Computational Biology Relevant Seminars in Toronto

Upcoming

• This page has been superseded by http://compbio.cs.toronto.edu/cbl/events.htm

Past

• Thu.June.14.2007 - Probabilistic model building heuristics and dynamic systems for bioinformatics - Dr. Robin Gras, Associate Professor and Canadian Research Chair in Probabilistic Heuristics and Bioinformatics, School of Computer Science, University of Windsor - Centre for Addiction and Mental Health, 250 College Street, Room G50 (Ground Floor), 10:00 am
• Mon.June.25.2007 - Tools for Protein Research: "Proteome Analyst" and Metacomputing for Prion Research - Paul Lu, Department of Computing Science, University of Alberta - Bahen 1230, 11:00 am
• Wed.May.30.2007 - Complex network analysis of free-energy landscapes: from a clustering to a coarse-graining strategy - David Gfeller, Laboratoire de Biophysique Statistique, SB/ITP, Ecole Polytechnique Fédérale de Lausanne, Switzerland - CCBR Red room at 3:30pm
• Tues.May.29.2007 - A network perspective on the evolution of metabolism by gene duplication. - Juan Javier Díaz-Mejía - 11am. CCBR Red room
• Fri.May.25.2007 - Computer Simulation as a Tool for Exploring Cytoskeletal Dynamics - Garrett Odell - 12:00 pm. ESCB142
• Mon.May.7.2007 - Learning from The Worm: Predicting Phenotype From Genotype - Dr. Andrew Fraser - 2:00 p.m. CCBR, 2nd floor, Red room
• Mon.May.7.2007 - Physical Module Networks: An Integrative Probabilistic Model of Transcription Regulation - Noa Novershtern - 11:00 a.m. Pratt 290C
• Fri.May.4.2007 - Deciphering and Modulating Cellular Signaling with Combinatorial Biology - Dr. Sachdev Sidhu - 11:00 a.m. CCBR, 2nd floor, Red room
• Mon.Apr.30.2007 - The Value of Protein-Protein Interaction Networks for Disease Research - Dr. Eric Wanker, Neuroproteomics, Max Delbrueck Center for Molecular Medicine (MDC), Berlin-Buch, Germany - 11:30 a.m. CCBR Red Seminar Room
• Mon.Apr.30.2007 - Collapse or Collaborate: Experimental and Mathematical Analyses of a Synthetic Cooperative System - Wenying Shou - 1.10pm CCBR Red Seminar Room.
• Fri.Apr.20.2007 - Integrated computational biology: avoiding fusion of illusion and confusion - Igor Jurisica, Ph.D. Scientist, Division of Signaling Biology, Ontario Cancer Institute - 3:00 p.m. Samuel Lunenfeld Research Institute of Mount Sinai Hospital, 9th Floor, Room 968
• Tue.Apr.24.2007 - Microarray Technologies for Genome Analysis and Drug Discovery - Corey Nislow - 11:00 a.m. CCBR, 2nd floor, Red room
• Thu.Mar.1.2007 - The Role of Microtubules in the Establishment of Cellular Coordinates - Dr. Rafael Carazo-Salas, Cancer Research UK. - 11.00 am, Ramsey Wright, Rm. 432, 25 Harbord St.

• Mon.Feb.26.2007 - MouseFunc: A Competition for Mouse Gene Function Prediction - Lourdes Peña Castillo, Banting & Best Dept. of Medical Research, University of Toronto. - 11.00 am in Pratt 290C

  • Abstract: In this talk I will describe the MouseFunc project where the goal is to evaluate various computational methods to predict mouse gene functions using genomic data from heterogeneus sources. Several algorithms using diverse genomic data have been applied to gene function prediction, but these have been primarily tested on the unicellular yeast S. cerevisiae. To facilitate prediction of mouse gene function, identify strengths and weaknesses of existing functional genomic datasets and compare algorithm performance, we assembled a collection of genomic data on the mouse M. Musculus. Nine bioinformatics teams used this dataset to independently train classifiers and generate predictions of function for 21,603 mouse genes. Performance between the teams was assessed using both a held-out test set of genes and a prospective evaluation of novel predictions.

• Mon.Feb.26.2007 - Evolution of Regulatory Sequences and Systems - Dr. Alan Moses, Wellcome-Trust Sanger Institute, UK. - 11.00 am, Ramsey Wright, Rm. 432, 25 Harbord St.
• Wed.Feb.21.2007 - Regulation by negative feedback in systems biology: a control- theoretic approach - Dr. Brian Ingalls, University of Waterloo - 11.00 am, Red seminar room (2nd floor), Donnelly CCBR, 160 College Street
• Thu.Feb.22.2007 - Decoding the Regulatory Genome - Dr. Olivier Elemento, Lewis-Sigler Institute for Integrative Genomics, Princeton U. - 11.00 am, Ramsey Wright, Rm. 432, 25 Harbord St.
• Tue.Feb.20.2007 - Predicting protein-protein interactions by machine learning methods - Xuejian Xiong, Tyers Lab - 12.00 pm, MSH, Rm. 968
• Mon.Feb.19.2007 - Systems Biology of Cancer - Dr. Jussi Taipale, Institute of Biomedicine, University of Helsinki - 4.00 pm, Red Room CCBR
• Mon.Feb.19.2007 - Evolution of Chromosome Organization is Driven by Selection for Reduced Gene Expression Noise - Dr. Nizar Batada, University of Bath, UK. - 11.00 am, Ramsey Wright, Rm. 432, 25 Harbord St.

• Thu.Feb.15.2007 - Phenotypic Robustness & Variation: Molecular Mechanisms & Evolutionary Impact - Dr. Christine Queitsch, FAS Center for Systems Biology, Harvard U. - 11.30 am, Ramsey Wright, Rm. 432, 25 Harbord St.

• Wed.Feb.14.2007 - GYF Domains - Binding Specificities and Interaction Partners - Michael Kofler. Ph.D - 1.00 pm, MSH, Rm. 968
• Mon.Feb.12.2007 - From Static Interaction Networks to Dynamic Biological Systems - Dr. Denis Dupuy, Dana Farber Cancer Institute - 11.00 am, Ramsey Wright, Rm. 432, 25 Harbord St.
• Fri.Feb.2.2007 - Probing Cell Death with Small Molecules - Brent Stockwell - 12.00 pm, Earth Sciences Centre, Rm. B142, 5 Bancroft Avenue, basement level
• Thu.Feb.1.2007 - Gene-centered transcription regulatory networks in the nematode - A.J. Marian Walhout, Assistant Professor - 2:00 pm, Red seminar room (2nd floor), Donnelly CCBR, 160 College Street
• Mon.Jan.22.2007 - Active site specificity profiling of protein kinases - Benjamin E. Turk, Ph.D - 1.00pm, Red seminar room (2nd floor), Donnelly CCBR, 160 College Street

• Fri.Jan.19.2007 - Spatio-Temporal Simulations of Cellular Processes - Dr. John Parkinson, Hospital for Sick Children Research Institute - 4:00 p.m., at Fields Institute, Room 230 More info

• Tue.Jan.16.2007 - The Integrity of the Genome: Tiling arrays and other technologies to understand function - Corey Nislow - 2:00 p.m., Red Seminar Room, CCBR

• Mon.Dec.18.2006 - BioEdge: A tool box for advanced analyses of biochemical networks - Dr. Yves Deville - 2:30 p.m., at Sick Kids, Room 1527 (Hill Wing)

• Tue.Dec.12.2006 - High Resolution Models of Genome Regulatory Events - David K. Gifford, Computational Genomics Research Group, MIT - 2:00 p.m., Red Seminar Room

• Mon.Dec11.2006 - Finding Differences between Proteomes: A Modern Day Needle in a Haystack Problem - Michael MacCoss, University of Washington - 4:00 p.m. in the Red Seminar Room

• Mon.Dec.11.2006 - Convergent Evolution of Common Structural Features in Antifreeze Proteins - Brendan McConkey, University of Waterloo - 1:00pm - 2:00pm, Room 1250 Elm Wing, Hospital for Sick Children

• Fri.Dec.8.2006 - Nick Morrice - Identification of Protein Phosphorylation Sites by mass spectrometry; what's possible and what's not - University of Dundee - SLRI 968 @ 2pm
• Tues.Dec.5.2006 - The Third Rebuttal of the Random Breakage Theory - Pavel Pevzner - UCSD - 11:00AM Bahen 1180

  • Rearrangements are genomic earthquakes that change the chromosomal architectures. The fundamental question in molecular evolution is whether there exist chromosomal faults where rearrangements are happening over and over again. In 1984 Nadeau and Taylor proposed Random Breakage Model (RBM) of chromosome evolution that recently caused a controversy. RBM postulates that rearrangements are random, and thus there is no rearrangement hot-spots in mammalian genomes. It was embraced by biologists from the very beginning (due to its prophetic prediction power) but in 2003 was refuted by Pevzner and Tesler who gave a non-constructive argument against RBM using a combinatorial theorem. They further proposed Fragile Breakage Model that postulates that mammalian genomes represent a mosaic of fragile and solid regions. However, the rebuttal of RBM caused a controversy and shortly after RBM was refuted, Sankoff and Trinh, 2004 gave a rebuttal of the rebuttal of RBM. Sankoff and Trinh, 2004 did not question the validity of combinatorial arguments in Pevzner and Tesler, 2003 but instead argued that the synteny block generation algorithm is parameter-dependent and that rebuttal of RBM is more subtle than it may look like at the first glance. Recently, Peng et al., 2006 re-examined the Sankoff-Trinh arguments and demonstrated that they fell victims to their inaccurate synteny block generation algorithm that fails even on small toy examples. They further demonstrated that if Sankoff and Trinh had fixed these problems and chosen realistic parameters, their arguments against Pevzner and Tesler, 2003 would disappear. Sankoff, 2006 recently acknowledged the flaw in Sankoff and Trinh, 2004 but still appeared reluctant to acknowledge the validity of the Pevzner-Tesler rebuttal of RBM, this time arguing that a larger set of rearrangement operations (e.g., transpositions) may explain the "fragile regions" and that the "block deletion" argument in Sankoff and Trinh, 2004 is still valid. In this talk we give a rebuttal of the rebuttal (Sankoff, 2006) } of the rebuttal (Peng et al., 2006) of the rebuttal (sankoff and Trinh, 2004) of the rebuttal (Pevzner and Tesler, 2003) of RBM. This is a joint work with Max Alekseyev, Qian Peng, and Glenn Tesler.

• Tues.Dec.5.2006 - Genome-wide Assays and Chemical Genomics to Understand Drug Action and Gene Function - Guri Nina Giaever - CCBR Red Room
• Mon.Dec.4.2006 - Viruses in the Ocean: The largest unexplored reservoir of genetic diversity on Earth - Curtis Suttle - noon in the Red Room of CCBR
• Tues.Nov.28.2006 - Inventing Algorithms for Exploring the Biomolecular Universe - Brendan Frey - Rosebrugh Building, Rm 211 @ 4pm
• Mon.Nov.20.2006 - Integrating genomics and proteomics data to predict gene function - Quaid Morris - 4pm - MSB 4279
• Fri.Nov.17.2006 - Gary Bader - 1pm - CCBR Red Room
• Nov.6.2006 - How the brain learns representations - Geoff Hinton- 4:30 p.m., Room 140, University College, 15 King's College Circle, University of Toronto
  • Abstract: The brain converts the highly variable signals in millions of optic nerve fibres into stable internal representations of familiar objects. Computational neuroscientists are beginning to understand how to create self-organizing networks of simulated neurons in which sensible internal representations of the external world emerge from the interaction between simple learning rules and the richly structured sensory input.
• Nov.2.2006 - Dr. Nevan Krogan - Biology without bias: functional insights from high resolution genetic and protein-protein interaction maps - Department of Cellular and Molecular Pharmacology, California Institute for Quantitative Biomedical Research School of Medicine - 12:00 - 1:00pm @ 7-605; 610 University Avenue, Toronto, Ontario

• Nov.2.2006 - Construction of Gene Network via Composite Likelihood Approach - Xin Gao, York University - 4pm in Sidney Smith Hall 1074

• July.18.2006 (Tuesday) @ 10am in CCBR Red Room - Genomic Analyses of Transcription Factors and Cis Regulatory Elements - Dr. Martha L. Bulyk, Division of Genetics, Department of Medicine; Department of Pathology; Harvard-MIT Division of Health Sciences & Technology; Brigham & Women's Hospital and Harvard Medical School, Boston, Massachusetts

  • The interactions between transcription factors (TFs) and their DNA binding sites are an integral part of the cellular regulatory networks that control gene expression. Previously, we developed a DNA microarray-based in vitro technology that allows the rapid, high-throughput characterization of the DNA binding site sequence specificities of TFs in a single day. We plan to use PBM data on the DNA binding specificities of metazoan TFs for more accurate prediction of cis regulatory modules within the vast noncoding portions of those organisms' genomes. Specifically, we are inferring co-regulation by sets of TFs through an integrated analysis of gene expression data, TF binding site motif data, and prediction of cis regulatory modules. Examples of the prediction of cis regulatory modules conforming to a core cis regulatory code inferred in such a way will be shown for the founder cell population in the Drosophila embryonic mesoderm.
• July 13, 2006 (Thursday) @ 12:00 in Rm. 4171 Medical Sciences Building - Information Discovery for Genome Data - Yi-Ping Phoebe Chen, Associate Professor, School of Engineering and Information Technology, Faculty of Science and Technology, Deakin University, Burwood Campus, Melbourne, Australia

  • Dr. Yi-Ping Phoebe Chen is a Group Leader of Bioinformatics Research and head of the Multimedia Stream. She leads two research areas: Bioinformatics and Multimedia and hosts the ARC Centre in Bioinformatics from 2003 to 2007. She is also a founder of the Asia-Pacific Bioinformatics Conference. http://www.deakin.edu.au/~phoebe/

• July.10.2006 (Monday) @ 4pm in MSB room 4279 - Predicting Links in Biological Systems of PDZ Domains - Gary Bader
• July.6.2006 (Thursday) @ 4pm in 6th floor, Room 6-604, OCI (610 University Ave) Application of shot-gun proteomics to mammalian biology Dr. Thomas Kislinger

• June.1.2006 (Thursday) @ 4pm in SidSmith 1072 - Biomarker discovery: fact or artefact? - Robert Tibshirani, Stanford University

• May.25.2006 (Thursday) @ noon in CCBR red room - Rapidly Evolving Transcription Factors: Investigating Their Role in Shaping Species-Specific Regulatory Networks and Biological Traits - Lisa Stubbs, LLNL poster.pdf CANCELLED

• May.18.2006 (Thursday) @ 2pm in PrattBuilding 290C - Predicting links in biological networks - Gary Bader

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