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