Our Team

• (2020) David and Harriet Seligson Thesis Prize for outstanding thesis in the area of laboratory medicine
• (2019) Best Scientific Paper Award of all manuscripts published in European Urology
• (2017) AACR Scholar-in-Training Award
• (2016) International Conference on Machine Learning Computational Biology Workshop Spotlight Presentation
• (2016) NIH National Institute of Diabetes and Digestive and Kidney Diseases Research Award
• (2014) Tau Beta Pi Engineering Honor Society Inductee
• (2012) President’s Award for Academic Excellence
• (2011) National Merit Scholar

• Combes AJ*, Courau T*, Kuhn NF*, Hu KH*, Ray A*, Chen WS, Cleary SJ, Chew NW, Kushnoor D, Reeder GC, Shen A, Tsui J, Hiam-Galvez J, Munoz-Sandoval P, Zhu WS, Lee DS, Sun Y, You R, Magnen M, Rodriguez L, Leligdowicz A, Zamecnik CR, Loudermilk RP, Wilson MR, Ye CJ, Fragiadakis GK, Looney MR, Chan V, Ward A, Carrillo S, The UCSF COMET Consortium, Matthay M, Erle DJ, Woodruff PG, Langelier C, Kangelaris K, Hendrickson CM, Calfee C, Rao AA, Krummel MF. Global Absence and Targeting of Protective Immune States in Severe COVID-19. Nature, 591(7848):124-130, 2021.*These authors contributed equally”
• Chen WS*, Haynes WA*, Waitz R*, Kamath K, Vega-Crespo A, Shrestha R, Zhang M, Foye A, Baselga Carretero I, Garcilazo Perez I, Zhang M, Zhao SG, Sjöström M, Quigley DA, Chou J, Beer TM, Rettig M, Gleave M, Evans CP, Lara P, Chi KN, Reiter RE, Alumkal JJ, Aggarwal R, Small EJ, Daugherty PS, Ribas A, Oh DY, Shon JC, Feng FY. Autoantibody landscape of advanced prostate cancer. Clinical Cancer Research, 26(23):6204-6214, 2020.
• Guan X, Sun D, Lu E, Urrutia JA, Reiter RE, Rettig M, Evans CP, Lara P, Gleave M, Beer TM, Thomas GV, Huang J, Aggarwal RR, Quigley DA, Foye A, Chen WS, Youngren J, Weinstein AS, Stuart JM, Feng FY, Small EJ, Xia Z, Alumkal JJ. Copy Number Loss of 17q22 is Associated with Enzalutamide Resistance and Poor Prognosis in Metastatic Castration-Resistant Prostate Cancer. Clinical Cancer Research, 26(17):4616-4624, 2020.
• Kwon DH, Zhang L, Quigley DA, Foye A, Chen WS, …, Small EJ, Aggarwal RR. Downregulation of ADRB2 Expression is Associated with Small Cell Neuroendocrine Prostate Cancer and Adverse Clinical Outcomes in Castration-Resistant Prostate Cancer. Urol Oncol, 38(12):931.e9-931.e16, 2020.
• Zhao SG*, Chen WS*, Li H*, Foye A, Zhang M, Sjostrom M, Aggarwal R, Playdle D, …, Chinnaiyan AM, Maher CA, Small EJ, Quigley DA, Feng FY. The DNA methylation landscape of advanced prostate cancer. Nature Genetics, 52(8):778-789, 2020.
• Chen WS*, Zivanovic N*, van Dijk D, Wolf G, Bodenmiller B, Krishnaswamy S. Uncovering axes of variation among single-cell cancer specimens. Nature Methods, 17(3):302-310, 2020.
• Moon KR*, van Dijk D*, Wang Z*, Gigante S*, Burkhardt DB, Chen WS, Yim K, van den Elzen A, Hirn MJ, Coifman RR, Ivanova NB, Wolf G, Krishnaswamy S. Visualizing Structure and Transitions for Biological Data Exploration. Nature Biotechnology, 37(12):1482-1492, 2019.
• Amodio M*, van Dijk D*, Srinivasan K, Chen WS, Mohsen H, Moon KR, Campbell A, Zhao Y, Wang X, Venkataswamy M, Desai A, Ravi V, Kumar P, Montgomery R, Wolf G, Krishnaswamy S. Exploring Single-Cell Data with Deep Multitasking Neural Networks. Nature Methods, 16(11):1139-1145, 2019.
• Chen WS*, Feng E*, Aggarwal R, Foye A, Beer TM, Alumkal JJ, Gleave M, Chi KN, Reiter RE, Rettig MB, Evans CP, Small EJ, Sharifi N, Zhao SG. Germline polymorphisms associated with impaired survival outcomes and somatic tumor alterations in advanced prostate cancer. Prostate Cancer and Prostatic Diseases, 23(2):316-323, 2019.
• Alshalalfa M, Nguyen PL, Beltran H, Chen WS, Davicioni E, Zhao SG, Rebbeck TR, Schaeffer EM, Lotan TL, Feng FY, Mahal BA. Transcriptomic and Clinical Characterization of Neuropeptide Y Expression in Localized and Metastatic Prostate Cancer: Identification of Novel Prostate Cancer Subtype with Clinical Implications. European Urology Oncology, 2(4):405-412, 2019.
• Chen WS, Aggarwal R, Zhang L, Zhao SG, Thomas GV, Beer TM, Quigley DA, Foye A, Playdle D, Huang J, Lloyd P, Lu E, Sun D, Guan X, Rettig M, Gleave M, Evans CP, Youngren J, True L, Lara P, Kothari V, Xia Z, Chi KN, Reiter RE, Maher CA, Feng FY, Small EJ, Alumkal JJ, on behalf of the West Coast Prostate Cancer Dream Team. Genomic drivers of poor prognosis and enzalutamide resistance in metastatic castration-resistant prostate cancer. European Urology, 76(5):562-571, 2019.
• Chen WS*, Alshalalfa M*, Zhao SG, Liu Y, Mahal BA, Quigley DA, Wei T, Davicioni E, Rebbeck TR, Kantoff PW, Maher CA, Knudsen KE, Small EJ, Nguyen PL, Feng FY. Novel RB1-loss transcriptomic signature is associated with poor clinical outcomes across cancer types. Clinical Cancer Research, 25(14):4290-4299, 2019.
• Zhao SG*, Chen WS*, Das R, Chang SL, Tomlins SA, Chou J, Quigley DA, Dang HX, Barnard TJ, Mahal BA, Gibb EA, Liu Y, Davicioni E, Duska LR, Posadas EM, Jolly S, Spratt DE, Nguyen PL, Maher CA, Small EJ, Feng FY. Clinical and Genomic Implications of Luminal and Basal Subtypes Across Carcinomas. Clinical Cancer Research, 25(8):2450-2457, 2019.
• Chen WS, Bindra RS, Mo A, Hayman T, Husain Z, Contessa JN, Gaffney SG, Townsend JP, Yu JB. CDKN2A copy number loss indicates poor prognosis in HPV- head and neck cancer. Front Oncol., 8:95, 2018.
• Chen WS, Townsend JP, Yu JB. Radiation-specific clinical data should be included in existing large-scale genomic datasets. International Journal of Radiation Oncology • Biology • Physics, 98(1):8-10, 2017.
• Low YS, Daugherty AC, Schroeder EA, Chen W, Seto T, Weber S, Lim M, Hastie T, Mathur M, Desai M, Farrington C, Radin AA, Sirota M, Kenkare P, Thompson CA, Yu PP, Gomez SL, Sledge GW, Jr., Kurian AW, Shah NH. Synergistic drug combinations from electronic health records & gene expression. Journal of the American Medical Informatics Association, 24(3):565-576, 2017.
• Burt BM, Leung AN, Yanagawa M, Chen W, Hoang CD, Nair VS, Shrager JB. Diameter of solid tumor component alone should be used to establish T-stage in lung adenocarcinoma. Annals of Surgical Oncology, 22(Suppl 3):S1318-23, 2015.
• Jung K, LePendu P, Chen WS, Iyer SV, Readhead B, Dudley JT, Shah NH. Automated detection of off-label drug use. PLoS ONE, 9(2):e89324, 2014.
• Zhao SG, Chen WS, Alshalalfa M, Liu Y, Schaeffer EM, Davicioni E, Knudsen K, Small EJ, Feng FY, Nguyen PL. Novel transcriptomic signature for predicting functional RB1-loss with clinical implications in localized and metastatic castration-resistant prostate cancer. Prostate Cancer Foundation 25th Annual Scientific Retreat, 2018.
• Chen WS, Lam AE, Glover J, Yu JB. Role of radiotherapy in the optimal management of urethral carcinoma. Int J Radiat Oncol Biol Phys. 99(2 Suppl):abstr 2526, 2017.
• Chen WS, Bindra R, Mo A, Hayman T, Husain Z, Contessa JN, Gaffney SG, Townsend JP, Yu JB. CDKN2A copy number loss in HPV- and HPV+ head and neck cancer to indicate poor prognosis: An integrated genomic and clinical TCGA analysis. J Clin Oncol, 35(15 suppl):abstr 6060, 2017.
• Chen WS, Zivanovic N, Pe’er D, Bodenmiller B, Krishnaswamy S. Phenotypic analysis of single-cell breast cancer inhibition data reveals insights into EMT. Cancer Res. 77(13 Suppl):abstr 977, 2017.
• Burt B, Leung A, Yanagawa M, Chen W, Hoang C, Nair V, Shrager J. Diameter of solid tumor component alone should be used to establish T-stage in lung adenocarcinoma. Proceedings of the Society of Thoracic Surgeons 51st Annual Meeting, 2015.

Oral Presentations:

• Chen WS, Mahal BA, Alshalalfa M, Zhao SG, Beltran H, Davicioni E, Karnes RJ, Ku S, Lotan T, Rebbeck TR, Schaeffer EM, Feng FY, Nguyen PL. Associations of stromal infiltration with prognosis and response to postoperative radiotherapy in prostate cancer. ASTRO 61st Annual Meeting, Chicago, IL, Sep 2019.
• Chen WS, Aggarwal R, Zhang L, Zhao SG, Thomas GV, Beer TM, Quigley DA, Foye A, Playdle D, Huang J, Lloyd P, Lu E, Sun D, Guan X, Rettig M, Gleave M, Evans CP, Youngren J, True L, Lara P, Kothari V, Xia Z, Chi KN, Reiter RE, Maher CA, Feng FY, Small EJ, Alumkal JJ, on behalf of the West Coast Prostate Cancer Dream Team. Genomic drivers of poor prognosis and enzalutamide resistance in metastatic castration-resistant prostate cancer. ASCO Genitourinary Cancers Symposium Annual Meeting, San Francisco, CA, Feb 2019.
• Chen WS, Bindra RS, Mo A, Hayman T, Husain Z, Contessa JN, Yu JB. Investigating CDKN2A copy number loss in HPV- and HPV+ head and neck cancer: Integrated genomic and clinical analyses using TCGA. American Radium Society (ARS) 99th Annual Meeting, Colorado Springs, CO, May 2017.
• Chen WS, Zivanovic N, Pe’er D, Bodenmiller B, Krishnaswamy S. Phenotypic analysis of single-cell breast cancer inhibition data reveals insights into EMT. AACR Annual Meeting, Washington, DC, Apr 2017.
• Chen WS, Zivanovic N, Pe’er D, Bodenmiller B, Krishnaswamy S. Using Earth Mover’s Distance to compare the effects of drug inhibitions on EMT in single-cell breast cancer data. “Spotlight Presentation.” 33rd International Conference on Machine Learning (ICML) Computational Biology Workshop, New York, NY, Jun 2016.

Poster presentations:

• Chen WS, Lometti M, Wustrack R, Zimel M, O’Donnell RA, Horvai A, Cho S, Okimoto R, Jahan T, Gottschalk A, Braunstein SE. Intraoperative Radiotherapy Without External Beam Radiotherapy in the Management of Primary Soft Tissue Sarcomas of the Extremities. ASTRO 62nd Annual Meeting, Miami Convention Center (virtual), FL, Oct 2020.
• Moon KR, van Dijk D, Wang Z, Burkhardt D, Chen WS, Hirn MJ, Coifman RR, Ivanova NB, Wolf G, Krishnaswamy S. Visualization Beyond tSNE: PHATE for Visualizing and Analyzing Transition Structures in High-Dimensional Biological Data. Single Cell Genomics Annual Conference, Rehovot, Israel, Oct 2017.
• Chen WS, Lam AE, Glover J, Yu JB. Role of radiotherapy in the optimal management of urethral carcinoma. ASTRO 59th Annual Meeting, San Diego, CA, Sep 2017.
• Chen WS, Bindra R, Mo A, Hayman T, Husain Z, Contessa JN, Gaffney SG, Townsend JP, Yu JB. CDKN2A copy number loss in HPV- and HPV+ head and neck cancer to indicate poor prognosis: An integrated genomic and clinical TCGA analysis. ASCO Annual Meeting, Chicago, IL, Jun 2017.
• Ragavan M, Svec D, Bacaj T, Bezabeh I, Chen W, Irmak S, Shieh L. Barriers to timely discharge from the general medicine ward at an academic tertiary care center. American College of Physicians (ACP) Northern CA Conference. Oct 2014.