Curriculum Vitae

Raunak Shrestha

Ph.D. Candidate in Bioinformatics, University of British Columbia.
Laboratory of Advanced Genome Analysis (LAGA), Vancouver Prostate Centre,
2660 Oak Street, Vancouver, BC, Canada V6H 3Z6
Phone: 604-875-4111 (Ext: 21773), Email: rshrestha@prostatecentre.com

Research Interests

My main interest lies in the development and application of computational tools to enable precision medicine in cancer. I use machine learning and statistical techniques to understand the genetic basis of cancer. My research focus is on developing network-based algorithms to prioritize driver genes of cancer exploiting the genotype-phenotype relationships of individual cancer patients. Lately, I’ve been focusing on developing computational tools to predict therapeutics that target the drivers of cancer. My other research interests lies in cancer biomarker discovery using multi-omics data.

Research & Training Experience

Sept 2012 – Current   PhD Scholar at Laboratory for Advanced Genome AnalysisVancouver Prostate Centre

A Bioinformatician supervised by Dr. Colin Collins and Dr. Cenk Sahinalp (Laboratory for Computational Biology at Simon Fraser University). My research works revolves around development and application of methods to integrate various -omics data using systems biology approaches to study cancer.

May – Aug 2012         Research Student at Vancouver Prostate Centre

Bioinformatics research student under supervision of Dr. Colin Collins.Project title: “Exploring the Biology of Prostate Cancer Progression using Systems Biology Approach.”

Jan – April 2012          Research Student at Dr. Fiona Brinkman’s Laboratory. Simon Fraser University

Bioinformatics research student under supervision of Dr. Fiona Brinkman. Project title: “Motif discovery in Pseudomonas aeruginosa using RNA seq data.”

Sept – Dec 2011          Research Student at Dr. Jack Chen’s Laboratory. Simon Fraser University

Bioinformatics research student under supervision of Dr. Jack Chen. Project title: “Computational discovery of alleles in Caenorhabditis genomes.”

July 2009 – July 2011   Research Associate at Center for Molecular Dynamics Nepal, Kathmandu, Nepal

Worked as a leader in bioinformatics and genomics-data analysis works was involved in various research projects spanning bioinformatics, medical genomics, wildlife genetics and public health. I was also involved in performing routine laboratory works in molecular biology and immunology.

Jan-June 2009             Research Student at Genetics Nepal, Kathmandu, Nepal

Project titled: ”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.”

Post-Secondary Education

Sept 2012 – Current       Doctor of Philosophy in Bioinformatics, University of British Columbia, Canada

under CIHR/MFSHR Bioinformatics Training Program for Health Research

Supervisors: Prof. Dr. Colin Collins and Prof. Dr. S. Cenk Sahinalp

Sept 2011 – Aug 2012    Master of Science in Bioinformatics, Simon Fraser University, Canada

under CIHR/MFSHR Bioinformatics Training Program for Health Research (Transferred to PhD program)

2005 – 2009                  Bachelors of Technology (B.Tech.) in Biotechnology, Kathmandu University, Nepal

Awards and Honors

  • 2016-2018   Mitacs Accelerate PhD Fellowship
  • 2015-2016   Prostate Cancer Foundation – BC (PCF-BC) Research Awards – 2015
  • 2014- 2016   Faculty of Science Graduate Award, University of British Columbia
  • 2014     International Society for Computational Biology (ISCB) Travel Fellowship (RECOMB-2014)
  • 2011-2013   CIHR Bioinformatics Training Program for Health Research

Publications

  • Luk I, Shrestha R, Xue H, Wang Y, Zhang F, Lin D, Haegert A, Wu R, Dong X, Collins CC, Zoubeidi A, Gleave ME, Gout PW, and Wang Y. (2016) BIRC6-targeting as potential therapy for advanced, enzalutamide-resistant prostate cancer. Clin Cancer Res. 2016 Sep 23
  • Gill E, Chan L, Winsor G, Dobson N, Lo R, Sui SH, Dhillon B, Taylor P, Shrestha R, Spencer C, Hancock R, Unrau P, and Brinkman F. High-throughput detection of RNA processing in bacteria. (2016) (Preprint: http://biorxiv.org/content/early/2016/09/06/073791)
  • Yamada M, Tang J, Lugo-Martinez J, Hodzic E, Shrestha R, Saha A, Ouyang H, Yin D, Mamitsuka H, Sahinalp C, Radivojac P, Menczer F, and Chang Y. Ultra High-Dimensional Nonlinear Feature Selection for Big Biological Data. (2016) (Preprint: http://arxiv.org/abs/1608.04048)
  • Wyatt A, Mo F, Wang K, McConeghy B, Brahmbhatt S, Jong L, Mitchell D, Johnston R, Haegert A, Li E, Liew J, Yeung J, Shrestha R, Lapuk A, McPherson A, Shukin R, Bell R, Anderson S, Bishop J, Hurtado-Coll A, Xiao H, Chinnaiyan A, Mehra R, Lin D, Wang Y, Fazli L, Gleave M, Volik S, and Collins CC.  (2014) Heterogeneity in the inter-tumor transcriptome of high risk prostate cancer. Genome Biol. 15(8):426 (PubMed) (PDF)
  • Shrestha R., Joshi RN.,  Joshi K., Poudel BH. and 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 1 (1), 14-21. (PDF)

Oral Presentations

  • Translating Big-Data to Precision Oncology. Vancouver Prostate Centre / Terry Fox Seminar, February 17, 2017, Vancouver General Hospital, Vancouver, Canada.
  • HIT’nDRIVE: Patient-Specific Multi-Driver Gene Prioritization for Precision Oncology. Vancouver Bioinformatics User Group (VanBUG) November 3, 2016, Vancouver, Canada
  • HIT’nDRIVE: Patient-Specific Multi-Driver Gene Prioritization for Precision Oncology. 10th Annual Lorne D. Sullivan Lectureship & Research Day. June 21, 2016, Vancouver General Hospital, Vancouver, Canada.
  • HIT’nDRIVE: Patient-Specific Multi-Driver Gene Prioritization to Guide Precision Cancer Medicine. Workshop on Network Biology, Algorithmic Challenges in Genomics. April 11-15, 2016. Simons Institute, UC Berkley, Berkley, CA, USA. [url: https://simons.berkeley.edu/talks/raunak-shrestha-04-12-16]
  • Computational Detection and Prioritization of Driver Alterations in Cancer. Vancouver Prostate Centre / Terry Fox Seminar, November 3, 2014, Vancouver General Hospital, Vancouver, Canada.
  • 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. 2nd International Symposium on Biotechnology, June 29-30, 2010, Kathmandu,Nepal (Oral presentation)

Posters Presentations (only selected few)

  • Raunak Shrestha, Ermin Hodzic, Thomas Sauerwald, Phuong Dao, Kendric Wang, Jake Yeung, Shawn Anderson, Fabio Vandin, Gholamreza Haffari, Colin C. Collins and S. Cenk Sahinalp.(2016). HIT’nDRIVE: Patient-Specific Multi-Driver Gene Prioritization for Precision Oncology. The 27th International Conference on
    Genome Informatics, October 3-5, 2016, Fudan University, Shanghai, China.
  • Noushin Nabavi, Raunak Shrestha, Yuzhuo Wang and Colin C. Collins (2016). Characterization of intertumor heterogeneity in Malignant Mesothelioma. 13th International Conference of the International Mesothelioma Interest Group (iMIG 2016), May 1-4, 2016, Birmingham, UK. (As a first co-author).
  • Raunak Shrestha, Ermin Hodzic, Fan Mo, Anna Lapuk, S. Cenk Sahinalp and Colin C. Collins (2015). Computational Detection and Prioritization of Driver Alterations in Prostate Cancer from Multi-Omics Data. Eighth Annual Prostate Cancer Program Retreat (SPORE), March 15-17, 2015, Fort Lauderdale, Florida, USA. (Selected among the top-eight poster of the conference)
  • Raunak Shrestha, Kendric Wang, S. Cenk Sahinalp, Anna Lapuk and Colin Collins (2013). Exploring the Biology of Prostate Cancer Progression using Systems Biology Approach. The Eleventh Asia Pacific Bioinformatics Conference, January 21-23, 2013, Vancouver, Canada.

 Programming Language Skills

  • R, perl (Expert)
  • C, C++, php, css, sql (proficient)

Professional Memberships