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2020 – today
- 2024
[j73]Zhikang Wang
, Jiani Ma, Qian Gao, Chris Bain, Seiya Imoto, Pietro Liò, Hongmin Cai, Hao Chen, Jiangning Song:
Dual-stream multi-dependency graph neural network enables precise cancer survival analysis. Medical Image Anal. 97: 103252 (2024)- [i2]Zhikang Wang, Yumeng Zhang, Yingxue Xu, Seiya Imoto, Hao Chen, Jiangning Song:
Histo-Genomic Knowledge Distillation For Cancer Prognosis From Histopathology Whole Slide Images. CoRR abs/2403.10040 (2024) - 2023
- [j72]Jing Xu, Fuyi Li, Chen Li, Xudong Guo, Cornelia B. Landersdorfer, Hsin-Hui Shen, Anton Y. Peleg, Jian Li, Seiya Imoto, Jianhua Yao, Tatsuya Akutsu, Jiangning Song:
iAMPCN: a deep-learning approach for identifying antimicrobial peptides and their functional activities. Briefings Bioinform. 24(4) (2023) - [j71]Yao-zhong Zhang, Yunjie Liu, Zeheng Bai, Kosuke Fujimoto, Satoshi Uematsu, Seiya Imoto:
Zero-shot-capable identification of phage-host relationships with whole-genome sequence representation by contrastive learning. Briefings Bioinform. 24(5) (2023) - [j70]Tong Pan, Chen Li, Yue Bi, Zhikang Wang, Robin B. Gasser, Anthony W. Purcell, Tatsuya Akutsu, Geoffrey I. Webb, Seiya Imoto, Jiangning Song:
PFresGO: an attention mechanism-based deep-learning approach for protein annotation by integrating gene ontology inter-relationships. Bioinform. 39(3) (2023) - [j69]Zhikang Wang, Yue Bi, Tong Pan, Xiaoyu Wang, Chris Bain, Richard Bassed, Seiya Imoto, Jianhua Yao, Roger J. Daly, Jiangning Song:
Targeting tumor heterogeneity: multiplex-detection-based multiple instance learning for whole slide image classification. Bioinform. 39(3) (2023) - [j68]Noriaki Sato, Miho Uematsu, Kosuke Fujimoto, Satoshi Uematsu, Seiya Imoto:
ggkegg: analysis and visualization of KEGG data utilizing the grammar of graphics. Bioinform. 39(10) (2023) - [j67]Yao-zhong Zhang, Zeheng Bai, Seiya Imoto:
Investigation of the BERT model on nucleotide sequences with non-standard pre-training and evaluation of different k-mer embeddings. Bioinform. 39(10) (2023) - [j66]Zhikang Wang, Qian Gao, Xiaoping Yi, Xinyu Zhang, Yiwen Zhang, Daokun Zhang, Pietro Liò, Chris Bain, Richard Bassed, Shanshan Li, Yuming Guo, Seiya Imoto, Jianhua Yao, Roger J. Daly, Jiangning Song:
Surformer: An interpretable pattern-perceptive survival transformer for cancer survival prediction from histopathology whole slide images. Comput. Methods Programs Biomed. 241: 107733 (2023) - [j65]Heewon Park, Seiya Imoto, Satoru Miyano:
Gene Regulatory Network-Classifier: Gene Regulatory Network-Based Classifier and Its Applications to Gastric Cancer Drug (5-Fluorouracil) Marker Identification. J. Comput. Biol. 30(2): 223-243 (2023) - [c51]Misato Seki, Yao-Zhong Zhang, Seiya Imoto:
Imputing time-series microbiome abundance profiles with diffusion model. BIBM 2023: 914-919 - 2022
- [j64]Zeheng Bai, Yao-zhong Zhang, Satoru Miyano, Rui Yamaguchi, Kosuke Fujimoto, Satoshi Uematsu, Seiya Imoto:
Identification of bacteriophage genome sequences with representation learning. Bioinform. 38(18): 4264-4270 (2022) - [j63]Heewon Park, Seiya Imoto, Satoru Miyano:
PredictiveNetwork: predictive gene network estimation with application to gastric cancer drug response-predictive network analysis. BMC Bioinform. 23(1): 342 (2022) - [j62]Kohei Takeshita, Hiroyuki Takao, Seiya Imoto, Yuichi Murayama:
Improvement of the Japanese healthcare data system for the effective management of patients with COVID-19: A national survey. Int. J. Medical Informatics 162: 104752 (2022) - [j61]Heewon Park, Rui Yamaguchi, Seiya Imoto, Satoru Miyano:
Uncovering Molecular Mechanisms of Drug Resistance via Network-Constrained Common Structure Identification. J. Comput. Biol. 29(3): 257-275 (2022) - [i1]Zhikang Wang, Yue Bi, Tong Pan, Xiaoyu Wang, Chris Bain, Richard Bassed, Seiya Imoto, Jianhua Yao, Jiangning Song:
Multiplex-detection Based Multiple Instance Learning Network for Whole Slide Image Classification. CoRR abs/2208.03526 (2022) - 2021
- [j60]Hiroki Konishi, Rui Yamaguchi, Kiyoshi Yamaguchi, Yoichi Furukawa, Seiya Imoto:
Halcyon: an accurate basecaller exploiting an encoder-decoder model with monotonic attention. Bioinform. 37(9): 1211-1217 (2021) - [j59]Yanan Wang, Nicolas Coudray, Yun Zhao, Fuyi Li, Changyuan Hu, Yao-Zhong Zhang, Seiya Imoto, Aristotelis Tsirigos, Geoffrey I. Webb, Roger J. Daly, Jiangning Song:
HEAL: an automated deep learning framework for cancer histopathology image analysis. Bioinform. 37(22): 4291-4295 (2021) - [j58]Yao-Zhong Zhang, Seiya Imoto, Satoru Miyano, Rui Yamaguchi:
Enhancing breakpoint resolution with deep segmentation model: A general refinement method for read-depth based structural variant callers. PLoS Comput. Biol. 17(10) (2021) - [c50]Yao-Zhong Zhang, Kiyoshi Yamaguchi, Sera Hatakeyama, Yoichi Furukawa, Satoru Miyano, Rui Yamaguchi, Seiya Imoto:
On the application of BERT models for nanopore methylation detection. BIBM 2021: 320-327 - [c49]Yunjie Liu, Yaozhong Zhang, Seiya Imoto:
Discovering microbe functionality in human disease with a gene-ontology-aware model. BIBM 2021: 1873-1880 - 2020
- [j57]Takanori Hasegawa, Shuto Hayashi, Eigo Shimizu, Shinichi Mizuno, Atsushi Niida, Rui Yamaguchi, Satoru Miyano, Hidewaki Nakagawa, Seiya Imoto:
Neoantimon: a multifunctional R package for identification of tumor-specific neoantigens. Bioinform. 36(18): 4813-4816 (2020) - [j56]Yao-zhong Zhang, Arda Akdemir, Georg Tremmel, Seiya Imoto, Satoru Miyano, Tetsuo Shibuya, Rui Yamaguchi:
Nanopore basecalling from a perspective of instance segmentation. BMC Bioinform. 21-S(3): 136 (2020) - [j55]Takanori Hasegawa, Rui Yamaguchi, Atsushi Niida, Satoru Miyano, Seiya Imoto:
Ensemble smoothers for inference of hidden states and parameters in combinatorial regulatory model. J. Frankl. Inst. 357(5): 2916-2933 (2020) - [c48]Takuya Moriyama, Seiya Imoto, Satoru Miyano, Rui Yamaguchi:
Theoretical Foundation of the Performance of Phylogeny-Based Somatic Variant Detection. ISMCO 2020: 87-101
2010 – 2019
- 2019
- [j54]Takuya Moriyama, Seiya Imoto, Shuto Hayashi, Yuichi Shiraishi, Satoru Miyano, Rui Yamaguchi:
A Bayesian model integration for mutation calling through data partitioning. Bioinform. 35(21): 4247-4254 (2019) - [j53]Hiroki Konishi, Daisuke Komura, Hiroto Katoh, Shinichiro Atsumi, Hirotomo Koda, Asami Yamamoto, Yasuyuki Seto, Masashi Fukayama, Rui Yamaguchi, Seiya Imoto, Shumpei Ishikawa:
Capturing the differences between humoral immunity in the normal and tumor environments from repertoire-seq of B-cell receptors using supervised machine learning. BMC Bioinform. 20(1): 267:1-267:11 (2019) - [j52]Heewon Park, Makoto Yamada, Seiya Imoto, Satoru Miyano:
Robust Sample-Specific Stability Selection with Effective Error Control. J. Comput. Biol. 26(3): 202-217 (2019) - [j51]Shuto Hayashi, Takuya Moriyama, Rui Yamaguchi, Shinichi Mizuno, Mitsuhiro Komura, Satoru Miyano, Hidewaki Nakagawa, Seiya Imoto:
ALPHLARD-NT: Bayesian Method for Human Leukocyte Antigen Genotyping and Mutation Calling through Simultaneous Analysis of Normal and Tumor Whole-Genome Sequence Data. J. Comput. Biol. 26(9): 923-937 (2019) - [c47]Takuya Moriyama, Seiya Imoto, Satoru Miyano, Rui Yamaguchi:
Accurate and Flexible Bayesian Mutation Call from Multi-regional Tumor Samples. ISMCO 2019: 47-61 - 2018
- [j50]Heewon Park, Teppei Shimamura, Seiya Imoto, Satoru Miyano:
Adaptive NetworkProfiler for Identifying Cancer Characteristic-Specific Gene Regulatory Networks. J. Comput. Biol. 25(2): 130-145 (2018) - 2017
- [j49]Heewon Park, Atsushi Niida, Seiya Imoto, Satoru Miyano:
Interaction-Based Feature Selection for Uncovering Cancer Driver Genes Through Copy Number-Driven Expression Level. J. Comput. Biol. 24(2): 138-152 (2017) - [j48]Heewon Park, Yuichi Shiraishi, Seiya Imoto, Satoru Miyano:
A Novel Adaptive Penalized Logistic Regression for Uncovering Biomarker Associated with Anti-Cancer Drug Sensitivity. IEEE ACM Trans. Comput. Biol. Bioinform. 14(4): 771-782 (2017) - [c46]Yao-Zhong Zhang, Seiya Imoto, Satoru Miyano, Rui Yamaguchi:
Reconstruction of high read-depth signals from low-depth whole genome sequencing data using deep learning. BIBM 2017: 1227-1232 - 2016
- [j47]Takanori Hasegawa, Atsushi Niida, Tomoya Mori, Teppei Shimamura, Rui Yamaguchi, Satoru Miyano, Tatsuya Akutsu, Seiya Imoto:
A likelihood-free filtering method via approximate Bayesian computation in evaluating biological simulation models. Comput. Stat. Data Anal. 94: 63-74 (2016) - [j46]Emi Ayada, Takanori Hasegawa, Atsushi Niida, Satoru Miyano, Seiya Imoto:
Binary contingency table method for analysing gene mutation in cancer genome. Int. J. Bioinform. Res. Appl. 12(3): 211-226 (2016) - [j45]Harsh Saini, Gaurav Raicar, Sunil Pranit Lal, Abdollah Dehzangi, Seiya Imoto, Alok Sharma:
Protein Fold Recognition Using Genetic Algorithm Optimized Voting Scheme and Profile Bigram. J. Softw. 11(8): 756-767 (2016) - [j44]Tetsuhiro Yoshino, Kotoe Katayama, Yuko Horiba, Kaori Munakata, Rui Yamaguchi, Seiya Imoto, Satoru Miyano, Hideki Mima, Kenji Watanabe:
Predicting Japanese Kampo formulas by analyzing database of medical records: a preliminary observational study. BMC Medical Informatics Decis. Mak. 16: 118 (2016) - [c45]Takuya Moriyama, Yuichi Shiraishi, Kenichi Chiba, Rui Yamaguchi, Seiya Imoto, Satoru Miyano:
OVarCall: Bayesian Mutation Calling Method Utilizing Overlapping Paired-End Reads. ISBRA 2016: 40-51 - 2015
- [j43]Kenichi Chiba, Yuichi Shiraishi, Yasunobu Nagata, Kenichi Yoshida, Seiya Imoto, Seishi Ogawa, Satoru Miyano:
Genomon ITDetector: a tool for somatic internal tandem duplication detection from cancer genome sequencing data. Bioinform. 31(1): 116-118 (2015) - [j42]Takanori Hasegawa, Tomoya Mori, Rui Yamaguchi, Teppei Shimamura, Satoru Miyano, Seiya Imoto, Tatsuya Akutsu:
Genomic data assimilation using a higher moment filtering technique for restoration of gene regulatory networks. BMC Syst. Biol. 9: 14 (2015) - [j41]Heewon Park, Atsushi Niida, Satoru Miyano, Seiya Imoto:
Sparse Overlapping Group Lasso for Integrative Multi-Omics Analysis. J. Comput. Biol. 22(2): 73-84 (2015) - [c44]Emi Ayada, Atsushi Niida, Takanori Hasegawa, Satoru Miyano, Seiya Imoto:
Binary Contingency Table Method for Analyzing Gene Mutation in Cancer Genome. ISBRA 2015: 12-23 - 2014
- [j40]Naoto Usuyama, Yuichi Shiraishi, Yusuke Sato, Haruki Kume, Yukio Homma, Seishi Ogawa, Satoru Miyano, Seiya Imoto:
HapMuC: somatic mutation calling using heterozygous germ line variants near candidate mutations. Bioinform. 30(23): 3302-3309 (2014) - [j39]Takanori Hasegawa, Masao Nagasaki, Rui Yamaguchi, Seiya Imoto, Satoru Miyano:
An efficient method of exploring simulation models by assimilating literature and biological observational data. Biosyst. 121: 54-66 (2014) - [j38]Takanori Hasegawa, Tomoya Mori, Rui Yamaguchi, Seiya Imoto, Satoru Miyano, Tatsuya Akutsu:
An Efficient Data Assimilation Schema for Restoration and Extension of Gene Regulatory Networks Using Time-Course Observation Data. J. Comput. Biol. 21(11): 785-798 (2014) - [j37]Alok Sharma, Kuldip K. Paliwal, Seiya Imoto, Satoru Miyano, Vandana Sharma, Rajeshkannan Ananthanarayanan:
A feature selection method using fixed-point algorithm for DNA microarray gene expression data. Int. J. Knowl. Based Intell. Eng. Syst. 18(1): 55-59 (2014) - [j36]Alok Sharma, Kuldip K. Paliwal, Seiya Imoto, Satoru Miyano:
A feature selection method using improved regularized linear discriminant analysis. Mach. Vis. Appl. 25(3): 775-786 (2014) - [c43]Masaya M. Saito, Seiya Imoto, Rui Yamaguchi, Satoru Miyano, Tomoyuki Higuchi:
Parameter estimation in multi-compartment SIR model. FUSION 2014: 1-5 - 2013
- [j35]Alok Sharma, Kuldip K. Paliwal, Abdollah Dehzangi, James G. Lyons, Seiya Imoto, Satoru Miyano:
A strategy to select suitable physicochemical attributes of amino acids for protein fold recognition. BMC Bioinform. 14: 233 (2013) - [j34]Mitsunori Kayano, Seiya Imoto, Rui Yamaguchi, Satoru Miyano:
Multi-omics Approach for Estimating Metabolic Networks Using Low-Order Partial Correlations. J. Comput. Biol. 20(8): 571-582 (2013) - [j33]Alok Sharma, Kuldip K. Paliwal, Seiya Imoto, Satoru Miyano:
Principal component analysis using QR decomposition. Int. J. Mach. Learn. Cybern. 4(6): 679-683 (2013) - [c42]Masaya M. Saito, Seiya Imoto, Rui Yamaguchi, Satoru Miyano, Tomoyuki Higuchi:
Estimation of abrupt changes in sentinel observation data of influenza epidemics in Japan. FUSION 2013: 1385-1390 - [c41]Atsushi Niida, Georg Tremmel, Seiya Imoto, Satoru Miyano:
Multilayer Cluster Heat Map Visualizing Biological Tensor Data. BSB 2013: 116-125 - 2012
- [j32]Atsushi Niida, Seiya Imoto, Teppei Shimamura, Satoru Miyano:
Statistical model-based testing to evaluate the recurrence of genomic aberrations. Bioinform. 28(12): 115-120 (2012) - [j31]Kaname Kojima, Seiya Imoto, Rui Yamaguchi, André Fujita, Mai Yamauchi, Noriko Gotoh, Satoru Miyano:
Identifying regulational alterations in gene regulatory networks by state space representation of vector autoregressive models and variational annealing. BMC Genom. 13(S-1): S6 (2012) - [j30]Kentaro Ogami, Rui Yamaguchi, Seiya Imoto, Yoshinori Tamada, Hiromitsu Araki, Cristin G. Print, Satoru Miyano:
Computational gene network analysis reveals TNF-induced angiogenesis. BMC Syst. Biol. 6(S-2): S12 (2012) - [j29]Alok Sharma, Seiya Imoto, Satoru Miyano:
A between-Class Overlapping Filter-Based Method for transcriptome Data Analysis. J. Bioinform. Comput. Biol. 10(5) (2012) - [j28]Alok Sharma, Seiya Imoto, Satoru Miyano, Vandana Sharma:
Null space based feature selection method for gene expression data. Int. J. Mach. Learn. Cybern. 3(4): 269-276 (2012) - [j27]Kotoe Katayama, Rui Yamaguchi, Seiya Imoto, Keiko Matsuura, Kenji Watanabe:
Connection between traditional medicine and disease. SIGHIT Rec. 2(1): 21 (2012) - [j26]Alok Sharma, Seiya Imoto, Satoru Miyano:
A Top-r Feature Selection Algorithm for Microarray Gene Expression Data. IEEE ACM Trans. Comput. Biol. Bioinform. 9(3): 754-764 (2012) - [j25]Shuichi Kawano, Teppei Shimamura, Atsushi Niida, Seiya Imoto, Rui Yamaguchi, Masao Nagasaki, Ryo Yoshida, Cristin G. Print, Satoru Miyano:
Identifying Gene Pathways Associated with Cancer Characteristics via Sparse Statistical Methods. IEEE ACM Trans. Comput. Biol. Bioinform. 9(4): 966-972 (2012) - [c40]Kotoe Katayama, Seiya Imoto, Kenji Watanabe, Rui Yamaguchi, Keiko Matsuura, Satoru Miyano:
Analysis of questionnaire for traditional medical and develop decision support system. BIBM Workshops 2012: 762-763 - [c39]Masaya M. Saito, Seiya Imoto, Rui Yamaguchi, Satoru Miyano, Tomoyuki Higuchi:
Identifiability of local transmissibility parameters in agent-based pandemic simulation. FUSION 2012: 2466-2471 - 2011
- [j24]Yoshinori Tamada, Rui Yamaguchi, Seiya Imoto, Osamu Hirose, Ryo Yoshida, Masao Nagasaki, Satoru Miyano:
SiGN-SSM: open source parallel software for estimating gene networks with state space models. Bioinform. 27(8): 1172-1173 (2011) - [j23]Kotoe Katayama, Rui Yamaguchi, Seiya Imoto, Keiko Matsuura, Kenji Watanabe, Satoru Miyano:
Transform of visual analogue scale data and their clustering. Int. J. Knowl. Eng. Soft Data Paradigms 3(2): 143-151 (2011) - [j22]Yoshinori Tamada, Seiya Imoto, Satoru Miyano:
Parallel Algorithm for Learning Optimal Bayesian Network Structure. J. Mach. Learn. Res. 12: 2437-2459 (2011) - [j21]Yasuhiro Sogawa, Shohei Shimizu, Teppei Shimamura, Aapo Hyvärinen, Takashi Washio, Seiya Imoto:
Estimating exogenous variables in data with more variables than observations. Neural Networks 24(8): 875-880 (2011) - [j20]Yoshinori Tamada, Seiya Imoto, Hiromitsu Araki, Masao Nagasaki, Cristin G. Print, Stephen D. Charnock-Jones, Satoru Miyano:
Estimating Genome-Wide Gene Networks Using Nonparametric Bayesian Network Models on Massively Parallel Computers. IEEE ACM Trans. Comput. Biol. Bioinform. 8(3): 683-697 (2011) - [c38]Masaya M. Saito, Seiya Imoto, Rui Yamaguchi, Satoru Miyano, Tomoyuki Higuchi:
Parallel Agent-Based Simulator for Influenza Pandemic. AAMAS Workshops 2011: 361-370 - [c37]Masaya M. Saito, Seiya Imoto, Rui Yamaguchi, Satoru Miyano, Tomoyuki Higuchi:
Estimation of macroscopic parameter in agent-based pandemic simulation. FUSION 2011: 1-6 - [c36]Takanori Hasegawa, Rui Yamaguchi, Masao Nagasaki, Seiya Imoto, Satoru Miyano:
Poster: Comprehensive pharmacogenomic pathway screening by data assimilation. ICCABS 2011: 246 - [c35]Takanori Hasegawa, Rui Yamaguchi, Masao Nagasaki, Seiya Imoto, Satoru Miyano:
Comprehensive Pharmacogenomic Pathway Screening by Data Assimilation. ISBRA 2011: 160-171 - [c34]Kotoe Katayama, Rui Yamaguchi, Seiya Imoto, Keiko Matsuura, Kenji Watanabe, Satoru Miyano:
Clustering for Visual Analogue Scale Data in Symbolic Data Analysis. Complex Adaptive Systems 2011: 370-374 - [p1]Seiya Imoto, Yoshinori Tamada, Hiromitsu Araki, Satoru Miyano:
Computational Drug Target Pathway Discovery: A Bayesian Network Approach. Handbook of Statistical Bioinformatics 2011: 501-532 - 2010
- [j19]Teppei Shimamura, Seiya Imoto, Rui Yamaguchi, Masao Nagasaki, Satoru Miyano:
Inferring dynamic gene networks under varying conditions for transcriptomic network comparison. Bioinform. 26(8): 1064-1072 (2010) - [j18]Atsushi Niida, Seiya Imoto, Rui Yamaguchi, Masao Nagasaki, André Fujita, Teppei Shimamura, Satoru Miyano:
Model-free unsupervised gene set screening based on information enrichment in expression profiles. Bioinform. 26(24): 3090-3097 (2010) - [j17]Kaname Kojima, Eric Perrier, Seiya Imoto, Satoru Miyano:
Optimal Search on Clustered Structural Constraint for Learning Bayesian Network Structure. J. Mach. Learn. Res. 11: 285-310 (2010) - [c33]Tomoya Higashigaki, Kaname Kojima, Rui Yamaguchi, Masato Inoue, Seiya Imoto, Satoru Miyano:
Identifying Hidden Confounders in Gene Networks by Bayesian Networks. BIBE 2010: 168-173 - [c32]Shuichi Kawano, Teppei Shimamura, Atsushi Niida, Seiya Imoto, Rui Yamaguchi, Masao Nagasaki, Ryo Yoshida, Cristin G. Print, Satoru Miyano:
Discovering functional gene pathways associated with cancer heterogeneity via sparse supervised learning. BIBM 2010: 253-258 - [c31]Teppei Shimamura, Seiya Imoto, Atsushi Niida, Masao Nagasaki, Rui Yamaguchi, Satoru Miyano:
Network profiling analysis for generating modulator-dependent gene networks. BIBM Workshops 2010: 836 - [c30]Yasuhiro Sogawa, Shohei Shimizu, Aapo Hyvärinen, Takashi Washio, Teppei Shimamura, Seiya Imoto:
Discovery of Exogenous Variables in Data with More Variables Than Observations. ICANN (1) 2010: 67-76 - [c29]Seiya Imoto, Kaname Kojima, Eric Perrier, Yoshinori Tamada, Satoru Miyano:
Searching Optimal Bayesian Network Structure on Constraint Search Space: Super-Structure Approach. JSAI-isAI Workshops 2010: 210-218
2000 – 2009
- 2009
- [j16]Atsushi Niida, Andrew D. Smith, Seiya Imoto, Hiroyuki Aburatani, Michael Q. Zhang, Tetsu Akiyama:
Gene set-based module discovery in the breast cancer transcriptome. BMC Bioinform. 10 (2009) - [j15]Teppei Shimamura, Seiya Imoto, Rui Yamaguchi, André Fujita, Masao Nagasaki, Satoru Miyano:
Recursive regularization for inferring gene networks from time-course gene expression profiles. BMC Syst. Biol. 3: 41 (2009) - [j14]Rui Yamaguchi, Seiya Imoto, Satoru Miyano:
Network-Based Predictions and Simulations by Biological State Space Models: Search for Drug Mode of Action. J. Comput. Sci. Technol. 25(1): 131-153 (2009) - [c28]Satoru Miyano, Rui Yamaguchi, Yoshinori Tamada, Masao Nagasaki, Seiya Imoto:
Gene Networks Viewed through Two Models. BICoB 2009: 54-66 - [c27]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, Stephen D. Charnock-Jones, Kousuke Tashiro, Satoru Kuhara, Satoru Miyano:
Unraveling Dynamic Activities of Autocrine Pathways that Control Drug-Response Transcriptome Networks. Pacific Symposium on Biocomputing 2009: 251-263 - 2008
- [j13]Osamu Hirose, Ryo Yoshida, Seiya Imoto, Rui Yamaguchi, Tomoyuki Higuchi, Stephen D. Charnock-Jones, Cristin G. Print, Satoru Miyano:
Statistical inference of transcriptional module-based gene networks from time course gene expression profiles by using state space models. Bioinform. 24(7): 932-942 (2008) - [j12]Ryo Yoshida, Masao Nagasaki, Rui Yamaguchi, Seiya Imoto, Satoru Miyano, Tomoyuki Higuchi:
Bayesian learning of biological pathways on genomic data assimilation. Bioinform. 24(22): 2592-2601 (2008) - [j11]Atsushi Niida, Andrew D. Smith, Seiya Imoto, Shuichi Tsutsumi, Hiroyuki Aburatani, Michael Q. Zhang, Tetsu Akiyama:
Integrative bioinformatics analysis of transcriptional regulatory programs in breast cancer cells. BMC Bioinform. 9 (2008) - [j10]Kazuyuki Numata, Ryo Yoshida, Masao Nagasaki, Ayumu Saito, Seiya Imoto, Satoru Miyano:
ExonMiner: Web service for analysis of GeneChip Exon array data. BMC Bioinform. 9 (2008) - [c26]Osamu Hirose, Ryo Yoshida, Rui Yamaguchi, Seiya Imoto, Tomoyuki Higuchi, Satoru Miyano:
Analyzing Time Course Gene Expression Data with Biological and Technical Replicates to Estimate Gene Networks by State Space Models. Asia International Conference on Modelling and Simulation 2008: 940-946 - [c25]Kazuyuki Numata, Seiya Imoto, Satoru Miyano:
Partial Order-Based Bayesian Network Learning Algorithm for Estimating Gene Networks. BIBM 2008: 357-360 - 2007
- [j9]Rui Yamaguchi, Ryo Yoshida, Seiya Imoto, Tomoyuki Higuchi, Satoru Miyano:
Finding module-based gene networks with state-space models - Mining high-dimensional and short time-course gene expression data. IEEE Signal Process. Mag. 24(1): 37-46 (2007) - [c24]Ryo Yoshida, Kazuyuki Numata, Seiya Imoto, Masao Nagasaki, Atsushi Doi, Kazuko Ueno, Satoru Miyano:
Computational Genome-Wide Discovery of Aberrant Splice Variations with Exon Expression Profiles. BIBE 2007: 715-722 - [c23]Kazuyuki Numata, Seiya Imoto, Satoru Miyano:
A Structure Learning Algorithm for Inference of Gene Networks from Microarray Gene Expression Data Using Bayesian Networks. BIBE 2007: 1280-1284 - [c22]Pramod K. Gupta, Ryo Yoshida, Seiya Imoto, Rui Yamaguchi, Satoru Miyano:
Statistical Absolute Evaluation of Gene Ontology Terms with Gene Expression Data. ISBRA 2007: 146-157 - [c21]Alexandre Termier, Yoshinori Tamada, Kazuyuki Numata, Seiya Imoto, Takashi Washio, Tomoyuki Higuchi:
DIGDAG, a First Algorithm to Mine Closed Frequent Embedded Sub-DAGs. MLG 2007 - 2006
- [j8]Ryo Yoshida, Tomoyuki Higuchi, Seiya Imoto, Satoru Miyano:
ArrayCluster: an analytic tool for clustering, data visualization and module finder on gene expression profiles. Bioinform. 22(12): 1538-1539 (2006) - [j7]Reiichiro Nakamichi, Seiya Imoto, Satoru Miyano:
Statistical Model Selection Method to Analyze Combinatorial Effects of Snps and Environmental Factors for Binary Disease. Int. J. Artif. Intell. Tools 15(5): 711-724 (2006) - [c20]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:
Computational Strategy for Discovering Druggable Gene Networks from Genome-Wide RNA Expression Profiles. Pacific Symposium on Biocomputing 2006: 559-571 - 2005
- [j6]Yoshinori Tamada, Hideo Bannai, Seiya Imoto, Toshiaki Katayama, Minoru Kanehisa, Satoru Miyano:
Utilizing Evolutionary Information and Gene Expression Data for Estimating Gene Networks with Bayesian Network Models. J. Bioinform. Comput. Biol. 3(6): 1295-1314 (2005) - [c19]Ryo Yoshida, Seiya Imoto, Tomoyuki Higuchi:
Estimating Time-Dependent Gene Networks from Time Series Microarray Data by Dynamic Linear Models with Markov Switching. CSB 2005: 289-298 - [c18]Naoki Nariai, Yoshinori Tamada, Seiya Imoto, Satoru Miyano:
Estimating gene regulatory networks and protein-protein interactions of Saccharomyces cerevisiae from multiple genome-wide data. ECCB/JBI 2005: 212 - [c17]Osamu Hirose, Naoki Nariai, Yoshinori Tamada, Hideo Bannai, Seiya Imoto, Satoru Miyano:
Estimating Gene Networks from Expression Data and Binding Location Data via Boolean Networks. ICCSA (3) 2005: 349-356 - [c16]Ryo Yoshida, Seiya Imoto, Tomoyuki Higuchi:
A Penalized Likelihood Estimation on Transcriptional Module-Based Clustering. ICCSA (3) 2005: 389-401 - 2004
- [j5]Seiya Imoto, Tomoyuki Higuchi, Takao Goto, Kousuke Tashiro, Satoru Kuhara, Satoru Miyano:
Combining Microarrays and Biological Knowledge for Estimating Gene Networks via Bayesian Networks. J. Bioinform. Comput. Biol. 2(1): 77-98 (2004) - [c15]Reiichiro Nakamichi, Seiya Imoto, Satoru Miyano:
Case-Control Study of Binary Disease Trait Considering Interactions between SNPs and Environmental Effects using Logistic Regression. BIBE 2004: 73-78 - [c14]Seiya Imoto, Tomoyuki Higuchi, SunYong Kim, Euna Jeong, Satoru Miyano:
Residual Bootstrapping and Median Filtering for Robust Estimation of Gene Networks from Microarray Data. CMSB 2004: 149-160 - [c13]Ryo Yoshida, Tomoyuki Higuchi, Seiya Imoto:
A Mixed Factors Model for Dimension Reduction and Extraction of a Group Structure in Gene Expression Data. CSB 2004: 161-172 - [c12]Michiel J. L. de Hoon, Yuko Makita, Seiya Imoto, Kazuo Kobayashi, Naotake Ogasawara, Kenta Nakai, Satoru Miyano:
Predicting gene regulation by sigma factors in Bacillus subtilis from genome-wide data. ISMB/ECCB (Supplement of Bioinformatics) 2004: 101-108 - [c11]Tomohiro Ando, Seiya Imoto, Satoru Miyano:
Functional Data Analysis of the Dynamics of Gene Regulatory Networks. KELSI 2004: 69-83 - [c10]Michiel J. L. de Hoon, Seiya Imoto, Kazuo Kobayashi, Naotake Ogasawara, Satoru Miyano:
Predicting the Operon Structure of Bacillus subtilis Using Operon Length, Intergene Distance, and Gene Expression Information. Pacific Symposium on Biocomputing 2004: 276-287 - [c9]Naoki Nariai, SunYong Kim, Seiya Imoto, Satoru Miyano:
Using Protein-Protein Interactions for Refining Gene Networks Estimated from Microarray Data by Bayesian Networks. Pacific Symposium on Biocomputing 2004: 336-347 - [c8]Sascha Ott, Seiya Imoto, Satoru Miyano:
Finding Optimal Models for Small Gene Networks. Pacific Symposium on Biocomputing 2004: 557-567 - 2003
- [j4]SunYong Kim, Seiya Imoto, Satoru Miyano:
Inferring gene networks from time series microarray data using dynamic Bayesian networks. Briefings Bioinform. 4(3): 228 (2003) - [j3]Seiya Imoto, SunYong Kim, Takao Goto, Sachiyo Aburatani, Kousuke Tashiro, Satoru Kuhara, Satoru Miyano:
Bayesian Network and Nonparametric Heteroscedastic Regression for Nonlinear Modeling of Genetic Network. J. Bioinform. Comput. Biol. 1(2): 231-252 (2003) - [j2]Seiya Imoto, Christopher J. Savoie, Sachiyo Aburatani, SunYong Kim, Kousuke Tashiro, Satoru Kuhara, Satoru Miyano:
Use of Gene Networks for Identifying and Validating Drug Targets. J. Bioinform. Comput. Biol. 1(3): 459-474 (2003) - [c7]SunYong Kim, Seiya Imoto, Satoru Miyano:
Dynamic Bayesian Network and Nonparametric Regression for Nonlinear Modeling of Gene Networks from Time Series Gene Expression Data. CMSB 2003: 104-113 - [c6]Seiya Imoto, Tomoyuki Higuchi, Takao Goto, Kousuke Tashiro, Satoru Kuhara, Satoru Miyano:
Combining Microarrays and Biological Knowledge for Estimating Gene Networks via Bayesian Networks. CSB 2003: 104-113 - [c5]Yoshinori Tamada, SunYong Kim, Hideo Bannai, Seiya Imoto, Kousuke Tashiro, Satoru Kuhara, Satoru Miyano:
Estimating gene networks from gene expression data by combining Bayesian network model with promoter element detection. ECCB 2003: 227-236 - [c4]Michiel J. L. de Hoon, Seiya Imoto, Kazuo Kobayashi, Naotake Ogasawara, Satoru Miyano:
Inferring Gene Regulatory Networks from Time-Ordered Gene Expression Data of Bacillus Subtilis Using Differential Equations. Pacific Symposium on Biocomputing 2003: 17-28 - 2002
- [j1]Michiel J. L. de Hoon, Seiya Imoto, Satoru Miyano:
Statistical analysis of a small set of time-ordered gene expression data using linear splines. Bioinform. 18(11): 1477-1485 (2002) - [c3]Seiya Imoto, SunYong Kim, Takao Goto, Sachiyo Aburatani, Kousuke Tashiro, Satoru Kuhara, Satoru Miyano:
Bayesian Network and Nonparametric Heteroscedastic Regression for Nonlinear Modeling of Genetic Network. CSB 2002: 219-227 - [c2]Michiel J. L. de Hoon, Seiya Imoto, Satoru Miyano:
Inferring Gene Regulatory Networks from Time-Ordered Gene Expression Data Using Differential Equations. Discovery Science 2002: 267-274 - [c1]Seiya Imoto, Takao Goto, Satoru Miyano:
Estimation of Genetic Networks and Functional Structures Between Genes by Using Bayesian Networks and Nonparametric Regression. Pacific Symposium on Biocomputing 2002: 175-186
Coauthor Index
[j65] [j64] [j63] [j61] [j58] [c50] [j57] [j56] [j55] [c48] [j54] [j52] [j51] [c47] [j50] [j49] [j48] [c46] [j47] [j46] [j44] [c45] [j43] [j42] [j41] [c44] [j40] [j39] [j38] [j37] [j36] [c43] [j35] [j34] [j33] [c42] [c41] [j32] [j31] [j30] [j29] [j28] [j26] [j25] [c40] [c39] [j24] [j23] [j22] [j20] [c38] [c37] [c36] [c35] [c34] [p1] [j19] [j18] [j17] [c33] [c32] [c31] [c29] [j15] [j14] [c28] [c27] [j13] [j12] [j10] [c26] [c25] [j9] [c24] [c23] [c22] [j8] [j7] [c20] [j6] [c18] [c17] [j5] [c15] [c14] [c12] [c11] [c10] [c9] [c8] [j4] [j3] [j2] [c7] [c6] [c5] [c4] [j1] [c3] [c2] [c1]
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