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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

Estimating Gene Networks from Expression Data and Binding Location Data via Boolean Networks. - Osamu Hirose; Naoki Nariai; Yoshinori Tamada; Hideo Bannai; Seiya Imoto; Satoru Miyano (ICCSA (3), 2005)

A Penalized Likelihood Estimation on Transcriptional Module-Based Clustering. - Ryo Yoshida; Seiya Imoto; Tomoyuki Higuchi (ICCSA (3), 2005)

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

Discovery of Exogenous Variables in Data with More Variables Than Observations. - Yasuhiro Sogawa; Shohei Shimizu; Aapo Hyvärinen; Takashi Washio; Teppei Shimamura; Seiya Imoto (ICANN (1), 2010)

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

A Bayesian model integration for mutation calling through data partitioning. - Takuya Moriyama; Seiya Imoto; Shuto Hayashi; Yuichi Shiraishi; Satoru Miyano; Rui Yamaguchi (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. - Hiroki Konishi; Daisuke Komura; Hiroto Katoh; Shinichiro Atsumi; Hirotomo Koda; Asami Yamamoto; Yasuyuki Seto; Masashi Fukayama; Rui Yamaguchi; Seiya Imoto; Shumpei Ishikawa (BMC Bioinform., 2019)

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

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

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

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

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

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

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

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

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

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

HEAL: an automated deep learning framework for cancer histopathology image analysis. - Yanan Wang 003; Nicolas Coudray; Yun Zhao 004; Fuyi Li; Changyuan Hu; Yao-Zhong Zhang; Seiya Imoto; Aristotelis Tsirigos; Geoffrey I. Webb; Roger J. Daly; Jiangning Song (Bioinform., 2021)

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

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

Multiplex-detection Based Multiple Instance Learning Network for Whole Slide Image Classification. - Zhikang Wang; Yue Bi; Tong Pan; Xiaoyu Wang 016; Chris Bain; Richard Bassed; Seiya Imoto; Jianhua Yao 001; Jiangning Song (CoRR, 2022)

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

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

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

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

PFresGO: an attention mechanism-based deep-learning approach for protein annotation by integrating gene ontology inter-relationships. - Tong Pan; Chen Li 021; Yue Bi; Zhikang Wang; Robin B. Gasser; Anthony W. Purcell; Tatsuya Akutsu; Geoffrey I. Webb; Seiya Imoto; Jiangning Song (Bioinform., 2023)

Targeting tumor heterogeneity: multiplex-detection-based multiple instance learning for whole slide image classification. - Zhikang Wang; Yue Bi; Tong Pan; Xiaoyu Wang 016; Chris Bain; Richard Bassed; Seiya Imoto; Jianhua Yao 001; Roger J. Daly; Jiangning Song (Bioinform., 2023)

iAMPCN: a deep-learning approach for identifying antimicrobial peptides and their functional activities. - Jing Xu 008; Fuyi Li; Chen Li 021; Xudong Guo; Cornelia B. Landersdorfer; Hsin-Hui Shen; Anton Y. Peleg; Jian Li 052; Seiya Imoto; Jianhua Yao 001; Tatsuya Akutsu; Jiangning Song (Briefings Bioinform., 2023)

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

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

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

Surformer: An interpretable pattern-perceptive survival transformer for cancer survival prediction from histopathology whole slide images. - Zhikang Wang; Qian Gao; Xiaoping Yi; Xinyu Zhang 017; Yiwen Zhang; Daokun Zhang; Pietro Liò; Chris Bain; Richard Bassed; Shanshan Li; Yuming Guo 001; Seiya Imoto; et al. (Comput. Methods Programs Biomed., 2023)

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

Deep learning approaches for non-coding genetic variant effect prediction: current progress and future prospects. - Xiaoyu Wang 016; Fuyi Li; Yiwen Zhang; Seiya Imoto; Hsin-Hui Shen; Shanshan Li; Yuming Guo 001; Jian Yang 005; Jiangning Song (Briefings Bioinform., 2024)

Histo-Genomic Knowledge Distillation For Cancer Prognosis From Histopathology Whole Slide Images. - Zhikang Wang; Yumeng Zhang; Yingxue Xu; Seiya Imoto; Hao Chen 011; Jiangning Song (CoRR, 2024)

Dual-stream multi-dependency graph neural network enables precise cancer survival analysis. - Zhikang Wang; Jiani Ma; Qian Gao; Chris Bain; Seiya Imoto; Pietro Liò; Hongmin Cai; Hao Chen 011; Jiangning Song (Medical Image Anal., 2024)

Histo-Genomic Knowledge Association for Cancer Prognosis From Histopathology Whole Slide Images. - Zhikang Wang; Yumeng Zhang; Yingxue Xu; Seiya Imoto; Hao Chen 011; Jiangning Song (IEEE Trans. Medical Imaging, 2025)