Encyclopedia of Bioinformatics and Computational Biology

Shoba Ranganathan is an Honorary Professor of Bioinformatics in Applied Biosciences, Macquarie University. She was the first Chair of Bioinformatics in Australia (2004-22). She has held research and academic positions in India, USA, Singapore and Australia as well as a consultancy in industry. Shoba's research addresses several key areas of bioinformatics to understand biological systems using computational approaches. Her group has achieved both experience and expertise in different aspects of computational biology, ranging from metabolites and small molecules to biochemical networks, pathway analysis and computational systems biology. She has authored as well as edited several books and contributed several articles to the 1st edition of this Encyclopedia. She was awarded the 2023 Outstanding Contributions to the International Society for Computational Biology (ISCB) Award. She is an Honorary Senior Fellow of the Australian Society for Bioinformatics and Computational Biology since 2018 and an ISCB Fellow since 2023. Kenta Nakai is Professor at the Human Genome Center, the Institute of Medical Science, the University of Tokyo, Japan. He received his PhD degree from Kyoto University, Japan, in 1992. From 1989, he has worked at several institutions in Japan, including Kyoto University, National Institute of Basic Biology, and Osaka University. He joined the Human Genome Center, the Institute of Medical Science, the University of Tokyo, as Associate Professor in 1999, becoming Professor in 2003. He was elected President of the Japanese Society for Bioinformatics in 2006 and 2007. His main research interest is to develop computational ways to interpret biological information, especially transcriptional regulation. Two of his papers reporting the development of a knowledge-based prediction system of subcellular localization sites have been cited more than 1,200 times so far. He has played a central role in editing the Encyclopedia on Bioinformatics (in Japanese), which was published by Kyoritsu Shuppan Co. Ltd. in 2006. Christian Schönbach is Professor in the Department of Biology, School of Science & Technology, Nazarbayev University, Astana, Kazakhstan and Visiting Professor, Center for AIDS Research, Kumamoto University, Kumamoto, Japan, since 2013. He was awarded Dr. rer. nat. (Genetics) by Eberhard-Karls University, Tübingen (1993), after which he undertook post-doctoral training, at the Department of Tumor Biology, Institute of Medical Science, University of Tokyo. Since then, he has held research positions in Japan and Singapore, in academia, research institutes as well as industry, including Kent Ridge Digital Labs, Singapore and RIKEN Genomic Sciences Center, Yokohama, Japan, prior to becoming Professor, Department of Biology, School of Computer Science and Systems Engineering, Kyushu Institute of Technology, Fukuoka, Japan (2009-2013). He has served as Vice President Conferences of the Asia-Pacific Bioinformatics Network (APBioNet) (2010-present). His research interests include bioinformatics and genomics, data integration and biological knowledge discovery from databases; immunoinformatics and viral immunology; novel peroxisome targeting signal-containing proteins and their role in lipid metabolic/peroxisomal disease pathways; HIV escape mutants, TCR repertoire; bioinformatics transcriptional regulation of the host cell response and immunopathogenesis. His publications have been cited over 7500 times. He has authored and edited several books in Immunoinformatics and Immunomics, as well as contributed to the Encyclopedia of Systems Biology, published by Springer in 2013.

Draft/preliminary table of contents

Sections Biological Database Searching Computational Systems Biology Applications Computational pipelines and workflows in Bioinformatics Sequence Analysis Epigenomic Analysis Genetics and Population Analysis Genome Analysis Metabolome Analysis Biomolecular Structure Prediction and Analysis Transcriptome analysis Proteomics analysis Phylogenetic analysis Genome Informatics Text mining Applications Data models, representation and storage From Topics Algorithms Artificial Intelligence and Machine Learning Search strategies Solving Problems by Informed Search Greedy search Genetic Algorithms Agents and unknown environment Constraint Satisfaction Problems Linear Programming Backtracking search Biostatistics Computing for Bioinformatics Integrative Bioinformatics Ontology Text Mining Biological Networks Pathways in Biology Simulated annealing Transcriptome informatics Computational Systems Biology Gene and Protein informatics Advanced biocomputing strategies Cheminformatics Biological databases Functional Genomics Molecular Phylogeny Metabolome Informatics Structural Bioinformatics Translational Bioinformatics Bioimage informatics