33718838.
53. Wang F, Wang Q, Mohanty V, Liang S, Dou J, Han J, Minussi DC, Gao R, Ding L, Navin N, Chen K. MEDALT: Single-cell copy number lineage tracing enabling gene discovery. Genome Biol 22(1):70, 2021. e-Pub 2021. PMID: 33622385.
54. Gao R, Bai S, Henderson YC, Lin Y, Schalck A, Yan Y, Kumar T, Hu M, Sei E, Davis A, Wang F, Shaitelman SF, Wang JR, Chen K, Moulder S, Lai SY, Navin NE. Delineating copy number and clonal substructure in human tumors from single-cell transcriptomes. Nat Biotechnol. e-Pub 2021. PMID: 33462507.
55. Wang R, Dang M, Harada K, Han G, Wang F, Pool Pizzi M, Zhao M, Tatlonghari G, Zhang S, Hao D, Lu Y, Zhao S, Badgwell BD, Blum Murphy M, Shanbhag N, Estrella JS, Roy-Chowdhuri S, Abdelhakeem AAF, Wang Y, Peng G, Hanash S, Calin GA, Song X, Chu Y, Zhang J, Li M, Chen K, Lazar AJ, Futreal A, Song S, Ajani JA, Wang L. Single-Cell Dissection of Intratumoral Heterogeneity and Lineage Diversity in Metastatic Gastric Adenocarcinoma. Nat Med 27(1):141-151, 2021. e-Pub 2021. PMID: 33398161.
56. Abbas HA, Reville PK, Jiang X, Yang H, Reuben A, Im JS, Little L, Sinson JC, Chen K, Futreal A, Garcia-Manero G. Response to Hypomethylating Agents in Myelodysplastic Syndrome Is Associated With Emergence of Novel TCR Clonotypes. Front Immunol 12:659625, 2021. e-Pub 2021. PMID: 33912187.
57. Mendt M, Daher M, Basar R, Shanley M, Kumar B, Wei Inng FL, Acharya S, Shaim H, Fowlkes N, Tran JP, Gokdemir E, Uprety N, Nunez-Cortes AK, Ensley E, Mai T, Kerbauy LN, Melo-Garcia L, Lin P, Shen Y, Mohanty V, Lu J, Li S, Nandivada V, Wang J, Banerjee P, Reyes-Silva F, Liu E, Ang S, Gilbert A, Li Y, Wan X, Gu J, Zhao M, Baran N, Muniz-Feliciano L, Wilson J, Kaur I, Gagea M, Konopleva M, Marin D, Tang G, Chen K, Champlin R, Rezvani K, Shpall EJ. Metabolic Reprogramming of GMP Grade Cord Tissue Derived Mesenchymal Stem Cells Enhances Their Suppressive Potential in GVHD. Front Immunol 12:631353, 2021. e-Pub 2021. PMID: 34017325.
58. Liu E, Ang SOT, Kerbauy L, Basar R, Kaur I, Kaplan M, Li L, Tong Y, Daher M, Ensley EL, Uprety N, Nunez Cortes AK, Yang RZ, Li Y, Shaim H, Reyes Silva F, Lin P, Mohanty V, Acharya S, Shanley M, Muniz-Feliciano L, Banerjee PP, Chen K, Champlin RE, Shpall EJ, Rezvani K. GMP-Compliant Universal Antigen Presenting Cells (uAPC) Promote the Metabolic Fitness and Antitumor Activity of Armored Cord Blood CAR-NK Cells. Front Immunol 12:626098, 2021. e-Pub 2021. PMID: 33717142.
59. Abbas HA, Mohanty V, Wang R, Huang Y, Liang S, Wang F, Zhang J, Qiu Y, Hu CW, Qutub AA, Dail M, Bolen CR, Daver N, Konopleva M, Futreal A, Chen K, Wang L, Kornblau SM. Decoupling Lineage-Associated Genes in Acute Myeloid Leukemia Reveals Inflammatory and Metabolic Signatures Associated with Outcomes. Front Oncol 11:705627, 2021. e-Pub 2021. PMID: 34422660.
60. Miao Q, Wang F, Dou J, Iqbal R, Muftuoglu M, Basar R, Li L, Rezvani K, Chen K. Ab initio Spillover Compensation in CyTOF Data. Cytometry A. e-Pub 2020. PMID: 33342071.
61. Daher M, Basar R, Gokdemir E, Baran N, Uprety N, Nunez Cortes AK, Mendt M, Kerbauy LN, Banerjee PP, Hernandez Sanabria M, Imahashi N, Li L, FLWIL L, Fathi M, Rezvan A, Mohanty V, Shen Y, Shaim H, Lu J, Ozcan G, Ensley EL, Kaplan M, Nandivada V, Bdiwi M, Acharya S, Xi Y, Wan X, Mak DH, Liu E, Jiang XR, Ang S, Muniz-Feliciano L, Li Y, Wang J, Kordasti S, Petrov N, Varadarajan N, Marin D, Brunetti L, Skinner RJ, Lyu S, Silva L, Turk R, Schubert MS, Rettig GR, McNeill MS, Kurgan G, Behlke MA, Li H, Fowlkes NW, Chen K, Konopleva M, Champlin R, Shpall EJ, Rezvani K. Targeting a cytokine checkpoint enhances the fitness of armored cord blood CAR-NK cells. Blood. e-Pub 2020. PMID: 32902645.
62. Zook JM, Hansen NF, Olson ND, Chapman L, Mullikin JC, Xiao C, Sherry S, Koren S, Phillippy AM, Boutros PC, Sahraeian SME, Huang V, Rouette A, Alexander N, Mason CE, Hajirasouliha I, Ricketts C, Lee J, Tearle R, Fiddes IT, Barrio AM, Wala J, Carroll A, Ghaffari N, Rodriguez OL, Bashir A, Jackman S, Farrell JJ, Wenger AM, Alkan C, Soylev A, Schatz MC, Garg S, Church G, Marschall T, Chen K, Fan X, English AC, Rosenfeld JA, Zhou W, Mills RE, Sage JM, Davis JR, Kaiser MD, Oliver JS, Catalano AP, Chaisson MJP, Spies N, Sedlazeck FJ, Salit M. A robust benchmark for detection of germline large deletions and insertions. Nat Biotechnol. e-Pub 2020. PMID: 32541955.
63. Lee JJ, Kopetz S, Vilar E, Shen JP, Chen K, Maitra A. Relative Abundance of SARS-CoV-2 Entry Genes in the Enterocytes of the Lower Gastrointestinal Tract. Genes (Basel) 11(6), 2020. e-Pub 2020. PMID: 32545271.
64. Liang S, Liang Q, Chen R, Chen K. Stratified Test Alleviates Batch Effects in Single-Cell Data. Lecture Notes in Computer Science, 2020. e-Pub 2020. PMID: None.
65. Liang S, Wang F, Han J, Chen K. Latent periodic process inference from single-cell RNA-seq data. Nat Commun 11(1):1441, 2020. e-Pub 2020. PMID: 32188848.
66. Akdemir KC, Le VT, Chandran S, Li Y, Verhaak RG, Beroukhim R, Campbell PJ, Chin L, Dixon JR, Futreal PA, Working Group PSV, Consortium P. Disruption of chromatin folding domains by somatic genomic rearrangements in human cancer. Nat Genet 52(3):294-305, 2020. e-Pub 2020. PMID: 32024999.
67. Cortés-Ciriano I, Lee JJ, Xi R, Jain D, Jung YL, Yang L, Gordenin D, Klimczak LJ, Zhang CZ, Pellman DS, Working Group PSV, Park PJ, Consortium P. Comprehensive analysis of chromothripsis in 2,658 human cancers using whole-genome sequencing. Nat Genet 52(3):331-341, 2020. e-Pub 2020. PMID: 32025003.
68. Paczkowska M, Barenboim J, Sintupisut N, Fox NS, Zhu H, Abd-Rabbo D, Mee MW, Boutros PC, Drivers P, Working Group FI, Reimand J, Consortium P. Integrative pathway enrichment analysis of multivariate omics data. Nat Commun 11(1):735, 2020. e-Pub 2020. PMID: 32024846.
69. Zhang Y, Chen F, Fonseca NA, He Y, Fujita M, Nakagawa H, Zhang Z, Brazma A, Working Group PT, Working Group PSV, Creighton CJ, Consortium P. High-coverage whole-genome analysis of 1220 cancers reveals hundreds of genes deregulated by rearrangement-mediated cis-regulatory alterations. Nat Commun 11(1):736, 2020. e-Pub 2020. PMID: 32024823.
70. Carlevaro-Fita J, Lanzós A, Feuerbach L, Hong C, Mas-Ponte D, Pedersen JS, Drivers P, Group FI, Johnson R, Consortium P. Cancer LncRNA Census reveals evidence for deep functional conservation of long noncoding RNAs in tumorigenesis. Commun Biol 3(1):56, 2020. e-Pub 2020. PMID: 32024996.
71. Reyna MA, Haan D, Paczkowska M, Verbeke LPC, Vazquez M, Kahraman A, Pulido-Tamayo S, Barenboim J, Wadi L, Dhingra P, Shrestha R, Getz G, Lawrence MS, Pedersen JS, Rubin MA, Wheeler DA, Brunak S, Izarzugaza JMG, Khurana E, Marchal K, von Mering C, Sahinalp SC, Valencia A, Drivers P, Working Group FI, Reimand J, Stuart JM, Raphael BJ, Consortium P. Pathway and network analysis of more than 2500 whole cancer genomes. Nat Commun 11(1):729, 2020. e-Pub 2020. PMID: 32024854.
72. Shuai S, Drivers P, Working Group FI, Gallinger S, Stein L, Consortium P. Combined burden and functional impact tests for cancer driver discovery using DriverPower. Nat Commun 11(1):734, 2020. e-Pub 2020. PMID: 32024818.
73. Rodriguez-Martin B, Alvarez EG, Baez-Ortega A, Zamora J, Supek F, Demeulemeester J, Santamarina M, Ju YS, Temes J, Garcia-Souto D, Detering H, Li Y, Rodriguez-Castro J, Dueso-Barroso A, Bruzos AL, Dentro SC, Blanco MG, Contino G, Ardeljan D, Tojo M, Roberts ND, Zumalave S, Edwards PAW, Weischenfeldt J, Puiggròs M, Chong Z, Chen K, Lee EA, Wala JA, Raine K, Butler A, Waszak SM, Navarro FCP, Schumacher SE, Monlong J, Maura F, Bolli N, Bourque G, Gerstein M, Park PJ, Wedge DC, Beroukhim R, Torrents D, Korbel JO, Martincorena I, Fitzgerald RC, Van Loo P, Kazazian HH, Burns KH, Working Group PSV, Campbell PJ, Tubio JMC, Consortium P. Pan - cancer analysis of whole genomes identifies driver rearrangements promoted by LINE - 1 retrotransposition. Nat Genet. e-Pub 2020. PMID: 32024998.
74. Li Y, Roberts ND, Wala JA, Shapira O, Schumacher SE, Kumar K, Khurana E, Waszak S, Korbel JO, Haber JE, Imielinski M, Working Group PSV, Weischenfeldt J, Beroukhim R, Campbell PJ, Consortium P. Patterns of somatic structural variation in human cancer genomes. Nature 578(7793):112-121, 2020. e-Pub 2020. PMID: 32025012.
75. Genomes Consortium IPAOW. Pan-cancer analysis of whole genomes. Nature 578(7793):82-93, 2020. e-Pub 2020. PMID: 32025007.
76. Rheinbay E, Nielsen MM, Abascal F, Wala JA, Shapira O, Tiao G, Hornshøj H, Hess JM, Juul RI, Lin Z, Feuerbach L, Sabarinathan R, Madsen T, Kim J, Mularoni L, Shuai S, Lanzós A, Herrmann C, Maruvka YE, Shen C, Amin SB, Bandopadhayay P, Bertl J, Boroevich KA, Busanovich J, Carlevaro-Fita J, Chakravarty D, Chan CWY, Craft D, Dhingra P, Diamanti K, Fonseca NA, Gonzalez-Perez A, Guo Q, Hamilton MP, Haradhvala NJ, Hong C, Isaev K, Johnson TA, Juul M, Kahles A, Kahraman A, Kim Y, Komorowski J, Kumar K, Kumar S, Lee D, Lehmann KV, Li Y, Liu EM, Lochovsky L, Park K, Pich O, Roberts ND, Saksena G, Schumacher SE, Sidiropoulos N, Sieverling L, Sinnott-Armstrong N, Stewart C, Tamborero D, Tubio JMC, Umer HM, Uusküla-Reimand L, Wadelius C, Wadi L, Yao X, Zhang CZ, Zhang J, Haber JE, Hobolth A, Imielinski M, Kellis M, Lawrence MS, von Mering C, Nakagawa H, Raphael BJ, Rubin MA, Sander C, Stein LD, Stuart JM, Tsunoda T, Wheeler DA, Johnson R, Reimand J, Gerstein M, Khurana E, Campbell PJ, López-Bigas N, Drivers P, Working Group FI, Working Group PSV, Weischenfeldt J, Beroukhim R, Martincorena I, Pedersen JS, Getz G, Consortium P. Analyses of non-coding somatic drivers in 2,658 cancer whole genomes. Nature 578(7793):102-111, 2020. e-Pub 2020. PMID: 32025015.
77. Li L, Chen H, Marin D, Xi Y, Miao Q, Lv J, Banerjee PP, Shaim H, Daher M, Basar R, Imahashi N, Jimenez J, Hu B, Mehta RS, Kerbauy LN, Kaplan M, Mendt M, Ozcan G, Gokdemir E, Hernandez Sanabria M, Li Y, Chen K, Wang J, Muniz-Feliciano L, Zhao WL, Champlin RE, Shpall EJ, Rezvani K. A novel immature natural killer cell subpopulation predicts relapse after cord blood transplantation. Blood Adv 3(23):4117-4130, 2019. e-Pub 2019. PMID: 31821460.
78. Liang Q, Dharmat R, Owen L, Shakoor A, Li Y, Kim S, Vitale A, Kim I, Morgan D, Liang S, Wu N, Chen K, DeAngelis MM, Chen R. Single-nuclei RNA-seq on human retinal tissue provides improved transcriptome profiling. Nat Commun 10(1):5743, 2019. e-Pub 2019. PMID: 31848347.
79. Chattopadhyay C, Oba J, Roszik J, Marszalek JR, Chen K, Qi Y, Eterovic K, Robertson AG, Burks JK, McCannel TA, Grimm EA, Woodman SE. Elevated Endogenous SDHA Drives Pathological Metabolism in Highly Metastatic Uveal Melanoma. Invest Ophthalmol Vis Sci 60(13):4187-4195, 2019. e-Pub 2019. PMID: 31596927.
80. Zafar H, Navin N, Chen K, Nakhleh L. SiCloneFit: Bayesian inference of population structure, genotype, and phylogeny of tumor clones from single-cell genome sequencing data. Genome Res. e-Pub 2019. PMID: 31628257.
81. Lluch A, Gonzalez-Angulo A, Casadevall D, Eterovic A, Martínez de Dueñas E, Zheng Z, Guerrero-Zotano A, Liu S, Carrión RMP, Chen K, López-Muñiz JIC, Mills G, Antolín S, Blancas B, López-Serra P, Carrascal EC, Caballero R, Prat P, Rojo F, Gonzalez-Perez A, Meric-Bernstam F, Albanell J. Dynamic clonal remodeling in breast cancer metastases is associated to subtype conversion. European Journal of Cancer 120:54-64, 2019. e-Pub 2019. PMID: None.
82. Wang F, Liang S, Kumar T, Navin N, Chen K. SCMarker: ab initio marker selection for single cell transcriptome profiling. PLoS Comput Biol 15(10):e1007445, 2019. e-Pub 2019. PMID: 31658262.
83. Ruiz-Cordero R, Rao P, Li L, Qi Y, Atherton D, Peng B, Singh RR, Kim TB, Kawakami F, Routbort MJ, Alouch N, Chow CB, Tang X, Lu W, Brimo F, Matin SF, Wood CG, Tannir NM, Wistuba II, Chen K, Wang J, Jeffrey Medeiros L, Karam JA, Tamboli P, Sircar K. Hybrid Oncocytic/Chromophobe Renal Tumors Are Molecularly Distinct From Oncocytoma And Chromophobe Renal Cell Carcinoma. Mod Pathol. e-Pub 2019. PMID: 31231128.
84. Fang Y, McGrail DJ, Sun C, Labrie M, Chen X, Zhang D, Ju Z, Vellano CP, Lu Y, Li Y, Jeong KJ, Ding Z, Liang J, Wang SW, Dai H, Lee S, Sahni N, Mercado-Uribe I, Kim TB, Chen K, Lin SY, Peng G, Westin SN, Liu J, O'Connor MJ, Yap TA, Mills GB. Sequential therapy with PARP and WEE1 inhibitors minimizes toxicity while maintaining efficacy. Cancer Cell 35(6):851-867.e7, 2019. e-Pub 2019. PMID: 31185210.
85. Labrie M, Kim TB, Ju Z, Lee S, Zhao W, Fang Y, Lu Y, Chen K, Ramirez P, Frumovitz M, Meyer L, Fleming ND, Sood AK, Coleman RL, Mills GB, Westin SN. Adaptive responses in a PARP inhibitor window of opportunity trial illustrate limited functional interlesional heterogeneity and potential combination therapy options. Oncotarget 10(37):3533-3546, 2019. e-Pub 2019. PMID: 31191824.
86. Wang F, Zhang S, Kim TB, Lin YY, Iqbal R, Wang Z, Mohanty V, Sircar K, Karam JA, Wendl MC, Meric-Bernstam F, Weinstein JN, Ding L, Mills GB, Chen K. Integrated Transcriptomic-Genomic tool Texomer profiles cancer tissues. Nat Methods. e-Pub 2019. PMID: 30988467.
87. Dumbrava EI, Brusco L, Daniels M, Wathoo C, Shaw K, Lu K, Zheng X, Strong L, Litton J, Arun B, Eterovic A, Routbort M, Patel K, Piha-Paul S, Subbiah V, Hong D, Rodon J, Kopetz S, Mendelsohn J, Mills G, Chen K, Meric-Bernstam F. Expanded analysis of secondary germline findings from matched tumor/normal sequencing identifies additional clinically significant mutations. JCO Precision Oncology, 2019. e-Pub 2019. PMID: None.
88. Chaisson MJP, Sanders AD, Zhao X, Malhotra A, Porubsky D, Rausch T, Gardner EJ, Rodriguez OL, Guo L, Collins RL, Fan X, Wen J, Handsaker RE, Fairley S, Kronenberg ZN, Kong X, Hormozdiari F, Lee D, Wenger AM, Hastie AR, Antaki D, Anantharaman T, Audano PA, Brand H, Cantsilieris S, Cao H, Cerveira E, Chen C, Chen X, Chin CS, Chong Z, Chuang NT, Lambert CC, Church DM, Clarke L, Farrell A, Flores J, Galeev T, Gorkin DU, Gujral M, Guryev V, Heaton WH, Korlach J, Kumar S, Kwon JY, Lam ET, Lee JE, Lee J, Lee WP, Lee SP, Li S, Marks P, Viaud-Martinez K, Meiers S, Munson KM, Navarro FCP, Nelson BJ, Nodzak C, Noor A, Kyriazopoulou-Panagiotopoulou S, Pang AWC, Qiu Y, Rosanio G, Ryan M, Stütz A, Spierings DCJ, Ward A, Welch AE, Xiao M, Xu W, Zhang C, Zhu Q, Zheng-Bradley X, Lowy E, Yakneen S, McCarroll S, Jun G, Ding L, Koh CL, Ren B, Flicek P, Chen K, Gerstein MB, Kwok PY, Lansdorp PM, Marth GT, Sebat J, Shi X, Bashir A, Ye K, Devine SE, Talkowski ME, Mills RE, Marschall T, Korbel JO, Eichler EE, Lee C. Multi-platform discovery of haplotype-resolved structural variation in human genomes. Nat Commun 10(1):1784, 2019. e-Pub 2019. PMID: 30992455.
89. Beck CR, Carvalho CMB, Akdemir ZC, Sedlazeck FJ, Song X, Meng Q, Hu J, Doddapaneni H, Chong Z, Chen ES, Thornton PC, Liu P, Yuan B, Withers M, Jhangiani SN, Kalra D, Walker K, English AC, Han Y, Chen K, Muzny DM, Ira G, Shaw CA, Gibbs RA, Hastings PJ, Lupski JR. Megabase Length Hypermutation Accompanies Human Structural Variation at 17p11.2. Cell 176(6):1310-1324.e10, 2019. e-Pub 2019. PMID: 30827684.
90. Zheng S, Alfaro-Munoz K, Wei W, Wang X, Wang F, Eterovic AK, Shaw KRM, Meric-Bernstam F, Fuller GN, Chen K, Verhaak RG, Mills GB, Yung WKA, Weathers SP, de Groot JF. Prospective Clinical Sequencing of Adult Glioma. Mol Cancer Ther. e-Pub 2019. PMID: 30926639.
91. Klebanov N, Lin WM, Artomov M, Shaughnessy M, Njauw CN, Bloom R, Eterovic AK, Chen K, Kim TB, Tsao SS, Tsao H. Use of Targeted Next-Generation Sequencing to Identify Activating Hot Spot Mutations in Cherry Angiomas. JAMA Dermatol 155(2):211-215, 2019. e-Pub 2019. PMID: 30601876.
92. Nono AD, Chen K, Liu X. Comparison of different functional prediction scores using a gene-based permutation model for identifying cancer driver genes. BMC Medical Genomics 12 (Suppl)(22), 2019. e-Pub 2019. PMID: None.
93. Raghay K, Loree JM, Morris J, Overman MJ, Yu R, Bernstam FM, Menter D, Kee B, Muranyi A, Singh S, Routbourt M, Chen K, Shaw K, Katkhuda R, Shanmugam K, Maru D, Fakih M, Kopetz S. Validation of HER2 amplification as a predictive biomarker for anti-epidermal growth factor receptor antibody therapy in metastatic colorectal cancer. JCO Precision Oncology, 2019. e-Pub 2019. PMID: None.
94. Dumbrava EI, Brusco L, Daniels MS, Wathoo C, Shaw KR, Lu KH, Zheng Z, Strong LC, Litton J, Arun BK, Eterovic AK, Routbort MJ, Patel KP, Qi Y, Piha-Paul SA, Subbiah V, Hong DS, Rodon J, Kopetz S, Mendelsohn J, Mills GB, Chen K, Meric-Bernstam F. Expanded Analysis of Secondary Germline Findings From Matched Tumor/Normal Sequencing Identifies Additional Clinically Significant Mutations. JCO Precision Oncology 3:1-11, 2019. e-Pub 2019. PMID: None.
95. Lee AY, Ewing AD, Ellrott K, Hu Y, Houlahan KE, Bare JC, Espiritu SMG, Huang V, Dang K, Chong Z, Caloian C, Yamaguchi TN, Challenge Participants IDSMC, Kellen MR, Chen K, Norman TC, Friend SH, Guinney J, Stolovitzky G, Haussler D, Margolin AA, Stuart JM, Boutros PC. Combining accurate tumor genome simulation with crowdsourcing to benchmark somatic structural variant detection. Genome Biol 19(1):188, 2018. e-Pub 2018. PMID: 30400818.
96. Tetzlaff MT, Curry JL, Ning J, Sagiv O, Kandl T, Peng B, Bell D, Routbort MJ, Hudgens CW, Ivan D, Kim T, Chen K, Eterovic AK, Shaw KRM, Prieto VG, Yemelyanova A, Esmaeli B. Distinct biological types of ocular adnexal sebaceous carcinoma: HPV-driven and virus-negative tumors arise through non-overlapping molecular-genetic alterations. Clin Cancer Res. e-Pub 2018. PMID: 30420449.
97. Grzeskowiak CL, Kundu ST, Mo X, Ivanov AA, Zagorodna O, Lu H, Chapple RH, Tsang YH, Moreno D, Mosqueda M, Eterovic K, Fradette JJ, Ahmad S, Chen F, Chong Z, Chen K, Creighton CJ, Fu H, Mills GB, Gibbons DL, Scott KL. In Vivo Screening Identifies GATAD2B as a Metastasis Driver in Kras-Driven Lung Cancer. Nat Commun 9(1):2732, 2018. e-Pub 2018. PMID: 30013058.
98. Eterovic AK, Maher OM, Chandra J, Chen K, Huse J, Zaky W. Metachronous Medulloblastoma in a Child With Successfully Treated Neuroblastoma: Case Report and Novel Findings of DNA Sequencing. J Natl Compr Canc Netw 16(6):683-691, 2018. e-Pub 2018. PMID: 29891519.
99. Chyla B, Daver N, Doyle K, McKeegan E, Huang X, Ruvolo V, Wang Z, Chen K, Souers A, Leverson J, Potluri J, Boghaert E, Bhathena A, Konopleva M, Popovic R. Genetic Biomarkers Of Sensitivity and Resistance to Venetoclax Monotherapy in Patients With Relapsed Acute Myeloid Leukemia. Am J Hematol. e-Pub 2018. PMID: 29770480.
100. Raghav K, Bailey AM, Loree JM, Kopetz S, Holla V, Yap TA, Wang F, Chen K, Salgia R, Hong D. Untying the Gordion Knot of Targeting MET in Cancer. Cancer Treat Rev 66:95-103, 2018. e-Pub 2018. PMID: 29730462.
101. Somaiah N, Beird HC, Barbo A, Song J, Mills Shaw KR, Wang WL, Eterovic K, Chen K, Lazar A, Conley AP, Ravi V, Hwu P, Futreal A, Simon G, Meric-Bernstam F, Hong D. Targeted next generation sequencing of well-differentiated/dedifferentiated liposarcoma reveals novel gene amplifications and mutations. Oncotarget 9(28):19891-19899, 2018. e-Pub 2018. PMID: 29731991.
102. 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 WW, Hess JM, Yellapantula VD, Tamborero D, Gonzalez-Perez A, Suphavilai C, Ko JY, Khurana E, Park PJ, Van Allen EM, Liang H, Group MC, Research Network CGA, Lawrence MS, Godzik A, Lopez-Bigas N, Stuart J, Wheeler D, Getz G, Chen K, Lazar AJ, Mills GB, Karchin R, Ding L. Comprehensive Characterization of Cancer Driver Genes and Mutations. Cell 173(2):371-385.e18, 2018. e-Pub 2018. PMID: 29625053.
103. Thorsson V, Gibbs DL, Brown SD, Wolf D, Bortone DS, Ou Yang TH, Porta-Pardo E, Gao GF, Plaisier CL, Eddy JA, Ziv E, Culhane AC, Paull EO, Sivakumar IKA, Gentles AJ, Malhotra R, Farshidfar F, Colaprico A, Parker JS, Mose LE, Vo NS, Liu J, Liu Y, Rader J, Dhankani V, Reynolds SM, Bowlby R, Califano A, Cherniack AD, Anastassiou D, Bedognetti D, Rao A, Chen K, Krasnitz A, Hu H, Malta TM, Noushmehr H, Pedamallu CS, Bullman S, Ojesina AI, Lamb A, Zhou W, Shen H, Choueiri TK, Weinstein JN, Guinney J, Saltz J, Holt RA, Rabkin CE, Research Network CGA, Lazar AJ, Serody JS, Demicco EG, Disis ML, Vincent BG, Shmulevich L. The Immune Landscape of Cancer. Immunity 48(4):812-830.e14, 2018. e-Pub 2018. PMID: 29628290.
104. 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 WW, Wyczalkowski MA, Sengupta S, Li Z, Payne SH, Fenyö D, Miner JH, Walter MJ, Research Network CGA, Vincent B, Eyras E, Chen K, Shmulevich I, Chen F, Ding L. Systematic Analysis of Splice-Site-Creating Mutations in Cancer. Cell Rep 23(1):270-281.e3, 2018. e-Pub 2018. PMID: 29617666.
105. Gao Q, Liang WW, Foltz SM, Mutharasu G, Jayasinghe RG, Cao S, Liao WW, Reynolds SM, Wyczalkowski MA, Yao L, Yu L, Sun SQ, Working Group FA, Research Network CGA, Chen K, Lazar AJ, Fields RC, Wendl MC, Van Tine BA, Vij R, Chen F, Nykter M, Shmulevich I, Ding L. Driver Fusions and Their Implications in the Development and Treatment of Human Cancers. Cell Rep 23(1):227-238.e3, 2018. e-Pub 2018. PMID: 29617662.
106. 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 LB, Zhou DC, Liu D, Cao S, Kim YW, Koire A, McMichael JF, Hucthagowder V, Kim TB, Hahn A, Wang C, McLellan MD, Al-Mulla F, Johnson KJ, Research Network CGA, 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. Pathogenic Germline Variants in 10,389 Adult Cancers. Cell 173(2):355-370.e14, 2018. e-Pub 2018. PMID: 29625052.
107. Wang JF, Pu X, Zhang X, Chen K, Xi Y, Wang J, Mao X, Zhang J, Heymach JV, Antonoff MB, Hofstetter WL, Mehran RJ, Rice DC, Roth JA, Sepesi B, Swisher SG, Vaporciyan AA, Walsh GL, Meng QH, Shaw KR, Eterovic AK, Fang B. Variants with a low allele frequency detected in genomic DNA affect the accuracy of mutation detection in cell-free DNA by next-generation sequencing. Cancer 124(5):1061-1069, 2018. e-Pub 2018. PMID: 29178133.
108. 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. Systematic Functional Annotation of Somatic Mutations in Cancer. Cancer Cell 33(3):450-462.e10, 2018. e-Pub 2018. PMID: 29533785.
109. Chong Z, Chen K. Structural Variant Breakpoint Detection with novoBreak. Methods Mol Biol 1833:129-141, 2018. e-Pub 2018. PMID: 30039369.
110. Galloway-Peña J, DebRoy S, Brumlow C, Li X, Tran TT, Horstmann N, Yao H, Chen K, Wang F, Pan BF, Hawke DH, Thompson EJ, Arias CA, Fowler VG, Bhatti MM, Kalia A, Flores AR, Shelburne SA. Hypervirulent Group A Streptococcus Emergence in an Acaspular Background is Associated with Marked Remodeling of the Bacterial Cell Surface. PLoS One 13(12):e0207897, 2018. e-Pub 2018. PMID: 30517150.
111. Wang Z, Ng KS, Chen T, Kim TB, Wang F, Shaw K, Scott KL, Meric-Bernstam F, Mills GB, Chen K. Cancer driver mutation prediction through Bayesian integration of multi-omic data. PLoS One 13(5):e0196939, 2018. e-Pub 2018. PMID: 29738578.
112. Meric-Bernstam F, Zheng X, Shariati M, Damodaran S, Wathoo C, Brusco L, Demirhan ME, Tapia C, Eterovic AK, Basho RK, Ueno NT, Janku F, Sahin A, Rodon J, Broaddus R, Kim TB, Mendelsohn J, Mills Shaw KR, Tripathy D, Mills GB, Chen K. Survival Outcomes by TP53 Mutation Status in Metastatic Breast Cancer. JCO Precis Oncol 2018, 2018. e-Pub 2018. PMID: 30035249.
113. Morris V, Rao X, Pickering C, Foo WC, Rashid A, Eterovic K, Kim T, Chen K, Wang J, Shaw K, Eng C. Comprehensive Genomic Profiling of Metastatic Squamous Cell Carcinoma of the Anal Canal. Mol Cancer Res 15(11):1542-1550, 2017. e-Pub 2017. PMID: 28784613.
114. Evans KW, Yuca E, Akcakanat A, Scott SM, Arango NP, Zheng X, Chen K, Tapia C, Tarco E, Eterovic AK, Black DM, Litton JK, Yap TA, Tripathy D, Mills GB, Meric-Bernstam F. A Population of Heterogeneous Breast Cancer Patient Derived Xenografts Demonstrate Broad Activity of PARP Inhibitor in BRCA1/2 Wild Type Tumors. Clin Cancer Res 23(21):6468-6477, 2017. e-Pub 2017. PMID: 29093017.
115. Daniels M, Wathoo C, Brusco L, Lu KH, Shaw K, Dumbrava EE, Arun B, Strong L, Litton JK, Eterovic K, Aytac U, Mendelsohn J, Mills GB, Chen K, Meric-Bernstam F. Active Disclosure of Secondary Germline Findings to Deceased Research Participants’ Personal Representatives: Process and Outcomes. JCO Precision Oncology, 2017. e-Pub 2017. PMID: None.
116. Wyczalkowski MA, Wylie KM, Cao S, McLellan MD, Flynn J, Huang M, Ye K, Fan X, Chen K, Wendl MC, Ding L. BreakPoint Surveyor: a pipeline for structural variant visualization. Bioinformatics 33(19):3121-3122, 2017. e-Pub 2017. PMID: 28582538.
117. Zafar H, Tzen A, Navin N, Chen K, Nakhleh L. SiFit: inferring tumor trees from single-cell sequencing data under finite-sites models. Genome Biol 18(1):178, 2017. e-Pub 2017. PMID: 28927434.
118. Korphaisarn K, Loree JM, Nguyen V, Coulson R, Holla V, Litzenburger BC, Chen K, Mills GB, Maru DM, Meric-Bernstan F, Shaw KRM, Kopetz S. Genomic analysis of exceptional responder to regorafenib in treatment-refractory metastatic rectal cancer: a case report and review of the literature. Oncotarget 8(34):57882-57888, 2017. e-Pub 2017. PMID: 28915719.
119. Mashl RJ, Scott AD, Huang KL, Wyczalkowski MA, Yoon CJ, Niu B, DeNardo E, Yellapantula VD, Handsaker RE, Chen K, Koboldt DC, Ye K, Fenyö D, Raphael BJ, Wendl MC, Ding L. GenomeVIP: a cloud platform for genomic variant discovery and interpretation. Genome Res 27(8):1450-1459, 2017. e-Pub 2017. PMID: 28522612.
120. Wang Z, Kim TB, Peng B, Karam JA, Creighton CJ, Joon AY, Kawakami F, Trevisan P, Jonasch E, Chow CW, Rodriguez-Canales J, Tamboli P, Tannir NM, Wood CG, Monzon FA, Baggerly KA, Varella-Garcia M, Czerniak B, Wistuba II, Mills GB, Shaw K, Chen K, Sircar K. Sarcomatoid renal cell carcinoma has a distinct molecular pathogenesis, driver mutation profile and transcriptional landscape. Clin Cancer Res. e-Pub 2017. PMID: 28710314.
121. Arango NP, Brusco L, Mills Shaw KR, Chen K, Eterovic AK, Holla V, Johnson A, Litzenburger B, Khotskaya YB, Sanchez N, Bailey A, Zheng X, Horombe C, Kopetz S, Farhangfar CJ, Routbort M, Broaddus R, Bernstam EV, Mendelsohn J, Mills GB, Meric-Bernstam F. A Feasibility Study of Returning Clinically Actionable Somatic Genomic Alterations Identified in a Research Laboratory. Oncotarget. e-Pub 2017. PMID: 28415679.
122. Liu P, Yuan B, Carvalho CM, Wuster A, Walter K, Zhang L, Gambin T, Chong Z, Campbell IM, Coban Akdemir Z, Gelowani V, Writzl K, Bacino CA, Lindsay SJ, Withers M, Gonzaga-Jauregui C, Wiszniewska J, Scull J, Stankiewicz P, Jhangiani SN, Muzny DM, Zhang F, Chen K, Gibbs RA, Rautenstrauss B, Cheung SW, Smith J, Breman A, Shaw CA, Patel A, Hurles ME, Lupski JR. An Organismal CNV Mutator Phenotype Restricted to Early Human Development. Cell 168(5):830-842.e7, 2017. e-Pub 2017. PMID: 28235197.
123. Jain N, Roberts KG, Jabbour E, Patel K, Eterovic AK, Chen K, Zweidler-McKay P, Lu X, Fawcett G, Wang SA, Konoplev S, Harvey RC, Chen IM, Payne-Turner D, Valentine M, Thomas D, Garcia-Manero G, Ravandi F, Cortes J, Kornblau S, O'Brien S, Pierce S, Jorgensen J, Shaw KR, Willman CL, Mullighan CG, Kantarjian H, Konopleva M. Ph-like Acute Lymphoblastic Leukemia: A High-Risk Subtype in Adults. Blood 129(5):572-581, 2017. e-Pub 2017. PMID: 27919910.
124. Fan X, Chaisson M, Nakhleh L, Chen K. HySA: A Hybrid Structural variant Assembly approach using next generation and single-molecule sequencing technologies. Genome Res. e-Pub 2017. PMID: 28104618.
125. Chong Z, Ruan J, Gao M, Zhou W, Chen T, Fan X, Ding L, Lee AY, Boutros P, Chen J, Chen K. novoBreak: local assembly for breakpoint detection in cancer genomes. Nat Methods 14(1):65-67, 2017. e-Pub 2017. PMID: 27892959.
126. Research Network CGA. Integrated genomic and molecular characterization of cervical cancer. Nature. e-Pub 2017. PMID: 28112728.
127. Zhao Z, Liu Z, Chen K, Guo Y, Allen GI, Zhang J, Zheng WJ, Ruan J. The International Conference on Intelligent Biology and Medicine (ICIBM) 2016: summary and innovation in genomics. BMC Genomics(18(Suppl 6)):703, 2017. e-Pub 2017. PMID: None.
128. Dumbrava EE, Brusco L, Daniels MS, Wathoo C, Shaw KR, Lu KH, Zheng Z, Strong LC, Litton JK, Arun B, Eterovic AK, Routbort M, Piha-Paul SA, Subbiah V, Hong DS, Kopetz S, Mendelsohn J, Mills GB, Chen K, Meric-Bernstam F. Prevalence of incidental germline pathogenic (PV) and likely pathogenic (LPV) variants in hereditary cancer-related genes identified in matched tumor/normal sequencing of advanced solid tumors. Journal of Clinical Oncology 35(15_suppl):1524-1524, 2017. e-Pub 2017. PMID: None.
129. Roszik J, Haydu LE, Hess KR, Oba J, Joon AY, Siroy AE, Karpinets TV, Stingo FC, Baladandayuthapani V, Tetzlaff MT, Wargo JA, Chen K, Forget MA, Haymaker CL, Chen JQ, Meric-Bernstam F, Eterovic AK, Shaw KR, Mills GB, Gershenwald JE, Radvanyi LG, Hwu P, Futreal PA, Gibbons DL, Lazar AJ, Bernatchez C, Davies MA, Woodman SE. Novel algorithmic approach predicts tumor mutation load and correlates with immunotherapy clinical outcomes using a defined gene mutation set. BMC Med 14(1):168, 2016. e-Pub 2016. PMID: 27776519.
130. Raghav K, Morris V, Tang C, Morelli P, Amin HM, Chen K, Manyam GC, Broom B, Overman MJ, Shaw K, Meric-Bernstam F, Maru D, Menter D, Ellis LM, Eng C, Hong D, Kopetz S. MET Amplification in Metastatic Colorectal Cancer: An Acquired Response to EGFR Inhibition, Not a De Novo Phenomenon. Oncotarget 7(34):54627-54631, 2016. e-Pub 2016. PMID: 27421137.
131. Gerhard DS, Clemons PA, Shamji AF, Hon C, Wagner BK, Schreiber SL, Krasnitz A, Sordella R, Sander C, Lowe SW, Powers S, Smith K, Aburi M, Iavarone A, Lasorella A, Silva J, Stockwell BR, Califano A, Boehm JS, Vazquez F, Weir BA, Hahn WC, Khuri FR, Moreno CS, Johns M, Fu H, Nikolova O, Mendez E, Gadi VK, Margolin AA, Grandori C, Kemp CJ, Warren EH, Riddell SR, McIntosh MW, Gevaert O, Kuo CJ, Ji HP, Dhruv H, Finlay D, Kiefer J, Kim S, Vuori K, Berens ME, Hangauer M, Boettcher M, Weissman JS, Bivona TG, Bandyopadhyay S, McManus MT, McCormick F, Aksoy O, Simonds EF, Zheng T, Chen J, An Z, Balmain A, Weiss WA, Chen K, Liang H, Scott KL, Mills GB, Posner BA, MacMillan J, Minna J, White M, Roth MG, Jagu S, Mazerik J. Transforming Big Data into cancer-relevant insight: An initial, multi-tier approach to assess reproducibility and relevance. Mol Cancer Res. e-Pub 2016. PMID: 27401613.
132. Zafar H, Wang Y, Nakhleh L, Navin N, Chen K. Monovar: single nucleotide variant detection in single cells. Nat Methods 13(6):505-7, 2016. e-Pub 2016. PMID: 27088313.
133. Ledgerwood LG, Kumar D, Eterovic AK, Wick J, Chen K, Zhao H, Tazi L, Manna P, Kerley S, Joshi R, Wang L, Chiosea SI, Garnett JD, Tsue TT, Chien J, Mills GB, Grandis JR, Thomas SM. The degree of intratumor mutational heterogeneity varies by primary tumor sub-site. Oncotarget. e-Pub 2016. PMID: 27034009.
134. Meric-Bernstam F, Brusco L, Daniels M, Wathoo C, Bailey A, Strong L, Shaw K, Lu K, Qi Y, Zhao H, Lara-Guerra H, Litton J, Arun B, Eterovic AK, Aytac U, Routbort M, Subbiah V, Janku F, Davies MA, Kopetz S, Mendelsohn J, Mills GB, Chen K. Incidental germline variants in 1000 advanced cancers on a prospective somatic genomic profiling protocol. Ann Oncol. e-Pub 2016. PMID: 26787237.
135. Tsang YH, Dogruluk T, Tedeschi PM, Wardwell-Ozgo J, Lu H, Espitia M, Nair N, Minelli R, Chong Z, Chen F, Chang QE, Dennison JB, Dogruluk A, Li M, Ying H, Bertino JR, Gingras MC, Ittmann M, Kerrigan J, Chen K, Creighton CJ, Eterovic K, Mills GB, Scott KL. Functional annotation of rare gene aberration drivers of pancreatic cancer. Nat Commun 7:10500, 2016. e-Pub 2016. PMID: 26806015.
136. Cao S, Wendl MC, Wyczalkowski MA, Wylie K, Ye K, Jayasinghe R, Xie M, Wu S, Niu B, Grubb R, Johnson KJ, Gay H, Chen K, Rader JS, Dipersio JF, Chen F, Ding L. Divergent viral presentation among human tumors and adjacent normal tissues. Sci Rep 6:28294, 2016. e-Pub 2016. PMID: 27339696.
137. Chen T, Wang Z, Zhou W, Chong Z, Meric-Bernstam F, Mills GB, Chen K. Hotspot mutations delineating diverse mutational signatures and biological utilities across cancer types. BMC Genomics 17 Suppl 2:394, 2016. e-Pub 2016. PMID: 27356755.
138. Dogruluk T, Tsang YH, Espitia M, Chen F, Chen T, Chong Z, Appadurai V, Dogruluk A, Eterovic AK, Bonnen PE, Creighton CJ, Chen K, Mills GB, Scott KL. Identification of Variant-Specific Functions of PIK3CA by Rapid Phenotyping of Rare Mutations. Cancer Res 75(24):5341-54, 2015. e-Pub 2015. PMID: 26627007.
139. Zhou W, Chen T, Chong Z, Rohrdanz MA, Melott JM, Wakefield C, Zeng J, Weinstein JN, Meric-Bernstam F, Mills GB, Chen K. TransVar: a multi-level variant annotator for precision genomics. Nat Methods 12(11):1002-3, 2015. e-Pub 2015. PMID: 26513549.
140. Sudmant PH, Rausch T, Gardner EJ, Handsaker RE, Abyzov A, Huddleston J, Zhang Y, Ye K, Jun G, Fritz MH, Konkel MK, Malhotra A, Stütz AM, Shi X, Casale FP, Chen J, Hormozdiari F, Dayama G, Chen K, Malig M, Chaisson MJP, Walter K, Meiers S, Kashin S, Garrison E, Auton A, Lam HYK, Mu XJ, 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, Consortium GP, Mills RE, Gerstein MB, Bashir A, Stegle O, Devine SE, Lee C, Eichler EE, Korbel JO. An integrated map of structural variation in 2,504 human genomes. Nature 526(7571):75-81, 2015. e-Pub 2015. PMID: 26432246.
141. Consortium GP, authors C, committee S, group P, of Medicine BC, BGI-Shenzhen, Broad Institute of MIT, Harvard, Medical Research CIF, Biology Laboratory EM, Institute EB, Illumina, Molecular Genetics MPIF, Washington University MGIA, Health US, Oxford UO, Sanger Institute WT, group A, Affymetrix, of Medicine AEC, of Medicine BC, BGI-Shenzhen, University B, College B, Broad Institute of MIT, Harvard, Harbor Laboratory CS, University C, Biology Laboratory EM, Biology Laboratory EM, Institute EB, University H, Mutation Database HG, Illumina, Mount Sinai ISOMA, University LS, Hospital MG, Molecular Genetics MPIF, Washington University MGIA, University M, Institute NE, NIH, Genome Center NY, Cancer Research OIF, University PS, New Jersey RCIO, University S, University T, Genomic Medicine JLF, Scientific TF, Research Institute TG, Health US, California UO, Diego S, California UO, Francisco S, California UO, Cruz S, Chicago UO, London UC, Geneva UO, of Medicine UOMS, Michigan UO, Montréal UO, Chapel Hill UONCA, at Charlotte UONC, Oxford UO, Puerto Rico UO, at Houston UOTHSC, Utah UO, Washington UO, Medical College WC. A global reference for human genetic variation. Nature 526(7571):68-74, 2015. e-Pub 2015. PMID: 26432245.
142. Meric-Bernstam F, Johnson A, Holla V, Bailey AM, Brusco L, Chen K, Routbort M, Patel KP, Zeng J, Kopetz S, Davies MA, Piha-Paul SA, Hong DS, Eterovic AK, Tsimberidou AM, Broaddus R, Bernstam EV, Shaw KR, Mendelsohn J, Mills GB. A Decision Support Framework for Genomically Informed Investigational Cancer Therapy. J Natl Cancer Inst 107(7), 2015. e-Pub 2015. PMID: 25863335.
143. 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. Genome Modeling System: A Knowledge Management Platform for Genomics. PLoS Comput Biol 11(7):e1004274, 2015. e-Pub 2015. PMID: 26158448.
144. Chen K, Meric-Bernstam F, Zhao H, Zhang Q, Ezzeddine N, Tang LY, Qi Y, Mao Y, Chen T, Chong Z, Zhou W, Zheng X, Johnson A, Aldape KD, Routbort MJ, Luthra R, Kopetz S, Davies MA, de Groot J, Moulder S, Vinod R, Farhangfar CJ, Shaw KM, Mendelsohn J, Mills GB, Eterovic AK. Clinical Actionability Enhanced through Deep Targeted Sequencing of Solid Tumors. Clin Chem 61(3):544-53, 2015. e-Pub 2015. PMID: 25626406.
145. Grubbs EG, Ng PK, Bui J, Busaidy NL, Chen K, Lee JE, Lu X, Lu H, Meric-Bernstam F, Mills GB, Palmer G, Perrier ND, Scott KL, Shaw KR, Waguespack SG, Williams MD, Yelensky R, Cote GJ. RET Fusion as a Novel Driver of Medullary Thyroid Carcinoma. J Clin Endocrinol Metab 100(3):788-93, 2015. e-Pub 2015. PMID: 25546157.
146. Hao C, Wang L, Peng S, Cao M, Li H, Hu J, Huang X, Liu W, Zhang H, Wu S, Pataer A, Heymach JV, Eterovic AK, Zhang Q, Shaw KR, Chen K, Futreal A, Wang M, Hofstetter W, Mehran R, Rice D, Roth JA, Sepesi B, Swisher SG, Vaporciyan A, Walsh GL, Johnson FM, Fang B. Gene mutations in primary tumors and corresponding patient-derived xenografts derived from non-small cell lung cancer. Cancer Lett 357(1):179-85, 2015. e-Pub 2015. PMID: 25444907.
147. Liu S, Meric-Bernstam F, Parinyanitikul N, Wang B, Eterovic AK, Zheng X, Gagea M, Chavez-MacGregor M, Ueno NT, Lei X, Zhou W, Nair L, Tripathy D, Brown PH, Hortobagyi GN, Chen K, Mendelsohn J, Mills GB, Gonzalez-Angulo AM. Functional Consequence of the MET-T1010I polymorphism in Breast Cancer. Oncotarget 6(5):2604-14, 2015. e-Pub 2015. PMID: 25605252.
148. Malhotra A, Wang Y, Waters J, Chen K, Meric-Bernstam F, Hall IM, Navin NE. Ploidy-Seq: inferring mutational chronology by sequencing polyploid tumor subpopulations. Genome Med 7(1):6, 2015. e-Pub 2015. PMID: 25729435.
149. Zhou W, Zhao H, Chong Z, Mark RJ, Eterovic AK, Meric-Bernstam F, Chen K. ClinSeK: a targeted variant characterization framework for clinical sequencing. Genome Med 7(1):34, 2015. e-Pub 2015. PMID: 25918555.
150. Ince TA, Sousa AD, Jones MA, Harrell JC, Agoston ES, Krohn M, Selfors LM, Liu W, Chen K, Yong M, Buchwald P, Wang B, Hale KS, Cohick E, Sergent P, Witt A, Kozhekbaeva Z, Gao S, Agoston AT, Merritt MA, Foster R, Rueda BR, Crum CP, Brugge JS, Mills GB. Characterization of twenty-five ovarian tumour cell lines that phenocopy primary tumours. Nat Commun 6:7419, 2015. e-Pub 2015. PMID: 26080861.
151. McAuliffe PF, Evans KW, Akcakanat A, Chen K, Zheng X, Zhao H, Eterovic AK, Sangai T, Holder AM, Sharma C, Chen H, Do KA, Tarco E, Gagea M, Naff KA, Sahin A, Multani AS, Black DM, Mittendorf EA, Bedrosian I, Mills GB, Gonzalez-Angulo AM, Meric-Bernstam F. Ability to Generate Patient-Derived Breast Cancer Xenografts Is Enhanced in Chemoresistant Disease and Predicts Poor Patient Outcomes. PLoS One 10(9):e0136851, 2015. e-Pub 2015. PMID: 26325287.
152. Abyzov A, Li S, Kim DR, Mohiyuddin M, Stütz AM, Parrish NF, Mu XJ, Clark W, Chen K, Hurles M, Korbel JO, Lam HY, Lee C, Gerstein MB. Analysis of deletion breakpoints from 1,092 humans reveals details of mutation mechanisms. Nat Commun 6:7256, 2015. e-Pub 2015. PMID: 26028266.
153. Hassan B, Akcakanat A, Sangai T, Evans KW, Adkins F, Eterovic AK, Zhao H, Chen K, Chen H, Do KA, Xie SM, Holder AM, Naing A, Mills GB, Meric-Bernstam F. Catalytic mTOR inhibitors can overcome intrinsic and acquired resistance to allosteric mTOR inhibitors. Oncotarget 5(18):8544-57, 2014. e-Pub 2014. PMID: 25261369.
154. Wang Y, Waters J, Leung ML, Unruh A, Roh W, Shi X, Chen K, Scheet P, Vattathil S, Liang H, Multani A, Zhang H, Zhao R, Michor F, Meric-Bernstam F, Navin NE. Clonal evolution in breast cancer revealed by single nucleus genome sequencing. Nature. e-Pub 2014. PMID: 25079324.
155. Bailey AM, Mao Y, Zeng J, Holla V, Johnson A, Brusco L, Chen K, Mendelsohn J, Routbort MJ, Mills GB, Meric-Bernstam F. Implementation of biomarker-driven cancer therapy: existing tools and remaining gaps. Discov Med 17(92):101-14, 2014. e-Pub 2014. PMID: 24534473.
156. Zhou W, Chen T, Zhao H, Eterovic AK, Meric-Bernstam F, Mills GB, Chen K. Bias from removing read duplication in ultra-deep sequencing experiments. Bioinformatics. e-Pub 2014. PMID: 24389657.
157. Delaneau O, Marchini J, Consortium GP, Consortium GP. Integrating sequence and array data to create an improved 1000 Genomes Project haplotype reference panel. Nat Commun 5:3934, 2014. e-Pub 2014. PMID: 25653097.
158. Fan X, Zhou W, Chong Z, Nakhleh L, Chen K. Towards accurate characterization of clonal heterogeneity based on structural variation. BMC Bioinformatics 15(299):299, 2014. e-Pub 2014. PMID: 25201439.
159. Chen K, Chen L, Fan X, Wallis J, Ding L, Weinstock G. TIGRA: A Targeted Iterative Graph Routing Assembler for breakpoint assembly. Genome Res. e-Pub 2013. PMID: 24307552.
160. 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, Network TR. The somatic genomic landscape of glioblastoma. Cell 155(2):462-77, 2013. e-Pub 2013. PMID: 24120142.
161. 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. BreakTrans: uncovering the genomic architecture of gene fusions. Genome Biol 14(8):R87. e-Pub 2013. PMID: 23972288.
162. Zheng S, Fu J, Vegesna R, Mao Y, Heathcock LE, Torres-Garcia W, Ezhilarasan R, Wang S, McKenna A, Chin L, Brennan CW, Yung WK, Weinstein JN, Aldape KD, Sulman EP, Chen K, Koul D, Verhaak RG. A survey of intragenic breakpoints in glioblastoma identifies a distinct subset associated with poor survival. Genes Dev 27(13):1462-72, 2013. e-Pub 2013. PMID: 23796897.
163. Research Network TCGA. Genomic and Epigenomic Landscapes of Adult De Novo Acute Myeloid Leukemia. N Engl J Med. e-Pub 2013. PMID: 23634996.
164. Mao Y, Chen H, Liang H, Meric-Bernstam F, Mills GB, Chen K. CanDrA: Cancer-Specific Driver Missense Mutation Annotation with Optimized Features. PLoS One 8(10):e77945, 2013. e-Pub 2013. PMID: 24205039.
165. Consortium GP, Abecasis GR, Auton A, Brooks LD, DePristo MA, Durbin RM, Handsaker RE, Kang HM, Marth GT, McVean GA. An integrated map of genetic variation from 1,092 human genomes. Nature 491(7422):56-65, 2012. e-Pub 2012. PMID: 23128226.
166. 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. Genomic landscape of non-small cell lung cancer in smokers and never-smokers. Cell 150(6):1121-34, 2012. e-Pub 2012. PMID: 22980976.
167. 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. The origin and evolution of mutations in acute myeloid leukemia. Cell 150(2):264-78, 2012. e-Pub 2012. PMID: 22817890.
168. 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. Whole-genome analysis informs breast cancer response to aromatase inhibition. Nature 486(7403):353-60, 2012. e-Pub 2012. PMID: 22722193.
169. 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. BreakFusion: Targeted Assembly-based Identification of Gene Fusions in Whole Transcriptome Paired-end Sequencing Data. Bioinformatics. e-Pub 2012. PMID: 22563071.
170. 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. Background mutations in parental cells account for most of the genetic heterogeneity of induced pluripotent stem cells. Cell Stem Cell 10(5):570-82, 2012. e-Pub 2012. PMID: 22542160.
171. 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. Clonal architecture of secondary acute myeloid leukemia. N Engl J Med 366(12):1090-1098, 2012. e-Pub 2012. PMID: 22417201.
172. Ding L, Ley T, Larson DE, Miller CA, Koboldt DC, Welch JS, Ritchey JK, Young MA, Lamprecht T, McLellan MD, McMichael JF, Wallis J, Lu C, Shen D, Harris CC, Dooling DJ, Fulton RS, Fulton LL, Chen K, Schmidt H, Kalicki-Veizer J, Magrini V, Cook L, McGrath SD, Vickery TL, Wendi MC, Heath S, Watson MA, Link DC, Tomasson MH, Shannon WD, Payton JE, Kulkarni S, Westervelt P, Walter MJ, Graubert TA, Mardis E, Wilson R, Dipersio JF. Clonal evolution in relapsed acute myeloid leukemia revealed by whole-genome sequencing. Nature 481, 2012. e-Pub 2012. PMID: 22237025.
173. Koboldt DC, Larson DE, Chen K, Ding L, Wilson RK. Massively parallel sequencing approaches for characterization of structural variation. Methods Mol Biol 838:369-84, 2012. e-Pub 2012. PMID: 22228022.
174. Larson DE, Harris CC, Chen K, Koboldt DC, Abbott TE, Dooling DJ, Ley TJ, Mardis ER, Wilson RK, Ding L. SomaticSniper: Identification of somatic point mutations in whole genome sequencing data. Bioinformatics. e-Pub 2011. PMID: 22155872.
175. 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. Sequencing a mouse acute promyelocytic leukemia genome reveals genetic events relevant for disease progression. J Clin Invest 121(4):1445-55, 2011. e-Pub 2011. PMID: 21436584.
176. Mills RE, Walter K, Stewart C, Handsaker RE, Chen K, Alkan C, Abyzov A, Yoon SC, Ye K, Cheetham RK, Chinwalla A, Conrad DF, Fu Y, Grubert F, Hajirasouliha I, Hormozdiari F, Iakoucheva LM, Iqbal Z, Kang S, Kidd JM, Konkel MK, Korn J, Khurana E, Kural D, Lam HY, Leng J, Li R, Li Y, Lin CY, Luo R, Mu XJ, Nemesh J, Peckham HE, Rausch T, Scally A, Shi X, Stromberg MP, Stütz AM, Urban AE, Walker JA, Wu J, Zhang Y, Zhang ZD, Batzer MA, Ding L, Marth GT, McVean G, Sebat J, Snyder M, Wang J, Ye K, Eichler EE, Gerstein MB, Hurles ME, Lee C, McCarroll SA, Korbel JO, Project G. Mapping copy number variation by population-scale genome sequencing. Nature 470(7332):59-65, 2011. e-Pub 2011. PMID: 21293372.
177. 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. CREST maps somatic structural variation in cancer genomes with base-pair resolution. Nat Methods 8(8):652-4, 2011. e-Pub 2011. PMID: 21666668.
178. Consortium GP. A map of human genome variation from population-scale sequencing. Nature 467(7319):1061-73, 2010. e-Pub 2010. PMID: 20981092.
179. 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, Ivanovich JL, Goodfellow PJ, Perou CM, Weinstock GM, Aft R, Watson M, Ley TJ, Wilson RK, Mardis ER. Genome remodelling in a basal-like breast cancer metastasis and xenograft. Nature 464(7291):999-1005, 2010. e-Pub 2010. PMID: 20393555.
180. Zhang Q, Ding L, Larson DE, Koboldt DC, McLellan MD, Chen K, Shi X, Kraja A, Mardis ER, Wilson RK, Borecki IB, Province MA. CMDS: a population-based method for identifying recurrent DNA copy number aberrations in cancer from high-resolution data. Bioinformatics 26(4):464-9, 2010. e-Pub 2010. PMID: 20031968.
181. 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. BreakDancer: an algorithm for high-resolution mapping of genomic structural variation. Nat Methods 6(9):677-81, 2009. e-Pub 2009. PMID: 19668202.
182. Koboldt DC, Chen K, Wylie T, Larson DE, McLellan MD, Mardis ER, Weinstock GM, Wilson RK, Ding L. VarScan: variant detection in massively parallel sequencing of individual and pooled samples. Bioinformatics 25(17):2283-5, 2009. e-Pub 2009. PMID: 19542151.
183. 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. DNA sequencing of a cytogenetically normal acute myeloid leukaemia genome. Nature 456(7218):66-72, 2008. e-Pub 2008. PMID: 18987736.
184. Research Network CGA. Comprehensive genomic characterization defines human glioblastoma genes and core pathways. Nature 455(7216):1061-8, 2008. e-Pub 2008. PMID: 18772890.
185. 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. Somatic mutations affect key pathways in lung adenocarcinoma. Nature 455(7216):1069-75, 2008. e-Pub 2008. PMID: 18948947.
186. Chen K, McLellan MD, Ding L, Wendl MC, Kasai Y, Wilson RK, Mardis ER. PolyScan: an automatic indel and SNP detection approach to the analysis of human resequencing data. Genome Res 17(5):659-66, 2007. e-Pub 2007. PMID: 17416743.
187. McLaughlin WA, Chen K, Hou T, Wang W. On the detection of functionally coherent groups of protein domains with an extension to protein annotation. BMC Bioinformatics 8:390, 2007. e-Pub 2007. PMID: 17937820.
188. Hou T, McLaughlin W, Lu B, Chen K, Wang W. Prediction of binding affinities between the human amphiphysin-1 SH3 domain and its peptide ligands using homology modeling, molecular dynamics and molecular field analysis. J Proteome Res 5(1):32-43, 2006. e-Pub 2006. PMID: 16396493.
189. Hou T, Chen K, McLaughlin WA, Lu B, Wang W. Computational analysis and prediction of the binding motif and protein interacting partners of the Abl SH3 domain. PLoS Comput Biol 2(1):e1, 2006. e-Pub 2006. PMID: 16446784.
190. Chen K, Hasegawa-Johnson M, Cohen A, Borys S, Kim S, Cole J, Choi JY. Prosody dependent speech recognition on radio news corpus of American English. IEEE Transactions on Speech and Audio Processing 14(1):232-245, 2006. e-Pub 2006. PMID: None.
191. Hasegawa-Johnson M, Chen K, Cole J, Borys S, Kim S, Cohen A, Zhang T, Choi J, Kim H, Yoon T, and Chavarria S. Spontaneous recognition of words and prosody in the Boston University Radio Speech Corpus. Speech Communication, 2005. e-Pub 2005. PMID: None.
192. Kim S, Hasegawa-Johnson M, Chen K. Automatic recognition of pitch movements using time-delayed recurrent neural network. IEEE Signal Processing Letter, 2004. e-Pub 2004. PMID: None.
193. Park EM, Watowich SS. Improved tumor control with immune checkpoint blockade following metronidazole treatment. None. PMID: None.
194. Muhhamed, al WE. CoCo-ST: Comparing and Contrasting Spatial Transcriptomics data sets using graph contrastive learning. Nature Genetics. PMID: None.
195. Zhu B, et al JZ. Spatial Single-Cell Analysis Reveals the Transition of Tumor Microenvironment Organization from Precancer to Invasive Lung Adenocarcinoma. None. PMID: None.
196. Tseng C, al ME. A Phase II Study of Talazoparib Tosylate in Advanced Cancer Patients with Somatic and Germline (Not Breast or Ovarian Cancer) Alterations of BRCA1/2, Mutations/Deletions/Amplification in Other Homologous Recombination Repair Pathway Genes and PTEN or PTEN loss. npj Precision Oncology. PMID: None.
197. Yam, Ueno. Targeting the EGFR pathway in chemotherapy-resistant triple-negative breast cancer - a phase II study. Clinical Cancer Research. PMID: None.
198. Jiang XL, et al. Depletion of effector regulatory T cells drives major response to induction dual immune checkpoint blockade. None. PMID: None.
199. al GE. Neoantigen Cancer Vaccines and Distinct Immune Checkpoint Therapies Each Utilize Both Converging and Discrete Mechanisms. Science Immunology. PMID: None.
200. et al YG. Compartmentalized Responses to Endogenous Retroviruses Govern Adult Tissue Regeneration. None. PMID: None.
201. Lyu Y, Kim SJ, Humphrey ES, Deliu LP, Guan Y, Liang Q, Kim KH, Dou J, Tan Y, Jin K, Liu V, Hassan RH, Song X, Sun H, Zhang J, Lu Y, Mohanty V, Chen K, Yang YJ, Chen T, Ge Y. SETDB1 erosion unleashes endogenous retrovirus in aging. Cell. PMID: None.
202. Kumar S, et al MD. Integrated analysis of molecular and clinical features associated with overall survival in melanoma patients with brain metastasis. Acta Neuropathologica Communications Brain Metastasis Series. PMID: None.
203. Zhang J, et al BZ. Spatial profiling reveals distinct molecular and immune evolution of mouse lung adenocarcinoma precancers with or without carcinogen exposure. Nature Communications. PMID: None.
204. et al YG. Stem Cell Activity Coupled Suppression of Endogenous Retrovirus Governs Adult Tissue Regeneration. Cell. PMID: None.
205. Liang Q, Soto L, Haymaker C, Chen K. Interpretable Spatial Gradient Analysis for Spatial Transcriptomics Data. None. PMID: None.
206. Stepheni, Gubin. Metronidazole alters gut microbes and improves cancer immunotherapy results. None. PMID: None.
207. et al BZC. Acquired resistance of AML to menin inhibition is mediated by targetable alterations in. None. PMID: None.
208. Foltz SM, Ding L, et al. Somatic mutation phasing and haplotype extension using linked-reads in multiple myeloma. Nature Comm. PMID: None.
209. Kanishicar Sircar RREA. Genomic and Epigenomic Signatures Can Risk-Stratify Renal Oncocytic Tumors from Clinical-Grade Samples. None. PMID: None.
210. et al MH. Insights, opportunities and challenges provided by large cell atlases. None. PMID: None.
211. al ZE. Spatial single-cell analysis of human and murine lung adenocarcinoma precursors reveals TIM-3 as a putative target for lung cancer interception. None. PMID: None.
212. et al MW. Interrogation of Signaling Dysregulation and Drug Efficacy for Precision Medicine in Mantle Cell Lymphoma. Haematologica. PMID: None.
213. et al HR. CREM is a regulatory checkpoint of CAR and IL-15 signaling in NK cells. Nature. PMID: None.
214. et al JW. Joint multi-omics discriminant analysis with consistent representation learning using PANDA. None. PMID: None.
215. Chen W, Zhang P, Tran TN, Li S, Li L, Youker K, Fang L, Brannan KW, Chen S, Ma Q, Chen K, Song Q, Cooke J, Wang G. A visual – omics foundation model to bridge histopathology image with transcriptomics. None. PMID: None.
216. al HE. Navigating BTK Inhibitor Resistance in Mantle Cell Lymphoma: Integrative Profiling Strategies. npj Precision Oncology. PMID: None.
217. al VE. Transcriptional and phenotypic heterogeneity underpinning venetoclax resistance in AML. None. PMID: None.

Invited Articles

1. Zafar H, Navi N, Nakhleh L, Chen K. Computational approaches for inferring tumor evolution from single-cell genomic data. Current Opinion on Systems Biology 7:16-25, 2018. e-Pub 2018. PMID: None.
2. Navin NE, Chen K. Genotyping tumor clones from single-cell data. Nat Methods 13(7):555-6, 2016. e-Pub 2016. PMID: 27355792.
3. Djotsa Nono AB, Chen K, Liu X. Computational Prediction of Genetic Drivers in Cancer. beLS, 2016. e-Pub 2016. PMID: None.
4. Chen K, Meric-Bernstam F. Whole genome sequencing in cancer clinics. EBioMedicine 2(1):15-6, 2015. e-Pub 2015. PMID: 26137530.
5. Fan X, Abbott TE, Larson D, Chen K. BreakDancer: Identification of Genomic Structural Variation from Paired-End Read Mapping. Curr Protoc Bioinformatics 2014, 2014. e-Pub 2014. PMID: 25152801.

Other Articles

1. Hahn, WC, Bader, JS, Braun, TP, Califano, A, Clemons, PA, Druker, BJ, Ewald, AJ, Fu, H, Jagu, S, Kemp, CJ, Kim, W, Kuo, CJ, McManus, M, Mills, GB, Mo, X, Sahni, N, Schreiber, SL, Talamas, JA, Tamayo, P, Tyner, JW, Wagner, BK, Weiss, WA, Gerhard, DS, Dancik, V, Gill, S, Hua, B, Sharifnia, T, Viswanathan, V, Zou, Y, Dela Cruz, F, Kung, AL, Stockwell, BR, Boehm, JS, Dempster, J, Manguso, R, Vazquez, F, Cooper, LA, Du, Y, Ivanov, AA, Lonial, S, Moreno, CS, Niu, Q, Owonikoko, TK, Ramalingam, SS, Reyna, MA, Zhou, W, Grandori, C, Shmulevich, I, Chen, K, Liang, H An expanded universe of cancer targets. Cell 184(5):1142-1155, 2021. PMID: 33667368.
2. Korphaisarn K, Loree JM, Nguyen V, Coulson R, Holla V, Litzenburger BC, Chen K, Mills GB, Maru DM, Meric-Bernstan F, Mills Shaw KR, Kopetz S Genomic analysis of exceptional responder to regorafenib in treatment-refractory metastatic rectal cancer: a case report and review of the literature. Oncotarget. PMID: 28621683.
3. 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 Use of whole-genome sequencing to diagnose a cryptic fusion oncogene. JAMA 305(15):1577-84, 2011. PMID: 21505136.
4. 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 Identification of a novel TP53 cancer susceptibility mutation through whole-genome sequencing of a patient with therapy-related AML. JAMA 305(15):1568-76, 2011. PMID: 21505135.
5. 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 Recurring mutations found by sequencing an acute myeloid leukemia genome. N Engl J Med 361(11):1058-66, 2009. PMID: 19657110.

Editorials

1. Bebis G, Kato M, Kohandel M, Wilkie K, Antunes DA, Chen K, Dou J. Advances in mathematical and computational oncology, volume III. Frontiers in Oncology 13, 2023. PMID: None.
2. Bebis, G, Kato, M, Kohandel, M, Wilkie, KP, Antunes, DA, Chen, K, Dou, J. Editorial. Frontiers in Oncology 13, 2023. PMID: 37817766.
3. Bebis G, Benos T, Chen K, Jahn K, Lima E. 1st International Symposium on Mathematical and Computational Oncology. Frontiers Abstract Book, 2020. PMID: None.

Book Chapters

1. Chen K, Hasegawa-Johnson M, Cole J. A Factored Language Model for Prosody-Dependent Speech Recognition. In: Speech Synthesis and Recognition, Advanced Robotic Systems. None. None, 2007.