Limsoon Wong

Martin Vingron

This book constitutes the refereed proceedings of the 12th Annual International Conference on Research in Computational Molecular Biology, RECOMB 2008. It presents current issues in algorithmic, theoretical, and experimental bioinformatics.

12th Annual International Conference, RECOMB 2008, Singapore, March 30 - April 2, 2008, Proceedings

Research in Computational Molecular Biology

Sriganesh Srihari

Chern Han Yong

Complexes of physically interacting proteins constitute fundamental functional units that drive almost all biological processes within cells. A faithful reconstruction of the entire set of protein complexes (the "complexosome") is therefore important not only to understand the composition of complexes but also the higher level functional organization within cells. Advances over the last several years, particularly through the use of high-throughput proteomics techniques, have made it possible to map substantial fractions of protein interactions (the "interactomes") from model organisms including Arabidopsis thaliana (a flowering plant), Caenorhabditis elegans (a nematode), Drosophila melanogaster (fruit fly), and Saccharomyces cerevisiae (budding yeast). These interaction datasets have enabled systematic inquiry into the identification and study of protein complexes from organisms. Computational methods have played a significant role in this context, by contributing accurate, efficient, and exhaustive ways to analyze the enormous amounts of data. These methods have helped to compensate for some of the limitations in experimental datasets including the presence of biological and technical noise and the relative paucity of credible interactions. In this book, we systematically walk through computational methods devised to date (approximately between 2000 and 2016) for identifying protein complexes from the network of protein interactions (the protein-protein interaction (PPI) network). We present a detailed taxonomy of these methods, and comprehensively evaluate them for protein complex identification across a variety of scenarios including the absence of many true interactions and the presence of false-positive interactions (noise) in PPI networks. Based on this evaluation, we highlight challenges faced by the methods, for instance in identifying sparse, sub-, or small complexes and in discerning overlapping complexes, and reveal how a combination of strategies is necessary to accurately reconstruct the entire complexosome.

Computational Prediction of Protein Complexes from Protein Interaction Networks

Leonid Libkin

Wenfei Fan

Val Tannen

Wang-Chiew Tan

Michael Fourman

This Festschrift volume, published in honour of Peter Buneman, contains contributions written by some of his colleagues, former students, and friends. In celebration of his distinguished career a colloquium was held in Edinburgh, Scotland, 27-29 October, 2013. The articles presented herein belong to some of the many areas of Peter's research interests.

Essays dedicated to Peter Buneman

In Search of Elegance in the Theory and Practice of Computation

Yi-Ping Phoebe Chen

High-throughput sequencing and functional genomics technologies have given us a draft human genome sequence and have enabled large-scale genotyping and gene expression profiling of human populations. Databases containing large number of sequences, polymorphisms, and gene expression profiles of normal and diseased tissues in different clinical states are rapidly being generated for human and model organisms. Bioinformatics is thus rapidly growing in importance in the annotation of genomic sequences, in the understanding of the interplay between genes and proteins, in the analysis the genetic variability of species, etc. The 3rd APBC brings together researchers, professionals, and industrial practitioners for interaction and exchange of knowledge and ideas. The proceedings contains the latest results that address conceptual and practical issues of bioinformatics. Papers presented at APBC'05 and included in this proceedings volume span the following: Novel Applications in Bioinformatics, Computational Analysis of Biological Data, Data Mining & Statistical Modeling of Biological Data, Modeling and Simulation of Biological Processes, Visualization of Biological Processes and Data, Management, Migration, and Integration of Biological Databases, Access, Indexing, and Search in Biological Databases. Contents:A Better Gap Penalty for Pairwise-SVM (H N Chua & W-K Sung)A Graph Database with Visual Queries for Genomics (G Butler et al.)Consensus Fold Recognition by Predicted Model Quality (J Xu et al.)Toward Discovering Disease-Specific Gene Networks from Online Literature (Z Zhang et al.)Hybrid Registration for Two-Dimensional Gel Protein Images (X Wang & D D Feng)Exact Algorithms for Motif Search (S Rajasekaran et al.)Voting Algorithms for Discovering Long Motifs (F Y L Chin & H C M Leung)A Highly Scalable Algorithm for the Extraction of Cis-Regulatory Regions (A M Carvalho et al.)A Support Vector Machine Approach for Prediction of T Cell Epitopes (L Huang & Y Dai)Protein Informations Towards Integration of Data Grid and Computing Grid (H Nakamura)Computing the Assignment of Orthologous Genes via Genome Rearrangement (X Chen et al.)and other papers Readership: Computational biologists, bioinformaticists, computer scientists, biologists. Keywords:Bioinformatics;Computational Biology;Datamining;Biological Data;Modeling;Visualization;Database Management;Database Integration;Biological Database Indexing;Biological Database Search

Proceedings of the 3rd Asia-Pacific Bioinformatics Conference

See-Kiong Ng

Hiroshi Mamitsuka

Proceedings of the 18th International Conference, Biopolis, Singapore, 3-5 December 2007

Genome Informatics 2007

Limsoon Wong

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