Publications | Raunak Shrestha

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, admni, X Zhu, A Foye, H Li, LM Kim, M Bhalla, T O’loughlin, 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

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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RK Shrestha, Raunak Shrestha, S Shneiderman, J Baniya (2023). Beyond Reconstruction: What Leads to Satisfaction in Post-Disaster Recovery?. Journal of Happiness Studies.

Code Project DOI Journal

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.

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WS Chen, WA Haynes, R Waitz, K Kamath, A Vega-Crespo, Raunak Shrestha, M Zhang, 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).

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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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RK Shrestha, Raunak Shrestha (2020). Group segmentation and heterogeneity in the choice of cooking fuels in post-earthquake Nepal. (in submission).

Code Dataset Project Preprint

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.

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MA Reyna, D Haan, M Paczkowska, LPC Verbeke, M Vazquez, A Kahraman, S Pulido-Tamayo, J Barenboim, L Wadi, P Dhingra, Raunak Shrestha, G Getz, MS Lawrence, JS Pedersen, MA Rubin, DA Wheeler, S Brunak, JMG Izarzugaza, E Khurana, K Marchal, C von Mering, SC Sahinalp, A Valencia, J Reimand, JM Stuart, BJ Raphael, PCAWG Consortium (2020). Pathway and network analysis of more than 2,500 whole cancer genomes. Nature Communications.

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

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Raunak Shrestha, N Nabavi, Y Lin, F Mo, S Anderson, S Volik, H H Adomat, D Lin, H Xue, X Dong, R Shukin, RH Bell, B McConeghy, A Haegert, S Brahmbhatt, E Li, HZ Oo, A Hurtado-Coll, L Fazli, J Zhou, Y McConnell, A McCart, A Lowy, GB Morin, T Chen, M Daugaard, SC Sahinalp, F Hach, S Le Bihan, ME Gleave, Y Wang, A Churg, CC Collins (2019). BAP1 Haploinsufficiency Predicts a Distinct Immunogenic Class of Malignant Peritoneal Mesothelioma. Genome Medicine.

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E Hodzic, Raunak Shrestha, K Zhu, K Cheng, CC Collins, SC Sahinalp (2019). Combinatorial Detection of Conserved Alteration Patterns for Identifying Cancer Subnetworks. GigaScience.

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Raunak Shrestha (2018). Computational prioritization of cancer driver genes for precision oncology. University of British Columbia (PhD Thesis).

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EE Gill, LS Chan, GL Winsor, N Dobson, R Lo, SJH Sui, BK Dhillon, PK Taylor, Raunak Shrestha, CoSpencer, REW Hancock, PJ Unrau, FSL Brinkman (2018). High-throughput detection of RNA processing in bacteria. BMC Genomics.

DOI Journal PubMed

H Sharifi-Noghabi, Y Liu, N Erho, Raunak Shrestha, M Alshalalfa, E Davicioni, CC Collins, M Ester (2018). Deep Genomic Signature for early metastasis prediction in Prostate Cancer. (in submission).

DOI Preprint

M Yamada, J Tang, J Lugo-Martinez, E Hodzic, Raunak Shrestha, A Saha, H Ouyang, D Yin, H Mamitsuka, SC Sahinalp, P Radivojac, F Menczer, Y Chang (2018). Ultra High-Dimensional Nonlinear Feature Selection for Big Biological Data. IEEE Transactions on Knowledge and Data Engineering.

DOI Journal

Raunak Shrestha, E Hodzic, T Sauerwald, P Dao, K Wang, J Yeung, S Anderson, F Vandin, G Haffari, CC Collins, SC Sahinalp (2017). HIT'nDRIVE: Patient-Specific Multi-Driver Gene Prioritization for Precision Oncology. Genome Research.

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ISU Luk, Raunak Shrestha, H Xue, Y Wang, F Zhang, D Lin, A Haegert, R Wu, X Dong, CC Collins, A Zoubeidi, ME Gleave, PW Gout, Y Wang (2016). BIRC6-targeting as potential therapy for advanced, enzalutamide-resistant prostate cancer. Clinical Cancer Research.

DOI Journal PubMed

AW Wyatt, F Mo, K Wang, B McConeghy, S Brahmbhatt, L Jong, DM Mitchell, RL Johnston, A Haegert, E Li, J Liew, J Yeung, Raunak Shrestha, A Lapuk, A McPherson, R Shukin, RH Bell, S Anderson, J Bishop, A Hurtado-Coll, H Xiao, AM Chinnaiyan, R Mehra, D Lin, Y Wang, L Fazli, ME Gleave, S Volik, CC Collins (2014). Heterogeneity in the inter-tumor transcriptome of high risk prostate cancer. Genome Biology.

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K Wang, Raunak Shrestha, AW Wyatt, A Reddy, J Lehar, Y Wang, A Lapuk, CC Collins (2014). A Meta-Analysis Approach for Characterizing Pan-Cancer Mechanisms of Drug Sensitivity in Cell Lines. PLoS ONE.

DOI Journal PubMed

Raunak Shrestha, E Hodzic, J Yeung, K Wang, T Sauerwald, P Dao, S Anderson, H Beltran, MA Rubin, CC Collins, G Haffari, SC Sahinalp (2014). HIT'nDRIVE: Multi-driver gene prioritization based on hitting time. RECOMB-2014.

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Raunak Shrestha, RN Joshi, K Joshi, BH Poudel, BG Shrestha (2011). Analysis of KatG Ser315Thr Mutation in Multidrug Resistant Mycobacterium tuberculosis and SLC11A1 Polymorphism in Multidrug Resistance Tuberculosis in Central Development Region of Nepal Using PCR-RFLP Technique: A Pilot Study. Nepal Journal of Biotechnology.

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