Publications

PubMed | Google Scholar | Computer Science Bibliography (dblp)

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

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

PDF Dataset DOI PubMed Journal

Raunak Shrestha, M Llaurado-Fernandez, A Dawson, J Hoenisch, S Volik, Y Lin, S Anderson, H Kim, A Haegert, S Colborne, N Wong, B McConeghy, RH Bell, S Brahmbhatt, C Lee, GE DiMattia, S Le Bihan, GB Morin, CC Collins, MS Carey (2021). Multiomics Characterization of Low-grade Serous Ovarian Carcinoma Identifies Potential Biomarkers of MEK-inhibitor Sensitivity and Therapeutic Vulnerability. Cancer Research.

PDF Dataset DOI Journal PubMed Dataset2

WS Chen, WA Haynes, R Waitz, K Kamath, A Vega-Crespo, Raunak Shrestha, A Foye, IB Carretero, IG Perez, M Zhang, SG Zhao, M Sjostrom, DA Quigley, J Chou, TM Beer, M Rettig, M Gleave, CP Evans, P Lara, KN Chi, RE Reiter, JJ Alumkal, R Aggarwal, EJ Small, PS Daugherty, A Ribas, DY Oh, JC Shon, FY Feng (2020). Autoantibody landscape in patients with advanced prostate cancer. Clinical Cancer Research.

DOI Journal PubMed

E Hodzic, Raunak Shrestha, S Malikic, CC Collins, K Litchfield, S Turajlic, SC Sahinalp (2020). Identification of Conserved Evolutionary Trajectories in Tumors. Bioinformatics (ISMB 2020).

PDF Code DOI Journal PubMed

Raunak Shrestha, N Nabavi, S Volik, S Anderson, A Haegert, B McConeghy, F Sar, S Brahmbhatt, RH Bell, S Le Bihan, Y Wang, CC Collins, A Churg (2020). Well-Differentiated Papillary Mesothelioma of the Peritoneum is Genetically Distinct from Malignant Mesothelioma. Cancers.

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NM D’Costa, MR Lowerison, PA Raven, Z Tan, ME Roberts, Raunak Shrestha, MW Urban, CU Monjaras-Avila, HZ Oo, A Hurtado-Coll, C Chavez-Munoz, AI So (2020). Y-box Binding Protein-1 is Crucial in Acquired Drug Resistance Development in Metastatic Clear-Cell Renal Cell Carcinoma. Journal of Experimental & Clinical Cancer Research.

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NM D'Costa, D Cina, Raunak Shrestha, RH Bell, YLin, H Asghari, CU Monjaras-Avila, C Kollmannsberger, F Hach, CI Chavez-Munoz, AI So (2020). Identification of Predictive Gene Signature to Guide Precision Oncology of Clear-Cell Renal Cell Carcinoma. Scientific Reports.

PDF DOI Journal PubMed

PCAWG Consortium (2020). Pan-cancer Analysis of Whole Genomes. Nature.

PDF Code Dataset DOI Journal PubMed