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Author Details

Hiroshi Mamitsuka
Institute for Chemical Research, Kyoto University
1994
115
26
PMIDPaper TitleJournal TitlePublished Year
36576008Sc2Mol: a scaffold-based two-step molecule generator with variational autoencoder and transformer.Bioinformatics2023
37669154DeepMHCI: an anchor position-aware deep interaction model for accurate MHC-I peptide binding affinity prediction.Bioinformatics2023
37018091Central-Smoothing Hypergraph Neural Networks for Predicting Drug-Drug Interactions.IEEE Trans Neural Netw Learn Syst2023
34672333HPODNets: deep graph convolutional networks for predicting human protein-phenotype associations.Bioinformatics2022
35758803SPARSE: a sparse hypergraph neural network for learning multiple types of latent combinations to accurately predict drug-drug interactions.Bioinformatics2022
35758790DeepMHCII: a novel binding core-aware deep interaction model for accurate MHC-II peptide binding affinity prediction.Bioinformatics2022
33705322DIVERSE: Bayesian Data IntegratiVE Learning for Precise Drug ResponSE Prediction.IEEE/ACM Trans Comput Biol Bioinform2022
32976559BERTMeSH: deep contextual representation learning for large-scale high-performance MeSH indexing with full text.Bioinformatics2021
33515011XGSEA: CROSS-species gene set enrichment analysis via domain adaptation.Brief Bioinform2021
33822886HPOFiller: identifying missing protein-phenotype associations by graph convolutional network.Bioinformatics2021
34914721Crop loss identification at field parcel scale using satellite remote sensing and machine learning.PLoS One2021
34252926DeepGraphGO: graph neural network for large-scale, multispecies protein function prediction.Bioinformatics2021
34368832Machine learning approaches for drug combination therapies.Brief Bioinform2021
32086195Learning on Hypergraphs With Sparsity.IEEE Trans Pattern Anal Mach Intell2021
31838499A survey on adverse drug reaction studies: data, tasks and machine learning methods.Brief Bioinform2021
31838491Improving drug response prediction by integrating multiple data sources: matrix factorization, kernel and network-based approaches.Brief Bioinform2021
31596475FullMeSH: improving large-scale MeSH indexing with full text.Bioinformatics2020
33490910Eukaryotic virus composition can predict the efficiency of carbon export in the global ocean.iScience2020
31835002Scaled Coupled Norms and Coupled Higher-Order Tensor Completion.Neural Comput2020
32379868HPOLabeler: improving prediction of human protein-phenotype associations by learning to rank.Bioinformatics2020
30617801CalCleaveMKL: a Tool for Calpain Cleavage Prediction.Methods Mol Biol2019
31865916HPOAnnotator: improving large-scale prediction of HPO annotations by low-rank approximation with HPO semantic similarities and multiple PPI networks.BMC Med Genomics2019
30099485Recent advances and prospects of computational methods for metabolite identification: a review with emphasis on machine learning approaches.Brief Bioinform2019
31510641ADAPTIVE: leArning DAta-dePendenT, concIse molecular VEctors for fast, accurate metabolite identification from tandem mass spectra.Bioinformatics2019
30977782Modelling GÿE with historical weather information improves genomic prediction in new environments.Bioinformatics2019
31106361NetGO: improving large-scale protein function prediction with massive network information.Nucleic Acids Res2019
29522145GOLabeler: improving sequence-based large-scale protein function prediction by learning to rank.Bioinformatics2018
30148706Convex Coupled Matrix and Tensor Completion.Neural Comput2018
29950009SIMPLE: Sparse Interaction Model over Peaks of moLEcules for fast, interpretable metabolite identification from tandem mass spectra.Bioinformatics2018
30030813MeSHLabeler and DeepMeSH: Recent Progress in Large-Scale MeSH Indexing.Methods Mol Biol2018
30030812DrugE-Rank: Predicting Drug-Target Interactions by Learning to Rank.Methods Mol Biol2018
30030806SiBIC: A Tool for Generating a Network of Biclusters Captured by Maximal Frequent Itemset Mining.Methods Mol Biol2018
26839320Computational recognition for long non-coding RNA (lncRNA): Software and databases.Brief Bioinform2017
28988802A Community Challenge for Inferring Genetic Predictors of Gene Essentialities through Analysis of a Functional Screen of Cancer Cell Lines.Cell Syst2017
27197545Exploring phenotype patterns of breast cancer within somatic mutations: a modicum in the intrinsic code.Brief Bioinform2017
27187949Generalized Sparse Learning of Linear Models Over the Complete Subgraph Feature Set.IEEE Trans Pattern Anal Mach Intell2017
26153512Current status and prospects of computational resources for natural product dereplication: a review.Brief Bioinform2016
27696928Introduction to the special issue on GIW 2016.J Bioinform Comput Biol2016
27153725NMRPro: an integrated web component for interactive processing and visualization of NMR spectra.Bioinformatics2016
27307646DeepMeSH: deep semantic representation for improving large-scale MeSH indexing.Bioinformatics2016
27307615DrugE-Rank: improving drug-target interaction prediction of new candidate drugs or targets by ensemble learning to rank.Bioinformatics2016
26796116Predictions of Cleavability of Calpain Proteolysis by Quantitative Structure-Activity Relationship Analysis Using Newly Determined Cleavage Sites and Catalytic Efficiencies of an Oligopeptide Array.Mol Cell Proteomics2016
27003446Classification of Promoters Based on the Combination of Core Promoter Elements Exhibits Different Histone Modification Patterns.PLoS One2016
27076335MetaMHCpan, A Meta Approach for Pan-Specific MHC Peptide Binding Prediction.Methods Mol Biol2016
25459666Evaluation of serum-based cancer biomarkers: a brief review from a clinical and computational viewpoint.Crit Rev Oncol Hematol2015
26671801BMExpert: Mining MEDLINE for Finding Experts in Biomedical Domains Based on Language Model.IEEE/ACM Trans Comput Biol Bioinform2015
26471719MeSHSim: An R/Bioconductor package for measuring semantic similarity over MeSH headings and MEDLINE documents.J Bioinform Comput Biol2015
26072501MeSHLabeler: improving the accuracy of large-scale MeSH indexing by integrating diverse evidence.Bioinformatics2015
25616540In Silico Predictions of Human Skin Permeability using Nonlinear Quantitative Structure-Property Relationship Models.Pharm Res2015
23933754Similarity-based machine learning methods for predicting drug-target interactions: a brief review.Brief Bioinform2014
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Collaborators

Shanfeng Zhu
Shanghai Qi Zhi Institute
Co-authored papers 30
Minoru Kanehisa
Co-authored papers 9
Ronghui You
Fudan University
Co-authored papers 8
Kiyoko F Aoki-Kinoshita
Co-authored papers 7
Samuel Kaski
Aalto University
Co-authored papers 5
Shengwen Peng
Fudan University
Co-authored papers 4
Masayuki Karasuyama
Nagoya Institute of Technology
Co-authored papers 3
Chengxiang Zhai
University of Illinois Urbana-Champaign
Co-authored papers 2
Guanghua Xiao
The University of Texas Southwestern Medical Center
Co-authored papers 1
William C Hahn
Broad Institute of MIT and Harvard, USA Dana-Farber Cancer Institute
Co-authored papers 1
Adam A Margolin
Icahn School of Medicine
Co-authored papers 1
Yulia Newton
University of California, Santa Cruz Genomics Institute
Co-authored papers 1
Tapio Pahikkala
University of Turku
Co-authored papers 1
Takuji Yamada
Tokyo Institute of Technology
Co-authored papers 1
Thea Norman
Bill & Melinda Gates Foundation
Co-authored papers 1
Alden Deran
University of California Santa Cruz
Co-authored papers 1
Jesse S Boehm
Broad Institute of Harvard and MIT
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Yasushi Ishihama
Graduate School of Pharmaceutical Sciences, Kyoto University
Co-authored papers 1
Yuanfang Guan
University of Michigan ann arbor
Co-authored papers 1
Shuichi Kawashima
Database Center for Life Science, Joint Support-Center for Data Science Research
Co-authored papers 1
Vladislav Uzunangelov
University of California
Co-authored papers 1
Jing Tang
University of Helsinki
Co-authored papers 1
Alessandro Sette
Center for Infectious Disease and Vaccine Research, La Jolla Institute for Immunology
Co-authored papers 1
Tadashi Kondo
Nagasaki University Graduate School of Biomedical Sciences
Co-authored papers 1
Tao Wang
University of Texas Southwestern Medical Center
Co-authored papers 1
Jieyao Deng
Fudan University
Co-authored papers 1
Barbara A Weir
Janssen Research and Development LLC
Co-authored papers 1
Daniel Marbach
Roche Pharma Research and Early Development
Co-authored papers 1
Adrian Bivol
University of California
Co-authored papers 1
Joshua M Stuart
University of California at Santa Cruz
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Release 1.2