Network evaluation from the consistency of the graph structure with the measured data (2008)
Saito, Shigeru, Aburatani, Sachiyo, Horimoto, Katsuhisa
Abstract Background A knowledge-based network, which is constructed by extracting as many relationships identified by experimental studies as possible and then superimposing them, is one of the...
Sachiyo Aburatani, Fuyan Sun, Shigeru Saito, Masao Honda, Shu-ichi Kaneko, Katsuhisa Horimoto
Hepatocellular carcinoma (HCC) in a liver with advanced-stage chronic hepatitis C (CHC) is induced by hepatitis C virus, which chronically infects about 170 million people worldwide. To elucidate the...
Profile-Profile Comparison Based on Hidden Markov Model Profiles (2004)
Makihiko Sato, Nobuyoshi Sugaya, Hiroo Murakami, Sachiyo Aburatani, Katsuhisa Horimoto
Introduction The detection of sequence similarity within the twilight zone has been a challenging problem in sequence analysis. Among various types of approaches for sequence similarity detection,...
Genome Informatics 14: 278--279 (2003) ASIAN: A Web Site for Network Inference (2004)
Katsuhisa Horimoto, Hiroyuki Toh, Sachiyo Aburatani, Nobuyoshi Sugaya, Hiroo Murakami, Makihiko Sato, ...
Introduction Recently, we have developed a system, named "ASIAN", for inferring a network by the combination of clustering and graphical Gaussian modeling (GGM) [1, 2, 3, 4, 5]. The feasibility of...
Genome Informatics 14: 440--441 (2003) Identifying Obscure Periodic Patterns in Genomic DNA (2004)
Hiroo Murakami, Natsuhiro Ichinose, Tetsushi Yada, Sachiyo Aburatani, Nobuyoshi Sugaya, Makihiko Sato, ...
Introduction Genomic DNA sequence is very abundant in periodic patterns, which play important biological roles, such as gene expression, genome structural stabilization, and recombination. Tandem...
Nobuyoshi Sugaya, Hiroo Murakami, Makihiko Satoh, Sachiyo Aburatani, Katsuhisa Horimoto
Introduction In the phylum Cyanobacteria, complete genome sequences have been already reported in seven species and strains [1, 4, 5, 6, 7, 8]. Very interestingly, only one speices of these...
Genome Informatics 14: 496--497 (2003) Prediction of Protein-Protein Interactions from (2004)
Tetsuya Sato, Yoshihiro Yamanishi, Katsuhisa Horimoto, Hiroyuki Toh, Minoru Kanehisa
This paper presents a new method to predict protein-protein interactions from the evolutionary information by using partial correlation coe#cient in order to extract direct interactions rather than...
Genome Informatics 14: 480--481 (2003) Algorithms for Computing an Optimal Protein (2004)
Tatsuya Akutsu, Morihiro Hayashida, Etsuji Tomita, Katsuhisa Horimoto
Introduction Protein threading is one of the powerful methods for protein structure prediction. Some advances are recently made by the significant utilization of distance restraints. Xu et al....
Sachiyo Aburatani, Nobuyoshi Sugaya, Hiroo Murakami, Makihiko Sato, Katsuhisa Horimoto
Introduction DNA microarray data provide us with a large amount of information on gene expressions in the living cell. One of the important goals of such expression analysis is to estimate the...
Genome Informatics 12: 268--269 (2001) Correspondence between a Genetic Network Inferred (2002)
Sachiyo Aburatani, Katsuhisa Horimoto, Hiroyuki Toh, Ayumi Shinohara, Keisuke Iida, Kosuke Tashiro, ...
Introduction The recent advance of microarray techniques provides a chance to comprehensively understand the regulatory relationship in a genome scale. In particular, monitoring of gene expression by...
A Comprehensive Comparison between Locations of Orthologs in Circular Microbial Genomes (2001)
Hiroaki Saitoh, Kentaro Mori, Satoshi Fukuchi, Katsuhisa Horimoto, Japan Netwob
Introduction Fo[F wing an extensive searchfo oL9x.2B9]S genes between theco29]][ geno]] fro archaea and bacteria, the spatialasso ciatioo theoe2S[F]] has been investigated in termso synteny, the...
Inference of Genetic Networks from Expression Profile by Graphical Gaussian Modeling (2001)
Hiroyuki Toh, Katsuhisa Horimoto, Furuedai Suita Osaka
Introduction Recen t advanv of DNA microarray technk#Hw.H has made it possible to measure theexpression levels of thousanw ofgen[ simultan.zkAw ,un]v di#eren tconwzkAwv. Elucidatin pattern from the...
A Procedure for Estimating Cluster Boundaries in Gene Expression Profile Data (2001)
Katsuhisa Horimoto, Hiroyuki Toh
Gene expression profile data are rapidly accumulated by the advance of microarray techniques. The abundant data are analyzed by some clustering procedures to extract the useful information on the...
ASIAN: a web server for inferring a regulatory network framework from gene expression profiles
Aburatani, Sachiyo, Goto, Kousuke, Saito, Shigeru, Toh, Hiroyuki, Horimoto, Katsuhisa
The standard workflow in gene expression profile analysis to identify gene function is the clustering by various metrics and techniques, and the following analyses, such as sequence analyses of...
ASIAN: a web server for inferring a regulatory network framework from gene expression profiles
Aburatani, Sachiyo, Goto, Kousuke, Saito, Shigeru, Toh, Hiroyuki, Horimoto, Katsuhisa
The standard workflow in gene expression profile analysis to identify gene function is the clustering by various metrics and techniques, and the following analyses, such as sequence analyses of...
Aburatani, Sachiyo, Sun, Fuyan, Saito, Shigeru, Honda, Masao, Kaneko, Shu-Ichi, Horimoto, Katsuhisa
Hepatocellular carcinoma (HCC) in a liver with advanced-stage chronic hepatitis C (CHC) is induced by hepatitis C virus, which chronically infects about 170 million people worldwide. To elucidate the...