Biology by other means



Monday, September 22

8:00 Registration opens
9:30 Workshop 1:
Annotation, interpretation and management of Mutations (AIMM): What makes sense?
Workshop 2:
Networks: Theory and Practice in Biology
Tutorial 1:
From sequence to structure and function: Structural modeling of proteins and protein-DNA complexes by comparative methods
Tutorial 2:
Microarray data analysis and quality assessment, ArrayExpress and BioConductor
Tutorial 3:
Exploration and analysis of Protein-Protein Interactions (PPIs)
Tutorial 4:
Interoperability of bioinformatics software and databases
11:00 Coffee break
11:30 Workshop 1:
Workshop 2:
Tutorial 1:
Tutorial 2:
Tutorial 3:
Tutorial 4:
13:00 Lunch
14:00 Workshop 1:
Workshop 2:
Tutorial 1:
Tutorial 2:
Tutorial 3:
Tutorial 4:
15:30 Coffee break
16:00 Workshop 1:
Workshop 2:
Tutorial 1:
Tutorial 2:
Tutorial 3:
Tutorial 4:
17:30 Conference opening
18:00 Keynote: Eric Davidson 
The global logic of development, as visualized in the sea urchin embryo gene regulatory network
18:50 Annotation of Metagenome Short Reads Using Proxygenes
Victor Markowitz, Daniel Dalevi, Konstantinos Mavrommatis, Natalia Ivanova, Ernest Szeto, Philip Hugenholtz and Nikos Kyrpides
19:15 PhosphoPOINT: a comprehensive human kinase interactome and phospho-protein database
Chia-Ying Yang, Chao-Hui Chang, Ya-Ling Yu, Tsu-Chun Emma Lin, Sheng-An Lee, Chueh-Chuan Yen, Jinn-Moon Yang, Jin-Mei Lai, Yi-Ren Hong, Tzu-Ling Tseng, Kun-Mao Chao and Chi-Ying F Huang
19:40 Organization and integration of biomedical knowledge with concept maps for key peroxisomal pathways
Marcel Willemsen, Gerbert Jansen, Jasper Komen, Sander van Hooff, Hans Waterham, Pedro Brites, Ronald Wanders and Antoine van Kampen

Opening reception

Tuesday, September 23

8:30 Registration opens
9:00 Keynote: Trey Ideker
Protein Networks in Cancer
9:50 Functional Coherence in Domain Interaction Networks
Jayesh Pandey, Mehmet Koyuturk, Shankar Subramaniam and Ananth Grama
10:15 An Integrative Approach for Predicting Interactions of Protein Regions
Sven-Eric Schelhorn, Thomas Lengauer and Mario Albrecht
10:40 Nonparametric estimation of posterior error probabilities associated with peptides identified by tandem mass spectrometry
Lukas Käll, John D Storey and William Stafford Noble
11:05 Coffee break and poster viewing
12:10 De novo identification of metabolites by analyzing tandem mass spectra
Sebastian Boecker and Florian Rasche
12:35 An environmental perspective on large-scale genome clustering based on metabolic capabilities
Gabi Kastenmüller, Johann Gasteiger and Hans-Werner Mewes
13:00 Lunch
14:30 Fusing Time Series Expression Data through Hybrid Aggregation and Hierarchical Merge
Elena Tsiporkova and Veselka Boeva
14:55 Gaussian Process Modelling of Latent Chemical Species: Applications to Inferring Transcription Fact
Pei Gao, Antti Honkela, Magnus Rattray and Neil Lawrence
16:10 Coffee break and poster session 1
18:00 SIRENE: Supervised Inference of Regulatory Networks
Fantine Mordelet and Jean-Phlippe Vert
18:25 PhyloDetect: A likelihood-based strategy for detecting microorganisms with diagnostic microarrays
Hubert Rehrauer, Susan Schönmann, Leo Eberl and Ralph Schlapbach
18:50 Clinically driven semi-supervised class discovery in gene expression data
Israel Steinfeld, Roy Navon, Diego Ardigò, Ivana Zavaroni and Zohar Yakhini
19:15 Elixir: The European Life sciences Infrastructure for Biological Information
Janet Thornton
19:30 Keynote: Eske Willerslev
Ancient DNA
20:20 Reception and poster viewing

Wednesday, September 24

8:30 Registration opens
9:00 Keynote: Christine Orengo
Predicting Protein Functions and Networks - a Family Centric Approach
9:50 Protein Structure Alignment considering Phenotypic Plasticity
Gergely Csaba, Fabian Birzele and Ralf Zimmer
10:15 Detection of 3D atomic similarities and their use in the discrimination of small-molecule protein binding sites
Rafael Najmanovich, Natalja Kurbatova and Janet M Thornton
10:40 RNA structure alignment by a unit-vector approach
Emidio Capriotti and Marc A. Marti-Renom.
11:05 Coffee break and poster viewing
11:45 Comparison of vocabularies, representations and ranking algorithms for gene prioritization by text mining
Shi Yu, Steven Van Vooren, Leon-Charles Tranchevent, Bart De Moor and Yves Moreau
12:10 Inter–species normalization of gene mentions with GNAT
Joerg Hakenberg, Conrad Plake, Robert Leaman, Michael Schroeder and Graciela Gonzalez


Conference Outing

Thursday, September 25

8:30 Registration opens
9:30   Burkhard Rost
ISMB/ECCB 09 Advertisement
9:50 Analysis of Segmental Duplications via Duplication Distance
Crystal Kahn and Benjamin Raphael
10:15 A Fast and Flexible Method for the Segmentation of aCGH Data
Erez Ben-Yaacov and Yonina Eldar
10:40 Poisson Adjacency Distributions in Genome Comparison: Multichromosomal, Circular, Signed and Unsign
Wei Xu, Benoît Alain and David Sankoff
11:05 Coffee break and poster viewing
11:45 HapCUT: An efficient and accurate Algorithm for the Haplotype Assembly Problem
Vikas Bansal and Vineet Bafna
12:10 Efficient representation and p-value computation for high order Markov motifs
Paulo Fonseca, Christian Gautier, Katia Guimarães and Marie-France Sagot
12:35 Mining significant tree patterns in carbohydrate sugar chains
Kosuke Hashimoto, Ichigaku Takigawa, Motoki Shiga, Minoru Kanehisa and Hiroshi Mamitsuka
13:00 Lunch
14:30 Optimal Spliced Alignments of Short Sequence Reads
Fabio de Bona, Stephan Ossowski, Korbinian Schneeberger and Gunnar Rätsch
14:55 ChIPmix: Mixture model of regressions for two-color ChIP-chip analysis
Marie-Laure Martin-Magniette, Tristan Mary-Huard, Caroline Bérard and Stéphane Robin
15:30 Segment-based multiple sequence alignment
Tobias Rausch, Anne-Katrin Emde, David Weese, Andreas Döring, Cedric Notredame and Knut Reinert
16:10 Coffee break and poster session 2
18:00 Connect the dots: Exposing hidden protein family connections from the entire sequence tree
Yaniv Loewenstein and Michal Linial
18:25 Improved Network-based Identification of Protein Orthologs
Nir Yosef, Roded Sharan and William Stafford Noble
18:50 Comprehensive in silico mutagenesis highlights functionally important residues in proteins
Yana Bromberg and Burkhard Rost
19:15 Italian Bioinformatics Society (BITS) award for the best italian PhD thesis in Bioinformatics
19:30 Computational simulations of protein-protein recognition:
predicting mutational effects on the binding thermodynamics

Daniele Dell'Orco
20:20 Reception and poster viewing

Friday, September 26

8:30 Registration opens
9:00 Automatic decomposition of kinetic models of signaling networks minimizing the retroactivity among modules
Julio Saez-Rodriguez, Stefan Gayer, Martin Ginkel and Ernst Dieter Gilles
9:25 From minimal signed circuits to the dynamics of Boolean regulatory networks
Elisabeth Remy and Paul Ruet
9:50 Temporal Logic Patterns for Querying Dynamic Models of Cellular Interaction Networks
Pedro T Monteiro, Delphine Ropers, Radu Mateescu, Ana T. Freitas and Hidde de Jong.
10:15 Logical modelling of the role of the Hh pathway in the patterning of the Drosophila wing disc.
Aitor Gonzalez, Claudine Chaouiya and Denis Thieffry
10:40 Coffee break and poster viewing
11:10 Gain and Loss of Phosphorylation Sites as an Active Mechanism in Cancer
Predrag Radivojac, Peter Baenziger, Maricel Kann, Matthew Hahn, Matthew Mort and Sean Mooney
11:35 Logical Analysis of Survival Data: Prognostic survival models by detecting high degree interactions
Louis-Philippe Kronek and Reddy Anupama
12:00 Keynote: Alfonso Valencia
Protein interactions, an evolutionary perspective
12:50 Closing cerimony



Demo sessions
Date Time Room Presenter
September 23rd 10:00-11:00   Hall B
  14:30-15:30   Hall B wwPDB
September 24th 10:00-11:00   Hall B IBM
September 25th 10:00-11:00   Hall B Oxford University Press
14:30-15:30   Hall B Instituto Nacional de Bioinformática