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Proceedings of the 6th Asia-Pacific Bioinformatics Conference
High-throughput sequencing and functional genomics technologies have given us the human genome sequence as well as those of other experimentally, medically, and agriculturally important species, thus enabling large-scale genotyping and gene expression profiling of human populations. Databases containing large numbers of sequences, polymorphisms, structures, metabolic pathways, and gene expression profiles of normal and diseased tissues are rapidly being generated for human and model organisms. Bioinformatics is therefore gaining importance in the annotation of genomic sequences; the understanding of the interplay among and between genes and proteins; the analysis of the genetic variability o...
Similarity Joins in Relational Database Systems
State-of-the-art database systems manage and process a variety of complex objects, including strings and trees. For such objects equality comparisons are often not meaningful and must be replaced by similarity comparisons. This book describes the concepts and techniques to incorporate similarity into database systems. We start out by discussing the properties of strings and trees, and identify the edit distance as the de facto standard for comparing complex objects. Since the edit distance is computationally expensive, token-based distances have been introduced to speed up edit distance computations. The basic idea is to decompose complex objects into sets of tokens that can be compared effi...
Computer and Information Sciences -- ISCIS 2006
This book constitutes the refereed proceedings of the 21st International Symposium on Computer and Information Sciences, ISCIS 2006, held in Istanbul, Turkey in October 2006. The 106 revised full papers presented together with five invited lectures were carefully reviewed and selected from 606 submissions.
Proceedings of the 6th Asia-Pacific Bioinformatics Conference
High-throughput sequencing and functional genomics technologies have given us the human genome sequence as well as those of other experimentally, medically, and agriculturally important species, thus enabling large-scale genotyping and gene expression profiling of human populations. Databases containing large numbers of sequences, polymorphisms, structures, metabolic pathways, and gene expression profiles of normal and diseased tissues are rapidly being generated for human and model organisms. Bioinformatics is therefore gaining importance in the annotation of genomic sequences; the understanding of the interplay among and between genes and proteins; the analysis of the genetic variability of species; the identification of pharmacological targets; and the inference of evolutionary origins, mechanisms, and relationships. This proceedings volume contains an up-to-date exchange of knowledge, ideas, and solutions to conceptual and practical issues of bioinformatics by researchers, professionals, and industry practitioners at the 6th Asia-Pacific Bioinformatics Conference held in Kyoto, Japan, in January 2008.
Combinatorial Pattern Matching
The papers contained in this volume were presented at the 13th Annual S- posium on Combinatorial Pattern Matching, held July 3–5, 2002 at the Hotel Uminonakamichi, in Fukuoka, Japan. They were selected from 37 abstracts s- mitted in response to the call for papers. In addition, there were invited lectures by Shinichi Morishita (University of Tokyo) and Hiroki Arimura (Kyushu U- versity). Combinatorial Pattern Matching (CPM) addresses issues of searching and matching strings and more complicated patterns such as trees, regular expr- sions, graphs, point sets, and arrays, in various formats. The goal is to derive n- trivial combinatorial properties of such structures and to exploit these pro...
Computing and Combinatorics
Thepapersinthisvolumewereselectedforpresentationatthe10thInternational Computing and Combinatorics Conference (COCOON 2004), held on August 17–20, 2004 in Jeju Island, Korea. Previous meetings were held in Xi’an (1995), HongKong(1996),Shanghai(1997),Taipei(1998),Tokyo(1999),Sydney(2000), Guilin (2001), Singapore (2002), and Big Sky (2003). In response to the call for papers, 109 extended abstracts were submitted from 23 countries, of which 46 were accepted. The submitted papers were from Belgium (1), Canada (5), China (6), France (1), Germany (6), Hong Kong (8), India (6), Iran (1), Ireland (1), Israel (4), Italy (2), Japan (17), Korea (23), Mexico (3), New Zealand (1), Poland(1), Russia...
Algorithms For Analysis, Inference, And Control Of Boolean Networks
The Boolean network (BN) is a mathematical model of genetic networks and other biological networks. Although extensive studies have been done on BNs from a viewpoint of complex systems, not so many studies have been undertaken from a computational viewpoint. This book presents rigorous algorithmic results on important computational problems on BNs, which include inference of a BN, detection of singleton and periodic attractors in a BN, and control of a BN. This book also presents algorithmic results on fundamental computational problems on probabilistic Boolean networks and a Boolean model of metabolic networks. Although most contents of the book are based on the work by the author and colla...
Discovery Science
This volume contains 3 invited papers, 15 regular papers, and 22 poster papers that were selected for presentation at the Third International Conference on Discovery Science (DS 2000), which was held 4-6 December 2000 in Kyoto. The Program Committee selected the contributed papers from 48 submissions. Three distinguished researchers accepted our invitation to present talks: J- frey D. Ullman (Stanford University), Joseph Y. Halpern (Cornell University), and Masami Hagiya (University of Tokyo). The Program Committee would like to thank all those who submitted papers for consideration and the invited speakers. I would like to thank the Program Committee members, the Local Arrangements Committe...
Combinatorial Pattern Matching
This book constitutes the refereed proceedings of the 11th Annual Symposium on Combinatorial Pattern Matching, CPM 2000, held in Montreal, Canada, in June 2000.The 29 revised full papers presented together with 3 invited contributions and 2 tutorial lectures were carefully reviewed and selected from 44 submissions. The papers are devoted to current theoretical and algorithmic issues of searching and matching strings and more complicated patterns such as trees, regular expression graphs, point sets and arrays as well as to advanced applications of CPM in areas such as Internet, computational biology, multimedia systems, information retrieval, data compression, and pattern recognition.
Evolutionary Computation in Gene Regulatory Network Research
Introducing a handbook for gene regulatory network research using evolutionary computation, with applications for computer scientists, computational and system biologists This book is a step-by-step guideline for research in gene regulatory networks (GRN) using evolutionary computation (EC). The book is organized into four parts that deliver materials in a way equally attractive for a reader with training in computation or biology. Each of these sections, authored by well-known researchers and experienced practitioners, provides the relevant materials for the interested readers. The first part of this book contains an introductory background to the field. The second part presents the EC appr...
