Dr. Roth's interdisciplinary research focuses on the application of statistical machine learning to problems in high dimensional cancer biology. This research program encompasses the development of computational methods for studying clonal population structures and tumour evolution, as well as methodological work in computational statistics

Members

Faculty/Leaders

Staff

Students/Trainees

Naila Adam

Graduate Student

Kevin Chern

Graduate Student

Matteo Lepur

Graduate Student

Austin Smith

Co-op Student

Shaocheng Wu

Graduate Student

Open Positions

Research Programmer

Job Information

Classification Title: Information Systems & Technology (A)

Business Title: Research Programmer

Department: Pathology

Job Summary

A position with the Department of Pathology and Laboratory Medicine of the University of British Columbia is open immediately for a research programmer to work with our interdisciplinary team of researchers and software developers within the Department of Molecular Oncology at BC Cancer, part of the Provincial Health Services Authority. We are seeking a creative, experienced, and dedicated individual to play a key role in the bioinformatics analysis of computational genomic research data.

The research programmer will work with other team members and researchers in the department to conduct computational analysis, ranging from routine runs to novel discovery tasks.  With detailed instructions, you will be finding and applying bioinformatics algorithms to computational genomics problems.  When appropriate, your solutions will be deployed in full production processes, and you will work closely with other programmers to ensure the successful implementation and  deployment of automated workflows and analyses.

You will be on-site in the Department of Molecular Oncology at BC Cancer, working closely with software developers, students and researchers operating at the leading edge of the field of cancer genomics.  Our department has recently made meaningful advances in the understanding of tumour evolution and the software platforms developed in the lab will be used by world-leading scientists at BC Cancer and international collaborators to gain insight into how cancers initiate, develop and acquire resistance to treatment. More information on the department and research we conduct can be found here http://molonc.bccrc.ca/

Organizational Status

We are a small team of software developers and scientists embedded within a larger cancer research department.  You will be working with students and researchers to tackle genomics problems, and collaborating with developers and bioinformaticians on the team to develop high-throughput and automated analysis solutions.  You will be reporting to the bioinformatics team lead or designate.

Work Performed

Research and implement bioinformatics solution as requested

Perform simple to complex bioinformatics analysis and requests with supervision

As a team member, develop, test and automate bioinformatics solutions

Handle bioinformatics data retrieval, processing and dissemination requests

Assist researchers in computational, statistical and visualization tasks for publication

Consequences of Error

You will be receiving instructions from researchers, students and collaborators and will be responsible for the correctness of your work.  Failure to perform may result in setbacks to research and operational activity.

Supervision Received

You will be supervised by the bioinformatics team lead or designate.

Supervision Given

You will help advise and recommend best course of actions to other members of the lab on subjects pertaining to bioinformatics analysis and your field of expertise.

Education / Work Experience

Essential

BSc in bioinformatics, computer science, or equivalent

Minimum 2 year of additional relevant work/educational experience in genomics

Proven bioinformatics research experience

Experience with data analysis in R and Python

Experience with command-line interfaces and scripting in UNIX operating systems

Experience designing and creating analysis workflows and pipelines

Experience with next-generation sequencing (NGS) data

Preferred

MSc in bioinformatics, computer science or equivalent

Experience with scientific high performance computing environments

Experience with bioinformatics data management solutions

Selected Publications

Divergent clonal selection dominates medulloblastoma at recurrence.

Nature, 2016
Morrissy, A Sorana, Garzia, Livia, Shih, David J H, Zuyderduyn, Scott, Huang, Xi, Skowron, Patryk, Remke, Marc, Cavalli, Florence M G, Ramaswamy, Vijay, Lindsay, Patricia E, Jelveh, Salomeh, Donovan, Laura K, Wang, Xin, Luu, Betty, Zayne, Kory, Li, Yisu, Mayoh, Chelsea, Thiessen, Nina, Mercier, Eloi, Mungall, Karen L, Ma, Yusanne, Tse, Kane, Zeng, Thomas, Shumansky, Karey, Roth, Andrew J L, Shah, Sohrab, Farooq, Hamza, Kijima, Noriyuki, Holgado, Borja L, Lee, John J Y, Matan-Lithwick, Stuart, Liu, Jessica, Mack, Stephen C, Manno, Alex, Michealraj, K A, Nor, Carolina, Peacock, John, Qin, Lei, Reimand, Juri, Rolider, Adi, Thompson, Yuan Y, Wu, Xiaochong, Pugh, Trevor, Ally, Adrian, Bilenky, Mikhail, Butterfield, Yaron S N, Carlsen, Rebecca, Cheng, Young, Chuah, Eric, Corbett, Richard D, Dhalla, Noreen, He, An, Lee, Darlene, Li, Haiyan I, Long, William, Mayo, Michael, Plettner, Patrick, Qian, Jenny Q, Schein, Jacqueline E, Tam, Angela, Wong, Tina, Birol, Inanc, Zhao, Yongjun, Faria, Claudia C, Pimentel, José, Nunes, Sofia, Shalaby, Tarek, Grotzer, Michael, Pollack, Ian F, Hamilton, Ronald L, Li, Xiao-Nan, Bendel, Anne E, Fults, Daniel W, Walter, Andrew W, Kumabe, Toshihiro, Tominaga, Teiji, Collins, V Peter, Cho, Yoon-Jae, Hoffman, Caitlin, Lyden, David, Wisoff, Jeffrey H, Garvin, James H, Stearns, Duncan S, Massimi, Luca, Schüller, Ulrich, Sterba, Jaroslav, Zitterbart, Karel, Puget, Stephanie, Ayrault, Olivier, Dunn, Sandra E, Tirapelli, Daniela P C, Carlotti, Carlos G, Wheeler, Helen, Hallahan, Andrew R, Ingram, Wendy, MacDonald, Tobey J, Olson, Jeffrey J, Van Meir, Erwin G, Lee, Ji-Yeoun, Wang, Kyu-Chang, Kim, Seung-Ki, Cho, Byung-Kyu, Pietsch, Torsten, Fleischhack, Gudrun, Tippelt, Stephan, Ra, Young Shin, Bailey, Simon, Lindsey, Janet C, Clifford, Steven C, Eberhart, Charles G, Cooper, Michael K, Packer, Roger J, Massimino, Maura, Garre, Maria Luisa, Bartels, Ute, Tabori, Uri, Hawkins, Cynthia E, Dirks, Peter, Bouffet, Eric, Rutka, James T, Wechsler-Reya, Robert J, Weiss, William A, Collier, Lara S, Dupuy, Adam J, Korshunov, Andrey, Jones, David T W, Kool, Marcel, Northcott, Paul A, Pfister, Stefan M, Largaespada, David A, Mungall, Andrew J, Moore, Richard A, Jabado, Nada, Bader, Gary D, Jones, Steven J M, Malkin, David, Marra, Marco A, Taylor, Michael D

Distinct evolutionary trajectories of primary high-grade serous ovarian cancers revealed through spatial mutational profiling.

The Journal of pathology, 2013
Bashashati, Ali, Ha, Gavin, Tone, Alicia, Ding, Jiarui, Prentice, Leah M, Roth, Andrew, Rosner, Jamie, Shumansky, Karey, Kalloger, Steve, Senz, Janine, Yang, Winnie, McConechy, Melissa, Melnyk, Nataliya, Anglesio, Michael, Luk, Margaret T Y, Tse, Kane, Zeng, Thomas, Moore, Richard, Zhao, Yongjun, Marra, Marco A, Gilks, Blake, Yip, Stephen, Huntsman, David G, McAlpine, Jessica N, Shah, Sohrab P

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