Publications

PubMed | Google Scholar | Computer Science Bibliography (dblp)

H Li, JE Melnyk, BXH Fu, Raunak Shrestha, M Zhang, M Sjostrom, S Feng, JA Anderson, W Han, LN Chesner, HJ Shin, T Farsh, HJ Suarez, S Nath, J Chou, R Das, EA Egusa, M Calvert, A Kishishita, A Barpanda, J Zhu, A Maheshwari, WS Chen, M Alshalalfa, A Winters, JT Hua, T Liu, E Davicioni, AP Witta, BA Stohr, J Siddiqui, B Huang, EJ Small, KM Shokat, P Nelson, DA Quigley, EV Wasmuth, LA Gilbert, FY Feng (2025). Genome-scale CRISPR screens identify PTGES3 as a direct modulator of androgen receptor function in advanced prostate cancer. Nature Genetics.

DOI PubMed Journal

C Ye, Y Ma, Raunak Shrestha, J Cai, Y Liu, L Peng, J Yu, H Cai (2025). Extracellular vesicles-mediated delivery of CRISPR machinery silences androgen receptor in castration-resistant prostate cancer cells. Molecular Therapy.

DOI PubMed Journal

LN Chesner, F Polesso, JN Graff, JE Hawley, AK Smith, A Lundberg, R Das, T Shenoy, M Sjostrom, F Zhao, Y Hu, S Linder, WS Chen, ReM Hawkins, Raunak Shrestha, X Zhu, A Foye, H Li, LM Kim, M Bhalla, T Oloughlin, D Kuzuoglu-Ozturk, J T Hua, ML Badura, S Wilkinson, SY Trostel, AM Bergman, D Ruggero, CG Drake, AG Sowalsky, L Fong, MR Cooperberg, W Zwart, X Guan, A Ashworth, Z Xia, DA Quigley, LA Gilbert, FY Feng, AE Moran (2024). Androgen receptor inhibition increases MHC Class I expression and improves immune response in prostate cancer. Cancer Discovery.

DOI PubMed Journal

X Zhu, T Farsh, D Vis, I Yu, H Li, T Liu, M Sjostrom, Raunak Shrestha, J Kneppers, T Severson, MmZhang, A Lundberg, TM Rodriguez, AS Weinstein, A Foye, N Mehra, RR Aggarwal, AM Bergman, EJ Small, NA Lack, W Zwart, DA Quigley, MS Heijden, FY Feng (2024). Genomic and transcriptomic features of androgen receptor signaling inhibitor resistance in metastatic castration-resistant prostate cancer. The Journal of Clinical Investigation.

DOI PubMed Journal

Raunak Shrestha, LN Chesner, M Zhang, S Zhou, A Foye, A Lundberg, AS Weinstein, M Sjostrom, X Zhu, T Moreno-Rodriguez, H Li, JJ Alumkal, R Aggarwal, EJ Small, M Lupien, DA Quigley, FY Feng (2024). An Atlas of Accessible Chromatin in Advanced Prostate Cancer Reveals the Epigenetic Evolution during Tumor Progression. Cancer Research.

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S Zhao, M Bootsma, S Zhou, Raunak Shrestha, T Moreno-Rodriguez, A Lundberg, C Pan, C Arlidge, J Hawley, A Foye, A Weinstein, M Sjostrom, M Zhang, H Li, LN Chesner, N Rydzewski, K Helzer, Y Shi, S Dehm, J Lang, J Alumkal, H He, A Wyatt, R Aggarwal, W Zwart, E Small, D Quigley, M Lupien, FY Feng (2024). Integrated analyses highlight interactions between the three-dimensional genome and DNA, RNA and epigenomic alterations in metastatic prostate cancer. Nature Genetics.

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M Zhang, M Sjostrom, X Cui, A Foye, K Farh, Raunak Shrestha, A Lundberg, HX Dang, PG Febbo, R Aggarwal, J Alkumal, EJ Small, CA Maher, FY Feng, DA Quigley (2024). Integrative analysis of ultra-deep RNA-seq reveals alternative promoter usage as a mechanism of activating oncogenic programmes during prostate cancer progression. Nature Cell Biology.

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A Lundberg, M Zhang, R Aggarwal, H Li, L Zhang, A Foye, M Sjostrom, J Chou, K Chang, T Moreno-Rodriguez, Raunak Shrestha, A Baskin, X Zhu, AS Weinstein, N Younger, JJ Alumkal, TM Beer, KN Chi, CP Evans, M Gleave, PN Lara, RE Reiter, MB Rettig, ON Witte, AW Wyatt, FY Feng, EJ Small, DA Quigley (2023). The genomic and epigenomic landscape of double-negative metastatic prostate cancer. Cancer Research.

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

DOI PubMed Journal

N Rydzewski, JM Lang, M Yu, M Sjostrom, SL Chang, W Chen, Raunak Shrestha, M Zhang, DA Quigley, R Aggarwal, E Small, DR Wahl, FY Feng, SG Zhao (2021). Predicting Cancer Drug TARGETS - TreAtment Response GlmnET Signatures. NPJ genomic medicine.

DOI PubMed