Current Students

Click on each year to see the list of students in that cohort. Click on each student’s name to learn more about their background and interests.

2011 Cohorts

• Nathan Corbett

  • Supervisor: BTP student – UBC
  • Personal background: I hold a BScH Biology, Acadia University; and will shortly complete an MSc Experimental Medicine, UBC. I came to Vancouver with the aim of joining the vibrant biomedical research and industry communities here. As a biomedical researcher, I am acutely aware of the need for bioinformatics, and it was an obvious next step for my career. I am keen to add programming and database management to my skill set.
  • Research interests: My interests focus on the innate immune system and cancer. I think that the changes that occur within cancer cells which allow evasion from the innate immune responses are extremely interesting, as the ability to immunologically bypass these cancerous adaptations can yield dramatic remission with relatively few side-effects.
  • Selected publications: Corbett, N. P., Blimkie, D., Ho, K. C., Cai, B., Sutherland, D. P., Kallos, A., Crabtree, J., et al. (2010). Ontogeny of Toll-like receptor mediated cytokine responses of human blood mononuclear cells PloS one, 5(11), e15041. doi:10.1371/journal.pone.001504
  • Hobbies: I like to run, sail, play acoustic guitar/sing, play ultimate frisbee, and appreciate going to a good live show or a film
  • Personal website: www.nathancorbett.ca

• Calvin Lefebvre

  • Supervisor: BTP student – UBC
  • Personal background: For my undergraduate degree I completed an Honors of Bachelor of Science from University of Toronto with a Bioinformatics Specialist, Computer Science Major and Math Minor. I am really interested in molecular biology and computer science, especially algorithms, so pursuing bioinformatics was the obvious choice.
  • Research interests: Research interests include visual computing, machine learning, algorithms, cancer and next-generation sequencing.
  • Hobbies: My interests outside of academia are chess, reading, traveling and participating in various sports including snowboarding, mountain biking, scuba diving, wakeboarding, spelunking, ultimate frisbee, and surfing.

• Carolyn Ch’ng

  • Supervisor: BTP student – UBC. MSc; Rotation at the Hallam Lab (September to December 2011)
  • Personal background: I obtained my undergraduate degree in Cell and Molecular Biology, and Life Science Informatics at the University of Michigan, Ann Arbor. Given the opportunity to explore life science in a novel perspective, I learned that the interdisciplinary approach in Bioinformatics leverages the robustness of large-scale analyses in various biological dimensions. It is an exciting field that I look forward to further pursue here at UBC, and I believe that Bioinformatics has considerable potential in yielding rewarding results by providing a collaborative environment in Life Science research and development.
  • Hobbies: Beyond school, I would probably be attending live concerts and shows, travelling, or wandering around the city or the outdoors to enjoy and explore the picturesque landscapes of British Columbia.
  • Research interests: I am interested in the development of biological frameworks and interfaces, using an interdisciplinary approach in handling biological data.

• Tyler Funnel

  • Supervisor: BTP student – UBC
  • Personal background: I received a B.Sc. in Computer Science from the University of Northern British Columbia in 2009 then went on to work as a software engineer for a small publishing company for two years. I decided to pursue a future in bioinformatics as it combines my interest and background in computer science and my personal interest in biology and genetics. I’m currently working towards a M.Sc. in Bioinformatics and undertaking a research rotation with Dr. Paul Pavlidis.

• Adrin Jalali

  • Supervisor: PhD student with Dr. Ryan Brinkman
  • Personal background: In Jul. 2002, I got my Diploma in mathematics and physics, Shahid Soltani High School (Part of National Organization for Development of Exceptional Talents), Karaj, Tehran, Iran. My thesis was titled “Design and Implementation of a Genetic Algorithm to Solve Time Table of a School”. From Sep. 2002 – Jul. 2006, I did my B.S. in Computer Science, School of Math and Computer Science, Amirkabir University of Technology, Tehran, Iran. From Sep. 2006 – Oct. 2009, I did a M.S. in Computer Science in School of Math, Statistics, and Computer Science at University of Tehran, Tehran, Iran. My thesis was titled “Finding DNA Motifs Using Bidirectional Recurrent Neural Networks”.
  • Research interests: Computational Intelligence, Computational Biology, Data mining, Data warehousing

• Alborz Mazloomianli – PhD student with Irmtraud Meyer

• Raunak Shrestha

  • Supervisor: BTP student – SFU
  • Personal background: B.Tech. Biotechnology, Kathmandu University, Nepal. Bioinformatics plays a key role in any biology research.Undoubtedly, advances in computational technology hold promises to decipher the mysteries behind many disease systems. This is what fascinates me about Bioinformatics.
  • Research interests: Comparative Pathogenomics, Cancer Genomics and Molecular Modelling
  • Hobbies: I’m a freelance graphic designer, an avid music listener and love traveling.
  • Personal website: http://raunakms.wordpress.com

• Alvin Tian

  • Supervisor: MSc. at Dr. Suttle lab.
  • Personal background: I completed my major of biology and computer science at UBC. I choose to join the bioinformatics program to enrich my knowledge in the field of bioinformatics and aid my current research.
  • Research interests: Investigate the composition of viral community in fresh and coastal waters using a PCR amplicon approach.
  • Hobbies: Outside of school, I enjoy practicing photography and play competitive sports such as hockey and basketball.

• Ian Wood – BTP student – UBC

• Shing Zhan

  • Supervisor: PhD student with Steve Jones
  • Personal background: Undergraduate degree: UBC B.Sc (Hon) Genetics. I like both computational and life sciences. Bioinformatics is the perfect combo.
  • Research interests: Polyploidy and gene duplication (and their evolutionary consequences), genome architecture of eukaryotes (especially non-model organisms), mutation discovery using next-generation sequencing.
  • Selected publications: 1. Mayrose I, Zhan SH, Rothfels CJ, Magnuson-Ford K, Barker MS, Rieseberg LH, and Otto SP. Recently formed polyploid plants diversify at lower rates. Science. 333:1257. 2. Kane NC, Barker MS, Zhan SH, and Rieseberg LH. Molecular evolution across the Asteraceae: micro- and macroevolutionary processes. Mol Biol Evol. Advanced Access.
  • Hobbies: Traveling.

• Julie Chen – PhD student with Wyeth Wasserman

2010 Cohorts

• Luisa Chan – CIHR MSc student

• Ryan Guilliany- MSc student with David Huntsman (BCCA, UBC)

• Daniel Lai

  • Supervisor: PhD in Dr. Irmtraud Meyer’s lab at CHiBi (UBC).
  • Personal background: BSc: Combined Major in Computer Science and Microbiology & Immunology (UBC, 2010). Why bioinformatics? Came up as something to do with my undergrad degree on Google…
  • Research interests: Will need to figure this out before comps, probably something with high throughput sequencing
  • Hobbies: Anime, PSP

• Huifang Li

  • Supervisor: PhD student with Art Cherkasov (Urological Sciences, VGH)
  • Personal background: I graduated from China Pharmaceutical University with a MSc in Pharmacoinformatics and a BSc in Information Management and Information System. Being a bioinformatics graduate due to the great interest in computational drug design which is closely related in Bioinfomatics.
  • Research interests: Research interest is mainly focusing on the in silico screening, structure-activity relationship studies, and rational molecular design of anticancer targets. Currently a PhD. student in Dr. Artem Cherkasov’s lab in vancouver prostate centre, working on the molecular discovery and design of Androgen Receptor antagonists against Prostate Cancer.
  • Selected publications: Huifang Li, Yadong Chen, Shasha Rao, Tao Lu, et al. Recent Advances in the Research and Development of B-Raf Inhibitors. Curr. Med. Chem. 2010, 17: 1618-1634. Huifang Li, Tao Lu, Yadong Chen, et al. Virtual screening for Raf-1 kinase inhibitors based on pharmacophore model of substituted ureas. Eur. J. Med. Chem. 2009, 44, 1240-1249.

• Emilia Lim

  • Supervisor: PhD student with Dr. Marco Marra (GSC, BCCA)
  • Personal background: I completed my undergraduate degree in Bioinformatics at the University of Alberta (Edmonton, AB) before moving to Vancouver to pursue graduate studies. I chose to enroll in the Bioinformatics Training Program here because it was well-structured and I knew that if I did so, I would be given numerous opportunities to learn from the best and brightest in genome science.
  • Research interests: I am interested in applying high through-put sequencing technologies to answering questions in human health and disease. In particular, I am focusing on understanding how specific mutations in genes contribute to tumor development in various cancers.

• Eloi Mercier – PhD student with Paul Pavlidis (CHiBi, UBC)

• Michael Peabody

  • Supervisor: CIHR MSc student with Dr. Fiona Brinkman
  • Personal background: I did the my undergrad degree at Simon Fraser University (SFU) with a joint Molecular Biology and Biochemistry and Computer Science major. My interests outside academia are reading, capoeira and other martial arts, snowboarding, board games, traveling, and volunteering.
  • Research interests: Within bioinformatics my specific research interest is the metagenomics of watersheds.

• Jeff Proctor

  • Supervisor: CIHR MSc student with Dr. Irmtraud Meyer
  • Personal background: I began a bachelor in software engineering at the University of Victoria in 2005. While doing a coop term at GenoLogics, a laboratory informatics software company, my interest in biology was sparked. I added a minor in molecular biology, and finished my undergraduate degree in 2010. I immediately started the Bioinformatics Training Program the following semester. I am now in my second year, and currently working on an MSc with Irmtraud Meyer at the Center for High-Throughput Biology (CHiBi) at UBC.
  • Research interests: RNA secondary structure prediction, theoretical computer science.

• Casper Shyr

  • Supervisor: PhD student with Dr. Wyeth Wasserman
  • Personal background: I did my undergraduate at UBC pursuing a combined honors computer science and biology degree. My undergraduate thesis studied the interaction of transcription factor with regulatory sequences with Dr. Wyeth Wasserman and Dr. Elodie Portales-Casamar. After I graduated, I enrolled in CIHR bioinformatics Masters program, doing 3-month rotations in 3 different labs, studying liver transcriptome, metagenomics, and RNA secondary structures. Starting September 2011, I will be re-joining Wasserman lab to pursue my PhD.
  • Research interests: My research interests rest on developing and applying computational methods to analyze high-throughput dataset and tackle interesting biological questions. I am also keen to be in project environments that bridge the gap between computational biologists and experimental scientists.
  • Selected publications:Deepti Malhotra, Elodie Portales-Casamar, Anju Singh, Siddhartha Srivastava, David Arenillas, Christine Happel, Casper Shyr, Nobunao Wakabayashi, Thomas W. Kensler, Wyeth W. Wasserman,and Shyam Biswal. Global mapping of binding sites for Nrf2 identifies novel targets in cell survival response through ChIP-Seq profiling and network analysis. Nucl. Acids Res. (2010)
  • Hobbies: I enjoyed playing guitar, hiking, tennis and reading science fictions. I am also a big fan of rodents.
  • Personal website: personal website

• Young Song

  • Supervisor: MSc with Dr. Steven Hallm (Microbiology & Immunology dept. at UBC)
  • Personal background: I received my BSc (Hon. Biology) at the University of Waterloo in ’09. I also have a minors in Computer Science. I was actually an honours bioinformatics student at Waterloo, but switched by program to Biology by the end of second year, because I just didn’t like the lack of flexibility in the program. During my undergrad, I did four co-op terms, and by the end of third co-op term, I realized bioinformatics was definitely something that I wanted to do. However, it also came to my understanding that health research wasn’t something that I would focus my research on. Near the end of my time as undergraduate, I worked under Dr.Hallam as summer student, and that work term for me was the catalyst for my motivation in the field of environmental metagenomics and other related studies.
  • Research interests: In general, my research interests lie in field of environmental microbiology and agriculture. My current research though mainly involves employing various computational methods to predict metabolic potentials in various environmental samples, especially those related to hydrocarbon degradation. I work on computational prediction of microbial community structuresin various environments from time to time.
  • Selected publications: Hallam SJ, Page AP, Constan L, Song YC, Norbeck AD, Brewer H, Pasa-Tolic L. 2011. Molecular tools for investigating ANME communities structure and function. Methods in Enzymology. 494: 75-90. Shulze-Makuch D, Haque S, Antonio MR, Ali D, Hosein R, Song YC, Yang J, Zaikova E, Beckles DM, Guinan J, Lehto HJ and SJ Hallam. 2011. Microbial life in liquid asphalt desert. Astrobiology. 11(3): 241-258.
  • Hobbies: Sports: I am a loyal fan of Liverpool FC and Pittsburgh Steelers. I also play soccer in recreational level. Music: I listen to metal, classic rock/country and Tejano. I recently started collecting miniature figurines for wargaming (eg. Warhammer Fantasy and 40K).

• Patrick Tan

  • Supervisor: CIHR MSc student with Dr. Paul Pavlidis, Centre for High-Throughput Biology, UBC.
  • Personal background: I am currently a CIHR Masters student in the UBC Bioinformatics program since September 2010. One of my Masters rotations looked at the relationships between gene expression, cell types and connectivity in the adult mouse brain. Prior to this, I graduated with a Bachelor’s degree (honours) in the Computing Science and Molecular Biology and Biochemistry program at Simon Fraser University where I studied the BRCA protein-protein interaction complex for my honour’s thesis. In addition, I have also developed software for companies such as Zymeworks and Actuate-Xenos Group.
  • Research interests: My current interest is to further understand the fascinating world of molecular biology for developing novel therapeutics to combat human disease. To do this, I develop software pipelines that integrate various publicly available biological data such as common single nucleotide polymorphisms, gene expression and gene networks, epigenetics, and protein-protein interaction. Once the results are available, I apply data mining and statistical methods such as clustering and principal components analysis to help put the data back into the biological context.
  • Selected publications: French L, Tan PC and Pavlidis P (2011). Large-scale analysis of gene expression and connectivity in the rodent brain: insights through data integration. Front. Neuroinform. 5:12. doi:10.3389/fninf.2011.00012. Tan PP, Dargahi D, Pio F. Predicting protein complexes by data integration of different types of interactions. Int J Comput Biol Drug Des. 2010;3(1):19-30.doi: 10.1504/IJCBDD.2010.034464. Epub 2010 Aug 5.PubMed PMID: 20693608.
  • Hobbies: In my spare time, I hike, jog, play tennis, fold some origami, watch Japanese anime and Korean drama, snap some pictures, and volunteer.
  • Personal website: personal website

• Eric (Peichen) Xin

  • Supervisor: CIHR Masters student with Bob Hancock (Microbiology & Immunology, UBC)
  • Personal background: I majored in Computer Science and Technology as an undergraduate student and I chose bioinformatics because I believe new approaches to diagnose and treat cancer will be found through bioinformatics-related research.
  • Selected publications:Meng Zhang, Yi Zhang, Liang Hu, Peichen Xin: On the Structure of Consistent Partitions of Substring Set of a Word. FAW 2009: 326-335.
  • Hobbies: I also like travelling, reading, cooking, skateboarding, and swimming, which make life colorful.

2009 Cohorts

• Fong Chan

  • Supervisor: CIHR Masters student with Randy Gascoyne (BCCA, UBC)
  • Personal background: My undergraduate degree is in Bioinformatics at SFU. I chose to study Bioinformatics in a somewhat random way. After finishing high school, I went up to SFU to see a undergraduate advisor in computer science. While walking up to her office, I saw a flier for a joint degree between computer science and biology and jumped on it since I loved Biology in high school. Not really knowing what I was really jumping into. In any case, I ended up becoming the first group of graduates from the Bioinformatics program at SFU and have continued onto my graduate studies. I haven’t regretted or looked back since being in Bioinformatics has turned out to be one of the best choices I’ve ever made in my life!
  • Research interests: My research interests are still quite diverse since I am still learning about the field everyday. But I enjoy working with Next Generation Sequencing and Microarrays in trying to characterize genomic or transcriptomic differences between normal and cancerous patients. I also enjoy applying machine learning approaches and potentially developing new models to help interpret biological data.
  • Selected publications: Chan FC, Kawas EA, Wilkinson MD, Tebbutt SJ. DataBiNS-Viz: a web-based tool for visualization of non-synonymous SNP data. Journal of Proteomics and Bioinformatics 1, 233-236 (2008).
  • Hobbies: Aside from doing research, I love playing sports such as volleyball, hockey, badminton, and basically any sport. I also enjoy gathering with events to socialize over conversations and games.

• Melanie Courtout – PhD student with Ryan Brinkman (BCCRC, BCCA)

• Katayoon Kasaian – MSc student with Steven Jones (GSC, BCCA)

• Evan Morien

  • Supervisor: MSc student with Paul Pavlidis (CHiBi, UBC)
  • Personal background: Bachelor’s in Biology, concentration in Genetics. Class of 2007, University at Buffalo (SUNY). I chose Bioinformatics because I was drawn to the analytical techniques of it versus those of classical molecular biology.
  • Research interests: My research interests include microarray and sequence data analysis, epigenetics, and genetic disease.
  • Selected publications: Genome-wide survey reveals dynamic widespread tissue-specific changes in DNA methylation during development. Liang P, Song F, Ghosh S, Morien E, Qin M, Mahmood S, Fujiwara K, Igarashi J, Nagase H, Held WA, BMC Genomics 2011, 12:231
  • Hobbies: My interests outside of academia include photography, birding, and music.

• Kendric Wang

  • Supervisor: CIHR MSc student with Colin Collins (Prostate Centre, VGH) and Cenk Sahinalp (CS, SFU)
  • Personal background: I obtained my bachelor’s degree in Biomedical Computing from Queen’s University. Although my undergraduate research was focused on medical imaging, I found myself more drawn to the complexities of cancer systems and the need for novel computational approaches to model it at both cellular-level and molecular-level. I came to Vancouver for graduate research because it has a strong community of interdisciplinary researchers across applied and traditional sciences, and the Bioinformatics Training Program seemed one-of-a-kind in Canada with its unique rotation program. Not to mention, it was difficult to pass up an opportunity to come to one of the most livable cities in the world.
  • Research InterestsI am interested in translational research, where the focus is to translate basic research findings into clinical applications. My thesis research involves using a systems biology approach to integrate different -omics data (such as gene expression with genomic variations) for identifying biomarkers of sensitivity to chemotherapies. In addition, I’m interested in applying the next generation of high-throughput technologies to gain a greater understanding of diseases and improve subsequent their diagnosis and treatment.
  • Selected publications: Dao P, Wang K*, Collins C, Ester M, Lapuk A, Sahinalp C. Optimally discriminative subnetwork markers predict response to chemotherapy. Bioinformatics 2011, 27, 13:i205-13.
  • Hobbies: Tennis fanatic, food, pick-up sports.

2008 Cohorts

• Nima Aghaeepour

  • Supervisor: PhD student with Dr. Ryan Brinkman (BCCRC, BCCA) and Holger Hoos (CS, UBC)
  • Personal background: I did my undergrad in computer science. Now I’m doing a PhD on computational phenotyping of cytometry assays that measure the immune response to vaccination, infection or malignancies.
  • Research interests: High-throughput single-cell analysis
  • Personal website: personal website

• Gavin Ha – PhD student with Sam Aparicio (BCCRC, BCCA)

• Rodrigo Goya – PhD student with Marco Marra (GSC, BCCA) and Irmtraud Meyer (CS, UBC)

• Raymond Lim – CIHR MSc student with Paul Pavlidis (CHiBi, UBC)

• Ryan Morin

  • Supervisor: PhD student with Dr. Marco Marra (GSC, BCCA)
  • Personal background: The most exciting science is conducted and directed by people with post-graduate degrees. I did not feel properly prepared to do research with only a BSc. I wanted to stay in Vancouver and UBC has a great reputation and a great training program for bioinformatics. The BCCA is an awesome place to do such research owing to the presence of the Genome Sciences Centre.
  • Research interests: My project involves the analysis (data mining) of massively parallel sequence data from the tumours of more than 100 patients, mainly with non Hodgkin lymphoma. I am working on methods to identify protein-altering somatic mutations using RNA-seq and whole genome sequence data. By applying these methods to numerous samples, I hope to identify genes likely to be important in the development of these cancers. Finding such genes is the first step in pursuing new targeted therapies and may also enable the development of new diagnostic or prognostic tests that may guide treatment selection in the future. I hope to find multiple genes that drive lymphoma and potentially other cancers that present new treatment options for patients afflicted with cancer. Such genes may allow our lab and others to design new therapies to directly and rationally target individual cases of cancer. I hope that in the long run, my research helps lead to the discovery of new treatments that will extend the lives of cancer patients.

• Kieran O’Neill

  • Supervisor: PhD Candidate with Ryan Brinkman (BCCRC, BCCA)
  • Personal background: B.Sc. (majors Biochemistry and Computer Science) from University of Natal (South Africa). B.Sc. (Hons) in Computer Science at University from KwaZulu-Natal (South Africa). M.Sc. in Computer Science at Universtiy from KwaZulu-Natal (South Africa)
  • Research interests: Current work includes applying machine learning and high-dimensional statistics to a large retrospective clinical flow cytometry data set for AML diagnosis. Past work has included computational protein structure folding, visualization and ontologies within the context of functional genomics. In general I am interested in bringing together computational biomedical statistics and bioinformatic data integration.
  • Selected publications: Kieran O’Neill, Alexander Garcia, Anita Schwegmann, Rafael C Jimenez,Dan Jacobson and Henning Hermjakob; OntoDas – a tool for facilitating the construction of complex queries to the Gene Ontology; BMC Bioinformatics 2008, 9:437

2007 Cohorts

• Rebecca Hunt Newbury – PhD student with Wyeth Wasserman (Medical Genetics:CMMT, UBC)

• Soroosh Samadian – PhD student with Mark Wilkinson (iCapture Centre, St. Paul’s Hospital)

2006 Cohorts

• Anthony Fejes

  • Supervisor: PhD student with Steven Jones (GSC, BCCA)
  • Personal background: 2000 – Bachelors of Science, Hon. Co-op Biochemistry, University of Waterloo. 2001 – Bachelors of Independent Studies, University of Waterloo. 2004 – Masters of Science, Microbiology and Immunology, University of British Columbia. See http://about.fejes.ca
  • Research interests: Chip-Seq, Next-Generation Sequencing, Databases, Human Variation, Breast Cancer, algorithm development
  • Selected publications: AP Fejes, G Robertson, M Bilenky, R Varhol, M Bainbridge, SJM Jones, 2008, FindPeaks 3.1: a tool for identifying areas of enrichment from massively parallel short-read sequencing technology. AP Fejes, AH Khodabakhshi, I Birol, SJM Jones, 2011, Human variation database: an open-source database template for genomic discovery
  • Personal website: personal website

• Leon French – PhD student with Paul Pavlidis (UBiC, UBC)

• Meeta Mistry

  • Supervisor: PhD student with Paul Pavlidis (UBiC, UBC)
  • Personal background: My undergraduate degree was in Computational and Physical Specialized Biochemistry at McMaster University in Hamilton, Ontario. After realizing that the wet-lab was not my forte I took the CBW Bioinformatics Workshop and picked up some programming courses on the side. In 2006 , I was accepted to the CIHR/MSFHR Bioinformatics Program and am hoping to finish soon.
  • Research interests: Statistical analysis of high-dimensional biology with application to neuropsychiatric disorders
  • Selected publications:Mistry, M. and Pavlidis P. A cross-laboratory comparison of expression profiling data from normal human postmortem brain. Neuroscience. 167(2):384-95. May 2010. Mistry M. and Pavlidis P. Gene Ontology term overlap as a measure of gene functional similarity. BMC Bioinformatics. 9(1):237. August 2008.

• Olena Morozova – PhD student with Marco Marra (Genome Sciences Centre, BCCA)

2005 Cohorts

• Warren Cheun

  • Supervisor: PhD student in Wyeth Wasserman Lab (Medical Genetics, UBC)
  • Personal background: I have an undergraduate degree in Microbiology, and a Master’s degree in Computer Science, and I entered the Bioinformatics program to combine these passions.
  • Research interests: I’m interested in novel methods and algorithms – the application of computational resources to more efficiently solve existing and novel problems to inform and improve our knowledge of the human biology. I want to use computers to live better lives!
  • Personal website: http://dnahelix.org

2004 Cohorts

• Yvonne Li – Ph.D. student in Steve Jones Lab (Genome Sciences Centre, UBC)