Bioinformatics Graduate Program

Graduates of the Program:

Caroline Ch'ng

B. Sc. (Cell and Molecular Biology & Informatics), University of Michigan, 2011

 

"Meta-analysis of gene expression in individuals with autism spectrum disorder"

M.Sc. Supervisor: Dr. Paul Pavlidis, CHiBi, UBC

                       

August 16th, 2013

 

Patrick Tan

B.Sc. Honours, Simon Fraser University, 2010

"Gene expression analysis of human and rodent brains".

M.Sc. Supervisor: Dr. Paul Pavlidis, CHiBi, UBC

                       

November 22, 2012

 

Post-Graduation: Working as a bioinformatician in Dr. Paul Pavlidis lab, UBC.

 

Nima Aghaeepour

B.Sc., University of Tehran, 2008

"Computational exploratory analysis of high-dimensional flow cytometry data for diagnosis and biomarker".

Ph.D. Supervisor: Dr. Ryan Brinkman, BC Cancer Research Centre, BCCA

                       

November 19 , 2012

 

Post-Graduation: Post-doctoral studies at Stanford School of Medicine, Califiornia, USA.

 

Jeff Proctor

B.SEng., University of Victoria, 2010

"Cofold: an rna predicition method that takes co-translational folding into account".

M.Sc. Supervisor: Dr. Irmtraud Meyer, Computer Science, UBC

                       

September 24 , 2012

Post-Graduation: Working as Bioinformatician in Dr. Irmtraud Meyer's lab, Computer Science, UBC.

 

Warren Cheung

B.Sc., University of British Columbia, 2003

M.Sc., University of British Columbia, 2007

"Inferring novel relationships through over-representation analysis of medical subjects in biomedical bibliographies".

Ph.D. Supervisors: Dr. Wyeth Wasserman, Medical Genetics, Centre for Molecular Medicine &Therapeutics, UBC

                          Francis Ouellette, Ontario Insitute fro Cancer Research, University of Toronto

July 27, 2012

Post-Graduation: Post-doctoral studies.

 

Meeta Mistry

B.Sc. Honours, McMaster University, 2005

"Meta-anaylses of expression profiling data in the postmortem human brain".

Ph.D. Supervisor: Dr. Paul Pavlidis, Psychiatry & CHiBi, UBC

July 6, 2012

Post-Graduation: Post-doctoral studies.

 

Olena Morozova

B.Sc. Honours, University of Toronto, 2006

"Genomic studies of the normal and malignant neural crest."

Ph.D. Supervisor: Dr. Marco Marra, Genome Sciences Centre, BC Cancer Agency

May 1 , 2012

Post-Graduation: Postdoctoral Scholar with David Haussler at the Howard Hughes Medical Institute; University of California, 

                          Santa Cruz

 

Kendric Wang

B. Cmp. Honours (Biomedical Computing), Queen's University, 2009

"A systems biology approach for identifying predictive markers for chemotherapy response."

M.Sc. Supervisor: Dr. Colin Collins, Prostate Centre, Vancouver General Hospital and Dr. Cenk Sahinalp, Computing Science, SFU

March 13 , 2012

Post-Graduation: Continuing studies towards a MD/PhD.

 

Leon French

B.Sc. Computer Science, University of Windsor, 2003
M.Sc. Computer Science, University of Windsor, 2005

"Bioinformatics for Neuroanatomical Connectivity."

Ph.D. Supervisor: Dr. Paul Pavlidis, Psychiatry & CHiBi, UBC

January 27, 2012

Post-Graduation: Post-doctoral studies in Neuroanatomy Dept., UBC

 

Fong Chun Chan

B.Sc., Simon Fraser University, 2009

"Detection of differentially expressed alternative transcripts using conventiaonal microarrays ."

M.Sc. Supervisor: Dr. Randy Gascoyne, BC Cancer Agency

December 16, 2011

Post-Graduation: Continue studies towards a PhD in the Bioinformatics Graduate Program.

 

Ryan Morin

B.Sc., Simon Fraser University, 2003

M.Sc. University of British Columbia, 2007

"Mutation discovery and characterization in lymphoid neoplasms using massively parallel RNA and DNA sequencing."

Ph.D. Supervisor: Dr. Marco Marra, Genome Sciences Centre

December 15, 2011

Post-Graduation: Assistant Professor in Molecular Biology and Biochemistry at Simon Fraser University.

Yvonne Li

B.Sc., University of British Columbia, 2003

"Bioinformatics approaches to drug repositioning."

Ph.D Supervisor: Dr. Steven Jones, Genome Sciences Centre, BCCA

November 21 , 2011

Post-Graduation: Post-doctoral studies at the Genome Sciences Centre, BCCA.

Raymond Lim

B.Sc., University of British Columbia, 2008

"Wide-scale comparison of transcriptome data and the role of microRNA in major depression and suicide."

M.Sc. Supervisor: Dr. Paul Pavlidis, Psychiatry and CHiBi, UBC

August 19 , 2011

Post-Graduation: Working for Dr. Randy Gascoyne, BCCA.

Hisanaga Mark Okada

B.Sc., Simon Fraser University, 2008

"Classification of coding and non-coding RNA in RNA-Seq data."

M.Sc. Supervisor: Dr. Martin Ester, Computing Science, SFU

February 28 , 2011

 

Post-Graduation: Working in the financial dostrict in Tokyo, Japan.

Denil Wickrama

B.Sc., McMaster University, 2006

"Mapping putative regulatory regions using histone H3 lysine 4 monomethylation marks in breast cancer cell lines."

M.Sc. Supervisor: Dr. Steven Jones, Genome Sciences Centre, BCCA

February 23 , 2011

 

Bora Uyar

B.Sc., Sabanci University, Turkey, 2008

"Homology and evidence-based genome annotation of Caenorhabditis species"

M.Sc. Supervisor: Dr. Jack Chen, Molecular Biology & Biochemistry, SFU

December 3 , 2010

Post-Graduation: Undertaking a PhD at EMBL in Heidelberg, Germany.

 

Adam Hall

B.Sc., University of Cambridge, 2007

"Short-read DNA sequence alignment with custom designed FPGA-based hardware"

M.Sc. Supervisor: Dr. Steven Jones, Genome Sciences Centre, BCCA

November 3, 2010

Post-Graduation: Undertaking a PhD at Cambridge Computer Lab, UK.

 

Anamaria Crisan

B.Comp., Queen's University, 2008

"Mutation discovery in regions of segmental cancer genome amplifications from next generation sequencing of tumours"

M.Sc. Supervisor: Drs. Sam Aparicio and Sohrab Shah, Pathology, UBC

September 14, 2010

Post-Graduation: Computational biologist at a Vancouver genomics company.

Nicholas Wiebe

B.Sc. Honors, University of Alberta, 2007

"Transat: a method for detecting evolutionarily conserved helices in alignment of RNA sequences and its application inidentifying transient or alternative structures."

M.Sc. Supervisor: Dr. Irmtraud Meyer, Computer Science, UBC

August 30, 2010

 

Carri-Lyn Mead

B.Sc. University of Waterloo, 2003

"Investigation of Novel Schizophrenia Candidate Genes through Biochemical and Computational Methods"

Ph.D. Supervisor: Dr. Robert Holt, Genome Sciences Centre, BCCA

April 1, 2010

Post-Graduation: Post-doctoral studies.

 

Kelvin (Xi) Zhang

B.Sc. Honors, East China Normal University, 1998

M.Sc. University of Windsor, 2004

"Knowledge Discovery from Large-scale Biological Networks and their Relationships"

Ph.D. Supervisor: Dr. Francis Ouellette, Informatics and BioComputing, Ontario Institute for Cancer Research

March 30, 2010

Post-Graduation: Post-doctoral studies.

 

Adrian Cortes

B.Sc. University of British Columbia, 2006

"Automated Analysis of High-Throughput Flow Cytometry Data from Hemoatopoietic Stem Cell Experiments"

M.Sc. Supervisor: Dr. Ryan Brinkman, BC Cancer Research Centre, UBC.

February 11 , 2010

Post-Graduation: Undertaking a  Ph.D in Brisbane, Australlia.

 

Michael Hsing

M.Sc. University of British Columbia, 2005

"Developing Bioinformatics Tools and Analyses on Protein Indels and Protein-Protein Interactions - Novel Applications for Drug Discovery in Staphyloccocus aureus"

Ph.D. Supervisor: Dr. Artem Cherkasov, Urologic Sciences, UBC

January 13 , 2010

Post-Graduation: Undertaking a post-doctoral fellowship at Harvard Medical School.

 

 

Debra Fulton

B.Sc. Simon Fraser University, 2002

"Computational Prediction of Regulatory Element Combinations and Transcription Factor Cooperativity"

Ph.D. Supervisor: Dr. Wyeth Wasserman, Centre for Molecular Medicine & Therapeutics, UBC

December 14, 2009

Post-Graduation:  Undertaking a post-doctoral fellowship in the Peterson Lab at McGill University, Montreal.

 

Kaida Ning

B.Sc., Zhejiang University, China, 2007

"Biological Insights for Transcription Factor Through Analysing ChIP-Seq Data"

M.Sc. Supervisor:  Dr. Raphael Gottardo, Statistics, UBC

September 21, 2009

Post-Graduation:  Working as a bioinformatician at the BCCA.

 

Daniel Horspool

B.Sc. University of Victoria, British Columbia, 2005

"Gene Sythesis by Assembly of Short Oligonucleotides"

M.Sc. Supervisor:  Dr. Rob Holt - Genome Sciences Centre, BC Cancer Agency

Aug 6, 2009

Post-Graduation:  Undertaking a Medical degree at McGill University, Montreal.

 

Morgan Langille

BSc. University of New Brunswick, St. John's, NB, 2004

"Computational prediction and characterization of genomic islands: insights into bacterial pathogenicity"

Ph.D Supervisor: Dr. Fiona Brinkman - Molecular Biology & Biochemistry, Simon Fraser University

April 16, 2009

Post-Graduation: Undertaking a post-doctoral fellowship with Dr. Jonathan Eisen at University of California, Davis.

Ben Good

BSc. University of California at San Diego, 1998

MSc. University of Sussex, 2000

"Strategies for amassing, characterizing, and applying third party metadata in bioinformatics"

Ph.D. Supervisor: Dr. Mark Wilkinson - Medical Genetics, iCapture Centre, St. Paul's Hosptial, University of British Columbia

April 3, 2009

 

Post-Graduation:  Undertaking post-doctoral studies at the Genome Institute for Novatis Research Foundation.

 

Tang Lee

BSc. University of British Columbia, 2006

"Outcome prediction and genome-transcriptome correlation analysis in classical Hodgkin's lymphoma"

M.Sc. Supervisor:  Dr. Randy Gascoyne - Clinical Professor, UBC, Pathology & Laboratory Medicine, University of British  Columbia

March 23, 2009

Post-Graduation: Working as a bioinformatician in Dr. Randy Gascoyne lab, Pathology & Laboratory Medicine, BC Cancer Agency.

 

James Wagner

BSc. University of Alberta, 2005

"Gibbs Sampling for Gapped Motif Discovery in Proteins"

M.Sc. Supervisor: Dr. Martin Ester - Computing Science, Simon Fraser University

August 28, 2008

Post-Graduation: Undertaking a PhD in Dr. Mathieu Blanchette's lab at McGill Centre for Bioinformatics.

 

Xiaohui Chen

BSc. Zhejiang University , Hangzhou , China, 2006

"COMPARISONS OF STATISTICAL MODELING FOR CONTRUCTING GENE REGULATORY NETWORKS"

M.Sc. Supervisor: Dr. Raphael Gottardo and Dr. Kevin Murphy - Statistics, University of British Columbia

August 12, 2008

Post-Graduation:  Undertaking a PhD in Dr. Z. Jane Wang's lab in the dept of Electrical & Computer Engineering, UBC.

 

Recep Colak

BSc. Bilkent University, Turkey, 2006

"TOWARDS FINDING THE COMPLETE MODULOME: DENSITY CONSTRAINED BICLUSTERING"

M.Sc. Supervisor: Dr. Martin Ester - Computing Science, Simon Fraser University

June 23, 2008

Post-graduation: Undertaking a PhD in Dr. M. Brudno's and Dr. P. Kim's lab in the department of Computer Science, University of Toronto.

Chi Kin Ho

B.Sc. University of Warwick, UK, 2005

"COMPUTATIONALLY IDENTIFYING NOVEL ESSENTIAL GENES, INCLUDING NON-CODING RNAS, IN INTERGENIC

SEQUENCES IN BACTERIAL GENOMES"

M.Sc. Supervisor: Dr. Fiona Brinkman - Molecular Biology & Biochemistry, Simon Fraser University

June 12, 2008

Post-graduation: Working as a bioinformatician for IBM in Burnaby, BC.

 

Nels Thorsteinson

B.Sc. Queen's University, Kingston, Ontario, 2005

"COMPUTATIONAL LIGAND DISCOVERY FOR THE HUMAN AND ZEBRAFISH SEX HORMONE BINDING GLOBULIN"

M.Sc. Supervisor: Dr. Artem Cherkasov - Experimental Medicine, University of British Columbia

May 26, 2008

Post-graduation: Working as an Applications scientist at a chemical company in Montreal, Quebec.

 

Shannan Ho Sui

B.Sc. Honours, University of British Columbia, 2000

"IN SILICO APPROACHES TO INVESTIGATING MECHANISMS OF GENE REGULATION"

Ph.D. Supervisor: Dr. Wyeth Wasserman - Centre for Molecular Medicine & Therapeutics, Medical Genetics, University of British Columbia

March 7, 2008

Post-graduation: Working as a post-doctoral fellow in Dr. Fiona Brinkman's lab in Molecular Biology & Biochemistry, Simon Fraser University.

 

Simon Chan

B.Sc. First Class Honors, Cellular & Molecular Biology, Simon Fraser University, 2005

"A BIOINFORMATICS META-ANALYSIS OF DIFFERENTIALLY EXPRESSED GENES IN COLORECTAL CANCER"

M.Sc. Suprvisor: Dr. Steven Jones - Genome Sciences Centre, Medical Genetics, University of British Columbia

November 27, 2007

Post-graduation: Working as a bioinformatician in Dr. Steven Jones' lab at the Genome Sciences Centre, BCCA.

 

Ryan Morin

B.Sc. Molecular Biology and Biochemistry, Simon Fraser University, 2003

"APPLICATION OF MASSIVELY PARALLEL SEQUENCING TO MicroRNA PROFILING AND DISCOVERY IN HUMAN EMBRYONIC STEM CELLS"

 

M.Sc. Supervisor: Dr. Marco Marra- Genome Sciences Centre, Medical Genetics, University of British Columbia

October 4, 2007

Post-graduation: Undertaking a Ph.D in Dr. Marco Marra's lab at the Genome Sciences Centre, BC Cancer Agency.

 

Siddhartha Srivastava

B.Sc. Computer Science and Biological Sciences, University of Calgary, 2005

"D-GRIP: DNA GENETIC RISK INFORMATION PROFILE"

M.Sc. Supervisor: Dr. Wyeth Wasserman - Centre for Molecular Medicine & Therapeutics, University of British Columbia

September 28, 2007

Post-graduation: Undertaking a Medical degree at the University of Calgary.

 

Gozde Cozen

B.Sc. Computer Engineering, BiLKENT University, Turkey, 2005

"EFFICIENT COMPUTATIONAL METHODS FOR SEQUENCE ANALYSIS OF SMALL RNAS"

M.Sc. Supervisor: Dr. Cenk Sahinalp - Computing Science, Simon Fraser University

Co-supervisor: Dr. Peter Unrau - Molecular Biology & Biochemistry, Simon Fraser University

August 7, 2007

Post-graduation: Working as a bioinformatician in Dr. Evan Eichler's lab in the Genome Sciences dept, University of

                          Washington in Seattle.

 

Chris Thachuk

B.S.C. Honors, Computer Science, University of Windsor, 2005

"NOVEL ALGORITHMS FOR IN VITOR GENE SYNTHESIS"

M.Sc. Supervisor: Dr. Arvind Gupta - Computing Science, Simon Fraser University

Co-supervisor: Dr. Anne Condon - Computer Science, University of British Columbia

August 3, 2007

Post-graduation: Undertaking a PhD in Dr. Anne Condon's lab in the Computer Science dept at UBC.

 

Jessica (Shung-Jung) Lee

B.Sc. Honors, Biochemistry, Queens University, 2003

"PREDICTION OF GRAFT-VERSUS-HOST DISEASE BASED ON SUPERVISEDTEMPORAL ANALYSIS ON HIGH-THROUGHPUT FLOW CYTOMETRY" 

 

M.Sc. Supervisor: Dr. Ryan Brinkman- Medical Genetics, University of British Columbia

April 24, 2007

Post-graduation: Undertaking a PhD in Dr. Robert Kearney's lab in the dept of Biomedical Engineering at McGill University,

                          Montreal.

 

Di Wang

B.Sc., with Distinction, Computer Science, Bishop's University, 2004

B.Sc. Animal Husbandry, Beijing Agricultural College, 1994

Bioinformatics Diploma: Molecular Biology & Biochemistry, Simon Fraser University

December, 2006

Post-graduation: Working as a bioinformatician at OmniRim Solution Inc., Vancouver, BC.

 

Keith Boroevich

B.Sc. First Class Honours, Cellular & Molecular Biology, Simon Fraser University, 2002

"INDENTIFICATION OF CIS-ACTING REGULATORY ELEMENTS USING ORTHOLOGY BIASED GIBBS SAMPLING"

 

M.Sc. Supervisor: Dr. David Baillie - Molecular Biology & Biochemistry, Simon Fraser University

Co-supervisor: Dr. Steven Jones - Molecular Biology & Biochemistry (adjunct), Simon Fraser University

October 14, 2005

Post-graduation: Working as a bioinformatician in Dr. William Davidson's lab in the dept of Molecular Biology & Biochemisty,

                          SFU.

 

Byron Kuo

B.Sc., Computer Science, University of British Columbia, 2002

B.Sc., Cell Biology and Genetics, University of British Columbia, 1999

" SAGE2SPLICE: UNMAPPED SAGE TAGS REVEAL NOVEL SPLICE JUNCTIONS"

M.Sc. Supervisor: Dr. Elizabeth M. Simpson - Centre for Molecular Medicine & Therapeutics, University of British Columbia

Co-supervisor: Dr. Wyeth Wasserman - Centre for Molecular Medicine & Therapeutics, University of British Columbia

September 1, 2005

Post-graduation: Working as a bioinformatician at Health Canada in Ottawa, Ontario.

Alison Meynert

B.Sc. Honours, Computer Science & Statistics, University of Victoria, 2002

"COMMON EVIDENCE NETWORK: AN INTEGRATED APPROACH TO INVESTIGATING GENE RELATIONSHIPS"

M.Sc. Supervisor: Dr. Arvind Gupta - Computing Science, Simon Fraser University

Co-Supervisor: Francis Ouellette - University Bioinformatics Centre, University of British Columbia

August 3, 2005

Post-graduation: Undertaking a PhD in Dr. Ewan Birney's lab at the European Bioinformatics Centre, Cambridge, UK.

 

Michael Hsing

B.Sc. Honours, Molecular Biology & Biochemistry, Simon Fraser University, 2002

"MODELING OF CELL SIGNALING PATHWAYS IN MACROPHAGES BY SEMANTIC NETWORKS"

M.Sc. Supervisor: Dr. Artem Cherkasov - Experimental Medicine, University of British Columbia

February 23, 2005

Post-graduation: Undertaking a PhD in Dr. Art Cherkasov's lab in the dept of Experimental Medicine at UBC.

 

Fred Yefang Peng

Ph.D. Plant Physiology, Sun Yat-sen University, Guangzhou, P.R. China, 1993

B.Sc. Botany, Sun Yat-sen University, Guangzhou, P.R. China, 1987

"COMPUTATIONAL DETECTION OF TRANSCIPTIONAL REGULATORS OF PROTEIN COMPLEXES IN APOPTOSIS"


M.Sc. Supervisor:  Dr. Frederic Pio - Molecular Biology & Biochemistry, Simon Fraser University

September 23, 2004

Post-graduation: Working as a bioinformatician at the Canola Genomics Lab at the University of Alberta .

 

Perseus Missirlis

B.Sc. Honours, Life Sciences, Queens University, 2002

"CIS-FEATURES MEDIATING CAG/CTG REPEAT INSTABILITY, THE SATELLOG DATABASE, AND CANDIDATE REPEAT PRIORITIZATION IN SCHIZOPHRENIA"

M.Sc. Supervisor:  Dr. Robert Holt - Genome Sciences Centre, British Columbia Cancer Agency

August 13, 2004

Post-graduation: Undertaking a Medical degree at UBC.

 

 

 

 

 

 

 

 
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(c) 2002 Training Program in Bioinformatics for Health Research at UBC, SFU and BCCA