Accepted Proceedings Papers

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 A.  Sequencing and sequence analysis for genomics

Lambda: The Local Aligner for Massive Biological Data. Hannes Hauswedell, Jochen Singer and Knut Reinert. [pdf]
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. [pdf]
Towards a piRNA prediction using multiple kernel fusion and support vector machine. Jocelyn Brayet, Farida Zehraoui, Laurence Jeanson-Leh, David Israeli and Fariza Tahi. [pdf]
FastHap: fast and accurate single individual haplotype reconstruction using fuzzy conflict graphs. Sepideh Mazrouee and Wei Wang. [pdf]
Probabilistic single-individual haplotyping. Volodymyr Kuleshov. [pdf]

   B.  Gene expression

Two-dimensional segmentation for analyzing HiC data. Celine Levy-Leduc, Maud Delattre, Tristan Mary-Huard and Stephane Robin. [pdf]
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. [pdf]
Estimating the activity of transcription factors by the effect on their target genes. Theresa Schacht, Marcus Oswald, Roland Eils, Stefan Eichmueller and Rainer Koenig. [pdf]
Modeling DNA methylation dynamics with approaches from phylogenetics. John A. Capra and Dennis Kostka. [pdf]

   C.  Pathways and molecular networks 

Identifying transcription factor complexes and their roles. Thorsten Will and Volkhard Helms. [pdf]
Personalized identification of altered pathways in cancer. Taejin Ahn, Eunjin Lee, Nam Huh and Taesung Park. [pdf]
Alignment-free protein interaction network comparison. Waqar Ali, Tiago Rito, Gesine Reinert, Fengzhu Sun and Charlotte M. Deane. [pdf]
HubAlign: An accurate and efficient method for global alignment of protein-protein interaction networks. Somaye Hashemifar and Jinbo Xu. [pdf]

   D.  Computational systems biology

Experimental design schemes for learning Boolean network models. Nir Atias, Michal Gershenzon, Katia Labazin and Roded Sharan. [pdf]
TEMPI: Probabilistic modeling Time-Evolving differential PPI networks with MultiPle Information. Yongsoo Kim, Jin-Hyeok Jang, Seungjin Choi and Daehee Hwang. [pdf]
Stronger findings for metabolomics through Bayesian modeling of multiple peaks and compound correlations. Tommi Suvitaival, Simon Rogers and Samuel Kaski. [pdf]
Causal network inference using biochemical kinetics. Chris Oates, Frank Dondelinger, Nora Bayani, James Korkola, Joe Gray and Sach Mukherjee. [pdf]
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. [pdf]

   E.  Structural bioinformatics

PconsFold: Improved contact predictions improve protein models. Mirco Michel, Sikander Hayat, Marcin J. Skwark, Chris Sander, Debora S. Marks and Arne Elofsson. [pdf]
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. [pdf]
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.  [pdf]
Assessing the local structural quality of transmembrane protein models using statistical potentials (QMEANBrane). Gabriel Studer, Marco Biasini and Torsten Schwede. [pdf]
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. [pdf]

   F.  Evolution and population genomics

Polytomy ReÔ¨Ānement for the Correction of Dubious Duplications in Gene Trees. Manuel Lafond, Cedric Chauve, Riccardo Dondi and Nadia El-Mabrouk. [pdf]
RidgeRace: Ridge regression for continuous ancestral character estimation on phylogenetic trees. Christina Kratsch and Alice McHardy. [pdf]
Point estimates in phylogenetic reconstructions. Philipp Benner, Miroslav Bacak and Pierre-Yves Bourguignon. [pdf]
ASTRAL: Genome-Scale Coalescent-Based Species Tree Estimation. Siavash Mirarab, Rezwana Reaz Rimpi, Md. Shamsuzzoha Bayzid, Théo Zimmermann, Shel Swenson and Tandy Warnow. [pdf]

   G.  Bioinformatics of health and disease

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. [pdf]
Drug susceptibility prediction against a panel of drugs using kernelized Bayesian multitask learning. Mehmet Gönen and Adam A. Margolin. [pdf]
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. [pdf]
ContrastRank: a new method for ranking putative cancer driver genes and classification of tumor samples. Rui Tian, Malay Basu and Emidio Capriotti. [pdf]

   H.  Biological knowledge discovery from data, texts and bio-images

Unveiling new biological relationships using shared hits of chemical screening assay pairs. Xueping Liu and Monica Campillos. [pdf]
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. [pdf]
Integration of molecular network data reconstructs Gene Ontology. Vladimir Gligorijevic, Vuk Janjic and Natasa Przulj. [pdf]
Extracting patterns of database and software usage from the bioinformatics literature. Geraint Duck, Goran Nenadic, Andy Brass, David Robertson and Robert Stevens. [pdf]
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. [pdf]

   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. [pdf]
Entropy driven partitioning of the hierarchical protein space. Nadav Rappoprt, Nati Linial, Michal Linial and Amos Stern. [pdf]
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. [pdf]
cnvOffSeq: detecting intergenic copy number variation using off-target exome sequencing data. Evangelos Bellos and Lachlan Coin. [pdf]

 

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