Raunak Shrestha, PhD

Title(s)Assistant Researcher, Radiation Oncology
SchoolSchool of Medicine
Address1600 Divisadero, #300
San Francisco CA 94115
PronounsHe/Him/His
ORCID ORCID Icon0000-0002-1144-1413 Additional info
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    Collapse Biography 
    Collapse Education and Training
    University of British Columbia, Vancouver, CanadaPhD2018Bioinformatics
    Kathmandu University, NepalB.Tech.2009Biotechnology
    Collapse Awards and Honors
    Prostate Cancer Foundation2022  - 2025Prostate Cancer Foundation Young Investigator Award

    Collapse Overview 

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    Collapse Bibliographic 
    Collapse Publications
    Publications listed below are automatically derived from MEDLINE/PubMed and other sources, which might result in incorrect or missing publications. Researchers can login to make corrections and additions, or contact us for help. to make corrections and additions.
    Newest   |   Oldest   |   Most Cited   |   Most Discussed   |   Timeline   |   Field Summary   |   Plain Text
    Altmetrics Details PMC Citations indicate the number of times the publication was cited by articles in PubMed Central, and the Altmetric score represents citations in news articles and social media. (Note that publications are often cited in additional ways that are not shown here.) Fields are based on how the National Library of Medicine (NLM) classifies the publication's journal and might not represent the specific topic of the publication. Translation tags are based on the publication type and the MeSH terms NLM assigns to the publication. Some publications (especially newer ones and publications not in PubMed) might not yet be assigned Field or Translation tags.) Click a Field or Translation tag to filter the publications.
    1. An Atlas of Accessible Chromatin in Advanced Prostate Cancer Reveals the Epigenetic Evolution during Tumor Progression. Cancer Res. 2024 Sep 16; 84(18):3086-3100. 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, Lupien M, Quigley DA, Feng FY. PMID: 38990734.
      View in: PubMed   Mentions:    Fields:    
    2. Integrated analyses highlight interactions between the three-dimensional genome and DNA, RNA and epigenomic alterations in metastatic prostate cancer. Nat Genet. 2024 Aug; 56(8):1689-1700. 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 Coast Dream Team Consortium, Lynch M, Dehm SM, Lang JM, Alumkal JJ, He HH, Wyatt AW, Aggarwal R, Zwart W, Small EJ, Quigley DA, Lupien M, Feng FY. PMID: 39020220; PMCID: PMC11319208.
      View in: PubMed   Mentions: 1     Fields:    Translation:HumansCells
    3. Integrative analysis of ultra-deep RNA-seq reveals alternative promoter usage as a mechanism of activating oncogenic programmes during prostate cancer progression. Nat Cell Biol. 2024 Jul; 26(7):1176-1186. 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, Quigley DA. PMID: 38871824.
      View in: PubMed   Mentions:    Fields:    Translation:HumansCells
    4. A prostate cancer gastrointestinal transcriptional phenotype may be associated with diminished response to AR-targeted therapy. bioRxiv. 2024 Jun 03. 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. PMID: 38895460; PMCID: PMC11185575.
      View in: PubMed   Mentions:
    5. The Genomic and Epigenomic Landscape of Double-Negative Metastatic Prostate Cancer. Cancer Res. 2023 08 15; 83(16):2763-2774. 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, Gleave M, Lara PN, Reiter RE, Rettig MB, Witte ON, Wyatt AW, Feng FY, Small EJ, Quigley DA. PMID: 37289025; PMCID: PMC10425725.
      View in: PubMed   Mentions: 9     Fields:    Translation:Humans
    6. Author Correction: Pathway and network analysis of more than 2500 whole cancer genomes. Nat Commun. 2022 Dec 08; 13(1):7566. 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, Izarzugaza JMG, Khurana E, Marchal K, von Mering C, Sahinalp SC, Valencia A, PCAWG Drivers and Functional Interpretation Working Group, Reimand J, Stuart JM, Raphael BJ, PCAWG Consortium. PMID: 36481610; PMCID: PMC9732045.
      View in: PubMed   Mentions:    Fields:    
    7. The 5-Hydroxymethylcytosine Landscape of Prostate Cancer. Cancer Res. 2022 11 02; 82(21):3888-3902. 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, Fraser M, Chesner L, Perry MD, Moreno-Rodriguez T, Chen WS, Alumkal JJ, Chou J, Morgans AK, Beer TM, Thomas GV, Gleave M, Lloyd P, Phillips T, McCarthy E, Haffner MC, Zoubeidi A, Annala M, Reiter RE, Rettig MB, Witte ON, Fong L, Bose R, Huang FW, Luo J, Bjartell A, Lang JM, Mahajan NP, Lara PN, Evans CP, Tran PT, Posadas EM, He C, Cui XL, Huang J, Zwart W, Gilbert LA, Maher CA, Boutros PC, Chi KN, Ashworth A, Small EJ, He HH, Wyatt AW, Quigley DA, Feng FY. PMID: 36251389; PMCID: PMC9627125.
      View in: PubMed   Mentions: 17     Fields:    Translation:Humans
    8. Predicting cancer drug TARGETS - TreAtment Response Generalized Elastic-neT Signatures. NPJ Genom Med. 2021 Sep 21; 6(1):76. 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 SG. PMID: 34548481; PMCID: PMC8455625.
      View in: PubMed   Mentions: 6  
    9. An integrated functional and clinical genomics approach reveals genes driving aggressive metastatic prostate cancer. Nat Commun. 2021 07 29; 12(1):4601. 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. PMID: 34326322; PMCID: PMC8322386.
      View in: PubMed   Mentions: 14     Fields:    Translation:HumansAnimalsCells
    10. Multiomics Characterization of Low-Grade Serous Ovarian Carcinoma Identifies Potential Biomarkers of MEK Inhibitor Sensitivity and Therapeutic Vulnerability. Cancer Res. 2021 04 01; 81(7):1681-1694. 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 GB, Collins CC, Carey MS. PMID: 33441310.
      View in: PubMed   Mentions: 16     Fields:    Translation:HumansCells
    11. Autoantibody Landscape in Patients with Advanced Prostate Cancer. Clin Cancer Res. 2020 12 01; 26(23):6204-6214. 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, Evans CP, Lara P, Chi KN, Reiter RE, Alumkal JJ, Ashworth A, Aggarwal R, Small EJ, Daugherty PS, Ribas A, Oh DY, Shon JC, Feng FY. PMID: 32967941; PMCID: PMC7710628.
      View in: PubMed   Mentions: 6     Fields:    Translation:Humans
    12. Identification of conserved evolutionary trajectories in tumors. Bioinformatics. 2020 07 01; 36(Suppl_1):i427-i435. Hodzic E, Shrestha R, Malikic S, Collins CC, Litchfield K, Turajlic S, Sahinalp SC. PMID: 32657374; PMCID: PMC7355238.
      View in: PubMed   Mentions: 5     Fields:    Translation:Humans
    13. Well-Differentiated Papillary Mesothelioma of the Peritoneum Is Genetically Distinct from Malignant Mesothelioma. Cancers (Basel). 2020 Jun 13; 12(6). 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. PMID: 32545767; PMCID: PMC7352777.
      View in: PubMed   Mentions: 4  
    14. Y-box binding protein-1 is crucial in acquired drug resistance development in metastatic clear-cell renal cell carcinoma. J Exp Clin Cancer Res. 2020 Feb 10; 39(1):33. 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. PMID: 32041631; PMCID: PMC7011538.
      View in: PubMed   Mentions: 9     Fields:    Translation:HumansAnimalsCells
    15. Identification of gene signature for treatment response to guide precision oncology in clear-cell renal cell carcinoma. Sci Rep. 2020 02 06; 10(1):2026. 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. PMID: 32029828; PMCID: PMC7005147.
      View in: PubMed   Mentions: 9     Fields:    Translation:HumansCells
    16. Pan-cancer analysis of whole genomes. Nature. 2020 02; 578(7793):82-93. ICGC/TCGA Pan-Cancer Analysis of Whole Genomes Consortium. PMID: 32025007; PMCID: PMC7025898.
      View in: PubMed   Mentions: 1023     Fields:    Translation:HumansCells
    17. Pathway and network analysis of more than 2500 whole cancer genomes. Nat Commun. 2020 02 05; 11(1):729. 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, Izarzugaza JMG, Khurana E, Marchal K, von Mering C, Sahinalp SC, Valencia A, PCAWG Drivers and Functional Interpretation Working Group, Reimand J, Stuart JM, Raphael BJ, PCAWG Consortium. PMID: 32024854; PMCID: PMC7002574.
      View in: PubMed   Mentions: 45     Fields:    Translation:HumansCells
    18. Combinatorial Detection of Conserved Alteration Patterns for Identifying Cancer Subnetworks. Gigascience. 2019 04 01; 8(4). Hodzic E, Shrestha R, Zhu K, Cheng K, Collins CC, Cenk Sahinalp S. PMID: 30978274; PMCID: PMC6458499.
      View in: PubMed   Mentions: 4     Fields:    Translation:HumansCells
    19. BAP1 haploinsufficiency predicts a distinct immunogenic class of malignant peritoneal mesothelioma. Genome Med. 2019 02 18; 11(1):8. 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, McConnell Y, McCart A, Lowy A, Morin GB, Chen T, Daugaard M, Sahinalp SC, Hach F, Le Bihan S, Gleave ME, Wang Y, Churg A, Collins CC. PMID: 30777124; PMCID: PMC6378747.
      View in: PubMed   Mentions: 65     Fields:    Translation:Humans
    20. High-throughput detection of RNA processing in bacteria. BMC Genomics. 2018 03 27; 19(1):223. 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. PMID: 29587634; PMCID: PMC5870498.
      View in: PubMed   Mentions: 18     Fields:    Translation:Cells
    21. HIT'nDRIVE: patient-specific multidriver gene prioritization for precision oncology. Genome Res. 2017 09; 27(9):1573-1588. Shrestha R, Hodzic E, Sauerwald T, Dao P, Wang K, Yeung J, Anderson S, Vandin F, Haffari G, Collins CC, Sahinalp SC. PMID: 28768687; PMCID: PMC5580716.
      View in: PubMed   Mentions: 25     Fields:    Translation:HumansCells
    22. BIRC6 Targeting as Potential Therapy for Advanced, Enzalutamide-Resistant Prostate Cancer. Clin Cancer Res. 2017 Mar 15; 23(6):1542-1551. 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. PMID: 27663589.
      View in: PubMed   Mentions: 18     Fields:    Translation:HumansAnimalsCells
    23. Heterogeneity in the inter-tumor transcriptome of high risk prostate cancer. Genome Biol. 2014 Aug 26; 15(8):426. 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, Hurtado-Coll A, Xiao H, Chinnaiyan AM, Mehra R, Lin D, Wang Y, Fazli L, Gleave ME, Volik SV, Collins CC. PMID: 25155515; PMCID: PMC4169643.
      View in: PubMed   Mentions: 52     Fields:    Translation:Humans
    24. A meta-analysis approach for characterizing pan-cancer mechanisms of drug sensitivity in cell lines. PLoS One. 2014; 9(7):e103050. Wang K, Shrestha R, Wyatt AW, Reddy A, Lehár J, Wang Y, Lapuk A, Collins CC. PMID: 25036042; PMCID: PMC4103868.
      View in: PubMed   Mentions: 6     Fields:    Translation:HumansCells
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