Chen WS, Moradi Tuchayi A, Sabbagh A, Kim I, Porter E, Ashraf-Ganjouei Amir, Li YR, Witztum A, Rajagopal A, Seyedin SN, Juarez R, Carroll PR, Feng FY, Small EJ, Hope TA, Hong JC. Utility of metastasis-directed radiotherapy with and without hormonal therapy in management of oligometastatic prostate cancer. JNCI Cancer Spectr. 9(6):pkaf096.

Sjöström M, Zhao SG, Levy S, Zhang M, Ning Y, Shrestha R, Lundberg A, Herberts C, Foye A, Aggarwal R, Hua JT, Li H, Bergamaschi A, Maurice-Dror C, Maheshwari A, Chen S, Ng SWS, Ye W, Petricca J, Fraser M, Chesner L, Perry MD, Moreno-Rodriguez T, Chen WS, Alumkal JJ, Chou J, Morgans AK, Beer TM, Thomas GV, Gleave M, Lloyd P, Phillips T, McCarthy E, Haffner MC, Zoubeidi A, Annala M, Reiter RE, Rettig MB, Witte ON, Fong L, Bose R, Huang FW, Luo J, Bjartell A, Lang JM, Mahajan NP, Lara PN, Evans CP, Tran PT, Posadas EM, He C, Cui XL, Huang J, Zwart W, Gilbert LA, Maher CA, Boutros PC, Chi KN, Ashworth A, Small EJ, He HH, Wyatt AW, Quigley DA, Feng FY. The 5-Hydroxymethylcytosine Landscape of Prostate Cancer. Cancer Research, 82(21):3888-3902, 2022.

Rydzewski NR, Peterson E, Lang JM, Yu M, Laura Chang S, Sjöström M, Bakhtiar H, Song G, Helzer KT, Bootsma ML, Chen WS, Shrestha RM, Zhang M, Quigley DA, Aggarwal R, Small EJ, Wahl DR, Feng FY, Zhao SG. Predicting cancer drug TARGETS - TreAtment Response Generalized Elastic-neT Signatures. npj Genomic Medicine, 6(1):76, 2021.

Das R, Sjöström M, Shrestha R, Yogodzinski C, Egusa EA, Chesner LN, Chen WS, Chou J, Dang DK, Swinderman JT, Ge A, Hua JT, Kabir S, Quigley DA, Small EJ, Ashworth A, Feng FY, Gilbert LA. An integrated functional and clinical genomics approach reveals genes driving aggressive metastatic prostate cancer. Nature Communications, 12(1):4601, 2021.

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, 591:124–130, 2021.

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, 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, 2020.

Mahal BA, Alshalalfa M, Zhao SG, Beltran H, Chen WS, Chipidza F, Davicioni E, Karnes RJ, Ku SY, Lotan TL, Muralidhar V, Rebbeck TR, Schaeffer EM, Spratt DE, Feng FY, Nguyen PL. Genomic and clinical characterization of stromal infiltration markers in prostate cancer. Cancer, 126(7):1407-1412, 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.

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.