1 / 23

PSB RECAP: Genomic Hula

PSB RECAP: Genomic Hula. 2002 Kaua’i, Hawaii. Na Pali Coast. Wailua and Jurassic Falls. Conference Site. Breakdown of PSB Schedule. Tutorials 2 Keynote Lectures 7 Diverse sessions most of which had discussion sections Poster session featured insane 1 minute overview.

speciale
Download Presentation

PSB RECAP: Genomic Hula

An Image/Link below is provided (as is) to download presentation Download Policy: Content on the Website is provided to you AS IS for your information and personal use and may not be sold / licensed / shared on other websites without getting consent from its author. Content is provided to you AS IS for your information and personal use only. Download presentation by click this link. While downloading, if for some reason you are not able to download a presentation, the publisher may have deleted the file from their server. During download, if you can't get a presentation, the file might be deleted by the publisher.

E N D

Presentation Transcript

  1. PSB RECAP: Genomic Hula 2002 Kaua’i, Hawaii

  2. Na Pali Coast

  3. Wailua and Jurassic Falls

  4. Conference Site

  5. Breakdown of PSB Schedule • Tutorials • 2 Keynote Lectures • 7 Diverse sessions • most of which had discussion sections • Poster session • featured insane 1 minute overview

  6. Genome-Wide Analysis and Comparative Genetics Goal: Bridge gap between comparative computational genomics and biology Emphasis on algorithms for comparative mapping and new approaches to analysis

  7. Genome-Wide Analysis and Comparative Genetics • Volkmuth and Alexandrov: Evidence for sequence-independent evolutionary traces in genomics data • fold: structural motif used as building block in proteins • traces: conservation of fold along the genome and genes that are correlated in expression are more apt to share a fold • use these traces to infer fold of protein and improve ability to predict biochemical function

  8. Genome-Wide Analysis and Comparative Genetics • Goldberg, McCouch & Kleinberg: Constructing comparative genome maps with unresolved map order • stack algorithm to compute marker order by optimizing parsimony criterion • casts mapping as labeling problem: two genomes are base and target. Need to label the segments of the target using names of linkage groups from the base. • Algorithm is generic - no species specific information

  9. Keynote Lecture 1: David Botstein “Extracting Biologically Interesting Information from Microarray” • Role of microarrays is to direct other experiments • “Charge Ahead!” • Major effects view -- opposite of hypothesis driven experiments • Interesting twist on talk given at Penn

  10. Literature Data Mining for Biology Most key information still free text in journals and comment fields of databases Need for consensus evaluation

  11. Literature Data Mining for Biology • Ding, Berleant, Nettleton and Wurtele: Mining Medline: abstracts, sentences or phrases? • Systematic comparison of using abstracts, sentences or phrases in automated mining information retrieval • Examined recall, precision, and effectiveness using these different units to mine interactions among biochemical terms based on term co-occurrences

  12. Keynote Lecture 2: Rebecca Eisenberg: Bioinformatics, Bioinformation and Biomolecules: the role and limitations of patents • Interesting discussion about fine line with patents between protecting work and common good

  13. Human Genome Variation: Disease, Drug Response and Clinical Phenotypes • Need for clinical phenotype annotations in analysis between genotype/haplotype and phenotype • Celera Infomercial on new high throughput SNP genotyping automated computer system • 95% accuracy with fully automated QC system

  14. Human Genome Variation: Disease, Drug Response and Clinical Phenotypes • Oliver, Rubin, Stuart, Hewett, Klein and Altman: Ontology development for a pharmacogenetics knowledge base • Issue of mapping ontologies to external data sources • http://www.pharmgkb.org

  15. Phylogenetic Genomics and Genomic Phylogenetics • Utilization of genomic order and information about duplication events • Wang, Jansen, Moret, Raubeson, and Warnow “Fast Phylogenetic Algorithms for the analysis of genome rearrangement data: an empirical study” • Presents 2 new methods of character coding for parsimony-based analysis of genomic rearrangement (i.e. gene orders as sequences of state characters)

  16. Genome Pathway and Interaction Bioinformatics • Collection and organization of pathway information is critical and needs to be addressed • Hartemink et al.: Bayesian approach that incorporates genomic location and expression data • Idea of simplifying subset used in model

  17. Genome Pathway and Interaction Bioinformatics: Discussion • Hartemink: need unification after proliferation of ideas • Shrager: fiction of pathways and stasis • Karp: comparative studies of pathways (convservation and divergence, correlation among pathways, idea of “pathway variance”) • need for systematic comparison of databases

  18. Genome Pathway and Interaction Bioinformatics: Discussion • Andre: Use of ontologies, connection with text mining (Geneways) • Garvey: Biospice.org Simulation program for integrated circuit evaluation and in silico experiments

  19. Proteins: Structure, Function and Evolution Approaches to determine protein structure and function New emphasis on evolutionary models to get at this problem

  20. Proteins: Structure, Function and Evolution • Nielsen and Huelsenbeck: Detecting positively selected amino acid sites using posterior predictive p-values • elegant approach to detecting selected sites that may have structural or functional importance • phylogenetic mapping of mutations from multiple sequence alignment

  21. Ab initio computations of protein structure - Harold Scheraga • Goal is to determine how interactions lead to folded structure (not to predict structure) • Modeling is based only on energy • Excellent results in CASP3 and CASP4 • Not actually clear if this approach achieves it goal

More Related