Limsoon Wong - Böcker

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.

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 numbers 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 of the genetic variability of species, and so on. This proceedings contains an up-to-date exchange of knowledge, ideas, and solutions to conceptual and practical issues of bioinformatics, by researchers, professionals, and industrial practitioners at the 4th Asia-Pacific Bioinformatics Conference held in Taipei in February 2006.

This volume contains papers presented at the 18th International Conference on Genome Informatics (GIW 2007) held at the Biopolis, Singapore from December 3 to 5, 2007. The GIW Series provides an international forum for the presentation and discussion of original research papers on all aspects of bioinformatics, computational biology and systems biology. Its scope includes biological sequence analysis, protein folding prediction, gene regulatory network, clustering algorithms, comparative genomics, and text mining. Boasting a history of 18 years, GIW is likely the longest-running international bioinformatics conference.A total of 16 papers were selected for presentation at GIW 2007 and inclusion in this book. The notable authors include Ming Li (University of Waterloo, Canada), Minoru Kanehisa (Kyoto University, Japan), Vladimir Kuznetsov (Genome Institute of Singapore), Tao Jiang (UC Riverside, USA), Christos Ouzounis (European Bioinformatics Institute, UK), and Satoru Miyano (University of Tokyo, Japan). In addition, this book contains abstracts from the five invited speakers: Frank Eisenhaber (Bioinformatics Institute, Singapore), Sir David Lane (Institute of Molecular and Cell Biology, Singapore), Hanah Margalit (The Hebrew University of Jerusalem, Israel), Lawrence Stanton (Genome Institute of Singapore), and Michael Zhang (Cold Spring Harbor Laboratory, USA).

The field of bioinformatics has two main objectives: the creation and maintenance of biological databases, and the discovery of knowledge from life sciences data in order to unravel the mysteries of biological function, leading to new drugs and therapies for human disease. Life sciences data come in the form of biological sequences, structures, pathways, or literature. One major aspect of discovering biological knowledge is to search, predict, or model specific patterns of a given dataset, which have some relevance to an important biological phenomenon or another dataset. To date, many pattern recognition algorithms have been applied or catered to address a wide range of bioinformatics problems. The 2006 Workshop of Bioinformatics in Pattern Recognition (PRIB 2006) marks the beginning of a series of workshops that is aimed at gathering researchers applying pattern recognition algorithms in an attempt to resolve problems in computational biology and bioinformatics. This volume presentsthe proceedings of Workshop PRIB 2006 held in Hong Kong, China, on August 20, 2006. It includes 19 technical contributions that were selected by the Program Committee from 43 submissions. We give a brief introduction to pattern recognition in bioinformatics in the first paper. The rest of the volume consists of three parts. Part 1: signal and motif detection, and gene selection. Part 2: models of DNA, RNA, and protein structures. Part 3: biological databases and imaging.

This volume contains the papers presented at the 12th Annual International ConferenceonREsearchin COmputationalMolecularBiology(RECOMB2008) held in Singapore, March 30-April 2, 2008. The RECOMB conference series was founded in 1997 by Sorin Istrail, Pavel Pevzner and Michael Waterman. Its history is summarized in the table herein. The general development of the RECOMB conference series is guided by a Steering Committee. RECOMB 2008 was hosted by the National University of Singapore and held at the University Cultural Centre. The Conference Chair was Limsoon Wong, who was supported by a 16-member-strong Organizing Committee. Out of 193 papers submitted to RECOMB 2008, the Program Committee (PC) selected 34 papers for presentation at the conference. The PC consisted of 46 members, who could further draw on the help of subreviewers. Three PC members with possible help of the external reviewers ?rst reviewed each paper, subsequently a Web-based discussion led to the ?nal selection of papers. This year, RECOMB and the journal Genome Research teamed up to - fer authors Genome Research as an alternative forum for publication.Appro- mately 55 of the RECOMB submissions, selected by a subset of the PC headed by Sera?m Batzoglou, were forwarded to Genome Research for consideration.

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.

The Institute for Mathematical Sciences at the National University of Singapore organized a program on “Post-Genome Knowledge Discovery” from January to June 2002. The program focused on the computational and statistical analysis of sequences and genetics, and the mathematical modeling of complex biological interactions, which are critical to the accurate annotation of genomic sequences, the study of the interplay between genes and proteins, and the study of the genetic variability of species. As part of the program, tutorials for graduate students and newcomers to this transdisciplinary area of research were given by experts in these fields.This important volume collects the expanded notes of some of the tutorials that were given during the program. The topics include comparison and alignment of biological sequences, modeling and analysis of biological pathways, data mining and knowledge discovery from biological and clinical data.

Computer scientists have increasingly been enlisted as “bioinformaticians” to assist molecular biologists in their research. This book is a practical introduction to bioinformatics for these computer scientists. The chapters are in-depth discussions by expert bioinformaticians on both general techniques and specific approaches to a range of selected bioinformatics problems. The book is organized into clusters of chapters on the following topics:• Overview of modern molecular biology and a broad spectrum of techniques from computer science — data mining, machine learning, mathematical modeling, sequence alignment, data integration, workflow development, etc.• In-depth discussion of computational recognition of functional and regulatory sites in DNA sequences.• Incisive discussion of computational prediction of secondary structure of RNA sequences.• Overview of computational prediction of protein cellular localization, and selected discussions of inference of protein function.• Overview of methods for discovering protein-protein interactions.• Detailed discussion of approaches to gene expression analysis for the diagnosis of diseases, the treatment of diseases, and the understanding of gene functions.• Case studies on analysis of phylogenies, functional annotation of proteins, construction of purpose-built integrated biological databases, and development of workflows underlying the large-scale-effort gene discovery.

Computer scientists have increasingly been enlisted as “bioinformaticians” to assist molecular biologists in their research. This book is a practical introduction to bioinformatics for these computer scientists. The chapters are in-depth discussions by expert bioinformaticians on both general techniques and specific approaches to a range of selected bioinformatics problems. The book is organized into clusters of chapters on the following topics:• Overview of modern molecular biology and a broad spectrum of techniques from computer science — data mining, machine learning, mathematical modeling, sequence alignment, data integration, workflow development, etc.• In-depth discussion of computational recognition of functional and regulatory sites in DNA sequences.• Incisive discussion of computational prediction of secondary structure of RNA sequences.• Overview of computational prediction of protein cellular localization, and selected discussions of inference of protein function.• Overview of methods for discovering protein-protein interactions.• Detailed discussion of approaches to gene expression analysis for the diagnosis of diseases, the treatment of diseases, and the understanding of gene functions.• Case studies on analysis of phylogenies, functional annotation of proteins, construction of purpose-built integrated biological databases, and development of workflows underlying the large-scale-effort gene discovery.