Schedule

FINAL SCHEDULE



Sunday, September 26 – Workshops and Tutorials


08:30

Workshop and tutorial registration

09:00

ESCS1 Student
Symposium

Tutorial 1 Working with next-generation sequencing data

Tutorial 2
Use of semantic web resources in computational biology and bioinformatics

Tutorial 3 Current methods and applications for regulatory sequence analysis

Tutorial 4 Protein structure validation

Workshop 1 Learning from perturbation effects

Workshop 2 Annotation, Interpretation and Management of Mutations (AIMM)

10:30

Coffee break

11:00

ESCS1 (cont’d)

Tutorial 1
(cont’d)

Tutorial 2
(cont’d)

Tutorial 3
(cont’d)

Tutorial 4
(cont’d)

Workshop 1
(cont’d)

Workshop 2
(cont’d)

12:30

Lunch

13:30

ESCS1 (cont’d)

Tutorial 1
(cont’d)

Tutorial 2
(cont’d)

Tutorial 3
(cont’d)

Tutorial 4
(cont’d)

Workshop 1
(cont’d)

Workshop 2
(cont’d)

15:00

Coffee break

15:30

ESCS1 (cont’d)

Tutorial 1
(cont’d)

Tutorial 2
(cont’d)

Tutorial 3
(cont’d)

Tutorial 4
(cont’d)

Workshop 1
(cont’d)

Workshop 2
(cont’d)

17:00

End of workshops and tutorials



Sunday, September 26 – Conference Opening


16:00

Conference registration open

17:30

Conference opening and welcome

17:40

Keynote 1 - Peer Bork
Systemic analysis of biological systems: lessons from a small single bacterium and a large complex community

18:30

PT1 - Utopia Documents: linking scholarly literature with research data. Teresa K. Attwood, Douglas B. Kell, Philip McDermott, James Marsh, Steve Pettifer and David Thorne.

18:50

PT2 - Integrating genome assemblies with MAIA. Jurgen Nijkamp, Wynand Winterbach, Marcel van den Broek, Jean-Marc Daran, Marcel Reinders and Dick de Ridder.

19:10

PT3 - A Graphical Method for Reducing and Relating Models in Systems Biology. Steven Gay, Sylvain Soliman and François Fages.

19:30

Walk to the reception venue

20:00

Welcome reception

21:30

End of welcome reception


Monday, September 27


08:30

Registration and welcome breakfast & business announcements

09:00

Keynote 2 - Michael J. E. Sternberg
Modeling protein structure, function, and interactions


PROCEEDINGS TRACK

TECH TRACK

09:50

PT4 - Vorescore - Fold Recognition improved by Rescoring of Protein Structure Models. Gergely Csaba and Ralf Zimmer.

TT1 - Software for the data-driven researcher of the future. Paul Fisher et al.

10:10

PT5 - Solenoid and Non-solenoid Protein Recognition Using Stationary Wavelet Packet Transform. An Vo, Nha Nguyen and Heng Huang.

10:30

PT6 - Discriminatory Power of RNA Family Models. Christian Hoener zu Siederdissen and Ivo L. Hofacker.

TT2 - Clinical genomic analysis at IBM: from HIV positive to Hypertension. Michal Rosen-Zvi et al.

10:50

PT7 - RactIP: fast and accurate prediction of RNA-RNA interaction using integer programming. Yuki Kato, Kengo Sato, Michiaki Hamada, Yoshihide Watanabe, Kiyoshi Asai and Tatsuya Akutsu.

11:10

Coffee break

11:40

PT8 - Semi-Supervised Multi-Task Learning for Predicting Interactions between HIV-1 and Human Proteins. Yanjun Qi, Oznur Tastan, Jaime G. Carbonell, Judith Klein-Seetharaman and Jason Weston.

TT3 - The Microsoft Biology Foundation. Simon Mercer et al.

12:00

PT9 - Candidate gene prioritization based on spatially mapped gene expression: an application to XLMR. Rosario M. Piro, Ivan Molineris, Ugo Ala, Paolo Provero and Ferdinando Di Cunto.


PROCEEDINGS TRACK

TECH TRACK

12:20

PT10 - Prediction of a prostate cancer regulatory network from gene expression, microRNA and clinical data. Eric Bonnet, Tom Michoel and Yves Van de Peer.

TT4 - Study capturing: from research question to sample annotation. Kees van Bochove et al.

12:40

PT11 - Inferring Cancer Subnetwork Markers using Density-Constrained Biclustering. Phuong Dao, Recep Colak, Raheleh Salari, Flavia Moser, Elai Davicioni, Alexander Schoenhuth and Martin Ester.

13:00

Lunch

14:15

PT12 - Modeling associations between genetic markers using Bayesian networks. Edwin Villanueva and Carlos Dias Maciel.

TT5 - NextGen biology with TIBCO Spotfire. Christof Gaenzler et al.

14:35

PT13 - Mass Spectrometry Data Processing Using Zero-Crossing Lines in Multi-Scale of Gaussian Derivative Wavelet. Nha Nguyen, Heng Huang, Soontorn Oraintara and An Vo.

14:55

PT14 - Detecting host factors involved in virus infection by observing the clustering of infected cells in siRNA screening images. Apichat Suratanee, Ilka Wörz, Petr Matula, Anil Kumar, Lars Kaderali, Karl Rohr, Ralf Bartenschlager, Roland Eils and Rainer König.

TT6 - Partitioning biological data with transitivity clustering. Jan Baumbach et al.

15:15

Announcement of ISMB/ECCB 2011 and ECCB 2012

15:30

Coffee break

16:00

Keynote 3 – Elaine Mardis. Analysis of whole-genome sequencing data from paired tumor and normal genomes

16:50

PT15 - Characteristics of 454 Pyrosequencing Data – Enabling Realistic Simulation with Flowsim. Susanne Balzer, Ketil Malde, Anders Lanzén, Animesh Sharma and Inge Jonassen.

ART MEETS SCIENCE
The Cosmopolitan Chicken Research Project. Koen Van Mechelen, Jean-Jacques Cassiman.

17:10

PT16 - A Fast algorithm for Exact Sequence search in Biological Sequences using Polyphase Decomposition. Abhilash Srikantha, Ajit Bopardikar, Kalyan Kaipa, Venkataraman Parthasarathy, KyuSang Lee, TaeJin Ahn and Rangavittal Narayanan.

17:30

PT17 - Classification of ncRNAs using position and size information in deep sequencing data. Florian Erhard and Ralf Zimmer.

17:50

Poster session (ODD numbers) & drinks

19:50

End of day


Tuesday, September 28


08:30

Registration and business announcements

9:00

Keynote 4 - Rainer Spang
From large data sets to small networks


PROCEEDINGS TRACK

TECH TRACK

09:50

PT18 - Prototypes of elementary functional loops unravel evolutionary connections between protein functions. Alexander Goncearenco and Igor Berezovsky.


10:10

PT19 - Improved sequence-based prediction of disordered regions with multilayer fusion of multiple information sources. Marcin J. Mizianty, Wojciech Stach, Ke Chen, Kanaka Durga Kedarisetti, Fatemeh Miri Disfani and Lukasz Kurgan.

TT7 - CLC bio, A Comprehensive Platform for NGS Data Analysis. Roald Forsberg

10:30

PT20 - A predictor for toxin-like proteins reveals cell modulators within viral genomes. Guy Naamati, Manor Askenazi and Michal Linial.

10:50

Coffee break

11:20

PT21 - Discriminative and informative features for biomolecular text mining with ensemble feature selection. Sofie Van Landeghem, Thomas Abeel, Yvan Saeys and Yves Van de Peer.

TT8 - DNA Sequencing with Illumina Instruments and Chemistry: Current and Future Applications. Klaus Maisinger

11:40

PT22 - BioXSD: the common data-exchange format for everyday bioinformatics Web services. Matúš Kalaš, Pål Puntervoll, Alexandre Joseph, Edita Bartaševičiūtė, Armin Töpfer, Prabakar Venkataraman, Steve Pettifer, Jan Christian Bryne, Jon Ison, Christophe Blanchet, Kristoffer Rapacki and Inge Jonassen.

12:00

PT23 - Improving Disease Gene Prioritization using the Semantic Similarity of Gene Ontology Terms. Andreas Schlicker, Thomas Lengauer and Mario Albrecht.

TT9 - Super-scale sequence data analysis with hybrid core computing. John Leidel

12:20

PT24 - Discovering drug interactions: a text-mining and reasoning approach based on properties of drug metabolism. Luis Tari, Saadat Anwar, Shanshan Liang, James Cai and Chitta Baral.

12:40

Lunch

14:10

PT25 - Nonlinear dimension reduction and clustering by Minimum Curvilinearity unfold neuropathic pain and tissue embryological classes. Carlo Vittorio Cannistraci, Timothy Ravasi, Franco Maria Montevecchi, Trey Ideker and Massimo Alessio.

TT10 - How robust are NGS whole-genome assemblies‌ A case study with plant genomes. Niina Haiminen, Laxmi Parida

14:30

PT26 - A Varying Threshold Method for ChIP Peak-Calling Using Multiple Sources of Information. - KuanBei Chen and Yu Zhang.

14:50

PT27 - is-rSNP: A novel technique for in silico regulatory SNP detection. Geoff Macintyre, James Bailey, Izhak Haviv and Adam Kowalczyk.


15:10

Poster session (EVEN numbers) with coffee

17:10

Bus departures to Bruges

17:30

Ride to Bruges

18:30

Free time in Bruges

20:00

Banquet Dinner

22:30

Busses to Ghent

00:00

Last bus to Ghent



Wednesday, September 29


08:30

Registration and business announcements

09:00

Keynote 4 - Hans Westerhoff
Computing the flows of life


PROCEEDINGS TRACK

TECH TRACK

09:50

PT28 - Efficient parameter search for qualitative models of regulatory networks using symbolic model checking. Gregory Batt, Michel Page, Irene Cantone, Gregor Goessler, Pedro Monteiro and Hidde de Jong.

TT11 - Data integration in proteomics through EnVsion and EnCore webservices. Rafael Jimenez et al.

10:10

PT29 - Bayesian experts in exploring reaction kinetics of transcription circuits. Ryo Yoshida, Masaya Saito, Hiromichi Nagao and Tomoyuki Higuchi.

10:30

PT30 - Dynamic Deterministic Effects Propagation Networks: learning signalling pathways from longitudinal protein array data. Christian Bender, Frauke Henjes, Holger Fröhlich, Stefan Wiemann, Ulrike Korf and Tim Beißbarth.

TT12 - ELIXIR: A Sustainable European Infrastructure for Biological Information. Andrew Lyall.

10:50

PT31 - A novel approach for determining environment-specific protein costs: The case of Arabidopsis thaliana. Max Sajitz-Hermstein and Zoran Nikoloski.

11:10

Coffee break

11:40

PT32 - Decorrelating expression in gene-set analysis. Dougu Nam.

TT13 - The Protein Data Bank in Europe (PDBe) - Bringing Structure to Biology. Wim Vranken et al.

12:00

PT33 - How threshold behaviour affects the use of subgraphs for network comparison. Tiago Rito, Zi Wang, Charlotte Deane and Gesine Reinert.


PROCEEDINGS TRACK

TECH TRACK

12:20

PT34 - Discovering Graphical Granger Causality Using the Truncating Lasso Penalty. Ali Shojaie and George Michailidis.

TT14 - The Universal Protein Resource (UniProt). Maria J. Martin.

12:40

Lunch

14:00

PT35 - Parsimony and Likelihood Reconstruction of Human Segmental Duplications. Crystal Kahn, Benjamin Raphael and Borislav Hristov.


TT15 - Accurate next gen sequencing data analysis on cloud computing. Attila Bérces et al.


14:20

PT36 - Maximum Likelihood Estimation of Locus-Specific Mutation Rates in Y-chromosome Short Tandem Repeats. Osnat Ravid-amir and Saharon Rosset.


14:40

Coffee break

15:10

Keynote 6 – Yves Van de Peer
The evolutionary significance of ancient whole genome duplications and computational approaches to unveiling them

16:00

Closing remarks and awards

16:30

END OF CONFERENCE