Raunak Shrestha

Post-doctoral Research Scholar (Computational Biology)

University of California, San Francisco (UCSF)

I am a Computational Biology Post-doctoral Research Fellow with Dr. Felix Feng at the University of California, San Francisco (UCSF). My primary research location is the UCSF HDFC Cancer Center. Additionally, I hold Adjunct Research Scientist position at the Nepal Applied Mathematics & Informatics Institute for Research (NAAMII), where I am leading the Computational Genomics Laboratory.

My main interest lies in understanding cancer progression and treatment resistance through the development and application of computational genomics approaches. [My Curriculum Vitae]

I am actively looking for academic positions.

Interests

Bioinformatics
Cancer Genomics
Epigenomics
Single-cell Genomics
Immuno-Oncogenomics
Precision Oncology
Infectious Disease Genomics
Machine Learning
Data Science

Education

PhD in Bioinformatics, 2018

University of British Columbia, Canada
BTech in Biotechnology, 2009

Kathmandu University, Nepal

Selected Publications

More Publications

An Atlas of Accessible Chromatin in Advanced Prostate Cancer Reveals the Epigenetic Evolution during Tumor Progression

Integration of a large cohort of transcriptome, whole genome, and ATAC-sequencing characterizes the chromatin accessibility changes in advanced prostate cancer and identifies therapy-resistant prostate cancer subtype-specific transcription factors that modulate oncogenic programs.

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

An Atlas of Accessible Chromatin in Advanced Prostate Cancer Reveals the Epigenetic Evolution during Tumor Progression

Integrated analyses highlight interactions between the three-dimensional genome and DNA, RNA and epigenomic alterations in metastatic prostate cancer

We discovered a group of metastatic prostate cancer patients with lower levels of DNA-DNA interactions around the Androgen Receptor (AR) gene, the main driver of prostate cancer. Interestingly, this group had an abundance of circular DNA outside of the chromosomes (extrachromosomal circular DNA (ecDNA)) that included parts of the AR gene resulting in AR gene amplification and become very active, which might explain why their cancer was resistant to treatment.

Multiomics Characterization of Low-grade Serous Ovarian Carcinoma Identifies Potential Biomarkers of MEK-inhibitor Sensitivity and Therapeutic Vulnerability

LGSOC is a rare tumor subtype with high case fatality rates in patients with metastatic disease. Here, we use multiomics integration of whole-exome sequencing, RNA sequencing, and mass spectrometry–based proteomics on LGSOC cell lines to elucidate novel biomarkers and therapeutic vulnerabilities.

BAP1 Haploinsufficiency Predicts a Distinct Immunogenic Class of Malignant Peritoneal Mesothelioma

Malignant peritoneal mesothelioma (PeM) is a rare and fatal cancer originating from the abdominal lining. Our study revealed that BAP1 could serve as a prognostic and predictive biomarker for immunotherapy in PeM.

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

BAP1 Haploinsufficiency Predicts a Distinct Immunogenic Class of Malignant Peritoneal Mesothelioma

HIT'nDRIVE: Patient-Specific Multi-Driver Gene Prioritization for Precision Oncology

An algorithm to identify cancer driver genes in individual cancer patients by measuring the influence of gene alterations on perturbing transcriptional networks.

Raunak Shrestha, E Hodzic, T Sauerwald, P Dao, K Wang, J Yeung, S Anderson, F Vandin, G Haffari, CC Collins, SC Sahinalp

HIT'nDRIVE: Patient-Specific Multi-Driver Gene Prioritization for Precision Oncology

Recent Publications

PubMed | Google Scholar | dblp | All publications

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.

PDF Code Dataset DOI PubMed Journal

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.

PDF DOI PubMed Journal

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.

Code 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.

PDF DOI PubMed Journal

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.

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.

PDF DOI Journal PubMed

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.

PDF DOI Journal PubMed

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

See all publications

Computational Genomics Lab at NAAMII

At NAAMII-Nepal, we aim to transform global health through the application of computational genomics. Our areas of focus encompass infectious disease genomics and complex disease genomics (cancer, diabetes), with a particular emphasis on better understanding disease progression and treatment resistance.

Insulin Resistance in Diabetes

Investigating biomarkers of Type-2 diabetes and insulin resistance

HPV-mediated Cancers

Biomarkers of HPV-negative head and neck cancer

Predicting drug-resistant Tuberculosis

Using systems genomics to understand and better coltrol TB multi-drug resistance

Developing efficient dengue vaccine

Mining Dengue virus immunopeptidome for next-generation dengue vaccine

Genomic epidemiology to understand virus evolution

Understanding transmission patterns of SARS-CoV-2

Software & Data Analytics

Software

HIT’nDRIVE - Combinatorial optimization algorithm for cancer driver genes prioritization
cd-CAP - Combinatorial Detection of Conserved Alteration Patterns for Identifying Cancer Subnetworks
CONETT - Combinatorial optimization algorithm for identification of conserved evolutionary trajectories in tumors

Data Analytics