Schedule

[Download the full program book - 100 pages pdf]

Sept. 6-7: WORKSHOPS, TUTORIALS and SATELLITE MEETINGS

Saturday, September 6th, 9:00 - 18:00 :  Workshops and Tutorials, Satellite meeting: ISCB European Student Council Symposium.

Sunday, September 7th, 9:00 - 17:30 : Workshops and Tutorials, Satellite meeting: Junior Principal Investigator Meeting.

Location: PMC and Forum, to know where will be your event, look at the summary table.

Sept. 7-10: MAIN CONFERENCE

Schedule

[Download the schedule "to go" - 5 pages pdf]

  Venue : PALAIS DE LA MUSIQUE ET DES CONGRES (PMC), Strasbourg, FRANCE

Sessions Contents

REMARKS
- The order of presentation is not defined yet.
- When the same topic is distributed over two sessions, the talk distribution between the sessions can still undergo modifications.
- Affiliation is indicated only for presenting author (underlined)

- The conference Proceedings will be available for download from the Bioinformatics Oxford University Press web site from August 27, 2014.

Sunday, September 7, 2014

Opening Session

Monday, September 8, 2014

[Download the program of Monday (schedule+abstracts) - 12 pages pdf]

Session Mon1 : Pathways and Molecular Networks 

Chair : Ralf Zimmer, Anaïs Baudot

• HubAlign: An accurate and efficient method for global alignment of protein-protein interaction networks. Daniella Boernigen, Somaye Hashemifar and Jinbo Xu. Toyota Technological Institute at Chicago, United States.
• Alignment-free protein interaction network comparison. Waqar Ali, Tiago Rito, Gesine Reinert,  Fengzhu Sun and Charlotte M. Deane. University of Oxford, United Kingdom.
• From Area J - Methods and Technologies for Computational Biology: Fast randomisation of large genomic datasets while preserving alteration counts. Andrea Gobbi, Francesco Iorio, Kevin J. Dawson, David C. Wedge, David Tamborero, Ludmil B. Alexandrov, Nuria Lopez-Bigas, Mathew J. Garnett, Giuseppe Jurman and Julio Saez-Rodriguez. EMBL - European Bioinformatics Institute, United Kingdom.

Session Mon2 : Pathways and Molecular Networks (2)

Chair : Ralf Zimmer, Anais Baudot

• Identifying transcription factor complexes and their roles. Thorsten Will and Volkhard Helms. Saarland University, Germany.
• Personalized identification of altered pathways in cancer. Taejin Ahn, Eunjin Lee, Nam Huh and Taesung Park. Seoul National University, Republic of Corea.
• Highlight Talk: Wiring miRNAs to pathways: a topological approach to integrate miRNA and mRNA expression profiles. Enrica Calura, Paolo Martini, Gabriele Sales and Chiara Romualdi. University of Padova, Italy.

Session Mon3 : Sequencing and Sequence Analysis for Genomics (1)

Chair : Dominique Lavenier

• Lambda: The Local Aligner for Massive Biological Data. Hannes Hauswedell, Jochen Singer and Knut Reinert. Freie Universität Berlin, Germany.
• Fiona: a parallel and automatic strategy for read error correction. Marcel Schulz, David Weese, Manuel Holtgrewe, Viktoria Dimitrova, Sijia Niu, Knut Reinert and Hugues Richard. Saarland University & Max Planck Institute for Informatics, Saarbrücken, Germany.
• Highlight Talk: Comparison of mapping algorithms used in high-throughput sequencing: application to Ion Torrent data. Ségolène Caboche, Christophe Audebert, Yves Lemoine and David Hot. Lille University, France.

Session Mon4 : Sequencing and Sequence Analysis for Genomics (2)

Chair : Stéphane Robin

• FastHap: fast and accurate single individual haplotype reconstruction using fuzzy conflict graphs. Sepideh Mazrouee and Wei Wang. University of California Los Angeles, United States.
• Probabilistic single-individual haplotyping. Volodymyr Kuleshov. Stanford University, United States.
• From Area J - Methods and Technologies for Computational Biology: cnvOffSeq: detecting intergenic copy number variation using off-target exome sequencing data. Evangelos Bellos and Lachlan Coin. Imperial College London, United Kingdom.

Session Mon5 : Evolution and Population genomics (1)

Chair : Romain Studer, Hélène Chiapello

• Polytomy Refinement for the Correction of Dubious Duplications in Gene Trees. Manuel Lafond, Cedric Chauve, Riccardo Dondi and Nadia El-Mabrouk. University of Montreal, Canada.
• RidgeRace: Ridge regression for continuous ancestral character estimation on phylogenetic trees. Christina Kratsch and Alice McHardy. Heinrich-Heine-University Düsseldorf, Germany.
• Point estimates in phylogenetic reconstructions. Philipp Benner, Miroslav Bacak and Pierre-Yves Bourguignon. Max Planck Institute for Mathematics in the Sciences, Leipzig, Germany.

Session Mon6 : Evolution and Population genomics (2)

Chair : Romain Studer, Hélène Chiapello

• ASTRAL: Genome-Scale Coalescent-Based Species Tree Estimation. Siavash Mirarab, Rezwana Reaz Rimpi, Md. Shamsuzzoha Bayzid, Théo Zimmermann, Shel Swenson and Tandy Warnow. University of Texas - Austin, United States.
• Highlight Talk: Patterns of positive selection in seven ant genomes. Julien Roux, Eyal Privman, Sébastien Moretti, Josephine Daub, Marc Robinson-Rechavi and Laurent Keller. University of Lausanne, Switzerland.

Session Mon7 : Structural Bioinformatics (1)

Chair : Torsten Schwede, Anna Tramontano

• Assessing the local structural quality of transmembrane protein models using statistical potentials (QMEANBrane). Gabriel Studer, Marco Biasini and Torsten Schwede. Biozentrum, Swiss Institute of Bioinformatics, Switzerland
• A new statistical framework to assess structural alignment quality using information compression. James Collier, Lloyd Allison, Arthur Lesk, Maria Garcia de La Banda and Arun Konagurthu. Monash University, Australia.
• From Area J - Methods and Technologies for Computational Biology: Entropy driven partitioning of the hierarchical protein space. Nadav Rappoport, Amos Stern, Nathan Linial and Michal Linial. The Hebrew University of Jerusalem, Israel.

Session Mon8 : Structural Bioinformatics (2)

Chair : Torsten Schwede, Anna Tramontano

• PconsFold: Improved contact predictions improve protein models. Mirco Michel, Sikander Hayat, Marcin J. Skwark, Chris Sander, Debora S. Marks and Arne Elofsson. Stockholm University, Sweden.
• From Area J - Methods and Technologies for Computational Biology: Microarray R-based Analysis of Complex Lysate Experiments with MIRACLE. Markus List, Ines Block, Marlene Lemvig Pedersen, Helle Christiansen, Steffen Schmidt, Mads Thomassen, Qihua Tan, Jan Baumbach and Jan Mollenhauer. University of Southern Denmark, Denmark.
• Highlight Talk: Comprehensive analysis of DNA polymerase III alpha subunits and their homologs in bacterial genomes. Kęstutis Timinskas, Monika Balvočiūtė, Albertas Timinskas and Česlovas Venclovas. Vilnius University, Lithuania.

Tuesday, September 9, 2014

[Download the program of Tuesday (schedule+abstracts) - 9 pages pdf]

Session Tue1 : Computational Systems Biology (1)

Chair : Oliver Kohlbacher, Anne Siegel

• Stronger findings for metabolomics through Bayesian modeling of multiple peaks and compound correlations. Tommi Suvitaival, Simon Rogers and Samuel Kaski. Aalto University, Finland.
• Causal network inference using biochemical kinetics. Chris Oates, Frank Dondelinger, Nora Bayani, James Korkola, Joe Gray and Sach Mukherjee. University of Warwick, United Kingdom.
• Highlight Talk: High-dimensional Bayesian parameter estimation: Case study for a model of JAK2/STAT5 signaling. Sabine Hug, Andreas Raue, Jan Hasenauer, Julie Bachmann, Ursula Klingmüller, Jens Timmer and Fabian J. Theis. Helmholtz Zentrum München, Germany.

Session Tue2 : Computational Systems Biology (2)

Chair : Oliver Kohlbacher, Anne Siegel

• Effects of small particle numbers on long-term behaviour in discrete biochemical systems. Peter Kreyssig, Christian Wozar, Stephan Peter, Tomas Veloz, Bashar Ibrahim and Peter Dittrich. Friedrich-Schiller-University Jena, Germany.
• TEMPI: Probabilistic modeling Time-Evolving differential PPI networks with MultiPle Information. Yongsoo Kim, Jin-Hyeok Jang, Seungjin Choi and Daehee Hwang. Daegu Gyeongbuk Institute of Science and Technology, Republic of Corea.
• Experimental design schemes for learning Boolean network models. Nir Atias, Michal Gershenzon, Katia Labazin and Roded Sharan. Tel Aviv University, Israel.

Session Tue3 : Bioinformatics of Health and Disease (1)

Chair : Emmanuel Barillot

• OncodriveROLE classifies cancer driver genes in Loss of Function and Activating mode of action. Michael Philipp Schroeder, Carlota Rubio-Perez, David Tamborero, Abel Gonzalez-Perez and Nuria Lopez-Bigas. Universitat Pompeu Fabra, Barcelona, Spain.
• ContrastRank: a new method for ranking putative cancer driver genes and classification of tumor samples. Rui Tian, Malay Basu and Emidio Capriotti. University of Alabama at Birmingham, United States.
• Drug susceptibility prediction against a panel of drugs using kernelized Bayesian multitask learning. Mehmet Gönen and Adam A. Margolin. Sage Bionetworks, Seattle, United States.

Session Tue4 : Biological Knowledge Discovery from data

Chair : Dietrich Rebholz-Schuhmann

• Unveiling new biological relationships using shared hits of chemical screening assay pairs. Xueping Liu and Monica Campillos. Helmholtz Center Munich, Germany.
• Identification of structural features in chemicals associated with cancer drug response: A systematic data-driven analysis. Suleiman Ali Khan, Seppo Virtanen, Olli Kallioniemi, Krister Wennerberg, Antti Poso and Samuel Kaski. Aalto University, Finland.
• Highlight Talk: Shaping the interaction landscape of bioactive molecules. David Gfeller, Aurelien Grosdidier, Matthias Wirth, Antoine Daina, Olivier Michielin and Vincent Zoete. Swiss Institute of Bioinformatics, Lausanne, Switzerland.

Session Tue5 : Gene Expression (1)

Chair : Morgane Thomas-Chollier, Caroline Friedel

• Estimating the activity of transcription factors by the effect on their target genes. Theresa Schacht, Marcus Oswald, Roland Eils, Stefan Eichmueller and Rainer Koenig. Jena University Hospital, Germany.
• Modeling DNA methylation dynamics with approaches from phylogenetics. John A. Capra and Dennis Kostka. University of Pittsburgh, United States.
• Highlight Talk: Key regulators control distinct transcriptional programmes in blood and progenitor and mast cells. Felicia Ng, Fernando Calero-Nieto, Nicola Wilson, Rebecca Hannah, Victoria Moignard, Ana Leal-Cervantes, Isabel Jimenez-Madrid, Evangelia Diamanti, Lorenz Wernisch and Berthold Gottgens. MRC et Welcome trust, Cambridge, United Kingdom.

Session Tue6 : Gene Expression (2)

Chair : Morgane Thomas-Chollier, Caroline Friedel

• Two-dimensional segmentation for analyzing HiC data. Celine Levy-Leduc, Maud Delattre, Tristan Mary-Huard and Stephane Robin. AgroParisTech, INRA, France.
• Broad-Enrich: Functional interpretation of large sets of broad genomic regions. Raymond Cavalcante, Chee Lee, Ryan Welch, Snehal Patil, Terry Weymouth, Laura Scott and Maureen Sartor. University of Michigan, United States.
• Highlight Talk: Chromatin Position Effects Quantified from Thousands of Reporters Integrated in Parallel. Lodewyk Wessels, Waseem Akhtar, Johann de Jong, Alex Pindyurin, Ludo Pagie, Wouter Meuleman, Jeroen de Ridder, Anton Berns, Maarten van Lohuizen and Bas van Steensel. Netherlands Cancer Institute, Amsterdam, The Netherlands.

Wednesday, September 10, 2014

[Download the program of Wednesday (schedule+abstracts) - 6 pages pdf] 

Session Wed1 : Biological Ontologies

Chair : Katy Wolstencroft

• The impact of incomplete knowledge on the evaluation of protein function prediction: a structured-output learning perspective. Yuxiang Jiang, Wyatt Clark, Iddo Friedberg and Predrag Radivojac. Indiana University Bloomington, United States.
• Integration of molecular network data reconstructs Gene Ontology. Vladimir Gligorijevic, Vuk Janjic and Natasa Przulj. Imperial College London, United Kingdom.

Session Wed2 : Bioinformatics of Health and Disease (2) and Bio-imaging

Chair : Lodewyk Wessels

• Transcriptome-guided amyloid imaging genetic analysis via a novel structured sparse learning algorithm. Jingwen Yan, Lei Du, Sungeun Kim, Shannon Risacher, Heng Huang, Jason Moore, Andrew Saykin and Li Shen. Indiana University, Indianapolis, United States.
• Large-Scale Automated Identification of Mouse Brain Cells in Confocal Light Sheet Microscopy Images. Paolo Frasconi, Ludovico Silvestri, Paolo Soda, Roberto Cortini, Francesco Pavone and Giulio Iannello. University of Florence, Italy.
• Highlight Talk: Novel Developments in computational clinical breath analysis and biomarker detection. Anne-Christin Hauschild, Jörg Ingo Baumbach and Jan Baumbach. University of Southern Denmark, Denmark.

Session Wed3 : Text Mining for Computational Biology

Chair : Claire Nedellec

• Extracting patterns of database and software usage from the bioinformatics literature. Geraint Duck, Goran Nenadic, Andy Brass, David Robertson and Robert Stevens. The University of Manchester, United Kingdom.
• Highlight Talk: Text mining technologies for database curation. Fabio Rinaldi, Simon Clematide, Simon Hafner, Gerold Schneider, Gintare Grigonyte, Martin Romacker and Therese Vachon. University of Zurich, Switzerland.

Session Wed4 : RNA prediction

Chair : Yann Ponty

• CRISPRstrand: Predicting repeat orientations to determine the crRNA-encoding strand at CRISPR loci. Omer S. Alkhnbashi, Fabrizio Costa, Shiraz A. Shah, Roger A. Garrett, Sita J. Saunders and Rolf Backofen. Albert-Ludwigs-University Freiburg, Germany.
• Towards a piRNA prediction using multiple kernel fusion and support vector machine. Jocelyn Brayet, Farida Zehraoui, Laurence Jeanson-Leh, David Israeli and Fariza Tahi. University of Evry, France.