Histo-Genomic Knowledge Association for Cancer Prognosis From Histopathology Whole Slide Images. - Wang, Zhikang; Zhang, Yumeng; Xu, Yingxue; Imoto, Seiya; Chen, Hao; Song, Jiangning (IEEE Trans. Medical Imaging, 2025)

Deep learning approaches for non-coding genetic variant effect prediction: current progress and future prospects. - Wang, Xiaoyu; Li, Fuyi; Zhang, Yiwen; Imoto, Seiya; Shen, Hsin-Hui; Li, Shanshan; Guo, Yuming; Yang, Jian; Song, Jiangning (Briefings Bioinform., 2024)

STForte: tissue context-specific encoding and consistency-aware spatial imputation for spatially resolved transcriptomics. - Pang, Yuxuan; Wang, Chunxuan; Zhang, Yao-zhong; Wang, Zhuo; Imoto, Seiya; Lee, Tzong-Yi (Briefings Bioinform., 2024)

Dual-stream multi-dependency graph neural network enables precise cancer survival analysis. - Wang, Zhikang; Ma, Jiani; Gao, Qian; Bain, Chris; Imoto, Seiya; Liò, Pietro; Cai, Hongmin; Chen, Hao; Song, Jiangning (Medical Image Anal., 2024)

Histo-Genomic Knowledge Distillation For Cancer Prognosis From Histopathology Whole Slide Images. - Wang, Zhikang; Zhang, Yumeng; Xu, Yingxue; Imoto, Seiya; Chen, Hao; Song, Jiangning (CoRR, 2024)

iAMPCN: a deep-learning approach for identifying antimicrobial peptides and their functional activities. - Xu, Jing; Li, Fuyi; Li, Chen; Guo, Xudong; Landersdorfer, Cornelia B.; Shen, Hsin-Hui; Peleg, Anton Y.; Li, Jian; Imoto, Seiya; Yao, Jianhua; Akutsu, Tatsuya; Song, Jiangning (Briefings Bioinform., 2023)

Zero-shot-capable identification of phage-host relationships with whole-genome sequence representation by contrastive learning. - Zhang, Yao-zhong; Liu, Yunjie; Bai, Zeheng; Fujimoto, Kosuke; Uematsu, Satoshi; Imoto, Seiya (Briefings Bioinform., 2023)

PFresGO: an attention mechanism-based deep-learning approach for protein annotation by integrating gene ontology inter-relationships. - Pan, Tong; Li, Chen; Bi, Yue; Wang, Zhikang; Gasser, Robin B.; Purcell, Anthony W.; Akutsu, Tatsuya; Webb, Geoffrey I.; Imoto, Seiya; Song, Jiangning (Bioinform., 2023)

Targeting tumor heterogeneity: multiplex-detection-based multiple instance learning for whole slide image classification. - Wang, Zhikang; Bi, Yue; Pan, Tong; Wang, Xiaoyu; Bain, Chris; Bassed, Richard; Imoto, Seiya; Yao, Jianhua; Daly, Roger J.; Song, Jiangning (Bioinform., 2023)

ggkegg: analysis and visualization of KEGG data utilizing the grammar of graphics. - Sato, Noriaki; Uematsu, Miho; Fujimoto, Kosuke; Uematsu, Satoshi; Imoto, Seiya (Bioinform., 2023)

Investigation of the BERT model on nucleotide sequences with non-standard pre-training and evaluation of different k-mer embeddings. - Zhang, Yao-zhong; Bai, Zeheng; Imoto, Seiya (Bioinform., 2023)

Surformer: An interpretable pattern-perceptive survival transformer for cancer survival prediction from histopathology whole slide images. - Wang, Zhikang; Gao, Qian; Yi, Xiaoping; Zhang, Xinyu; Zhang, Yiwen; Zhang, Daokun; Liò, Pietro; Bain, Chris; Bassed, Richard; Li, Shanshan; Guo, Yuming; Imoto, Seiya; et al. (Comput. Methods Programs Biomed., 2023)

Gene Regulatory Network-Classifier: Gene Regulatory Network-Based Classifier and Its Applications to Gastric Cancer Drug (5-Fluorouracil) Marker Identification. - Park, Heewon; Imoto, Seiya; Miyano, Satoru (J. Comput. Biol., 2023)

Imputing time-series microbiome abundance profiles with diffusion model. - Seki, Misato; Zhang, Yao-Zhong; Imoto, Seiya (2023)

Identification of bacteriophage genome sequences with representation learning. - Bai, Zeheng; Zhang, Yao-zhong; Miyano, Satoru; Yamaguchi, Rui; Fujimoto, Kosuke; Uematsu, Satoshi; Imoto, Seiya (Bioinform., 2022)

PredictiveNetwork: predictive gene network estimation with application to gastric cancer drug response-predictive network analysis. - Park, Heewon; Imoto, Seiya; Miyano, Satoru (BMC Bioinform., 2022)

Improvement of the Japanese healthcare data system for the effective management of patients with COVID-19: A national survey. - Takeshita, Kohei; Takao, Hiroyuki; Imoto, Seiya; Murayama, Yuichi (Int. J. Medical Informatics, 2022)

Uncovering Molecular Mechanisms of Drug Resistance via Network-Constrained Common Structure Identification. - Park, Heewon; Yamaguchi, Rui; Imoto, Seiya; Miyano, Satoru (J. Comput. Biol., 2022)

Multiplex-detection Based Multiple Instance Learning Network for Whole Slide Image Classification. - Wang, Zhikang; Bi, Yue; Pan, Tong; Wang, Xiaoyu; Bain, Chris; Bassed, Richard; Imoto, Seiya; Yao, Jianhua; Song, Jiangning (CoRR, 2022)

Halcyon: an accurate basecaller exploiting an encoder-decoder model with monotonic attention. - Konishi, Hiroki; Yamaguchi, Rui; Yamaguchi, Kiyoshi; Furukawa, Yoichi; Imoto, Seiya (Bioinform., 2021)

HEAL: an automated deep learning framework for cancer histopathology image analysis. - Wang, Yanan; Coudray, Nicolas; Zhao, Yun; Li, Fuyi; Hu, Changyuan; Zhang, Yao-Zhong; Imoto, Seiya; Tsirigos, Aristotelis; Webb, Geoffrey I.; Daly, Roger J.; Song, Jiangning (Bioinform., 2021)

Enhancing breakpoint resolution with deep segmentation model: A general refinement method for read-depth based structural variant callers. - Zhang, Yao-Zhong; Imoto, Seiya; Miyano, Satoru; Yamaguchi, Rui (PLoS Comput. Biol., 2021)

On the application of BERT models for nanopore methylation detection. - Zhang, Yao-Zhong; Yamaguchi, Kiyoshi; Hatakeyama, Sera; Furukawa, Yoichi; Miyano, Satoru; Yamaguchi, Rui; Imoto, Seiya (2021)

Discovering microbe functionality in human disease with a gene-ontology-aware model. - Liu, Yunjie; Zhang, Yaozhong; Imoto, Seiya (2021)

Neoantimon: a multifunctional R package for identification of tumor-specific neoantigens. - Hasegawa, Takanori; Hayashi, Shuto; Shimizu, Eigo; Mizuno, Shinichi; Niida, Atsushi; Yamaguchi, Rui; Miyano, Satoru; Nakagawa, Hidewaki; Imoto, Seiya (Bioinform., 2020)

Nanopore basecalling from a perspective of instance segmentation. - Zhang, Yao-zhong; Akdemir, Arda; Tremmel, Georg; Imoto, Seiya; Miyano, Satoru; Shibuya, Tetsuo; Yamaguchi, Rui (BMC Bioinform., 2020)

Ensemble smoothers for inference of hidden states and parameters in combinatorial regulatory model. - Hasegawa, Takanori; Yamaguchi, Rui; Niida, Atsushi; Miyano, Satoru; Imoto, Seiya (J. Frankl. Inst., 2020)

Theoretical Foundation of the Performance of Phylogeny-Based Somatic Variant Detection. - Moriyama, Takuya; Imoto, Seiya; Miyano, Satoru; Yamaguchi, Rui (2020)

A Bayesian model integration for mutation calling through data partitioning. - Moriyama, Takuya; Imoto, Seiya; Hayashi, Shuto; Shiraishi, Yuichi; Miyano, Satoru; Yamaguchi, Rui (Bioinform., 2019)

Capturing the differences between humoral immunity in the normal and tumor environments from repertoire-seq of B-cell receptors using supervised machine learning. - Konishi, Hiroki; Komura, Daisuke; Katoh, Hiroto; Atsumi, Shinichiro; Koda, Hirotomo; Yamamoto, Asami; Seto, Yasuyuki; Fukayama, Masashi; Yamaguchi, Rui; Imoto, Seiya; Ishikawa, Shumpei (BMC Bioinform., 2019)

Robust Sample-Specific Stability Selection with Effective Error Control. - Park, Heewon; Yamada, Makoto; Imoto, Seiya; Miyano, Satoru (J. Comput. Biol., 2019)

ALPHLARD-NT: Bayesian Method for Human Leukocyte Antigen Genotyping and Mutation Calling through Simultaneous Analysis of Normal and Tumor Whole-Genome Sequence Data. - Hayashi, Shuto; Moriyama, Takuya; Yamaguchi, Rui; Mizuno, Shinichi; Komura, Mitsuhiro; Miyano, Satoru; Nakagawa, Hidewaki; Imoto, Seiya (J. Comput. Biol., 2019)

Accurate and Flexible Bayesian Mutation Call from Multi-regional Tumor Samples. - Moriyama, Takuya; Imoto, Seiya; Miyano, Satoru; Yamaguchi, Rui (2019)

Adaptive NetworkProfiler for Identifying Cancer Characteristic-Specific Gene Regulatory Networks. - Park, Heewon; Shimamura, Teppei; Imoto, Seiya; Miyano, Satoru (J. Comput. Biol., 2018)

Interaction-Based Feature Selection for Uncovering Cancer Driver Genes Through Copy Number-Driven Expression Level. - Park, Heewon; Niida, Atsushi; Imoto, Seiya; Miyano, Satoru (J. Comput. Biol., 2017)

A Novel Adaptive Penalized Logistic Regression for Uncovering Biomarker Associated with Anti-Cancer Drug Sensitivity. - Park, Heewon; Shiraishi, Yuichi; Imoto, Seiya; Miyano, Satoru (IEEE ACM Trans. Comput. Biol. Bioinform., 2017)

Reconstruction of high read-depth signals from low-depth whole genome sequencing data using deep learning. - Zhang, Yao-Zhong; Imoto, Seiya; Miyano, Satoru; Yamaguchi, Rui (2017)

A likelihood-free filtering method via approximate Bayesian computation in evaluating biological simulation models. - Hasegawa, Takanori; Niida, Atsushi; Mori, Tomoya; Shimamura, Teppei; Yamaguchi, Rui; Miyano, Satoru; Akutsu, Tatsuya; Imoto, Seiya (Comput. Stat. Data Anal., 2016)

Binary contingency table method for analysing gene mutation in cancer genome. - Ayada, Emi; Hasegawa, Takanori; Niida, Atsushi; Miyano, Satoru; Imoto, Seiya (Int. J. Bioinform. Res. Appl., 2016)

Protein Fold Recognition Using Genetic Algorithm Optimized Voting Scheme and Profile Bigram. - Saini, Harsh; Raicar, Gaurav; Lal, Sunil Pranit; Dehzangi, Abdollah; Imoto, Seiya; Sharma, Alok (J. Softw., 2016)

Predicting Japanese Kampo formulas by analyzing database of medical records: a preliminary observational study. - Yoshino, Tetsuhiro; Katayama, Kotoe; Horiba, Yuko; Munakata, Kaori; Yamaguchi, Rui; Imoto, Seiya; Miyano, Satoru; Mima, Hideki; Watanabe, Kenji (BMC Medical Informatics Decis. Mak., 2016)

OVarCall: Bayesian Mutation Calling Method Utilizing Overlapping Paired-End Reads. - Moriyama, Takuya; Shiraishi, Yuichi; Chiba, Kenichi; Yamaguchi, Rui; Imoto, Seiya; Miyano, Satoru (2016)

Genomon ITDetector: a tool for somatic internal tandem duplication detection from cancer genome sequencing data. - Chiba, Kenichi; Shiraishi, Yuichi; Nagata, Yasunobu; Yoshida, Kenichi; Imoto, Seiya; Ogawa, Seishi; Miyano, Satoru (Bioinform., 2015)

Genomic data assimilation using a higher moment filtering technique for restoration of gene regulatory networks. - Hasegawa, Takanori; Mori, Tomoya; Yamaguchi, Rui; Shimamura, Teppei; Miyano, Satoru; Imoto, Seiya; Akutsu, Tatsuya (BMC Syst. Biol., 2015)

Sparse Overlapping Group Lasso for Integrative Multi-Omics Analysis. - Park, Heewon; Niida, Atsushi; Miyano, Satoru; Imoto, Seiya (J. Comput. Biol., 2015)

Binary Contingency Table Method for Analyzing Gene Mutation in Cancer Genome. - Ayada, Emi; Niida, Atsushi; Hasegawa, Takanori; Miyano, Satoru; Imoto, Seiya (2015)

HapMuC: somatic mutation calling using heterozygous germ line variants near candidate mutations. - Usuyama, Naoto; Shiraishi, Yuichi; Sato, Yusuke; Kume, Haruki; Homma, Yukio; Ogawa, Seishi; Miyano, Satoru; Imoto, Seiya (Bioinform., 2014)

An efficient method of exploring simulation models by assimilating literature and biological observational data. - Hasegawa, Takanori; Nagasaki, Masao; Yamaguchi, Rui; Imoto, Seiya; Miyano, Satoru (Biosyst., 2014)

An Efficient Data Assimilation Schema for Restoration and Extension of Gene Regulatory Networks Using Time-Course Observation Data. - Hasegawa, Takanori; Mori, Tomoya; Yamaguchi, Rui; Imoto, Seiya; Miyano, Satoru; Akutsu, Tatsuya (J. Comput. Biol., 2014)

A feature selection method using fixed-point algorithm for DNA microarray gene expression data. - Sharma, Alok; Paliwal, Kuldip K.; Imoto, Seiya; Miyano, Satoru; Sharma, Vandana; Ananthanarayanan, Rajeshkannan (Int. J. Knowl. Based Intell. Eng. Syst., 2014)

A feature selection method using improved regularized linear discriminant analysis. - Sharma, Alok; Paliwal, Kuldip K.; Imoto, Seiya; Miyano, Satoru (Mach. Vis. Appl., 2014)

Parameter estimation in multi-compartment SIR model. - Saito, Masaya M.; Imoto, Seiya; Yamaguchi, Rui; Miyano, Satoru; Higuchi, Tomoyuki (2014)

A strategy to select suitable physicochemical attributes of amino acids for protein fold recognition. - Sharma, Alok; Paliwal, Kuldip K.; Dehzangi, Abdollah; Lyons, James G.; Imoto, Seiya; Miyano, Satoru (BMC Bioinform., 2013)

Multi-omics Approach for Estimating Metabolic Networks Using Low-Order Partial Correlations. - Kayano, Mitsunori; Imoto, Seiya; Yamaguchi, Rui; Miyano, Satoru (J. Comput. Biol., 2013)

Principal component analysis using QR decomposition. - Sharma, Alok; Paliwal, Kuldip K.; Imoto, Seiya; Miyano, Satoru (Int. J. Mach. Learn. Cybern., 2013)

Estimation of abrupt changes in sentinel observation data of influenza epidemics in Japan. - Saito, Masaya M.; Imoto, Seiya; Yamaguchi, Rui; Miyano, Satoru; Higuchi, Tomoyuki (2013)

Multilayer Cluster Heat Map Visualizing Biological Tensor Data. - Niida, Atsushi; Tremmel, Georg; Imoto, Seiya; Miyano, Satoru (2013)

Statistical model-based testing to evaluate the recurrence of genomic aberrations. - Niida, Atsushi; Imoto, Seiya; Shimamura, Teppei; Miyano, Satoru (Bioinform., 2012)

Identifying regulational alterations in gene regulatory networks by state space representation of vector autoregressive models and variational annealing. - Kojima, Kaname; Imoto, Seiya; Yamaguchi, Rui; Fujita, André; Yamauchi, Mai; Gotoh, Noriko; Miyano, Satoru (BMC Genom., 2012)

Computational gene network analysis reveals TNF-induced angiogenesis. - Ogami, Kentaro; Yamaguchi, Rui; Imoto, Seiya; Tamada, Yoshinori; Araki, Hiromitsu; Print, Cristin G.; Miyano, Satoru (BMC Syst. Biol., 2012)

A between-Class Overlapping Filter-Based Method for transcriptome Data Analysis. - Sharma, Alok; Imoto, Seiya; Miyano, Satoru (J. Bioinform. Comput. Biol., 2012)

Null space based feature selection method for gene expression data. - Sharma, Alok; Imoto, Seiya; Miyano, Satoru; Sharma, Vandana (Int. J. Mach. Learn. Cybern., 2012)

Connection between traditional medicine and disease. - Katayama, Kotoe; Yamaguchi, Rui; Imoto, Seiya; Matsuura, Keiko; Watanabe, Kenji (SIGHIT Rec., 2012)

A Top-r Feature Selection Algorithm for Microarray Gene Expression Data. - Sharma, Alok; Imoto, Seiya; Miyano, Satoru (IEEE ACM Trans. Comput. Biol. Bioinform., 2012)

Identifying Gene Pathways Associated with Cancer Characteristics via Sparse Statistical Methods. - Kawano, Shuichi; Shimamura, Teppei; Niida, Atsushi; Imoto, Seiya; Yamaguchi, Rui; Nagasaki, Masao; Yoshida, Ryo; Print, Cristin G.; Miyano, Satoru (IEEE ACM Trans. Comput. Biol. Bioinform., 2012)

Analysis of questionnaire for traditional medical and develop decision support system. - Katayama, Kotoe; Imoto, Seiya; Watanabe, Kenji; Yamaguchi, Rui; Matsuura, Keiko; Miyano, Satoru (2012)

Identifiability of local transmissibility parameters in agent-based pandemic simulation. - Saito, Masaya M.; Imoto, Seiya; Yamaguchi, Rui; Miyano, Satoru; Higuchi, Tomoyuki (2012)

SiGN-SSM: open source parallel software for estimating gene networks with state space models. - Tamada, Yoshinori; Yamaguchi, Rui; Imoto, Seiya; Hirose, Osamu; Yoshida, Ryo; Nagasaki, Masao; Miyano, Satoru (Bioinform., 2011)

Transform of visual analogue scale data and their clustering. - Katayama, Kotoe; Yamaguchi, Rui; Imoto, Seiya; Matsuura, Keiko; Watanabe, Kenji; Miyano, Satoru (Int. J. Knowl. Eng. Soft Data Paradigms, 2011)

Parallel Algorithm for Learning Optimal Bayesian Network Structure. - Tamada, Yoshinori; Imoto, Seiya; Miyano, Satoru (J. Mach. Learn. Res., 2011)

Estimating exogenous variables in data with more variables than observations. - Sogawa, Yasuhiro; Shimizu, Shohei; Shimamura, Teppei; Hyvärinen, Aapo; Washio, Takashi; Imoto, Seiya (Neural Networks, 2011)

Estimating Genome-Wide Gene Networks Using Nonparametric Bayesian Network Models on Massively Parallel Computers. - Tamada, Yoshinori; Imoto, Seiya; Araki, Hiromitsu; Nagasaki, Masao; Print, Cristin G.; Charnock-Jones, Stephen D.; Miyano, Satoru (IEEE ACM Trans. Comput. Biol. Bioinform., 2011)

Parallel Agent-Based Simulator for Influenza Pandemic. - Saito, Masaya M.; Imoto, Seiya; Yamaguchi, Rui; Miyano, Satoru; Higuchi, Tomoyuki (2011)

Estimation of macroscopic parameter in agent-based pandemic simulation. - Saito, Masaya M.; Imoto, Seiya; Yamaguchi, Rui; Miyano, Satoru; Higuchi, Tomoyuki (2011)

Poster: Comprehensive pharmacogenomic pathway screening by data assimilation. - Hasegawa, Takanori; Yamaguchi, Rui; Nagasaki, Masao; Imoto, Seiya; Miyano, Satoru (2011)

Comprehensive Pharmacogenomic Pathway Screening by Data Assimilation. - Hasegawa, Takanori; Yamaguchi, Rui; Nagasaki, Masao; Imoto, Seiya; Miyano, Satoru (2011)

Clustering for Visual Analogue Scale Data in Symbolic Data Analysis. - Katayama, Kotoe; Yamaguchi, Rui; Imoto, Seiya; Matsuura, Keiko; Watanabe, Kenji; Miyano, Satoru (2011)

Computational Drug Target Pathway Discovery: A Bayesian Network Approach. - Imoto, Seiya; Tamada, Yoshinori; Araki, Hiromitsu; Miyano, Satoru (2011)

Inferring dynamic gene networks under varying conditions for transcriptomic network comparison. - Shimamura, Teppei; Imoto, Seiya; Yamaguchi, Rui; Nagasaki, Masao; Miyano, Satoru (Bioinform., 2010)

Model-free unsupervised gene set screening based on information enrichment in expression profiles. - Niida, Atsushi; Imoto, Seiya; Yamaguchi, Rui; Nagasaki, Masao; Fujita, André; Shimamura, Teppei; Miyano, Satoru (Bioinform., 2010)

Optimal Search on Clustered Structural Constraint for Learning Bayesian Network Structure. - Kojima, Kaname; Perrier, Eric; Imoto, Seiya; Miyano, Satoru (J. Mach. Learn. Res., 2010)

Identifying Hidden Confounders in Gene Networks by Bayesian Networks. - Higashigaki, Tomoya; Kojima, Kaname; Yamaguchi, Rui; Inoue, Masato; Imoto, Seiya; Miyano, Satoru (2010)

Discovering functional gene pathways associated with cancer heterogeneity via sparse supervised learning. - Kawano, Shuichi; Shimamura, Teppei; Niida, Atsushi; Imoto, Seiya; Yamaguchi, Rui; Nagasaki, Masao; Yoshida, Ryo; Print, Cristin G.; Miyano, Satoru (2010)

Network profiling analysis for generating modulator-dependent gene networks. - Shimamura, Teppei; Imoto, Seiya; Niida, Atsushi; Nagasaki, Masao; Yamaguchi, Rui; Miyano, Satoru (2010)

Discovery of Exogenous Variables in Data with More Variables Than Observations. - Sogawa, Yasuhiro; Shimizu, Shohei; Hyvärinen, Aapo; Washio, Takashi; Shimamura, Teppei; Imoto, Seiya (2010)

Searching Optimal Bayesian Network Structure on Constraint Search Space: Super-Structure Approach. - Imoto, Seiya; Kojima, Kaname; Perrier, Eric; Tamada, Yoshinori; Miyano, Satoru (2010)

Gene set-based module discovery in the breast cancer transcriptome. - Niida, Atsushi; Smith, Andrew D.; Imoto, Seiya; Aburatani, Hiroyuki; Zhang, Michael Q.; Akiyama, Tetsu (BMC Bioinform., 2009)

Recursive regularization for inferring gene networks from time-course gene expression profiles. - Shimamura, Teppei; Imoto, Seiya; Yamaguchi, Rui; Fujita, André; Nagasaki, Masao; Miyano, Satoru (BMC Syst. Biol., 2009)

Network-Based Predictions and Simulations by Biological State Space Models: Search for Drug Mode of Action. - Yamaguchi, Rui; Imoto, Seiya; Miyano, Satoru (J. Comput. Sci. Technol., 2009)

Gene Networks Viewed through Two Models. - Miyano, Satoru; Yamaguchi, Rui; Tamada, Yoshinori; Nagasaki, Masao; Imoto, Seiya (2009)

Unraveling Dynamic Activities of Autocrine Pathways that Control Drug-Response Transcriptome Networks. - Tamada, Yoshinori; Araki, Hiromitsu; Imoto, Seiya; Nagasaki, Masao; Doi, Atsushi; Nakanishi, Yukiko; Tomiyasu, Yuki; Yasuda, Kaori; Dunmore, Ben; Sanders, Deborah; Humphreys, Sally; Print, Cristin G.; et al. (2009)

Statistical inference of transcriptional module-based gene networks from time course gene expression profiles by using state space models. - Hirose, Osamu; Yoshida, Ryo; Imoto, Seiya; Yamaguchi, Rui; Higuchi, Tomoyuki; Charnock-Jones, Stephen D.; Print, Cristin G.; Miyano, Satoru (Bioinform., 2008)

Bayesian learning of biological pathways on genomic data assimilation. - Yoshida, Ryo; Nagasaki, Masao; Yamaguchi, Rui; Imoto, Seiya; Miyano, Satoru; Higuchi, Tomoyuki (Bioinform., 2008)

Integrative bioinformatics analysis of transcriptional regulatory programs in breast cancer cells. - Niida, Atsushi; Smith, Andrew D.; Imoto, Seiya; Tsutsumi, Shuichi; Aburatani, Hiroyuki; Zhang, Michael Q.; Akiyama, Tetsu (BMC Bioinform., 2008)

ExonMiner: Web service for analysis of GeneChip Exon array data. - Numata, Kazuyuki; Yoshida, Ryo; Nagasaki, Masao; Saito, Ayumu; Imoto, Seiya; Miyano, Satoru (BMC Bioinform., 2008)

Analyzing Time Course Gene Expression Data with Biological and Technical Replicates to Estimate Gene Networks by State Space Models. - Hirose, Osamu; Yoshida, Ryo; Yamaguchi, Rui; Imoto, Seiya; Higuchi, Tomoyuki; Miyano, Satoru (2008)

Partial Order-Based Bayesian Network Learning Algorithm for Estimating Gene Networks. - Numata, Kazuyuki; Imoto, Seiya; Miyano, Satoru (2008)

Finding module-based gene networks with state-space models - Mining high-dimensional and short time-course gene expression data. - Yamaguchi, Rui; Yoshida, Ryo; Imoto, Seiya; Higuchi, Tomoyuki; Miyano, Satoru (IEEE Signal Process. Mag., 2007)

Computational Genome-Wide Discovery of Aberrant Splice Variations with Exon Expression Profiles. - Yoshida, Ryo; Numata, Kazuyuki; Imoto, Seiya; Nagasaki, Masao; Doi, Atsushi; Ueno, Kazuko; Miyano, Satoru (2007)

A Structure Learning Algorithm for Inference of Gene Networks from Microarray Gene Expression Data Using Bayesian Networks. - Numata, Kazuyuki; Imoto, Seiya; Miyano, Satoru (2007)

Statistical Absolute Evaluation of Gene Ontology Terms with Gene Expression Data. - Gupta, Pramod K.; Yoshida, Ryo; Imoto, Seiya; Yamaguchi, Rui; Miyano, Satoru (2007)

DIGDAG, a First Algorithm to Mine Closed Frequent Embedded Sub-DAGs. - Termier, Alexandre; Tamada, Yoshinori; Numata, Kazuyuki; Imoto, Seiya; Washio, Takashi; Higuchi, Tomoyuki (2007)

ArrayCluster: an analytic tool for clustering, data visualization and module finder on gene expression profiles. - Yoshida, Ryo; Higuchi, Tomoyuki; Imoto, Seiya; Miyano, Satoru (Bioinform., 2006)

Statistical Model Selection Method to Analyze Combinatorial Effects of Snps and Environmental Factors for Binary Disease. - Nakamichi, Reiichiro; Imoto, Seiya; Miyano, Satoru (Int. J. Artif. Intell. Tools, 2006)

Computational Strategy for Discovering Druggable Gene Networks from Genome-Wide RNA Expression Profiles. - Imoto, Seiya; Tamada, Yoshinori; Araki, Hiromitsu; Yasuda, Kaori; Print, Cristin G.; Charnock-Jones, Stephen D.; Sanders, Deborah; Savoie, Christopher J.; Tashiro, Kousuke; Kuhara, Satoru; Miyano, Satoru (2006)

Utilizing Evolutionary Information and Gene Expression Data for Estimating Gene Networks with Bayesian Network Models. - Tamada, Yoshinori; Bannai, Hideo; Imoto, Seiya; Katayama, Toshiaki; Kanehisa, Minoru; Miyano, Satoru (J. Bioinform. Comput. Biol., 2005)

Estimating Time-Dependent Gene Networks from Time Series Microarray Data by Dynamic Linear Models with Markov Switching. - Yoshida, Ryo; Imoto, Seiya; Higuchi, Tomoyuki (2005)

Estimating gene regulatory networks and protein-protein interactions of Saccharomyces cerevisiae from multiple genome-wide data. - Nariai, Naoki; Tamada, Yoshinori; Imoto, Seiya; Miyano, Satoru (2005)

Estimating Gene Networks from Expression Data and Binding Location Data via Boolean Networks. - Hirose, Osamu; Nariai, Naoki; Tamada, Yoshinori; Bannai, Hideo; Imoto, Seiya; Miyano, Satoru (2005)

A Penalized Likelihood Estimation on Transcriptional Module-Based Clustering. - Yoshida, Ryo; Imoto, Seiya; Higuchi, Tomoyuki (2005)

Combining Microarrays and Biological Knowledge for Estimating Gene Networks via Bayesian Networks. - Imoto, Seiya; Higuchi, Tomoyuki; Goto, Takao; Tashiro, Kousuke; Kuhara, Satoru; Miyano, Satoru (J. Bioinform. Comput. Biol., 2004)

Case-Control Study of Binary Disease Trait Considering Interactions between SNPs and Environmental Effects using Logistic Regression. - Nakamichi, Reiichiro; Imoto, Seiya; Miyano, Satoru (2004)

Residual Bootstrapping and Median Filtering for Robust Estimation of Gene Networks from Microarray Data. - Imoto, Seiya; Higuchi, Tomoyuki; Kim, SunYong; Jeong, Euna; Miyano, Satoru (2004)

A Mixed Factors Model for Dimension Reduction and Extraction of a Group Structure in Gene Expression Data. - Yoshida, Ryo; Higuchi, Tomoyuki; Imoto, Seiya (2004)

Predicting gene regulation by sigma factors in Bacillus subtilis from genome-wide data. - Hoon, Michiel J. L. de; Makita, Yuko; Imoto, Seiya; Kobayashi, Kazuo; Ogasawara, Naotake; Nakai, Kenta; Miyano, Satoru (2004)

Functional Data Analysis of the Dynamics of Gene Regulatory Networks. - Ando, Tomohiro; Imoto, Seiya; Miyano, Satoru (2004)

Predicting the Operon Structure of Bacillus subtilis Using Operon Length, Intergene Distance, and Gene Expression Information. - Hoon, Michiel J. L. de; Imoto, Seiya; Kobayashi, Kazuo; Ogasawara, Naotake; Miyano, Satoru (2004)

Using Protein-Protein Interactions for Refining Gene Networks Estimated from Microarray Data by Bayesian Networks. - Nariai, Naoki; Kim, SunYong; Imoto, Seiya; Miyano, Satoru (2004)

Finding Optimal Models for Small Gene Networks. - Ott, Sascha; Imoto, Seiya; Miyano, Satoru (2004)

Inferring gene networks from time series microarray data using dynamic Bayesian networks. - Kim, SunYong; Imoto, Seiya; Miyano, Satoru (Briefings Bioinform., 2003)

Bayesian Network and Nonparametric Heteroscedastic Regression for Nonlinear Modeling of Genetic Network. - Imoto, Seiya; Kim, SunYong; Goto, Takao; Aburatani, Sachiyo; Tashiro, Kousuke; Kuhara, Satoru; Miyano, Satoru (J. Bioinform. Comput. Biol., 2003)

Use of Gene Networks for Identifying and Validating Drug Targets. - Imoto, Seiya; Savoie, Christopher J.; Aburatani, Sachiyo; Kim, SunYong; Tashiro, Kousuke; Kuhara, Satoru; Miyano, Satoru (J. Bioinform. Comput. Biol., 2003)

Dynamic Bayesian Network and Nonparametric Regression for Nonlinear Modeling of Gene Networks from Time Series Gene Expression Data. - Kim, SunYong; Imoto, Seiya; Miyano, Satoru (2003)

Combining Microarrays and Biological Knowledge for Estimating Gene Networks via Bayesian Networks. - Imoto, Seiya; Higuchi, Tomoyuki; Goto, Takao; Tashiro, Kousuke; Kuhara, Satoru; Miyano, Satoru (2003)

Estimating gene networks from gene expression data by combining Bayesian network model with promoter element detection. - Tamada, Yoshinori; Kim, SunYong; Bannai, Hideo; Imoto, Seiya; Tashiro, Kousuke; Kuhara, Satoru; Miyano, Satoru (2003)

Inferring Gene Regulatory Networks from Time-Ordered Gene Expression Data of Bacillus Subtilis Using Differential Equations. - Hoon, Michiel J. L. de; Imoto, Seiya; Kobayashi, Kazuo; Ogasawara, Naotake; Miyano, Satoru (2003)

Statistical analysis of a small set of time-ordered gene expression data using linear splines. - Hoon, Michiel J. L. de; Imoto, Seiya; Miyano, Satoru (Bioinform., 2002)

Bayesian Network and Nonparametric Heteroscedastic Regression for Nonlinear Modeling of Genetic Network. - Imoto, Seiya; Kim, SunYong; Goto, Takao; Aburatani, Sachiyo; Tashiro, Kousuke; Kuhara, Satoru; Miyano, Satoru (2002)

Inferring Gene Regulatory Networks from Time-Ordered Gene Expression Data Using Differential Equations. - Hoon, Michiel J. L. de; Imoto, Seiya; Miyano, Satoru (2002)

Estimation of Genetic Networks and Functional Structures Between Genes by Using Bayesian Networks and Nonparametric Regression. - Imoto, Seiya; Goto, Takao; Miyano, Satoru (2002)