List of works - Michiaki Hamada

A Classification of Bioinformatics Algorithms from the Viewpoint of Maximizing Expected Accuracy (MEA) ⬇️

scientific article published on February 7, 2012

A Novel Method for Assessing the Statistical Significance of RNA-RNA Interactions Between Two Long RNAs

scientific article published on 02 July 2018

A semi-supervised learning approach for RNA secondary structure prediction

scientific article

AMAP: A pipeline for whole-genome mutation detection in Arabidopsis thaliana

scientific article published on 25 July 2016

Analysis of base-pairing probabilities of RNA molecules involved in protein-RNA interactions.

scientific article

Antagonistic RNA aptamer specific to a heterodimeric form of human interleukin-17A/F ⬇️

scientific article published on April 19, 2011

Beyond similarity assessment: Selecting the optimal model for sequence alignment via the Factorized Asymptotic Bayesian algorithm

scientific article published on 12 October 2017

Bioinformatics tools for lncRNA research.

scientific article published on 10 August 2015

CENTROIDFOLD: a web server for RNA secondary structure prediction

scientific article published on 12 May 2009

CentroidAlign: fast and accurate aligner for structured RNAs by maximizing expected sum-of-pairs score

scientific article

CentroidHomfold-LAST: accurate prediction of RNA secondary structure using automatically collected homologous sequences

scientific article

Comprehensive prediction of lncRNA-RNA interactions in human transcriptome

scientific article published on 11 January 2016

Computational approaches for alternative and transient secondary structures of ribonucleic acids

scientific article published on 01 June 2018

Computational prediction of lncRNA-mRNA interactionsby integrating tissue specificity in human transcriptome

scientific article

DeepM6ASeq: prediction and characterization of m6A-containing sequences using deep learning

scholarly article by Yiqian Zhang & Michiaki Hamada published 31 December 2018 in BMC Bioinformatics

Discovering novel mutation signatures by latent Dirichlet allocation with variational Bayes inference

scientific article published on 01 November 2019

Efficient calculation of exact probability distributions of integer features on RNA secondary structures

scientific article

Estimating Energy Parameters for RNA Secondary Structure Predictions Using Both Experimental and Computational Data

scientific article published on 12 March 2018

Fighting against uncertainty: an essential issue in bioinformatics.

scientific article published on 26 June 2013

Generalized centroid estimators in bioinformatics

scientific article (publication date: 18 February 2011)

HT-SELEX-based identification of binding pre-miRNA hairpin-motif for small molecules

scientific article published on 29 November 2021

IPknot: fast and accurate prediction of RNA secondary structures with pseudoknots using integer programming

scientific article

Identification and analysis of ribosome-associated lncRNAs using ribosome profiling data.

scientific article

Identification of RNA biomarkers for chemical safety screening in neural cells derived from mouse embryonic stem cells using RNA deep sequencing analysis

scientific article published on 26 November 2018

Identification of Transposable Elements Contributing to Tissue-Specific Expression of Long Non-Coding RNAs

scientific article published on 9 January 2018

Identification of m<sup>6</sup>A-Associated RNA Binding Proteins Using an Integrative Computational Framework

scientific article published on 01 March 2021

Identifying sequence features that drive ribosomal association for lncRNA

Improved Accuracy in RNA-Protein Rigid Body Docking by Incorporating Force Field for Molecular Dynamics Simulation into the Scoring Function.

scientific article published on 5 August 2016

Improving the accuracy of predicting secondary structure for aligned RNA sequences

scientific article

In silico approaches to RNA aptamer design

scientific article published on 11 October 2017

Jonckheere-Terpstra-Kendall-based non-parametric analysis of temporal differential gene expression

scientific article published on 24 March 2021

Learning chromatin states with factorized information criteria

scientific article

LncRRIsearch: A Web Server for lncRNA-RNA Interaction Prediction Integrated With Tissue-Specific Expression and Subcellular Localization Data.

scientific article published on 28 May 2019

Long Non-Coding RNA CRNDE Is Involved in Resistance to EGFR Tyrosine Kinase Inhibitor in EGFR-Mutant Lung Cancer via eIF4A3/MUC1/EGFR Signaling

scientific article published on 13 April 2021

Mining frequent stem patterns from unaligned RNA sequences

scientific article

MoAIMS: efficient software for detection of enriched regions of MeRIP-Seq

scientific article published on 14 March 2020

PBSIM: PacBio reads simulator--toward accurate genome assembly

scientific article

Parallelized Latent Dirichlet Allocation Provides a Novel Interpretability of Mutation Signatures in Cancer Genomes

scientific article published on 25 September 2020

Prediction of RNA secondary structure by maximizing pseudo-expected accuracy

scientific article

Prediction of RNA secondary structure using generalized centroid estimators

scientific article

Predictions of RNA secondary structure by combining homologous sequence information

scientific article

Privacy-preserving search for chemical compound databases.

scientific article published on 9 December 2015

Probabilistic alignments with quality scores: an application to short-read mapping toward accurate SNP/indel detection

scientific article

RIblast: An ultrafast RNA-RNA interaction prediction system based on a seed-and-extension approach

scientific article published on 28 April 2017

RNA secondary structure prediction from multi-aligned sequences

scientific article published on January 2015

RNA structural alignments, part II: non-Sankoff approaches for structural alignments

scientific article published in January 2014

RNA-Seq Analysis Reveals Localization-Associated Alternative Splicing across 13 Cell Lines

scientific article published on 18 July 2020

RactIP: fast and accurate prediction of RNA-RNA interaction using integer programming

scientific article

RaptRanker: in silico RNA aptamer selection from HT-SELEX experiment based on local sequence and structure information

scientific article published on 15 June 2020

Reference-free prediction of rearrangement breakpoint reads

scientific article

Revealing the microbial assemblage structure in the human gut microbiome using latent Dirichlet allocation

scientific article published on 23 June 2020

Rtools: a web server for various secondary structural analyses on single RNA sequences.

scientific article published on 29 April 2016

Shape-based alignment of genomic landscapes in multi-scale resolution

scientific article

Software.ncrna.org: web servers for analyses of RNA sequences

scientific article published on 25 April 2008

Stromal fibroblasts induce metastatic tumor cell clusters via epithelial-mesenchymal plasticity

scientific article published on 22 July 2019

Targeting the TR4 nuclear receptor-mediated lncTASR/AXL signaling with tretinoin increases the sunitinib sensitivity to better suppress the RCC progression

scientific article published on 09 September 2019

Training alignment parameters for arbitrary sequencers with LAST-TRAIN.

scientific article published on 30 December 2016

List of works by Michiaki Hamada

A Classification of Bioinformatics Algorithms from the Viewpoint of Maximizing Expected Accuracy (MEA) ⬇️

A Novel Method for Assessing the Statistical Significance of RNA-RNA Interactions Between Two Long RNAs

A semi-supervised learning approach for RNA secondary structure prediction

AMAP: A pipeline for whole-genome mutation detection in Arabidopsis thaliana

Analysis of base-pairing probabilities of RNA molecules involved in protein-RNA interactions.

Antagonistic RNA aptamer specific to a heterodimeric form of human interleukin-17A/F ⬇️

Beyond similarity assessment: Selecting the optimal model for sequence alignment via the Factorized Asymptotic Bayesian algorithm

Bioinformatics tools for lncRNA research.

CENTROIDFOLD: a web server for RNA secondary structure prediction

CentroidAlign: fast and accurate aligner for structured RNAs by maximizing expected sum-of-pairs score

CentroidHomfold-LAST: accurate prediction of RNA secondary structure using automatically collected homologous sequences

Comprehensive prediction of lncRNA-RNA interactions in human transcriptome

Computational approaches for alternative and transient secondary structures of ribonucleic acids

Computational prediction of lncRNA-mRNA interactionsby integrating tissue specificity in human transcriptome

DeepM6ASeq: prediction and characterization of m6A-containing sequences using deep learning

Discovering novel mutation signatures by latent Dirichlet allocation with variational Bayes inference

Efficient calculation of exact probability distributions of integer features on RNA secondary structures

Estimating Energy Parameters for RNA Secondary Structure Predictions Using Both Experimental and Computational Data

Fighting against uncertainty: an essential issue in bioinformatics.

Generalized centroid estimators in bioinformatics

HT-SELEX-based identification of binding pre-miRNA hairpin-motif for small molecules

IPknot: fast and accurate prediction of RNA secondary structures with pseudoknots using integer programming

Identification and analysis of ribosome-associated lncRNAs using ribosome profiling data.

Identification of RNA biomarkers for chemical safety screening in neural cells derived from mouse embryonic stem cells using RNA deep sequencing analysis

Identification of Transposable Elements Contributing to Tissue-Specific Expression of Long Non-Coding RNAs

Identification of m<sup>6</sup>A-Associated RNA Binding Proteins Using an Integrative Computational Framework

Identifying sequence features that drive ribosomal association for lncRNA

Improved Accuracy in RNA-Protein Rigid Body Docking by Incorporating Force Field for Molecular Dynamics Simulation into the Scoring Function.

Improving the accuracy of predicting secondary structure for aligned RNA sequences

In silico approaches to RNA aptamer design

Jonckheere-Terpstra-Kendall-based non-parametric analysis of temporal differential gene expression

Learning chromatin states with factorized information criteria

LncRRIsearch: A Web Server for lncRNA-RNA Interaction Prediction Integrated With Tissue-Specific Expression and Subcellular Localization Data.

Long Non-Coding RNA CRNDE Is Involved in Resistance to EGFR Tyrosine Kinase Inhibitor in EGFR-Mutant Lung Cancer via eIF4A3/MUC1/EGFR Signaling

Mining frequent stem patterns from unaligned RNA sequences

MoAIMS: efficient software for detection of enriched regions of MeRIP-Seq

PBSIM: PacBio reads simulator--toward accurate genome assembly

Parallelized Latent Dirichlet Allocation Provides a Novel Interpretability of Mutation Signatures in Cancer Genomes

Prediction of RNA secondary structure by maximizing pseudo-expected accuracy

Prediction of RNA secondary structure using generalized centroid estimators

Predictions of RNA secondary structure by combining homologous sequence information

Privacy-preserving search for chemical compound databases.

Probabilistic alignments with quality scores: an application to short-read mapping toward accurate SNP/indel detection

RIblast: An ultrafast RNA-RNA interaction prediction system based on a seed-and-extension approach

RNA secondary structure prediction from multi-aligned sequences

RNA structural alignments, part II: non-Sankoff approaches for structural alignments

RNA-Seq Analysis Reveals Localization-Associated Alternative Splicing across 13 Cell Lines

RactIP: fast and accurate prediction of RNA-RNA interaction using integer programming

RaptRanker: in silico RNA aptamer selection from HT-SELEX experiment based on local sequence and structure information

Reference-free prediction of rearrangement breakpoint reads

Revealing the microbial assemblage structure in the human gut microbiome using latent Dirichlet allocation

Rtools: a web server for various secondary structural analyses on single RNA sequences.

Shape-based alignment of genomic landscapes in multi-scale resolution

Software.ncrna.org: web servers for analyses of RNA sequences

Stromal fibroblasts induce metastatic tumor cell clusters via epithelial-mesenchymal plasticity

Targeting the TR4 nuclear receptor-mediated lncTASR/AXL signaling with tretinoin increases the sunitinib sensitivity to better suppress the RCC progression

Training alignment parameters for arbitrary sequencers with LAST-TRAIN.