List of works - Hiroshi Mamitsuka

A Community Challenge for Inferring Genetic Predictors of Gene Essentialities through Analysis of a Functional Screen of Cancer Cell Lines

scientific article published on 3 October 2017

A framework for determining outlying microarray experiments.

scientific article published in January 2008

A hidden Markov model-based approach for identifying timing differences in gene expression under different experimental factors

scientific article published on 19 January 2007

A hierarchical mixture of Markov models for finding biologically active metabolic paths using gene expression and protein classes

scientific article published on 01 January 2004

A learning method of hidden Markov models for sequence discrimination

scientific article published in January 1996

A probabilistic model for mining implicit 'chemical compound-gene' relations from literature

scientific article published in September 2005

A probabilistic model for mining labeled ordered trees: capturing patterns in carbohydrate sugar chains

article by N. Ueda et al published August 2005 in IEEE Transactions on Knowledge and Data Engineering

A review of statistical methods for prediction of proteolytic cleavage ⬇️

scientific article published on 02 December 2011

Active pathway identification and classification with probabilistic ensembles

scientific article published in January 2010

An in silico model for interpreting polypharmacology in drug-target networks

scientific article published in January 2013

Annotating gene functions with integrative spectral clustering on microarray expressions and sequences.

scientific article published in January 2010

Application of a new probabilistic model for mining implicit associated cancer genes from OMIM and medline

scientific article published on January 2006

Application of a new probabilistic model for recognizing complex patterns in glycans

scientific article published in August 2004

BMExpert: Mining MEDLINE for Finding Experts in Biomedical Domains Based on Language Model

article

Boosted network classifiers for local feature selection

scientific article published in November 2012

CaMPDB: a resource for calpain and modulatory proteolysis.

scientific article published in January 2010

Calpain cleavage prediction using multiple kernel learning.

scientific article

Classification of Promoters Based on the Combination of Core Promoter Elements Exhibits Different Histone Modification Patterns.

scientific article published on 22 March 2016

Computational intelligence in solving bioinformatics problems

scientific article published in September 2005

Computational recognition for long non-coding RNA (lncRNA): Software and databases.

scientific article published on 2 February 2016

Convex Coupled Matrix and Tensor Completion

scientific article published on 27 August 2018

Current status and prospects of computational resources for natural product dereplication: a review

scientific article published on 7 July 2015

DeepMeSH: deep semantic representation for improving large-scale MeSH indexing

scientific article

Detecting Differentially Coexpressed Genes from Labeled Expression Data: A Brief Review.

scientific article

Discriminative graph embedding for label propagation

scientific article published on 22 July 2011

DrugE-Rank: Predicting Drug-Target Interactions by Learning to Rank

scientific article published on 01 January 2018

DrugE-Rank: improving drug-target interaction prediction of new candidate drugs or targets by ensemble learning to rank

scientific article

Efficient Semisupervised MEDLINE Document Clustering With MeSH-Semantic and Global-Content Constraints

scientific article published on August 2013

Efficient tree-matching methods for accurate carbohydrate database queries.

scientific article published in January 2003

Efficiently finding genome-wide three-way gene interactions from transcript- and genotype-data

scientific article published on 7 September 2009

Enhancing MEDLINE document clustering by incorporating MeSH semantic similarity

scientific article published on 03 June 2009

Ensemble approaches for improving HLA class I-peptide binding prediction.

scientific article

Essential latent knowledge for protein-protein interactions: analysis by an unsupervised learning approach

scientific article published in April 2005

Evaluation of serum-based cancer biomarkers: a brief review from a clinical and computational viewpoint.

scientific article published on 14 October 2014

Exploring phenotype patterns of breast cancer within somatic mutations: a modicum in the intrinsic code

scientific article

Finding the biologically optimal alignment of multiple sequences

scientific article published in September 2005

Finding the maximum common subgraph of a partial k-tree and a graph with a polynomially bounded number of spanning trees

article published in 2004

GOLabeler: Improving Sequence-based Large-scale Protein Function Prediction by Learning to Rank

scientific article published on 7 March 2018

Generalized Sparse Learning of Linear Models Over the Complete Subgraph Feature Set.

scientific article published on 12 May 2016

Genome-wide integration on transcription factors, histone acetylation and gene expression reveals genes co-regulated by histone modification patterns.

scientific article

Glycoinformatics: Data Mining-based Approaches ⬇️

scientific article published on January 1, 2011

Graph mining: procedure, application to drug discovery and recent advances ⬇️

scientific article published on August 5, 2012

HAMSTER: visualizing microarray experiments as a set of minimum spanning trees.

scientific article

Identification of endocrine disruptor biodegradation by integration of structure-activity relationship with pathway analysis.

scientific article published on December 2007

Identifying neighborhoods of coordinated gene expression and metabolite profiles

scientific article

Identifying pathways of coordinated gene expression

scientific article published in January 2013

Improving MHC binding peptide prediction by incorporating binding data of auxiliary MHC molecules

scientific article

In Silico Predictions of Human Skin Permeability using Nonlinear Quantitative Structure-Property Relationship Models.

scientific article published on 24 January 2015

Integrated view of the human chromosome X-centric proteome project

scientific article published on 21 December 2012

Introduction to the special issue on GIW 2016

scientific article published on 03 October 2016

KCaM (KEGG Carbohydrate Matcher): a software tool for analyzing the structures of carbohydrate sugar chains

scientific article published on July 2004

Latent feature kernels for link prediction on sparse graphs

scientific article

MeSHLabeler and DeepMeSH: Recent Progress in Large-Scale MeSH Indexing

scientific article published on 01 January 2018

MeSHLabeler: improving the accuracy of large-scale MeSH indexing by integrating diverse evidence

scientific article published on June 2015

MeSHSim: An R/Bioconductor package for measuring semantic similarity over MeSH headings and MEDLINE documents

scientific article published on 09 September 2015

MetaMHC: a meta approach to predict peptides binding to MHC molecules.

scientific article

MetaMHCpan, A Meta Approach for Pan-Specific MHC Peptide Binding Prediction

scientific article published on 01 January 2016

Mining metabolic pathways through gene expression

scientific article published on 29 June 2010

Mining new protein-protein interactions. Using a hierarchical latent-variable model to determine the function of a functionally unknown protein

scientific article published in May 2005

Mining significant substructure pairs for interpreting polypharmacology in drug-target network

scientific article

Mining significant tree patterns in carbohydrate sugar chains.

scientific article published in August 2008

Multiple graph label propagation by sparse integration

scientific article published in December 2013

NMRPro: an integrated web component for interactive processing and visualization of NMR spectra

scientific article

NetPathMiner: R/Bioconductor package for network path mining through gene expression

scientific article published on 28 July 2014

On the performance of methods for finding a switching mechanism in gene expression.

scientific article published in January 2010

PURE: a PubMed article recommendation system based on content-based filtering.

scientific article published in January 2007

Predicting location and structure of beta-sheet regions using stochastic tree grammars.

scientific article published in January 1994

Predicting peptides that bind to MHC molecules using supervised learning of hidden Markov models

scientific article published in December 1998

Predictions of Cleavability of Calpain Proteolysis by Quantitative Structure-Activity Relationship Analysis Using Newly Determined Cleavage Sites and Catalytic Efficiencies of an Oligopeptide Array

scientific article

Probabilistic path ranking based on adjacent pairwise coexpression for metabolic transcripts analysis

scientific article published on 24 November 2007

ProfilePSTMM: capturing tree-structure motifs in carbohydrate sugar chains

scientific article published in July 2006

ROS-DET: robust detector of switching mechanisms in gene expression ⬇️

scientific article published on April 1, 2011

Recent advances and prospects of computational methods for metabolite identification: a review with emphasis on machine learning approaches

scientific article published on 01 November 2019

Representing inter-residue dependencies in protein sequences with probabilistic networks

scientific article published in August 1995

SIMPLE: Sparse Interaction Model over Peaks of moLEcules for fast, interpretable metabolite identification from tandem mass spectra.

scientific article published in July 2018

Semi-supervised graph partitioning with decision trees

scientific article published on 01 January 2008

SiBIC: A Tool for Generating a Network of Biclusters Captured by Maximal Frequent Itemset Mining

scientific article published on 01 January 2018

SiBIC: a web server for generating gene set networks based on biclusters obtained by maximal frequent itemset mining

scientific article

TAP Hunter: a SVM-based system for predicting TAP ligands using local description of amino acid sequence ⬇️

scientific article published on September 27, 2010

TEPITOPEpan: extending TEPITOPE for peptide binding prediction covering over 700 HLA-DR molecules

scientific article

The evolutionary repertoires of the eukaryotic-type ABC transporters in terms of the phylogeny of ATP-binding domains in eukaryotes and prokaryotes

scientific article

Toward more accurate pan-specific MHC-peptide binding prediction: a review of current methods and tools.

scientific article published on 22 September 2011

Understanding the substrate specificity of conventional calpains.

scientific article published on September 2012

alpha-Helix region prediction with stochastic rule learning

scientific article published in August 1995

List of works by Hiroshi Mamitsuka

A Community Challenge for Inferring Genetic Predictors of Gene Essentialities through Analysis of a Functional Screen of Cancer Cell Lines

A framework for determining outlying microarray experiments.

A hidden Markov model-based approach for identifying timing differences in gene expression under different experimental factors

A hierarchical mixture of Markov models for finding biologically active metabolic paths using gene expression and protein classes

A learning method of hidden Markov models for sequence discrimination

A probabilistic model for mining implicit 'chemical compound-gene' relations from literature

A probabilistic model for mining labeled ordered trees: capturing patterns in carbohydrate sugar chains

A review of statistical methods for prediction of proteolytic cleavage ⬇️

Active pathway identification and classification with probabilistic ensembles

An in silico model for interpreting polypharmacology in drug-target networks

Annotating gene functions with integrative spectral clustering on microarray expressions and sequences.

Application of a new probabilistic model for mining implicit associated cancer genes from OMIM and medline

Application of a new probabilistic model for recognizing complex patterns in glycans

BMExpert: Mining MEDLINE for Finding Experts in Biomedical Domains Based on Language Model

Boosted network classifiers for local feature selection

CaMPDB: a resource for calpain and modulatory proteolysis.

Calpain cleavage prediction using multiple kernel learning.

Classification of Promoters Based on the Combination of Core Promoter Elements Exhibits Different Histone Modification Patterns.

Computational intelligence in solving bioinformatics problems

Computational recognition for long non-coding RNA (lncRNA): Software and databases.

Convex Coupled Matrix and Tensor Completion

Current status and prospects of computational resources for natural product dereplication: a review

DeepMeSH: deep semantic representation for improving large-scale MeSH indexing

Detecting Differentially Coexpressed Genes from Labeled Expression Data: A Brief Review.

Discriminative graph embedding for label propagation

DrugE-Rank: Predicting Drug-Target Interactions by Learning to Rank

DrugE-Rank: improving drug-target interaction prediction of new candidate drugs or targets by ensemble learning to rank

Efficient Semisupervised MEDLINE Document Clustering With MeSH-Semantic and Global-Content Constraints

Efficient tree-matching methods for accurate carbohydrate database queries.

Efficiently finding genome-wide three-way gene interactions from transcript- and genotype-data

Enhancing MEDLINE document clustering by incorporating MeSH semantic similarity

Ensemble approaches for improving HLA class I-peptide binding prediction.

Essential latent knowledge for protein-protein interactions: analysis by an unsupervised learning approach

Evaluation of serum-based cancer biomarkers: a brief review from a clinical and computational viewpoint.

Exploring phenotype patterns of breast cancer within somatic mutations: a modicum in the intrinsic code

Finding the biologically optimal alignment of multiple sequences

Finding the maximum common subgraph of a partial k-tree and a graph with a polynomially bounded number of spanning trees

GOLabeler: Improving Sequence-based Large-scale Protein Function Prediction by Learning to Rank

Generalized Sparse Learning of Linear Models Over the Complete Subgraph Feature Set.

Genome-wide integration on transcription factors, histone acetylation and gene expression reveals genes co-regulated by histone modification patterns.

Glycoinformatics: Data Mining-based Approaches ⬇️

Graph mining: procedure, application to drug discovery and recent advances ⬇️

HAMSTER: visualizing microarray experiments as a set of minimum spanning trees.

Identification of endocrine disruptor biodegradation by integration of structure-activity relationship with pathway analysis.

Identifying neighborhoods of coordinated gene expression and metabolite profiles

Identifying pathways of coordinated gene expression

Improving MHC binding peptide prediction by incorporating binding data of auxiliary MHC molecules

In Silico Predictions of Human Skin Permeability using Nonlinear Quantitative Structure-Property Relationship Models.

Integrated view of the human chromosome X-centric proteome project

Introduction to the special issue on GIW 2016

KCaM (KEGG Carbohydrate Matcher): a software tool for analyzing the structures of carbohydrate sugar chains

Latent feature kernels for link prediction on sparse graphs

MeSHLabeler and DeepMeSH: Recent Progress in Large-Scale MeSH Indexing

MeSHLabeler: improving the accuracy of large-scale MeSH indexing by integrating diverse evidence

MeSHSim: An R/Bioconductor package for measuring semantic similarity over MeSH headings and MEDLINE documents

MetaMHC: a meta approach to predict peptides binding to MHC molecules.

MetaMHCpan, A Meta Approach for Pan-Specific MHC Peptide Binding Prediction

Mining metabolic pathways through gene expression

Mining new protein-protein interactions. Using a hierarchical latent-variable model to determine the function of a functionally unknown protein

Mining significant substructure pairs for interpreting polypharmacology in drug-target network

Mining significant tree patterns in carbohydrate sugar chains.

Multiple graph label propagation by sparse integration

NMRPro: an integrated web component for interactive processing and visualization of NMR spectra

NetPathMiner: R/Bioconductor package for network path mining through gene expression

On the performance of methods for finding a switching mechanism in gene expression.

PURE: a PubMed article recommendation system based on content-based filtering.

Predicting location and structure of beta-sheet regions using stochastic tree grammars.

Predicting peptides that bind to MHC molecules using supervised learning of hidden Markov models

Predictions of Cleavability of Calpain Proteolysis by Quantitative Structure-Activity Relationship Analysis Using Newly Determined Cleavage Sites and Catalytic Efficiencies of an Oligopeptide Array

Probabilistic path ranking based on adjacent pairwise coexpression for metabolic transcripts analysis

ProfilePSTMM: capturing tree-structure motifs in carbohydrate sugar chains

ROS-DET: robust detector of switching mechanisms in gene expression ⬇️

Recent advances and prospects of computational methods for metabolite identification: a review with emphasis on machine learning approaches

Representing inter-residue dependencies in protein sequences with probabilistic networks

SIMPLE: Sparse Interaction Model over Peaks of moLEcules for fast, interpretable metabolite identification from tandem mass spectra.

Semi-supervised graph partitioning with decision trees

SiBIC: A Tool for Generating a Network of Biclusters Captured by Maximal Frequent Itemset Mining

SiBIC: a web server for generating gene set networks based on biclusters obtained by maximal frequent itemset mining

TAP Hunter: a SVM-based system for predicting TAP ligands using local description of amino acid sequence ⬇️