Ken Chen, Ph.D.

Peer-Reviewed Articles

1. Wang Y, Dede M, Mohanty V, Dou J, Li Z, Chen K. A statistical approach for systematic identification of transition cells from scRNA-seq data. Cell Rep Methods:100913. e-Pub 2024. PMID: 39644902.
2. Lyu Y, Kim SJ, Humphrey ES, Nayak R, Guan Y, Liang Q, Kim KH, Tan Y, Dou J, Sun H, Song X, Nagarajan P, Gerner-Mauro KN, Jin K, Liu V, Hassan RH, Johnson ML, Deliu LP, You Y, Sharma A, Pasolli HA, Lu Y, Zhang J, Mohanty V, Chen K, Yang YJ, Chen T, Ge Y. Stem Cell Activity Coupled Suppression of Endogenous Retrovirus Governs Adult Tissue Regeneration. Cell. e-Pub 2024. PMID: 39476839.
3. Keshari S, Shavkunov AS, Miao Q, Saha A, Minowa T, Molgora M, Williams CD, Chaib M, Highsmith AM, Pineda JE, Alekseev S, Alspach E, Hu KH, Colonna M, Pauken KE, Chen K, Gubin MM. Comparing Neoantigen Cancer Vaccines and Immune Checkpoint Therapy Unveils an Effective Vaccine and Anti-TREM2 Macrophage-Targeting Dual Therapy. Cell Rep 43(11):114875. e-Pub 2024. PMID: 39446585.
4. 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.
5. 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. PMID: 39137729.
6. 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.
7. 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.
8. 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.
9. 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.
10. 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.
11. 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.
12. 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.
13. 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.
14. 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.
15. 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, Lim FLWI, 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. PMID: 36543374.
16. 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.
17. 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.
18. 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.
19. 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.
20. 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. PMID: 35108036.
21. 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.
22. Mohanty V, Wang F, Mills GB, CTD2 Research Network, 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.
23. 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.
24. 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.
25. 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.
26. 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, Lim FLWIL, 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.
27. Liang S, Liang Q, Chen R, Chen K. Stratified Test Alleviates Batch Effects in Single-Cell Data. Lecture Notes in Computer Science, 2020.
28. 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.
29. Li Y, Roberts ND, Wala JA, Shapira O, Schumacher SE, Kumar K, Khurana E, Waszak S, Korbel JO, Haber JE, Imielinski M, PCAWG Structural Variation Working Group, Weischenfeldt J, Beroukhim R, Campbell PJ, PCAWG Consortium. Patterns of somatic structural variation in human cancer genomes. Nature 578(7793):112-121, 2020. e-Pub 2020. PMID: 32025012.
30. 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.
31. 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.
32. 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.
33. 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.
34. 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, 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. Pathogenic Germline Variants in 10,389 Adult Cancers. Cell 173(2):355-370.e14, 2018. PMID: 29625052.
35. 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, MC3 Working Group, Cancer Genome Atlas Research Network, 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. PMID: 29625053.
36. 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, Cancer Genome Atlas Research Network, 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.
37. 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.
38. 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.
39. 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. PMID: 28235197.
40. 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 2016. PMID: 27892959.
41. 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.
42. 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.
43. 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.
44. 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.
45. 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. PMID: 26513549.
46. 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.
47. 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.
48. 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.
49. 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.
50. 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.
51. 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.
52. 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 and Dipersio JF. Clonal evolution in relapsed acute myeloid leukemia revealed by whole-genome sequencing. Nature 481, 2012. e-Pub 2012. PMID: 22237025.
53. 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, 1000 Genomes Project. Mapping copy number variation by population-scale genome sequencing. Nature 470(7332):59-65, 2011. PMID: 21293372.
54. 1000 Genomes Project Consortium. A map of human genome variation from population-scale sequencing. Nature 467(7319):1061-73, 2010. PMID: 20981092.
55. 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.
56. 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.
57. 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. PMID: 18987736.
58. Cancer Genome Atlas Research Network. Comprehensive genomic characterization defines human glioblastoma genes and core pathways. Nature 455(7216):1061-8, 2008. e-Pub 2008. PMID: 18772890.
59. 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.
60. 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.

Invited Articles

1. Zafar H, Navi N, Nakhleh L and Chen K. Computational approaches for inferring tumor evolution from single-cell genomic data. Current Opinion on Systems Biology 7:16-25, 2018.
2. Navin NE, Chen K. Genotyping tumor clones from single-cell data. Nat Methods 13(7):555-6, 2016. PMID: 27355792.