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Papers:
Decoding the Genomic Architecture of Mammalian and Plant Genomes: Synteny Blocks and Large-Scale Duplications
Qian Peng (Univ of California, San Diego, USA)Max Alekseyev (Univ of South Carolina, USA)
Glenn Tesler (Univ of California, San Diego, USA)
Pavel Pevzner (Univ of California, San Diego, USA)
Linear-Time Protein 3-D Structure Searching with Insertions and Deletions
Tetsuo Shibuya (Univ of Tokyo, Japan)Jesper Jansson (Ochanomizu Univ, Japan)
Kunihiko Sadakane (National Institute of Informatic, Japan)
K-partite RNA Secondary Structures
Minghui Jiang (Utah State Univ, USA)Pedro J. Tejada (Utah State Univ, USA)
Ramoni O. Lasisi (Utah State Univ, USA)
Shanhong Cheng (Utah State Univ, USA)
D. Scott Fechser (Utah State Univ, USA)
A non-parametric Bayesian approach for predicting RNA secondary structures
Kengo Sato (Japan Biological Informatics Consortium, Japan)Michiaki Hamada (Mizuho Information & Research Institute, Inc, Japan)
Toutai Mituyama (National Institute of Advanced Industrial Science and Technology, Japan)
Kiyoshi Asai (Univ of Tokyo, Japan)
Yasubumi Sakakibara (Keio Univ, Japan)
A Tree Based Method for the Rapid Screening of Chemical Fingerprints
Thomas Greve Kristensen (Aarhus Univ, Denmark)Jesper Nielsen (Aarhus Univ, Denmark)
Christian Nørgaard Storm Pedersen (Aarhus Univ, Denmark)
Large-scale neighbor-joining with NINJA
Travis Wheeler (Univ of Arizon, USA)A Unifying View on Approximation and FPT of Agreement Forests
Chris Whidden (Dalhousie Univ, Canada)Norbert Zeh (Dalhousie Univ, Canada)
On the upper bound of the prediction accuracy of residue contacts in proteins with correlated mutations: the case study of the similarity matrices
Pietro Di Lena (Univ of Bologna, Italy)Piero Fariselli (Univ of Bologna, Italy)
Luciano Margara (Univ of Bologna, Italy)
Marco Vassura (Univ of Bologna, Italy)
Rita Casadio (UNIB, Italy)
A simulation study comparing supertree and combined analysis methods using SMIDGen
M. Shel Swenson (Univ of Texas at Austin, USA)Francois Barbancon (Univ of Texas at Austin, USA)
Randy Linder (Univ of Texas, USA)
Tandy Warnow (Univ of Texas at Austin, USA)
Minimum Factorization Agreement of Spliced ESTs
Paola Bonizzoni (Univ di Milano-Bicocca, Italy)Gianluca Della Vedova (Univ degli Studi Milano-Bicocca, Italy)
Riccardo Dondi (Univ degli Studi di Bergamo, Italy)
Yuri Pirola (DISCo, Università di Milano-Bicocca, Italy)
Raffaella Rizzi (Comunicazione Univ degli Studi di Milano - Bicocca, Italy)
Annotating fragmentation patterns
Sebastian Böcker (Jena Univ, Germany)Florian Rasche (Jena Univ, Germany)
Tamara Steijger (Friedrich-Schiller-Univ Jen, Germany)
Structural Alignment of RNA with Complex Pseudoknot Structure
Thomas Wong (Univ of Hong Kong, Hong Kong)Tak-Wah Lam (Univ of Hong Kong, Hong Kong)
Wing-Kin Sung (Nuational Univ of Singapore, Singapore)
SM Yiu (Univ of Hong Kong, Hong Kong)
MPSCAN: fast localisation of multiple reads in genomes
Eric Rivals (LIRMM - UMR 5506 CNRS UM2, France)Leena Salmela (Helsinki Univ of Technology, Finland)
Petteri Kiiskinen (Helsinki Univ of Technology, Finland)
Petri Kalsi (Helsinki Univ of Technology, Finland)
Jorma Tarhio (Helsinki Univ of Technology, Finland)
Phylogenetic Comparative Assembly
Peter Husemann (Bielefeld Univ, Germany)Jens Stoye (Bielefeld Univ, Germany)
Back-translation for discovering distant protein homologies
Marta Girdea (LIFL - Univ Lille 1 / INRIA Lille - Nord Europe, France)Laurent Noé (LIFL - Univ Lille 1 / INRIA Lille - Nord Europe, France)
Gregory Kucherov (LIFL/CNRS/INRIA, France)
Predicting Gene Structures from Multiple RT-PCR Tests
Jakub Kovac (fmfi uk, Slovakia)Tomas Vinar (Comenius Univ in Bratislava, Slovakia)
Bronislava Brejova (Comenius Univ in Bratislava, Slovakia)
PMFastR: A New Approach to Multiple RNA Structure Alignment
Daniel DeBlasio (Univ of Central Florida, USA)Jocelyne Bruand (Univ of California, San Diego, USA)
Shaojie Zhang (Univ of Central Florida, USA)
SCJ: a variant of breakpoint distance for which sorting, genome median and genome halving problems are easy
Pedro Feijão (UNICAMP - Univ of Campinas, Brazil)João Meidanis (Univ of Campinas / Scylla Bioinformatics, Brazil)
Generalizing the Four Gamete Condition and Splits Equivalence Theorem: Perfect Phylogeny on Three State Characters
Fumei Lam (Univ of California, Davis, USA)Dan Gusfield (Univ of California, Davis, USA)
Srinath Sridhar (Carnegie Mellon Univ, USA)
biRNA: Fast RNA-RNA Binding Sites Prediction
Hamidreza Chitsaz (Simon Fraser Univ, Canada)Rolf Backofen (Albert-Ludwigs-Univ Freiburg, Germany)
S. Cenk Sahinalp (Simon Fraser Univ, Canada)
Improving Inference of Transcriptional Regulatory Networks Based on Network Evolutionary Models
Xiuwei Zhang (EPFL, Switzerland)Bernard Moret (EPFL, Switzerland)
Aligning Biomolecular Networks Using Modular Graph Kernels
Fadi Towfic (Iowa State Univ, Ames, IA, USA)M. Heather West Greenlee (Iowa State Univ, Ames, IA, USA)
Vasant Honavar (Iowa State Univ, USA)
MADMX: A Novel Strategy for Maximal Dense Motif Extraction
Fabio Vandin (Univ of Padova, Italy)Roberto Grossi (Univ di Pisa, Italy)
Andrea Pietracaprina (Univ of Padova, Italy)
Nadia Pisanti (Univ di Pisa, Italy)
Geppino Pucci (DEI - Univ di Padova, Italy)
Eli Upfal (Brown Univ, USA)
Fast prediction of RNA-RNA Interaction
Raheleh Salari (Simon Fraser Univ, Canada)Rolf Backofen (Albert-Ludwigs-Univ Freiburg, Germany)
S. Cenk Sahinalp (Simon Fraser Univ, Canada)
A Markov Classification Model for Metabolic Pathways
Timothy Hancock (Kyoto Univ, Japan)Hiroshi Mamitsuka (Kyoto Univ, Japan)
FlexSnap: Flexible Non-Sequential Protein Structure Alignment
Saeed Salem (RPI, USA)Mohammed Zaki (RPI, USA)
Chris Bystroff (Rensselaer Polytechnic Institute, USA)
Constructing Majority-Rule Supertrees
Jianrong Dong (Iowa State Univ, Ames, IA, USA)David Fernández-Baca (Iowa State Univ, Ames, IA, USA)
F.R. McMorris (Illinois Institute of Technology, USA)
Mimosa – Mixture model of co-expression to detect modulators of regulatory interaction
Matthew Hansen (Univ of Pennsylvania, USA)Logan Everett (Univ of Pennsylvania, USA)
Larry Singh (Univ of Pennsylvania, USA)
Sridhar Hannenhalli (Univ of Pennsylvania, USA)
Efficient Algorithms for Analyzing Segmental Duplications, Deletions, and Inversions in Genomes
Crystal Kahn (Brown Univ, USA)Shay Mozes (Brown Univ, USA)
Ben Raphael (Brown Univ, USA)
Exact Score Distribution Computation for Similarity Searches in Ontologies
Marcel Schulz (Max Planck Institute for Molecular Genetics, Germany)Sebastian Köhler (Institut for Medizinische Genetik, Charite Universitätsmedizin Berlin, Germany)
Sebastian Bauer (Institut fuer Medizinische Genetik, Charite Universitätsmedizin Berlin, Germany)
Martin Vingron (Max Planck Institut fuer molekulare Genetik, Germany)
Peter Robinson (Charite Univ tsmedizin Berlin, Germany)
Quantifying Systemic Evolutionary Changes by Color Coding Confidence-Scored PPI Networks
Phuong Dao (Simon Fraser Univ, Canada)Alexander Schonhuth (Simon Fraser Univ, Canada)
Fereydoun Hormozdiari (Simon Fraser Univ, Canada)
Iman Hajirasouliha (Simon Fraser Univ, Canada)
S. Cenk Sahinalp (Simon Fraser Univ, Canada)
Martin Ester (Simon Fraser Univ, Canada)
A General Framework for Local Pairwise Alignment Statistics with Gaps
Pasi Rastas (Helsinki Institute for Information Technology HIIT, Helsinki Univ of Technology and Univ of Helsinki, Finland)Visualizing Phylogenetic Treespace Using Cartographic Projections
Kenneth Sundberg (Brigham Young Univ, USA)Mark Clement (Brigham Young Univ, USA)
Quinn Snell (Brigham Young Univ, USA)
A simple practical and complete 0 (n^3/log(n)) - time Algorithm for RNA folding
Yelena Frid (Univ of California, Davis, USA)Dan Gusfield (Univ of California, Davis, USA)
SATe: Simultaneous Alignment and Tree Estimation
Kevin Liu (University of Texas at Austin, USA)Serita Nelson (University of Texas at Austin, USA)
Randy Linder (University of Texas at Austin, USA)
Tandy Warnow (University of Texas at Austin, USA)
Upper bounds on the ability to reconstruct prokaryotic genomes with next generation sequencing technologies
Joshua Wetzel (Rutgers University, USA)Mike Schatz (University of Maryland, USA)
Carl Kingsford (University of Maryland, USA)
Mihai Pop (University of Maryland, USA)
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