ismb/eccb 2004
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ISMB/ECCB 2004 Meeting Report
Glasgow, July 31- August 4
ISMB/ECCB 2004 Meeting Report
Glasgow, July 31- August 4
(http://www.iscb.org/ismbeccb2004/)
Peter E.M. Taschner
PT 9-04
ISMB/ECCB 2004
• Intelligent Systems for Molecular Biology• European Conference on Computational
Biology• ~2000 participants• 8 keynote speakers• 50 long and 17 short talks
– published in Bioinformatics 20, Suppl 1• 900 posters
PT 9-04
Keynote Speakers
• Leroy Hood: Systems biology• Dennis Noble: Heart rhythm simulation• Eric Green: Multiple species comparison to
decode the human genome• Svante Pääbo: Primate transcriptome
evolution
Keynote Speakers
• Matthias Mann: Organellar & Time resolved proteomics
• Anna Tramontano: Protein structure prediction
• Uri Alon: Simplicity in complex networks• David Lipman: Message & meaning in
sequence comparison
Keynote Speaker: Eric Green
Multiple species comparison to decode the human genome – CFTR pilot study
• 1600 multiplely conserved sequences (MCS) in 1.8 Mb CFTR region
• 22% CDS, 3.5 % UTR, 2.5 % repeats• 72 % unknown function, mostly unique • 66 % of MCS mentioned in literature• Approach does not detect lineage-specific elements
Multiple species comparison
Which organism gives most information, when compared to man?
• Gap in metazoan evolutionary tree: mammals vs. others
• Marsupials and monotremes seem to fill the gap and should be sequenced
• Best choice: Platypus, bargain: chicken• Fugu: good for CDS, not for other elements
Keynote Speaker: Uri Alon
Simplicity in complex networks
• Most genes one step from transcription factor• Certain network patterns appear more often than
expected: – FFL: feed forward loop (40 x in E. coli, 74 in yeast)– IFFL: Incoherent feed forward loop– SIM: single input module– DOR: densely overlapping regulons
Network pattern functions
• Feed forward loop:– Asymmetric filter for
transient signals allowing fast shutdown
• Incoherent feed forward loop:– Pulse generator
Network pattern functions
• Single input module:– Just in time production,
matching temporal gene expression– flagellar synthesis
• Densely overlapping regulons: – Resemble hardwired decision
making systems– carbon utilization– osmotic stress response
ISMB/ECCB 2004 topics
• Data mining• Data visualization• Databases• Functional
genomics• Genome annotation• Microarrays
PT 9-04
• New frontiers• Phylogeny and
evolution• Predictive methods• Sequence comparison• Structural biology• Systems biology
Database maintenance and curation problems
• Data depositories (Genbank, Swiss-Prot, ..) are flooded by whole genome sequencing projects
• Manual annotation and curation not feasible
• Automatic annotation and curation error-prone– improved sequence annotation and prediction software
needed
Coin and Durbin: Pseudogene Identification
• Pseudogenes – often mis-annotated– regarded as fossils, but:
• Expressed pseudogenes (2-3%) may be functional as regulatory RNAs– Yano et al. J Mol Med 82: 414 (2004)
• PSILC: improved identification by including Pfam domain information
Dieterich et al.: Functional inference of transcription factor binding sites (TFBS)
• Prediction of conserved TFBS using CORG (http://corg.molgen.mpg.de) combine with
• Cell cycle phase assignment (Whitfield)
• 22 non-exonic and 11 5'-UTR functional TFBS predicted
Data mining
• Reactome – biological processes in man knowledgebase (http://www.reactome.org/)
• H-Invitational Database (H-Inv DB) (http://www.h-invitational.jp)
TraitMap (http://omicspace.riken.jp/gps/index.html)
New frontiers
Data integration:
• GRID computing: workflows
• Data access via web services– Simple Object Access Protocol (SOAP)
(messaging protocol for transporting information) – Web Services Description Language (WSDL)
Databases• cPath: Cancer pathway database
(www.cbio.mskcc.org/cpath/)
• Online Predicted Human Interaction Database (http://ophid.utoronto.ca/)
• Bioinformatics knowledge database (https://apps.bioneq.qc.ca/twiki/bin/view/Knowledgebase/)
Functional genomics• Comparative mouse genomics center consortium
genotype database(http://mrages.niehs.nih.gov/genotype)
• INCLUSive webportal: analysis of gene expression and discovery of cis-regulatory elements(http://www.esat.kuleuven.ac.be/inclusive)
Predictive methods
• Darogan – Enzyme function prediction from conserved functional residues (http://www.darogan.com/)
• Phobius – combined TM topology and signal peptide predictor (http://phobius.cgb.ki.se/)
Structural biology
• Macromolecular Structure Database (MSD) (http://www.ebi.ac.uk/msd/index.html)
Systems biology
• SciPath – Integrated environment for SB analysis (http://www.ucl.ac.uk/oncology/MicroCore/scipath.htm)
• Pathway and interaction network modeling
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