Our computational biology research is focused on genome analysis, with an emphasis on the identification and characterization of regulatory sequences controlling the transcription of genes. Cells respond to diverse stimuli by altering gene activity. Subtle alterations of the regulatory network can produce dramatic phenotypic consequences. Past and ongoing projects are linked to the central goals of understanding how genes are regulated and learning how to apply this knowledge to advance biomedical research. You can learn about many of our projects via our group homepage at http://www.cisreg.ca/.
IDENTIFICATION AND ANALYSIS OF SEQUENCES REGULATING TRANSCRIPTION
Regulatory sequence analysis is complicated by a signal-to-noise problem. Transcription is regulated at one level by proteins that bind to short segments of DNA. These transcription factors activate or suppress gene activity by modulating the recruitment of RNA polymerase enzymes to the beginning of genes. As the target sequences for transcription factors are short, and transcription factors are tolerant of considerable variation in the sequences to which they bind, it is extremely difficult to distinguish functional binding sites in the vastness of the human genome.
Using high-throughput ChIP-Seq and chromatin property data, we are developing a new generation of bioinformatics methods for the identification of regulatory sequences. Our work is increasingly focused on coupling the regulatory region discrimination with the interpretation of mutations detected by whole genome sequencing.
APPLIED BIOINFORMATICS AND GENOME ANALYSIS
At the CMMT and BC Children’s Hospital Research Institute we maintain a strong link between research and application. We work closely with both our research and clinical collaborators to impact human health by coming genetics and bioinformatics approaches to data analysis. At present we are engineering regulatory sequences to direct gene expression selectively to target cells and tissues in the CanEuCre/Pleiades Promoter Project. With clinical partners at BC Children’s Hospital, we have established methods for efficient analysis of exome and whole genome sequences for children with diagnosed genetic disorders. We are continuing to expand the ways in which we perform genome analysis and strive combine our expertise in transcriptional regulation with genome analysis in a way which directly impacts patient care.
NOTICE FOR POTENTIAL APPLICANTS
Our team is constantly changing. The students and post-docs in the group have historically done well, with alumni working in both industry and academia. We take pride in teamwork and maintaining a positive research environment. Opportunities are always available for exceptional students and post-docs. Computer programming skills are essential—we work in a linux/Macintosh environment and develop our own software.
Post-doc candidates with good publication records are strongly encouraged to apply. Graduate students should consider the UBC Bioinformatics Graduate Program, although on occasion we directly accept students with demonstrated interest in our research. Motivated undergraduate students with strong computer skills are welcomed, particularly during the summer (May-August). In all cases early contact is best—it gives us time to plan for space, resources and the scientific project.