Raunak Shrestha, PhD
Assistant Researcher
Radiation Oncology
School of Medicine

Awards

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• Prostate Cancer Foundation Young Investigator Award, Prostate Cancer Foundation, 2022-2025

Education & Training

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• PhD Bioinformatics University of British Columbia 2018
• B.Tech. Biotechnology Kathmandu University 2009

Interests

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• Cancer Genomics
• Data Science
• Bioinformatics
• single-cell genomics
• Computational Biology
• Prostate Cancer

Websites

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• Posts on X raunakms (X.com)
• http://raunakms.github.io/ (raunakms.github.io)

Publications (26)

Top publication keywords:
Ubiquitin Thiolesterase5-MethylcytosineDNA Mutational AnalysisGenomicsDrug Resistance, NeoplasmProstatic Neoplasms, Castration-ResistantPeritoneal NeoplasmsHaploinsufficiencyMitogen-Activated Protein Kinase KinasesMesotheliomaChromatinCystadenocarcinoma, SerousReceptors, AndrogenEpigenesis, GeneticBiomarkers, Pharmacological

• Androgen receptor inhibition increases MHC Class I expression and improves immune response in prostate cancer.
  Cancer discovery 2024 Chesner LN, Polesso F, Graff JN, Hawley JE, Smith AK, Lundberg A, Das R, Shenoy T, Sjöström M, Zhao F, Hu YM, Linder S, Chen WS, Hawkins RM, Shrestha R, Zhu X, Foye A, Li H, Kim LM, Bhalla M, O'…
• An Atlas of Accessible Chromatin in Advanced Prostate Cancer Reveals the Epigenetic Evolution during Tumor Progression.
  Cancer research 2024 Shrestha R, Chesner LN, Zhang M, Zhou S, Foye A, Lundberg A, Weinstein AS, Sjöström M, Zhu X, Moreno-Rodriguez T, Li H, SU2C/PCF West Coast Prostate Cancer Dream Team, Alumkal JJ, Aggarwal R, Small EJ…
• Genomic and transcriptomic features of androgen receptor signaling inhibitor resistance in metastatic castration-resistant prostate cancer.
  The Journal of clinical investigation 2024 Zhu X, Farsh T, Vis D, Yu I, Li H, Liu T, Sjöström M, Shrestha R, Kneppers J, Severson T, Zhang M, Lundberg A, Moreno Rodriguez T, Weinstein AS, Foye A, Mehra N, Aggarwal RR, Bergman AM, Small EJ, …
• Integrated analyses highlight interactions between the three-dimensional genome and DNA, RNA and epigenomic alterations in metastatic prostate cancer.
  Nature genetics 2024 Zhao SG, Bootsma M, Zhou S, Shrestha R, Moreno-Rodriguez T, Lundberg A, Pan C, Arlidge C, Hawley JR, Foye A, Weinstein AS, Sjöström M, Zhang M, Li H, Chesner LN, Rydzewski NR, Helzer KT, Shi Y, West …
• 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 2024 Zhang M, Sjöström M, Cui X, Foye A, Farh K, Shrestha R, Lundberg A, Dang HX, Li H, Febbo PG, Aggarwal R, Alumkal JJ, Small EJ, SU2C/PCF West Coast Prostate Cancer Dream Team, Maher CA, Feng FY, …

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• A prostate cancer gastrointestinal transcriptional phenotype may be associated with diminished response to AR-targeted therapy.
  bioRxiv : the preprint server for biology 2024 Subramanian A, Zhang M, Sharifi M, Moreno-Rodriguez T, Feng E, Rydzewski NR, Shrestha R, Zhu X, Zhao SG, Aggarwal R, Small EJ, Ding CC, Quigley DA, Sjöström M
• The Genomic and Epigenomic Landscape of Double-Negative Metastatic Prostate Cancer.
  Cancer research 2023 Lundberg A, Zhang M, Aggarwal R, Li H, Zhang L, Foye A, Sjöström M, Chou J, Chang K, Moreno-Rodriguez T, Shrestha R, Baskin A, Zhu X, Weinstein AS, Younger N, Alumkal JJ, Beer TM, Chi KN, Evans CP, …
• Author Correction: Pathway and network analysis of more than 2500 whole cancer genomes.
  Nature communications 2022 Reyna MA, Haan D, Paczkowska M, Verbeke LPC, Vazquez M, Kahraman A, Pulido-Tamayo S, Barenboim J, Wadi L, Dhingra P, Shrestha R, Getz G, Lawrence MS, Pedersen JS, Rubin MA, Wheeler DA, Brunak S, …
• The 5-Hydroxymethylcytosine Landscape of Prostate Cancer.
  Cancer research 2022 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, …
• Predicting cancer drug TARGETS - TreAtment Response Generalized Elastic-neT Signatures.
  NPJ genomic medicine 2021 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 …
• An integrated functional and clinical genomics approach reveals genes driving aggressive metastatic prostate cancer.
  Nature communications 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
• Multiomics Characterization of Low-Grade Serous Ovarian Carcinoma Identifies Potential Biomarkers of MEK Inhibitor Sensitivity and Therapeutic Vulnerability.
  Cancer research 2021 Shrestha R, Llaurado Fernandez M, Dawson A, Hoenisch J, Volik S, Lin YY, Anderson S, Kim H, Haegert AM, Colborne S, Wong NKY, McConeghy B, Bell RH, Brahmbhatt S, Lee CH, DiMattia GE, Le Bihan S, Morin…
• Autoantibody Landscape in Patients with Advanced Prostate Cancer.
  Clinical cancer research : an official journal of the American Association for Cancer Research 2020 Chen WS, Haynes WA, Waitz R, Kamath K, Vega-Crespo A, Shrestha R, Zhang M, Foye A, Baselga Carretero I, Perez Garcilazo I, Zhang M, Zhao SG, Sjöström M, Quigley DA, Chou J, Beer TM, Rettig M, Gleave M…
• Identification of conserved evolutionary trajectories in tumors.
  Bioinformatics (Oxford, England) 2020 Hodzic E, Shrestha R, Malikic S, Collins CC, Litchfield K, Turajlic S, Sahinalp SC
• Well-Differentiated Papillary Mesothelioma of the Peritoneum Is Genetically Distinct from Malignant Mesothelioma.
  Cancers 2020 Shrestha R, Nabavi N, Volik S, Anderson S, Haegert A, McConeghy B, Sar F, Brahmbhatt S, Bell R, Le Bihan S, Wang Y, Collins C, Churg A
• 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 : CR 2020 D'Costa NM, Lowerison MR, Raven PA, Tan Z, Roberts ME, Shrestha R, Urban MW, Monjaras-Avila CU, Oo HZ, Hurtado-Coll A, Chavez-Munoz C, So AI
• Identification of gene signature for treatment response to guide precision oncology in clear-cell renal cell carcinoma.
  Scientific reports 2020 D'Costa NM, Cina D, Shrestha R, Bell RH, Lin YY, Asghari H, Monjaras-Avila CU, Kollmannsberger C, Hach F, Chavez-Munoz CI, So AI
• Pan-cancer analysis of whole genomes.
  Nature 2020 ICGC/TCGA Pan-Cancer Analysis of Whole Genomes Consortium
• Pathway and network analysis of more than 2500 whole cancer genomes.
  Nature communications 2020 Reyna MA, Haan D, Paczkowska M, Verbeke LPC, Vazquez M, Kahraman A, Pulido-Tamayo S, Barenboim J, Wadi L, Dhingra P, Shrestha R, Getz G, Lawrence MS, Pedersen JS, Rubin MA, Wheeler DA, Brunak S, …
• Combinatorial Detection of Conserved Alteration Patterns for Identifying Cancer Subnetworks.
  GigaScience 2019 Hodzic E, Shrestha R, Zhu K, Cheng K, Collins CC, Cenk Sahinalp S
• BAP1 haploinsufficiency predicts a distinct immunogenic class of malignant peritoneal mesothelioma.
  Genome medicine 2019 Shrestha R, Nabavi N, Lin YY, Mo F, Anderson S, Volik S, Adomat HH, Lin D, Xue H, Dong X, Shukin R, Bell RH, McConeghy B, Haegert A, Brahmbhatt S, Li E, Oo HZ, Hurtado-Coll A, Fazli L, Zhou J, …
• High-throughput detection of RNA processing in bacteria.
  BMC genomics 2018 Gill EE, Chan LS, Winsor GL, Dobson N, Lo R, Ho Sui SJ, Dhillon BK, Taylor PK, Shrestha R, Spencer C, Hancock REW, Unrau PJ, Brinkman FSL
• HIT'nDRIVE: patient-specific multidriver gene prioritization for precision oncology.
  Genome research 2017 Shrestha R, Hodzic E, Sauerwald T, Dao P, Wang K, Yeung J, Anderson S, Vandin F, Haffari G, Collins CC, Sahinalp SC
• BIRC6 Targeting as Potential Therapy for Advanced, Enzalutamide-Resistant Prostate Cancer.
  Clinical cancer research : an official journal of the American Association for Cancer Research 2016 Luk IS, Shrestha R, Xue H, Wang Y, Zhang F, Lin D, Haegert A, Wu R, Dong X, Collins CC, Zoubeidi A, Gleave ME, Gout PW, Wang Y
• Heterogeneity in the inter-tumor transcriptome of high risk prostate cancer.
  Genome biology 2014 Wyatt AW, Mo F, Wang K, McConeghy B, Brahmbhatt S, Jong L, Mitchell DM, Johnston RL, Haegert A, Li E, Liew J, Yeung J, Shrestha R, Lapuk AV, McPherson A, Shukin R, Bell RH, Anderson S, Bishop J, …
• A meta-analysis approach for characterizing pan-cancer mechanisms of drug sensitivity in cell lines.
  PloS one 2014 Wang K, Shrestha R, Wyatt AW, Reddy A, Lehár J, Wang Y, Lapuk A, Collins CC