ECCB'12 Proceedings Presentations


All proceedings papers are available as open access at: OUP Bioinformatics.


Sequencing and Sequence Analysis


Telescoper: De novo Assembly of Highly Repetitive Regions. Ma'Ayan Bresler, Sara Sheehan, Andrew Chan and Yun S. Song.

  Long read alignment based on maximal exact match seeds. Yongchao Liu and Bertil Schmidt.
  Indel-tolerant Read Mapping with Trinucleotide Frequencies using Cache-Oblivious kd-Trees. Md Mahmud, John Wiedenhoeft and Alexander Schliep.

DELLY: Structural variant discovery by integrated paired-end and split-read analysis. Tobias Rausch, Thomas Zichner, Andreas Schlattl, Adrian Stütz, Vladimir Benes and Jan Korbel.

  Decoding properties of tRNA leave a detectable signal in codon usage bias. Alexander Roth.
  Accurate Estimation of Short Read Mapping Quality for Next Generation Genome Sequencing. Matthew Ruffalo, Mehmet Koyuturk, Soumya Ray and Thomas LaFramboise.

MetaCluster 5.0: A two-round binning approach for metagenomic data for low-abundance species in a noisy sample. Yi Wang, Henry C.M. Leung, S.M. Yiu and Francis Y.L. Chin.

  Stitching Gene Fragments with a Network Matching Algorithm Improves Gene Assembly for Metagenomics. Yu-Wei Wu, Mina Rho, Thomas Doak and Yuzhen Ye.

Mutations, Variations, and Population Genomics

  An exome sequencing pipeline for identifying and genotyping common CNVs associated with disease with application to psoriasis. Lachlan Coin, Dandan Cao, Xin Jin, Yingrui Li, Jun Wang and Ren Jingjing.

Nonlinear dimension reduction with Wright-Fisher kernel for genotype aggregation and association mapping. Hongjie Zhu, Lexin Li and Hua Zhou.

Evolution, Phylogeny, and Comparative Genomics


Is the arrangement of the genes in ancestral chromosomes linear? Sèverine Bérard, Coralie Gallien, Bastien Boussau, Gergely Szollosi, Vincent Daubin and Eric Tannier.


Uncovering the co-evolutionary network among prokaryotic genes. Ofir Cohen, Haim Ashkenazy, David Burstein and Tal Pupko.


Genomic context analysis reveals dense interaction network between vertebrate ultra-conserved non-coding elements. Slavica Dimitrieva and Philipp Bucher.


Fractionation, rearrangement and subgenome dominance. David Sankoff and Chunfang Zheng

  Inferring Duplications, Losses, Transfers, and Incomplete Lineage Sorting with Non-Binary Species Trees. Maureen Stolzer, Han Lai, Minli Xu, Deepa Sathaye, Benjamin Vernot and Dannie Durand

Macromolecular Structure, Dynamics and Function


Multiple instance learning of Calmodulin binding sites. Asa Ben-Hur and Fayyaz Minhas.

  Side-chain rotamer changes upon ligand binding: Common, crucial, correlate with entropy and rearrange hydrogen bonding. Francis Gaudreault, Matthieu Chartier and Rafael Najmanovich
  A structure based protocol for learning the family specific mechanisms of membrane binding domains. Morten Kallberg and Hui Lu.
  SANS: High-throughput retrieval of protein sequences allowing 50 % mismatches. Patrik Koskinen and Liisa Holm.
  Protein domain recurrence and order can enhance prediction of protein functions. Mario Messih, Meghana Chitale, Vladimir Bajic, Daisuke Kihara and Xin Gao. (presentation cancelled)

Protein Interactions, Molecular Networks, and Proteomics


EnrichNet: network-based gene set enrichment analysis. Enrico Glaab, Anaïs Baudot, Natalio Krasnogor, Reinhard Schneider and Alfonso Valencia.


LocTree2 predicts localization for all domains of life. Tatyana Goldberg, Tobias Hamp and Burkhard Rost.

  Techniques to cope with missing data in host-pathogen protein interaction prediction. Meghana Kshirsagar, Jaime Carbonell and Judith Klein-Seetharaman.
  Identifying Functional Modules in Protein Interaction Networks through Overlapping Markov Clustering. Yu-Keng Shih and Srinivasan Parthasarathy.
  Graphlet-based edge clustering reveals pathogen-interacting proteins. Ryan Solava, Ryan Michaels and Tijana Milenkovic.
  Identification of chemogenomic features from drug-target interaction networks using interpretable classifiers. Yasuo Tabei, Edouard Pauwels, Veronique Stoven, Kazuhiro Takemoto and Yoshihiro Yamanishi.

Regulation, Pathways, and Systems Biology

  Boolean Approach to Signaling Pathway Modeling in HGF-induced Keratinocyte Migration. Hauke Busch, Melanie Boerries, Amit Singh, Juliana Nascimento and Silke Kowar.
  Stoichiometric capacitance reveals the theoretical capabilities of metabolic networks. Abdelhalim Larhlimi, Georg Basler, Sergio Grimbs, Joachim Selbig and Zoran Nikoloski.
  The architecture of the gene regulatory networks for different tissues. Jie Li, Xu Hua, Martin Haubrock, Jin Wang and Edgar Wingender.
  Random Sampling of Elementary Flux Modes in Large-scale Metabolic Networks. Daniel Machado, Zita Soons, Kiran Patil, Eugénio Ferreira and Isabel Rocha.
  Relating drug-protein interaction network with drug side-effects. Sayaka Mizutani, Edouard Pauwels, Veronique Stoven, Susumu Goto and Yoshihiro Yamanishi.
  Comprehensive estimation of input signals and dynamics in biochemical reaction networks. Max Schelker, Andreas Raue, Jens Timmer and Clemens Kreutz.
  Trajectory-oriented Bayesian experiment design versus Fisher A-optimal design: An in depth comparison study. Patrick Weber, Andrei Kramer, Clemens Dingler and Nicole Radde.

Bioimaging, Spatial-temporal Modeling and Data Visualization


Reveal - Visual eQTL Analytics. Günter Jäger, Florian Battke and Kay Nieselt.


Hybrid Spatial Gillespie and Particle Tracking Simulation. Michael Klann, Arnab Ganguly and Koeppl Heinz.

  Imaging, quantification, and visualization of spatio-temporal patterning in mESC colonies under different culture conditions. Nico Scherf, Maria Herberg, Konstantin Thierbach, Thomas Zerjatke, Tuzer Kalkan, Peter Humphreys, Austin Smith, Ingmar Glauche and Ingo Roeder.

Databases, Ontologies, and Text Mining

  An approach to describing and analysing bulk biological annotation quality: A case study using UniProtKB. Michael Bell, Colin Gillespie, Daniel Swan and Phillip Lord.
  ReLiance: A machine learning and literature-based prioritization of Receptor - Ligand pairings. Ernesto Iacucci, Leon-Charles Tranchevent, Dusan Popovic, Georgios Pavlopoulos, Bart De Moor, Reinhard Schneider and Yves Moreau.
  Event extraction across multiple levels of biological organization. Sampo Pyysalo, Tomoko Ohta, Makoto Miwa, Han-Cheol Cho, Jun'Ichi Tsujii and Sophia Ananiadou.

Bioinformatics of Health and Disease, Biomarkers and Personalized Medicine


Gene-gene interaction analysis for the survival phenotype based on the Cox model. Seungyeoun Lee, Min-Seok Kwon, Jung Mi Oh and Taesung Park.

  Improving HIV coreceptor usage prediction in the clinic using hints from next generation sequencing data. Nico Pfeifer and Thomas Lengauer.
  An accurate paired sample test for count data. Thang Pham and Connie Jimenez.
  Bayesian Assignment of Gene Ontology Terms to Gene Expression Experiments. Peter Sykacek.
  Drug target prediction using adverse event report systems: a pharmacogenomic approach. Masataka Takarabe, Masaaki Kotera, Yosuke Nishimura, Susumu Goto and Yoshihiro Yamanishi.
  From Phenotype to Genotype: An Association Study of Longitudinal Phenotypic Markers to Alzheimer’s Disease Relevant SNPs. Hua Wang, Feiping Nie, Heng Huang, Jingwen Yan, Sungeun Kim, Kwangsik Nho, Shannon Risacher, Andrew Saykin and Li Shen.

Applied and Translational Bioinformatics

  A novel approach for resolving differences in single-cell gene expression patterns from zygote to blastocyst. Florian Buettner and Fabian Theis.
  Finding differentially expressed regions of arbitrary length in quantitative genomic data based on marked point process model. Hiroshi Hatsuda.
  PARADIGM-SHIFT predicts the function of mutations in multiple cancers using pathway impact analysis. Sam Ng, Eric A. Collisson, Artem Sokolov, Theodore Goldstein, Abel Gonzalez-Perez, Nuria Lopez-Bigas, Christopher Benz, David Haussler and Joshua M. Stuart.


ECCB'12 Proceedings will be published in a special open-access issue of the journal "Bioinformatics" in September.