Protein Superfamily Database (Prosup). - Katsuhisa Horimoto; Kunio Oshima; Akira Tsugita; Jinya Otsuka (CODATA, 1994)

A method for comparing circular genomes from gene locations: application to mitochondrial genomes. - Katsuhisa Horimoto; Mikita Suyama; Hiroyuki Toh; Kentaro Mori; Jinya Otsuka (Bioinform., 1998)

Comprehensive comparison between locations of orthologous genes on archaeal and bacterial genomes. - Katsuhisa Horimoto; Satoshi Fukuchi; Kentaro Mori (Bioinform., 2001)

Statistical estimation of cluster boundaries in gene expression profile data. - Katsuhisa Horimoto; Hiroyuki Toh (Bioinform., 2001)

Inference of a genetic network by a combined approach of cluster analysis and graphical Gaussian modeling. - Hiroyuki Toh; Katsuhisa Horimoto (Bioinform., 2002)

Deduction of a gene regulatory relationship framework from gene expression data by the application of graphical Gaussian modeling. - Sachiyo Aburatani; Satoru Kuhara; Hiroyuki Toh; Katsuhisa Horimoto (Signal Process., 2003)

Protein Threading with Profiles and Constraints. - Tatsuya Akutsu; Morihiro Hayashida; Etsuji Tomita; Jun'ichi Suzuki; Katsuhisa Horimoto (BIBE, 2004)

ASIAN: a website for network inference. - Sachiyo Aburatani; Kousuke Goto; Shigeru Saito; Masaki Fumoto; Akira Imaizumi; Nobuyoshi Sugaya; Hiroo Murakami; Makihiko Sato; Hiroyuki Toh; Katsuhisa Horimoto (Bioinform., 2004)

Clique-based algorithms for protein threading with profiles and constraints. - Dukka Bahadur; Etsuji Tomita; Jun'ichi Suzuki; Katsuhisa Horimoto; Tatsuya Akutsu (APBC, 2005)

ASIAN: a web server for inferring a regulatory network framework from gene expression profiles. - Sachiyo Aburatani; Kousuke Goto; Shigeru Saito; Hiroyuki Toh; Katsuhisa Horimoto (Nucleic Acids Res., 2005)

Partial correlation coefficient between distance matrices as a new indicator of protein-protein interactions. - Tetsuya Sato 003; Yoshihiro Yamanishi; Katsuhisa Horimoto; Minoru Kanehisa; Hiroyuki Toh (Bioinform., 2006)

Dynamic Programming and Clique Based Approaches for Protein Threading with Profiles and Constraints. - Tatsuya Akutsu; Morihiro Hayashida; Dukka Bahadur; Etsuji Tomita; Jun'ichi Suzuki; Katsuhisa Horimoto (IEICE Trans. Fundam. Electron. Commun. Comput. Sci., 2006)

Symbolic-numeric Estimation of Parameters in Biochemical Models by Quantifier Elimination. - Hirokazu Anai; Shigeo Orii; Katsuhisa Horimoto (J. Bioinform. Comput. Biol., 2006)

Protein Threading with Profiles and Distance Constraints Using Clique Based Algorithms. - K. C. Dukka Bahadur; Etsuji Tomita; Jun'ichi Suzuki; Katsuhisa Horimoto; Tatsuya Akutsu (J. Bioinform. Comput. Biol., 2006)

Inference of Protein-Protein Interactions by Using Co-evolutionary Information. - Tetsuya Sato 003; Yoshihiro Yamanishi; Katsuhisa Horimoto; Minoru Kanehisa; Hiroyuki Toh (AB, 2007)

Exact Parameter Determination for Parkinson's Disease Diagnosis with PET Using an Algebraic Approach. - Hiroshi Yoshida; Koji Nakagawa; Hirokazu Anai; Katsuhisa Horimoto (AB, 2007)

An Algebraic-Numeric Algorithm for the Model Selection in Kinetic Networks. - Hiroshi Yoshida; Koji Nakagawa; Hirokazu Anai; Katsuhisa Horimoto (CASC, 2007)

Derivation of rigorous conditions for high cell-type diversity by algebraic approach. - Hiroshi Yoshida; Hirokazu Anai; Katsuhisa Horimoto (Biosyst., 2007)

Gene Systems Network Inferred from Expression Profiles in Hepatocellular Carcinogenesis by Graphical Gaussian Model. - Sachiyo Aburatani; Fuyan Sun; Shigeru Saito; Masao Honda; Shuichi Kaneko; Katsuhisa Horimoto (EURASIP J. Bioinform. Syst. Biol., 2007)

Network evaluation from the consistency of the graph structure with the measured data. - Shigeru Saito; Sachiyo Aburatani; Katsuhisa Horimoto (BMC Syst. Biol., 2008)

Integer programming-based approach to allocation of reporter genes for cell array analysis. - Morihiro Hayashida; Fuyan Sun; Sachiyo Aburatani; Katsuhisa Horimoto; Tatsuya Akutsu (Int. J. Bioinform. Res. Appl., 2008)

High-throughput Automated Image Processing System for Cell Array Observations. - Daisuke Tominaga; Fukumi Iguchi; Katsuhisa Horimoto; Yutaka Akiyama (Inf. Media Technol., 2008)

Judgment Algorithm for Periodicity of Time Series Data Based on Bayesian Information Criterion. - Daisuke Tominaga; Katsuhisa Horimoto (J. Bioinform. Comput. Biol., 2008)

Inference of Probabilities over a Stochastic IL-System by Quantifier Elimination. - Hiroshi Yoshida; Katsuhisa Horimoto; Hirokazu Anai (Math. Comput. Sci., 2008)

Completing Networks Using Observed Data. - Tatsuya Akutsu; Takeyuki Tamura; Katsuhisa Horimoto (ALT, 2009)

Detection of network structure changes by graphical chain modeling: a case study of hepatitis C virus-related hepatocellular carcinoma. - Shigeru Saito; Masao Honda; Shuichi Kaneko; Katsuhisa Horimoto (CDC, 2009)

Co-Expressed Gene Assessment Based on the Path Consistency Algorithm: Operon Detention in Escherichia coli. - Katsuhisa Horimoto; Shigeru Saito (SMC, 2009)

Foreword. - Hirokazu Anai; Katsuhisa Horimoto (Math. Comput. Sci., 2009)

A General Procedure for Accurate Parameter Estimation in Dynamic Systems Using New Estimation Errors. - Masahiko Nakatsui; Alexandre Sedoglavic; François Lemaire; François Boulier; Asli Ürgüplü; Katsuhisa Horimoto (ANB, 2010)

A procedure for identifying master regulators in conjunction with network screening and inference. - Shigeru Saito; Xinrong Zhou; Taejeong Bae; Sunghoon Kim 001; Katsuhisa Horimoto (BIBM, 2010)

Improvement of estimation accuracy in parameter optimization by symbolic computation. - Masahiko Nakatsui; Katsuhisa Horimoto (CACSD, 2010)

Parameter optimization by using differential elimination: a general approach for introducing constraints into objective functions. - Masahiko Nakatsui; Katsuhisa Horimoto; Masahiro Okamoto; Yasuhito Tokumoto; Jun Miyake (BMC Syst. Biol., 2010)

Possible linkages between the inner and outer cellular states of human induced pluripotent stem cells. - Shigeru Saito; Yasuko Onuma; Yuzuru Ito; Hiroaki Tateno; Masashi Toyoda; Akutsu Hidenori; Koichiro Nishino; Emi Chikazawa; Yoshihiro Fukawatase; Yoshitaka Miyagawa; Hajime Okita; Nobutaka Kiyokawa; et al. (BMC Syst. Biol., 2011)

Network screening of Goto-Kakizaki rat liver microarray data during diabetic progression. - Huarong Zhou; Shigeru Saito; Guanying Piao; Zhi-Ping Liu; Jiguang Wang; Katsuhisa Horimoto; Luonan Chen (BMC Syst. Biol., 2011)

Discovery of Chemical Compound Groups with Common Structures by a Network Analysis Approach (Affinity Prediction Method). - Shigeru Saito; Takatsugu Hirokawa; Katsuhisa Horimoto (J. Chem. Inf. Model., 2011)

International Symposium on Symbolic Systems Biology (NII Shonan Meeting 2011-7). - Katsuhisa Horimoto; Katsumi Inoue; Oliver Ray (NII Shonan Meet. Rep., 2011)

Exploration of Cellular Relationships from Characteristically Expressed Genes by Partial Canonical Correlation Analysis. - Akiko Toshimori; Kunio Shimizu; Tingting Yu; Zhining Fan; Xinrong Zhou; Shigeru Saito; Katsuhisa Horimoto; Xia Jinrong; Huarong Zhou (CISIS, 2012)

A Gaussian graphical model for identifying significantly responsive regulatory networks from time series gene expression data. - Zhi-Ping Liu; Wanwei Zhang; Katsuhisa Horimoto; Luonan Chen (ISB, 2012)

Network clustering along diabetes progression in three tissues of Goto-Kakizaki rats. - Xinrong Zhou; Katsuhisa Horimoto; Shigeru Saito; Luonan Chen; Huarong Zhou (ISB, 2012)

A computational procedure for identifying master regulator candidates: a case study on diabetes progression in Goto-Kakizaki rats. - Guanying Piao; Shigeru Saito; Yidan Sun; Zhi-Ping Liu; Yong Wang 001; Xiao Han; Jiarui Wu; Huarong Zhou; Luonan Chen; Katsuhisa Horimoto (BMC Syst. Biol., 2012)

Identification of upstream regulators for prognostic expression signature genes in colorectal cancer. - Taejeong Bae; Kyoohyoung Rho; Jin Woo Choi; Katsuhisa Horimoto; Wan Kyu Kim; Sunghoon Kim 001 (BMC Syst. Biol., 2013)

Identification of master regulator candidates in conjunction with network screening and inference. - Shigeru Saito; Xinrong Zhou; Taejeong Bae; Sunghoon Kim 001; Katsuhisa Horimoto (Int. J. Data Min. Bioinform., 2013)

ToGo-WF: prediction of RNA tertiary structures and RNA-RNA/protein interactions using the KNIME workflow. - Satoshi Yamasaki; Takayuki Amemiya; Yukimitsu Yabuki; Katsuhisa Horimoto; Kazuhiko Fukui (J. Comput. Aided Mol. Des., 2019)

Phosprof: pathway analysis database of drug response based on phosphorylation activity measurements. - Harumi Kagiwada; Chie Motono; Katsuhisa Horimoto; Kazuhiko Fukui (Database J. Biol. Databases Curation, 2022)