Molecular and Computational Systems Biology Seminars
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We are now organizing the second seminar series entitled "SFU Molecular and
Computational Systems Biology Seminar" at the SFU Burnaby Campus. This
series of interdisciplinary seminars are devoted to reviewing the
progress in the emerging and exciting field of systems biology. More
importantly, it will promote interactions, collaborations, and bridge gaps
between computing science/mathematics and biology. Although presentations
will be given primarily by people from SFU campuses, as we did in 2007, we will bring
scientists in, but not limited to, the entire Greater Vancouver area to
present their exciting research activities in this field. Systems Biology has been regarded as the next major project after the genome sequencing projects. The success of the Human Genome Project, the many subsequent genome sequencing projects, and especially the functional genomics projects (microarray, proteomics, SAGE, RNA interference, transgenetics, gene knock-out, protein-protein interactions, protein-DNA interactions, etc.), have produced an enormous volume of data and set up a solid platform for understanding biology at the "systems" level (the "systems biology"). To achieve this goal, and to effectively mine these rich data resources, many molecular, statistical, and computational methods have been developed and applied. These approaches are producing predictive models of cellular systems which are providing novel insights into biological processes and disease. We will hear about these exciting new developments in these seminars. These seminars will be held once per month. We look forward to your participation and would encourage you to get your students involved as presenters. Please forward to us possible presentation topics and preferred dates so that we can continue to form a schedule for this series. Organizers Cenk Sahinalp, Ph.D. School of Computing Science Eldon Emberly, Ph.D. Department of Physics Jack Chen, Ph.D. Department of Molecular Biology and Biochemistry |
All seminars in 2008 will be held at 4:00 PM on the second Wednesday of each month. Most seminars will be held in SFU IRMACS Centre (room 10900) with a few exceptions (see the schedule below for details).
Schedule
| Date | Speakers/Titles | Room |
|---|---|---|
| Jan 16, 2008 |
Speaker: Eldon Emberly, Department of Physics Title:Oscillations in Biological Networks Abstract: Many biological processes such as circadian rhythms or the cell cycle rely upon an oscillating biochemical signal to set the timing of events. These oscillations are generated by groups of molecules whose interactions are such that they produce an oscillating chemical signal. In this talk I will discuss two specific systems: circadian oscillations in photosynthetic bacteria and the cell cycle network of the asymmetrically dividing bacteria, caulobacter. I will highlight how physical modeling of these systems has provided novel insights into the molecular mechanisms that govern their oscillatory behaviour. |
SSB6178 |
| Date | Speakers/Titles | Room |
| Feb 13, 2008 |
Speaker: Dr. Peter Unrau , Department of Molecular Biology and Biochemistry Title: RNA silencing in land plants Abstract: RNA silencing (RNA interference) is a process found in most eukaryotes that regulates gene expression via the expression of small RNAs. We initially became interested in RNA silencing after unexpectedly finding that the vast majority of small RNAs from an angiosperm (tobacco) are terminally modified (Ebhardt et al., PNAS 2005). The characterization of this biochemistry led us to perform a survey of small RNA expression across the land plants. We found that in contrast to the relatively well studied angiosperms, the conifers (i.e. pines) have a distinctive small RNA expression pattern. This difference was characterized further by comparing the sequences of small RNAs produced by a conifer (Lodgepool pine, 130,998 reads) and an angiosperm (Rice, 11,329 reads) using a variety of bioinformatic techniques. Interestingly, the unique small RNA profile found in the conifers may be correlated with the apparent presence of a novel Dicer family in the conifers that is not found in the angiosperms. |
IRMACS 10900 |
| Date | Speakers/Titles | Room |
| Mar 12, 2008 |
Speaker: Dr. Steven Hallam, Department of Microbiology and Immunology, UBC Title: Beautiful Monsters: Assembly Problems and Solutions in Metagenome Analysis Abstract: Microorganisms represent the invisible majority of living things on planet Earth. Interdependent constituents of this vast microbial biota play critical roles in defining the biogeochemical gradients that drive the cycling of essential elements and nutrients. Such cycles support the trophic needs of all life forms and regulate global-scale atmospheric, terrestrial and oceanic processes. At the same time, rampant or aberrant microbial growth has the potential to negatively impact the health of individuals and ecosystems. Because the vast majority of microorganisms resist laboratory cultivation, our views on the extent of this diversity have been severely limited. Environmental genomics, also known as metagenomics, applies methods of DNA library production, high-throughput sequencing and downstream in silico analysis to explore the taxonomic and metabolic diversity of naturally occurring microbial populations as they relate to ecosystem health and function. One of the fundamental challenges to this approach is the identification of sequences derived from discrete organisms or “species” within a complex and heterogeneous sequence space. This problem is further compounded by microdiversity within the genomes of closely related members of a single population. The identification of related and interacting gene repertoires within this landscape, and the functional annotation of hypothetical gene models represent central challenges to both genome assembly and metabolic reconstruction efforts. This seminar will review current computational methods used to chart metagenomic sequence space with special emphasis on the microbial species concept, taxonomic binning, and the assembly of ordered tiling paths from environmental genomic data sets. |
IRMACS 10900 |
| Date | Speakers/Titles | Room |
| Apr 9, 2008 |
Speaker: Dr. Cedric Chauve, Department of Mathematics Title: Using gene clusters for reconstructing ancestral gene orders Abstract: There was recently paper by Jian Ma et al. (UCSC), published in Genome Research (2006) and an interesting discussion in the same journal about the comparison of cytogenetics and bioinformatics methods for inferring the karyotype and genome architecture of the ancestral vertebrate genome. In collaboration with Eric Tannier (INRIA Lyon, France) we propose a general framework for reconstructing an ancestral genome architecture from current genome sequences, based on using (1) conserved gene clusters notions that generalize the conserved adjacencies used in Ma et al. (2) algorithmical and combinatorial tools used in the field of of physical mapping. We illustrate our method on two datasets: one (7 genomes, no outgroup) based on the paper of Murphy et al in Science (2005) and one (8 genomes, two outgroups) based on the whole genome alignments available on the UCSC Genome Browser. Our method suggest that an approach based on models of genome rearrangements, when used with synteny blocks of sufficiently large size, is able to capture an interesting signal that is in agreement with cytogenetics. More importantly, I will also point several methodoligical issues that are important when using genome rerrangements models for inferring ancestral genome architectures. |
IRMACS 10900 |
| Date | Speakers/Titles | Room |
| May 14, 2008 |
Speaker: Dr. Michel Leroux, Department of Molecular Biology and Biochemistry Title: Abstract: |
TBA |
| Date | Speakers/Titles | Room |
| Jun 11, 2008 |
Speaker: Mike Kobor, CMMT Title: Abstract: |
IRMACS 10900 |
| Date | Speakers/Titles | Room |
| July 9, 2008 |
Speaker: Title: Abstract: |
IRMACS 10900 |