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Ken Chen, Ph.D. - Publications

Affiliations: 
1991-1999 Precision Instrument and Mechanics Tsinghua University, China 
 1999-2004 Electrical and Computer Engineering University of Illinois, Urbana-Champaign, Urbana-Champaign, IL 
 2004-2005 Biochemistry and Biophysics University of California, San Diego, La Jolla, CA 
 2005-2011 Genome Institute Washington University, Saint Louis, St. Louis, MO 
 2011- Bioinformatics and Computational Biology The University of Texas MD Anderson Cancer Center 
Area:
Cancer, Genomics, Machine Learning, Statistical Signal Processing, Electrical and Computer Engineering, Linguistics Language, Computer Science
Website:
https://faculty.mdanderson.org/profiles/ken_chen.html
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144 high-probability publications. We are testing a new system for linking publications to authors. You can help! If you notice any inaccuracies, please sign in and mark papers as correct or incorrect matches. If you identify any major omissions or other inaccuracies in the publication list, please let us know.

Year Citation  Score
2022 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, et al. Occult polyclonality of preclinical pancreatic cancer models drives in vitro evolution. Nature Communications. 13: 3652. PMID 35752636 DOI: 10.1038/s41467-022-31376-3  0.416
2021 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, et al. Oxidative phosphorylation is a metabolic vulnerability in chemotherapy-resistant triple negative breast cancer. Cancer Research. PMID 34518211 DOI: 10.1158/0008-5472.CAN-20-3242  0.366
2020 Liang S, Dou J, Iqbal R, Chen K. Batch-Corrected Distance Mitigates Temporal and Spatial Variability for Clustering and Visualization of Single-Cell Gene Expression Data. Biorxiv : the Preprint Server For Biology. PMID 33052339 DOI: 10.1101/2020.10.08.332080  0.261
2020 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, ... ... Chen K, et al. Targeting a cytokine checkpoint enhances the fitness of armored cord blood CAR-NK cells. Blood. PMID 32902645 DOI: 10.1182/Blood.2020007748  0.393
2020 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, ... ... Chen K, et al. Author Correction: A robust benchmark for detection of germline large deletions and insertions. Nature Biotechnology. PMID 32699374 DOI: 10.1038/S41587-020-0640-Y  0.718
2020 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, ... ... Chen K, et al. A robust benchmark for detection of germline large deletions and insertions. Nature Biotechnology. PMID 32541955 DOI: 10.1038/S41587-020-0538-8  0.767
2020 Liang S, Wang F, Han J, Chen K. Latent periodic process inference from single-cell RNA-seq data. Nature Communications. 11: 1441. PMID 32188848 DOI: 10.1038/S41467-020-15295-9  0.406
2020 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, ... ... Chen K, et al. Pan-cancer analysis of whole genomes identifies driver rearrangements promoted by LINE-1 retrotransposition. Nature Genetics. PMID 32024998 DOI: 10.1038/S41588-019-0562-0  0.507
2020 Zhu L, Meric-Bernstam F, Holla V, Kim T, Shaw KR, Chen K, Routbort M, Kopetz S, Overman MJ. Clinical outcome for gastrointestinal cancers with polymerase epsilon mutations treated with immunotherapy. Journal of Clinical Oncology. 38: 828-828. DOI: 10.1200/Jco.2020.38.4_Suppl.828  0.499
2020 Goldberg J, Qiao N, Gross B, Meric-Bernstam F, Guerriero J, Chen K, Philips AV, Peoples GE, Alatrash G, Mittendorf EA. ESR1 mutations provide novel targets for breast cancer immunotherapy. Journal of Clinical Oncology. 38: 3135-3135. DOI: 10.1200/Jco.2020.38.15_Suppl.3135  0.416
2019 Wang F, Liang S, Kumar T, Navin N, Chen K. SCMarker: Ab initio marker selection for single cell transcriptome profiling. Plos Computational Biology. 15: e1007445. PMID 31658262 DOI: 10.1371/Journal.Pcbi.1007445  0.418
2019 Arango NP, Brusco L, Shaw KRM, Chen K, Eterovic AK, Holla V, Johnson A, Litzenburger B, Khotskaya YB, Sanchez N, Bailey A, Zheng X, Horombe C, Kopetz S, Farhangfar CJ, et al. Correction: A feasibility study of returning clinically actionable somatic genomic alterations identified in a research laboratory. Oncotarget. 10: 5254. PMID 31497255 DOI: 10.18632/Oncotarget.27176  0.427
2019 Lluch A, González-Angulo AM, Casadevall D, Eterovic AK, Martínez de Dueñas E, Zheng X, Guerrero-Zotano Á, Liu S, Pérez R, Chen K, Chacón JI, Mills GB, Antolín S, Blancas I, López-Serra P, et al. Dynamic clonal remodelling in breast cancer metastases is associated with subtype conversion. European Journal of Cancer (Oxford, England : 1990). 120: 54-64. PMID 31491604 DOI: 10.1016/J.Ejca.2019.07.003  0.455
2019 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, ... ... Chen K, et al. Hybrid oncocytic/chromophobe renal tumors are molecularly distinct from oncocytoma and chromophobe renal cell carcinoma. Modern Pathology : An Official Journal of the United States and Canadian Academy of Pathology, Inc. PMID 31231128 DOI: 10.1038/S41379-019-0304-Y  0.476
2019 Zafar H, Tzen A, Navin N, Chen K, Nakhleh L. Comments on the model parameters in "SiFit: inferring tumor trees from single-cell sequencing data under finite-sites models". Genome Biology. 20: 95. PMID 31096998 DOI: 10.1186/S13059-019-1692-5  0.41
2019 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, ... ... Chen K, et al. Multi-platform discovery of haplotype-resolved structural variation in human genomes. Nature Communications. 10: 1784. PMID 30992455 DOI: 10.1038/S41467-018-08148-Z  0.503
2019 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. Nature Methods. PMID 30988467 DOI: 10.1038/S41592-019-0388-9  0.496
2019 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. Molecular Cancer Therapeutics. PMID 30926639 DOI: 10.1158/1535-7163.Mct-18-1122  0.547
2019 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, ... ... Chen K, et al. Megabase Length Hypermutation Accompanies Human Structural Variation at 17p11.2. Cell. PMID 30827684 DOI: 10.1016/J.Cell.2019.01.045  0.508
2019 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: 22. PMID 30704472 DOI: 10.1186/s12920-018-0452-9  0.461
2019 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 Dermatology. PMID 30601876 DOI: 10.1001/Jamadermatol.2018.4231  0.503
2019 Issa GC, Benton CB, Mohanty V, Shen Y, Alaniz Z, Wang F, Futreal PA, Wang W, Jorgensen JL, Navin N, Konopleva MY, Chen K, Andreeff M. Identification of Gene Expression Signatures in Leukemia Stem Cells and Minimal Residual Disease Following Treatment of Adverse Risk Acute Myeloid Leukemia Blood. 134: 2717-2717. DOI: 10.1182/Blood-2019-130540  0.466
2019 Labrie M, Ju Z, Litton JK, Kim T, Lee S, Chen K, Soliman PT, Frumovitz M, Meyer LA, Moulder S, Jazaeri AA, Lu KH, Sood AK, Coleman RL, Mills GB, et al. Abstract 2070: Exploration of markers of synergistic lethality of PARP and PI3K-Akt-mTOR inhibitors in women's cancers Cancer Research. 79: 2070-2070. DOI: 10.1158/1538-7445.Am2019-2070  0.419
2019 Evans K, Moulder S, Yuca E, Scott S, Arango NP, Shariati M, Vellano CP, Saridogan T, Zheng X, Gonzalez-Angulo AM, Zhao M, Su X, Tapia C, Chen K, Akcakanat A, et al. Abstract C016: Oxidative phosphorylation is a metabolic vulnerability in chemotherapy resistant triple negative breast cancer Molecular Cancer Therapeutics. 18. DOI: 10.1158/1535-7163.Targ-19-C016  0.437
2018 Lee AY, Ewing AD, Ellrott K, Hu Y, Houlahan KE, Bare JC, Espiritu SMG, Huang V, Dang K, Chong Z, Caloian C, Yamaguchi TN, Kellen MR, Chen K, et al. Combining accurate tumor genome simulation with crowdsourcing to benchmark somatic structural variant detection. Genome Biology. 19: 188. PMID 30400818 DOI: 10.1186/S13059-018-1539-5  0.516
2018 Bailey MH, Tokheim C, Porta-Pardo E, Sengupta S, Bertrand D, Weerasinghe A, Colaprico A, Wendl MC, Kim J, Reardon B, Kwok-Shing Ng P, Jeong KJ, Cao S, Wang Z, Gao J, ... ... Chen K, et al. Comprehensive Characterization of Cancer Driver Genes and Mutations. Cell. 174: 1034-1035. PMID 30096302 DOI: 10.1016/J.Cell.2018.07.034  0.428
2018 Chong Z, Chen K. Structural Variant Breakpoint Detection with novoBreak. Methods in Molecular Biology (Clifton, N.J.). 1833: 129-141. PMID 30039369 DOI: 10.1007/978-1-4939-8666-8_10  0.524
2018 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, et al. In vivo screening identifies GATAD2B as a metastasis driver in KRAS-driven lung cancer. Nature Communications. 9: 2732. PMID 30013058 DOI: 10.1038/S41467-018-04572-3  0.432
2018 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. Journal of the National Comprehensive Cancer Network : Jnccn. 16: 683-691. PMID 29891519 DOI: 10.6004/Jnccn.2018.7009  0.493
2018 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: e0196939. PMID 29738578 DOI: 10.1371/Journal.Pone.0196939  0.539
2018 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, et al. Targeted next generation sequencing of well-differentiated/dedifferentiated liposarcoma reveals novel gene amplifications and mutations. Oncotarget. 9: 19891-19899. PMID 29731991 DOI: 10.18632/Oncotarget.24924  0.537
2018 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 Treatment Reviews. 66: 95-103. PMID 29730462 DOI: 10.1016/J.Ctrv.2018.04.008  0.436
2018 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, ... ... Chen K, et al. The Immune Landscape of Cancer. Immunity. PMID 29628290 DOI: 10.1016/J.Immuni.2018.03.023  0.456
2018 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, ... ... Chen K, et al. Comprehensive Characterization of Cancer Driver Genes and Mutations. Cell. 173: 371-385.e18. PMID 29625053 DOI: 10.1016/J.Cell.2018.02.060  0.554
2018 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, ... ... Chen K, et al. Pathogenic Germline Variants in 10,389 Adult Cancers. Cell. 173: 355-370.e14. PMID 29625052 DOI: 10.1016/J.Cell.2018.03.039  0.501
2018 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, ... ... Chen K, et al. Systematic Analysis of Splice-Site-Creating Mutations in Cancer. Cell Reports. 23: 270-281.e3. PMID 29617666 DOI: 10.1016/J.Celrep.2018.03.052  0.514
2018 Gao Q, Liang WW, Foltz SM, Mutharasu G, Jayasinghe RG, Cao S, Liao WW, Reynolds SM, Wyczalkowski MA, Yao L, Yu L, Sun SQ, Chen K, et al. Driver Fusions and Their Implications in the Development and Treatment of Human Cancers. Cell Reports. 23: 227-238.e3. PMID 29617662 DOI: 10.1016/J.Celrep.2018.03.050  0.46
2018 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, ... ... Chen K, et al. Systematic Functional Annotation of Somatic Mutations in Cancer. Cancer Cell. 33: 450-462.e10. PMID 29533785 DOI: 10.1016/J.Ccell.2018.01.021  0.547
2018 Jayasinghe RG, Cao S, Gao Q, Wyczalkowski MA, Sengupta S, Walter MJ, Maher C, Wendl MC, Chen F, Eyras E, Lazar AJ, Chen K, Shmulevich I, Ding L. Abstract 2362: Comprehensive portrait of canonical and non-canonical splicing in cancer Cancer Research. 78: 2362-2362. DOI: 10.1158/1538-7445.Am2018-2362  0.544
2018 Zafar H, Navin N, Nakhleh L, Chen K. Computational approaches for inferring tumor evolution from single-cell genomic data Current Opinion in Systems Biology. 7: 16-25. DOI: 10.1016/J.Coisb.2017.11.008  0.526
2017 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, et al. 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. PMID 29178133 DOI: 10.1002/cncr.31152  0.428
2017 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, et al. A Population of Heterogeneous Breast Cancer Patient-Derived Xenografts Demonstrate Broad Activity of PARP Inhibitor in BRCA1/2 Wild-Type Tumors. Clinical Cancer Research : An Official Journal of the American Association For Cancer Research. 23: 6468-6477. PMID 29093017 DOI: 10.1158/1078-0432.Ccr-17-0615  0.504
2017 Zafar H, Tzen A, Navin N, Chen K, Nakhleh L. SiFit: inferring tumor trees from single-cell sequencing data under finite-sites models. Genome Biology. 18: 178. PMID 28927434 DOI: 10.1186/S13059-017-1311-2  0.446
2017 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: 57882-57888. PMID 28915719 DOI: 10.18632/Oncotarget.18357  0.492
2017 Morris VK, Rao X, Pickering CR, Foo WC, Rashid A, Eterovic AK, Kim TB, Chen K, Wang J, Shaw K, Eng C. Comprehensive Genomic Profiling of Metastatic Squamous Cell Carcinoma of the Anal Canal. Molecular Cancer Research : McR. PMID 28784613 DOI: 10.1158/1541-7786.Mcr-17-0060  0.51
2017 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, ... ... Chen K, et al. Sarcomatoid renal cell carcinoma has a distinct molecular pathogenesis, driver mutation profile and transcriptional landscape. Clinical Cancer Research : An Official Journal of the American Association For Cancer Research. PMID 28710314 DOI: 10.1158/1078-0432.Ccr-17-1057  0.491
2017 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 (Oxford, England). PMID 28582538 DOI: 10.1093/Bioinformatics/Btx362  0.371
2017 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 B, Wendl MC, et al. GenomeVIP: a cloud platform for genomic variant discovery and interpretation. Genome Research. PMID 28522612 DOI: 10.1101/Gr.211656.116  0.399
2017 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, et al. A feasibility study of returning clinically actionable somatic genomic alterations identified in a research laboratory. Oncotarget. PMID 28415679 DOI: 10.18632/Oncotarget.16018  0.326
2017 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, ... ... Chen K, et al. An Organismal CNV Mutator Phenotype Restricted to Early Human Development. Cell. 168: 830-842.e7. PMID 28235197 DOI: 10.1016/J.Cell.2017.01.037  0.464
2017 Ileana Dumbrava EE, Brusco L, Daniels MS, Wathoo C, Shaw KR, Lu KH, Zheng X, Strong LC, Litton JK, Arun B, Eterovic AK, Routbort M, Piha-Paul SA, Subbiah V, Hong DS, ... ... Chen K, et al. 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: 1524-1524. DOI: 10.1200/Jco.2017.35.15_Suppl.1524  0.466
2017 Ileana Dumbrava EE, Brusco L, Daniels MS, Wathoo C, Shaw KR, Lu KH, Zheng X, Strong LC, Litton JK, Arun B, Eterovic AK, Piha-Paul SA, Subbiah V, Hong DS, Woodman SE, ... ... Chen K, et al. Pathogenic variants in DNA damage response (DDR) genes in patients with advanced solid tumors. Journal of Clinical Oncology. 35: 11567-11567. DOI: 10.1200/Jco.2017.35.15_Suppl.11567  0.402
2017 Baez Vallecillo L, Chang JT, Chen K, Moss TJ, Shaw KR, Meric-Bernstam F, Eterovic AK, Mills GB, Mani S, Li X(, Gilcrease M, Moulder SL. Whole exome sequencing of metaplastic breast cancer (MpBC): Effect of mutation status on survival. Journal of Clinical Oncology. 35: 1090-1090. DOI: 10.1200/Jco.2017.35.15_Suppl.1090  0.456
2017 Albanell J, Gonzalez A, Gonzalez-Angulo AM, Eterovic AK, Duenas EM, Zheng X, Guerrero A, Liu S, Pérez-Carrión R, Chen K, Chacon JI, Mills GB, Novoa SA, Blancas I, Sanchez-Arago M, et al. Genomic alterations driving breast cancer (BC) metastases and their relationship with the subtype switch in the GEICAM ConvertHER study. Journal of Clinical Oncology. 35: 1017-1017. DOI: 10.1200/Jco.2017.35.15_Suppl.1017  0.489
2017 Evans K, Yuca E, Akcakanat A, Scott S, Arango NP, Zheng X, Chen K, Tapia C, Tarco E, Eterovic A, Black D, Jennifer L, Tripathy D, Mills G, Meric-Bernstam F. Abstract P4-06-04: Triple negative breast cancer patient-derived xenografts: Molecular characteristics and sensitivity to emerging therapies Cancer Research. 77. DOI: 10.1158/1538-7445.Sabcs16-P4-06-04  0.301
2017 Amin S, Awadalla P, Biankin A, Boutros P, Brazma A, Brooks AN, Calabrese C, Chang D, Chateigner A, Chen K, Chong Z, Craft B, Creighton C, Demircioğlu D, Fonseca N, et al. Abstract SY10-02: Pan-cancer study of recurrent and heterogeneous RNA aberrations and association with whole-genome variants Cancer Research. 77. DOI: 10.1158/1538-7445.Am2017-Sy10-02  0.366
2017 Lausted C, Zhou Y, Lee J, Vellano C, Eterovic KA, Song P, Tang L, Fawcett G, Kim T, Chen K, Geiss G, Meredith G, Mei Q, Demirkan G, Dunaway D, et al. Abstract 2441: NanoString 3D Biology™ technology: simultaneous digital counting of DNA, RNA and protein Cancer Research. 77: 2441-2441. DOI: 10.1158/1538-7445.Am2017-2441  0.347
2017 Zheng S, Wei W, Chen K, Alfaro-Munoz K, Eterovic AK, Shaw K, Mills G, Meric-Bernstam F, Verhaak R, Yung WKA, Weathers S, de Groot J. GENE-29. DEEP PANEL SEQUENCING OF A PROSPECTIVELY COLLECTED GLIOMA COHORT Neuro-Oncology. 19: vi98-vi99. DOI: 10.1093/Neuonc/Nox168.403  0.357
2016 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. Nature Methods. PMID 27892959 DOI: 10.1038/Nmeth.4084  0.462
2016 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, et al. Novel algorithmic approach predicts tumor mutation load and correlates with immunotherapy clinical outcomes using a defined gene mutation set. Bmc Medicine. 14: 168. PMID 27776519 DOI: 10.1186/S12916-016-0705-4  0.39
2016 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, et al. MET amplification in metastatic colorectal cancer: An acquired response to EGFR inhibition, not a de novo phenomenon. Oncotarget. PMID 27421137 DOI: 10.18632/Oncotarget.10559  0.366
2016 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, ... ... Chen K, et al. Transforming Big Data into cancer-relevant insight: An initial, multi-tier approach to assess reproducibility and relevance. Molecular Cancer Research : McR. PMID 27401613 DOI: 10.1158/1541-7786.Mcr-16-0090  0.417
2016 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: 394. PMID 27356755 DOI: 10.1186/s12864-016-2727-x  0.315
2016 Navin NE, Chen K. Genotyping tumor clones from single-cell data. Nature Methods. 13: 555-556. PMID 27355792 DOI: 10.1038/Nmeth.3903  0.445
2016 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, et al. Divergent viral presentation among human tumors and adjacent normal tissues. Scientific Reports. 6: 28294. PMID 27339696 DOI: 10.1038/Srep28294  0.365
2016 Zafar H, Wang Y, Nakhleh L, Navin N, Chen K. Monovar: single-nucleotide variant detection in single cells. Nature Methods. PMID 27088313 DOI: 10.1038/Nmeth.3835  0.485
2016 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, et al. The degree of intratumor mutational heterogeneity varies by primary tumor sub-site. Oncotarget. PMID 27034009 DOI: 10.18632/Oncotarget.8448  0.449
2016 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, ... ... Chen K, et al. Functional annotation of rare gene aberration drivers of pancreatic cancer. Nature Communications. 7: 10500. PMID 26806015 DOI: 10.1038/Ncomms10500  0.427
2016 Evans KW, Yuca E, Scott SM, Paez NA, Zheng X, Chen K, Gonzales L, Tapia C, Tarco E, Black DM, Mills GB, Meric-Bernstam F. Abstract A39: Patient-derived xenografts to test emerging therapies for triple negative breast cancer Clinical Cancer Research. 22. DOI: 10.1158/1557-3265.Pdx16-A39  0.429
2016 Popovic R, Daver N, Ruvolo V, Chen K, Wang Z, Huang X, Mabry M, Potluri J, McKeegan E, Konopleva M, Chyla BJ. Abstract CT069: Correlative biomarkers of clinical activity of the BCL-2 inhibitor, venetoclax (ABT-199/ GDC-0199), in acute myeloid leukemia patients Cancer Research. 76. DOI: 10.1158/1538-7445.Am2016-Ct069  0.35
2015 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 Research. PMID 26627007 DOI: 10.1158/0008-5472.Can-15-1654  0.478
2015 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 multilevel variant annotator for precision genomics. Nature Methods. 12: 1002-3. PMID 26513549 DOI: 10.1038/Nmeth.3622  0.42
2015 Sudmant PH, Rausch T, Gardner EJ, Handsaker RE, Abyzov A, Huddleston J, Zhang Y, Ye K, Jun G, Hsi-Yang Fritz M, Konkel MK, Malhotra A, Stütz AM, Shi X, Paolo Casale F, ... ... Chen K, et al. An integrated map of structural variation in 2,504 human genomes. Nature. 526: 75-81. PMID 26432246 DOI: 10.1038/Nature15394  0.397
2015 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. Erratum: Analysis of deletion breakpoints from 1,092 humans reveals details of mutation mechanisms. Nature Communications. 6: 8389. PMID 26346554 DOI: 10.1038/Ncomms9389  0.373
2015 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, et al. Ability to Generate Patient-Derived Breast Cancer Xenografts Is Enhanced in Chemoresistant Disease and Predicts Poor Patient Outcomes. Plos One. 10: e0136851. PMID 26325287 DOI: 10.1371/Journal.Pone.0136851  0.33
2015 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, ... ... Chen K, et al. Genome Modeling System: A Knowledge Management Platform for Genomics. Plos Computational Biology. 11: e1004274. PMID 26158448 DOI: 10.1371/Journal.Pcbi.1004274  0.594
2015 Chen K, Meric-Bernstam F. Whole Genome Sequencing in Cancer Clinics. Ebiomedicine. 2: 15-6. PMID 26137530 DOI: 10.1016/J.Ebiom.2014.12.007  0.413
2015 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. Nature Communications. 6: 7256. PMID 26028266 DOI: 10.1038/ncomms8256  0.305
2015 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 Medicine. 7: 34. PMID 25918555 DOI: 10.1186/S13073-015-0155-1  0.439
2015 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, et al. A decision support framework for genomically informed investigational cancer therapy. Journal of the National Cancer Institute. 107. PMID 25863335 DOI: 10.1093/Jnci/Djv098  0.445
2015 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 Medicine. 7: 6. PMID 25729435 DOI: 10.1186/S13073-015-0127-5  0.513
2015 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, et al. Clinical actionability enhanced through deep targeted sequencing of solid tumors. Clinical Chemistry. 61: 544-53. PMID 25626406 DOI: 10.1373/Clinchem.2014.231100  0.399
2015 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, et al. Functional consequence of the MET-T1010I polymorphism in breast cancer. Oncotarget. 6: 2604-14. PMID 25605252 DOI: 10.18632/Oncotarget.3094  0.339
2015 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, et al. RET fusion as a novel driver of medullary thyroid carcinoma. The Journal of Clinical Endocrinology and Metabolism. 100: 788-93. PMID 25546157 DOI: 10.1210/Jc.2014-4153  0.446
2015 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, et al. Gene mutations in primary tumors and corresponding patient-derived xenografts derived from non-small cell lung cancer. Cancer Letters. 357: 179-85. PMID 25444907 DOI: 10.1016/J.Canlet.2014.11.024  0.424
2015 You YN, Chang K, Chen K, Mehdizadeh A, Cuddy A, Lieu CH, Shaw KR, Vilar Sanchez E, Eng C. Somatic mutations in young-onset colorectal cancer unrelated to hereditary syndromes: A comparative study using high-depth targeted exome sequencing. Journal of Clinical Oncology. 33: 623-623. DOI: 10.1200/Jco.2015.33.3_Suppl.623  0.435
2015 Raghav KPS, Tang C, Morelli MP, Amin HM, Chen K, Manyam GC, Broom BM, Talasaz A, Overman MJ, Shaw KR, Meric-Bernstam F, Maru DM, Eng C, Hong DS, Kopetz S. Multiple independent methods fail to confirm MET amplification rate reported in literature for metastatic colorectal cancer (mCRC). Journal of Clinical Oncology. 33: 572-572. DOI: 10.1200/Jco.2015.33.3_Suppl.572  0.366
2015 Davies MA, Joon A, Bassett RL, Roszik J, Siroy A, Haydu LE, Chen K, Stingo F, Baladandayuthapani V, Shaw KR, Meric-Bernstam F, Tetzlaff MT, Gershenwald JE, Woodman SE, Lazar AJF. Demographics, tumor characteristics, and clinical outcomes associated with somatic mutations in 201 cancer-related genes in advanced melanoma patients (pts). Journal of Clinical Oncology. 33: 9057-9057. DOI: 10.1200/Jco.2015.33.15_Suppl.9057  0.435
2015 Meric-Bernstam F, Brusco L, Daniels MS, Strong LC, Shaw KR, Lu KH, Qi Y, Lara-Guerra H, Litton JK, Zhao H, Eterovic AK, Arun B, Routbort M, Janku F, Davies MA, ... ... Chen K, et al. Prevalence of incidental actionable germline mutations in 1,000 advanced cancer patients on a prospective somatic genomic profiling program. Journal of Clinical Oncology. 33: 1510-1510. DOI: 10.1200/Jco.2015.33.15_Suppl.1510  0.503
2015 Chen K, Meric-Bernstam F, Zhao H, Chen T, Shaw K, Mendelsohn J, Eterovic A, Mills G. Abstract PR13: Investigating the importance of low allele frequency mutations for cancer patient management Cancer Research. 75. DOI: 10.1158/1538-7445.Transcagen-Pr13  0.516
2015 Gonzalez-Angulo AM, Lluch A, Eterovic AK, Guerrero A, Zheng X, Perez R, Liu S, Chacón JI, Chen K, Antolin S, Mills GB, Ferrer J, Burgues O, Bermejo B, Munoz E, et al. Abstract PD3-6: ConvertHER: Evolution of genomic alterations from primary to metastatic breast cancer Cancer Research. 75. DOI: 10.1158/1538-7445.Sabcs14-Pd3-6  0.442
2015 Chen K, Meric-Bernstam F, Zhao H, Chen T, Shaw K, Mendelsohn J, Eterovic A, Mills G. Abstract PR05: Investigating the importance of low allele frequency mutations for cancer patient management Cancer Research. 75. DOI: 10.1158/1538-7445.Compsysbio-Pr05  0.513
2014 Fan X, Zhou W, Chong Z, Nakhleh L, Chen K. Towards accurate characterization of clonal heterogeneity based on structural variation. Bmc Bioinformatics. 15: 299. PMID 25201439 DOI: 10.1186/1471-2105-15-299  0.398
2014 Fan X, Abbott TE, Larson D, Chen K. BreakDancer - Identification of Genomic Structural Variation from Paired-End Read Mapping. Current Protocols in Bioinformatics / Editoral Board, Andreas D. Baxevanis ... [Et Al.]. 2014. PMID 25152801 DOI: 10.1002/0471250953.Bi1506S45  0.397
2014 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, et al. Clonal evolution in breast cancer revealed by single nucleus genome sequencing. Nature. 512: 155-60. PMID 25079324 DOI: 10.1038/Nature13600  0.471
2014 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. Discovery Medicine. 17: 101-14. PMID 24534473  0.358
2014 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 (Oxford, England). PMID 24389657 DOI: 10.1093/Bioinformatics/Btt771  0.391
2014 Chen K, Chen L, Fan X, Wallis J, Ding L, Weinstock G. TIGRA: a targeted iterative graph routing assembler for breakpoint assembly. Genome Research. 24: 310-7. PMID 24307552 DOI: 10.1101/Gr.162883.113  0.402
2014 Kopetz S, Overman MJ, Chen K, Lucio-Eterovic AK, Kee BK, Fogelman DR, Dasari A, Raghav KPS, Vilar Sanchez E, Phillips J, Shureiqi I, Garrett CR, Wolff RA, Patel K, Aldape KD, et al. Mutation and copy number discordance in primary versus metastatic colorectal cancer (mCRC). Journal of Clinical Oncology. 32: 3509-3509. DOI: 10.1200/Jco.2014.32.15_Suppl.3509  0.369
2014 Wang Y, Navin N, Waters J, Leung M, Unruh A, Shi X, Roh W, Chen K, Scheet P, Vattathil S, Liang H, Multani A, Zhang H, Meric-Bernstam F, Michor F, et al. Abstract LB-310: Single cell genome sequencing reveals clonal stability and diversity in breast cancer Cancer Research. 74. DOI: 10.1158/1538-7445.Am2014-Lb-310  0.489
2014 Eterovic K, Chen K, Zhao H, Meric-Bernstam F, Luthra R, Kenneth A, Routbort M, Kopetz S, Davies M, Groot Jd, Moulder S, Mao Y, Horombe C, Tang L, Ping S, et al. Abstract 4276: T200: a high depth targeted exome sequencing platform to identify actionable alterations in FFPE solid tumor samples Cancer Research. 74: 4276-4276. DOI: 10.1158/1538-7445.Am2014-4276  0.473
2014 Chen T, Zhao H, Mao Y, Qi Y, Eterovic AK, Shaw KRM, Moulder SL, Davies MA, Degroot JF, Kopetz SE, Meric-Bernstam F, Mills GB, Chen K. Abstract 4275: Identifying cancer driver mutations in clinical sequencing data Cancer Research. 74: 4275-4275. DOI: 10.1158/1538-7445.Am2014-4275  0.495
2014 McAuliffe PF, Akcakanat A, Evans K, Eterovic AK, Zhao H, Chen K, Sangai T, Chen H, Do K, Holder AM, Sharma C, Symmans WF, Gagea M, Naff KA, Sahin A, et al. Abstract 1186: Patient-derived breast cancer xenografts demonstrate molecular evolution in the phosphatidylinositol 3-kinase pathway upon engraftment Cancer Research. 74: 1186-1186. DOI: 10.1158/1538-7445.Am2014-1186  0.396
2013 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: e77945. PMID 24205039 DOI: 10.1371/Journal.Pone.0077945  0.519
2013 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 Biology. 14: R87. PMID 23972288 DOI: 10.1186/Gb-2013-14-8-R87  0.577
2013 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, et al. A survey of intragenic breakpoints in glioblastoma identifies a distinct subset associated with poor survival. Genes & Development. 27: 1462-72. PMID 23796897 DOI: 10.1101/Gad.213686.113  0.532
2013 Ley TJ, Miller C, Ding L, Raphael BJ, Mungall AJ, Robertson G, Hoadley K, Triche TJ, Laird PW, Baty JD, Fulton LL, Fulton R, Heath SE, Kalicki-Veizer J, Kandoth C, ... ... Chen K, et al. Genomic and epigenomic landscapes of adult de novo acute myeloid leukemia New England Journal of Medicine. 368: 2059-2074. PMID 23634996 DOI: 10.1056/Nejmoa1301689  0.384
2013 Mao Y, Chen H, Liang H, Meric-Bernstam F, Mills G, Chen K. Abstract 5148: CanDrA: Cancer-specific driver missense mutation annotation with optimized features. Cancer Research. 73: 5148-5148. DOI: 10.1158/1538-7445.Am2013-5148  0.525
2012 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, et al. Genomic landscape of non-small cell lung cancer in smokers and never-smokers. Cell. 150: 1121-34. PMID 22980976 DOI: 10.1016/J.Cell.2012.08.024  0.639
2012 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, et al. The origin and evolution of mutations in acute myeloid leukemia. Cell. 150: 264-78. PMID 22817890 DOI: 10.1016/J.Cell.2012.06.023  0.647
2012 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, ... ... Chen K, et al. Whole-genome analysis informs breast cancer response to aromatase inhibition. Nature. 486: 353-60. PMID 22722193 DOI: 10.1038/Nature11143  0.645
2012 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 (Oxford, England). 28: 1923-4. PMID 22563071 DOI: 10.1093/Bioinformatics/Bts272  0.577
2012 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, et al. Background mutations in parental cells account for most of the genetic heterogeneity of induced pluripotent stem cells. Cell Stem Cell. 10: 570-82. PMID 22542160 DOI: 10.1016/J.Stem.2012.03.002  0.582
2012 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, et al. Clonal architecture of secondary acute myeloid leukemia. The New England Journal of Medicine. 366: 1090-8. PMID 22417201 DOI: 10.1056/Nejmoa1106968  0.6
2012 Ding L, Ley TJ, Larson DE, Miller CA, Koboldt DC, Welch JS, Ritchey JK, Young MA, Lamprecht T, McLellan MD, McMichael JF, Wallis JW, Lu C, Shen D, Harris CC, ... ... Chen K, et al. Clonal evolution in relapsed acute myeloid leukaemia revealed by whole-genome sequencing. Nature. 481: 506-10. PMID 22237025 DOI: 10.1038/Nature10738  0.632
2012 Koboldt DC, Larson DE, Chen K, Ding L, Wilson RK. Massively parallel sequencing approaches for characterization of structural variation. Methods in Molecular Biology (Clifton, N.J.). 838: 369-84. PMID 22228022 DOI: 10.1007/978-1-61779-507-7_18  0.426
2012 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 (Oxford, England). 28: 311-7. PMID 22155872 DOI: 10.1093/Bioinformatics/Btr665  0.643
2012 Ellis MJ, Ding L, Shen D, Luo J, Suman VJ, Goiffon RJ, Wallis JW, Goldstein TC, Chen K, Allred DC, Leitch AM, Olson JA, Ota DM, Watson M, Piwnica-Worms D, et al. Whole genome sequencing to characterize luminal-type breast cancer. Journal of Clinical Oncology. 30: 503-503. DOI: 10.1200/Jco.2012.30.15_Suppl.503  0.654
2012 Ellis MJ, Li D, Shen D, Luo J, Suman VJ, Wallis JW, Tine BAV, Hoog J, Crowder RJ, Snider JE, Ballman K, Chen K, Koboldt DC, Schierding WS, McMichael JF, et al. Abstract LB-423: Whole genome comparisons of pre- and post- aromatase inhibitor treatment in estrogen receptor positive breast cancer Cancer Research. 72. DOI: 10.1158/1538-7445.Am2012-Lb-423  0.441
2012 Navin NE, Wang Y, Waters J, Chen K, Hall I, Malhotra A, Quinlan A. Abstract 5054: Inferring mutational chronology in breast cancer by deep-sequencing tumor subpopulations Cancer Research. 72: 5054-5054. DOI: 10.1158/1538-7445.Am2012-5054  0.491
2011 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, et al. CREST maps somatic structural variation in cancer genomes with base-pair resolution. Nature Methods. 8: 652-4. PMID 21666668 DOI: 10.1038/Nmeth.1628  0.599
2011 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, et al. Use of whole-genome sequencing to diagnose a cryptic fusion oncogene. Jama. 305: 1577-84. PMID 21505136 DOI: 10.1001/Jama.2011.497  0.62
2011 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, ... ... Chen K, et al. Identification of a novel TP53 cancer susceptibility mutation through whole-genome sequencing of a patient with therapy-related AML. Jama. 305: 1568-76. PMID 21505135 DOI: 10.1001/Jama.2011.473  0.671
2011 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, et al. Sequencing a mouse acute promyelocytic leukemia genome reveals genetic events relevant for disease progression. The Journal of Clinical Investigation. 121: 1445-55. PMID 21436584 DOI: 10.1172/Jci45284  0.633
2011 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, et al. Mapping copy number variation by population-scale genome sequencing. Nature. 470: 59-65. PMID 21293372 DOI: 10.1038/Nature09708  0.398
2011 Ellis MJ, Ding L, Shen D, Wallis J, Suman V, Luo J, Tao Y, Hoog J, Davies S, Lin L, Perou C, Tine BV, Bose R, Chang LW, Chen K, et al. Abstract LB-87: Analysis of luminal-type breast cancer by massively parallel sequencing Cancer Research. 71. DOI: 10.1158/1538-7445.Am2011-Lb-87  0.65
2010 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, et al. Genome remodelling in a basal-like breast cancer metastasis and xenograft. Nature. 464: 999-1005. PMID 20393555 DOI: 10.1038/Nature08989  0.629
2010 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 (Oxford, England). 26: 464-9. PMID 20031968 DOI: 10.1093/Bioinformatics/Btp708  0.576
2010 Mardis E, Ding L, Li S, Larson DE, Chen K, Wallis J, Hoog J, Deshryver K, Wilson R, Ellis MJ. Massive parallel sequencing of an African-American basal-like breast cancer: Comparison of primary tumor, metastasis, and xenograft. Journal of Clinical Oncology. 28: 10500-10500. DOI: 10.1200/Jco.2010.28.15_Suppl.10500  0.638
2010 Schuettpelz L, Link DC, Shen D, Walter MJ, Koboldt DC, Dooling DJ, Fulton RS, Schmidt H, Maupin R, O'Laughlin M, Chen K, McLellan MD, Kulkarni S, Ivanovich J, Lebeau M, et al. DNA Sequence of the Cancer Genome of a Patient with Therapy-Related Acute Myeloid Leukemia Blood. 116: 580-580. DOI: 10.1182/Blood.V116.21.580.580  0.649
2010 Walter MJ, Shen D, Ding L, Shao J, Witowski S, Chen K, Koboldt DC, Dooling DJ, Maupin R, Fulton RS, Schmidt H, O'Laughlin M, McLellan MD, Frater J, Westervelt P, et al. Detection of Novel Mutations In MDS/AML by Whole Genome Sequencing Blood. 116: 299-299. DOI: 10.1182/Blood.V116.21.299.299  0.614
2010 Welch JS, Ding L, Chen K, Larson DE, Kulkarni S, Payton JE, Wallis J, Veizer J, McLellan MD, Vickery TL, Reed JP, Koboldt DC, Klco J, DiPersio JF, Mardis ER, et al. Resolution of a Clinical Dilemma with Whole Genome Sequencing, and Discovery of a New Mechanism for Generating PML-Rara: Insertional Fusion Blood. 116: 2755-2755. DOI: 10.1182/Blood.V116.21.2755.2755  0.606
2010 Mardis E, Ding L, Shen D, Wallis J, Chen K, Watson M, Hoog J, Ellis M, Rk W. Abstract ES7-1: Next Generation Sequencing for the Clinician: A Breast Cancer Study Cancer Research. 70. DOI: 10.1158/0008-5472.Sabcs10-Es7-1  0.626
2009 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, et al. BreakDancer: an algorithm for high-resolution mapping of genomic structural variation. Nature Methods. 6: 677-81. PMID 19668202 DOI: 10.1038/Nmeth.1363  0.599
2009 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, et al. Recurring mutations found by sequencing an acute myeloid leukemia genome. The New England Journal of Medicine. 361: 1058-66. PMID 19657110 DOI: 10.1056/Nejmoa0903840  0.66
2009 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 (Oxford, England). 25: 2283-5. PMID 19542151 DOI: 10.1093/Bioinformatics/Btp373  0.592
2008 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, et al. DNA sequencing of a cytogenetically normal acute myeloid leukaemia genome. Nature. 456: 66-72. PMID 18987736 DOI: 10.1038/Nature07485  0.663
2008 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, ... ... Chen K, et al. Somatic mutations affect key pathways in lung adenocarcinoma. Nature. 455: 1069-75. PMID 18948947 DOI: 10.1038/Nature07423  0.623
2008 McLendon R, Friedman A, Bigner D, Van Meir EG, Brat DJ, Mastrogianakis GM, Olson JJ, Mikkelsen T, Lehman N, Aldape K, Yung WKA, Bogler O, Weinstein JN, VandenBerg S, Berger M, ... ... Chen K, et al. Comprehensive genomic characterization defines human glioblastoma genes and core pathways Nature. 455: 1061-1068. PMID 18772890 DOI: 10.1038/Nature07385  0.635
2007 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 Research. 17: 659-66. PMID 17416743 DOI: 10.1101/Gr.6151507  0.626
2007 Ley TJ, DiPersio J, Ding L, Ries R, Magrini V, Payton J, McGrath S, Walter M, Wylie T, Dunford-Shore B, Chen K, McLellan M, Wendl M, Dooling D, Cook L, et al. Sequencing an Acute Myeloid Leukemia (AML) Genome with “Next Generation” Technologies. Blood. 110: 205-205. DOI: 10.1182/Blood.V110.11.205.205  0.662
2006 Chen K, Hasegawa-Johnson M, Cohen A, Borys S, Kim SS, Cole J, Choi JY. Prosody dependent speech recognition on radio news corpus of American English Ieee Transactions On Audio, Speech and Language Processing. 14: 232-244. DOI: 10.1109/Tsa.2005.853208  0.564
2005 Hasegawa-Johnson M, Baker J, Borys S, Chen K, Coogan E, Greenberg S, Juneja A, Kirchhoff K, Livescu K, Mohan S, Muller J, Sonmez K, Wang T. LANDMARK-BASED SPEECH RECOGNITION: REPORT OF THE 2004 JOHNS HOPKINS SUMMER WORKSHOP. Proceedings of the ... Ieee International Conference On Acoustics, Speech, and Signal Processing / Sponsored by the Institute of Electrical and Electronics Engineers Signal Processing Society. Icassp (Conference). 1: 1213-1216. PMID 19212454 DOI: 10.1109/ICASSP.2005.1415088  0.527
2005 Hasegawa-Johnson M, Chen K, Cole J, Borys S, Kim SS, Cohen A, Zhang T, Choi JY, Kim H, Yoon T, Chavarria S. Simultaneous recognition of words and prosody in the Boston University Radio Speech Corpus Speech Communication. 46: 418-439. DOI: 10.1016/J.Specom.2005.01.009  0.572
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