Michiaki Hamada

Work

Waseda University
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Professor

Japan

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National Institute of Advanced Industrial Science and Technology
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Team Leader

Japan

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Waseda University
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Associate Professor

Japan

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University of Tokyo
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Associate Professor

Japan

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Mizuho Joho Soken Kabushiki Kaisha
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Consultant

Japan

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Education

Tokyo Institute of Technology
Japan

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Doctor of Science

Tohoku University
Japan

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Master of science

Publications

Bioinformatics Approaches for Determining the Functional Impact of Repetitive Elements on Non-coding RNAs

Summary

working-paper

Deep learning challenge to generate apo RNA conformations with cryptic binding site

Summary

preprint

Multi-objective computational optimization of human 5′ UTR sequences

Published by

Briefings in Bioinformatics

Summary

journal-article

Hidden challenges in evaluating spillover risk of zoonotic viruses using machine learning models

Published by

Communications Medicine

Summary

journal-article

Deciphering the comprehensive relationship between 5′UTR and 3′UTR sequences with deep learning

Summary

preprint

Mitotic phosphorylation of ADAR1 regulates its centromeric localization and is required for faithful mitotic progression

Summary

preprint

Integrative epigenome and transcriptome analyses reveal transcriptional programs differentially regulated by ASCL1 and NEUROD1 in small cell lung cancer

Published by

Oncogene

Summary

journal-article

Screening and machine-learning assisted prediction of translation-enhancing peptides reducing ribosomal stalling in Escherichia coli

Summary

preprint

Landscape of Evolutionary Arms Races between Transposable Elements and KRAB-ZFP Family

Summary

preprint

Systematic discovery of directional regulatory motifs associated with human insulator sites

Summary

preprint

Prediction of antibiotic resistance mechanisms using a protein language model

Summary

preprint

RaptGen-UI: an integrated platform for exploring and analyzing the sequence landscape of HT-SELEX experiments

Published by

Bioinformatics Advances

Summary

journal-article

Multi-objective computational optimization of human 5′ UTR sequences

Summary

preprint

A chimeric RNA consisting of siRNA and aptamer for inhibiting dengue virus replication

Published by

NAR Molecular Medicine

Summary

journal-article

Prediction of antibiotic resistance mechanisms using a protein language model

Published by

Bioinformatics

Summary

journal-article

The Lomb-Scargle periodogram-based differentially expressed gene detection along pseudotime

Summary

preprint

Identification of a novel RNA transcript TISPL upregulated by stressors that stimulate ATF4

Published by

Gene

Summary

journal-article

Selection and characterization of aptamers targeting the Vif-CBFß-ELOB-ELOC-CUL5 complex

Summary

other

RaptGen-Assisted Generation of an RNA/DNA Hybrid Aptamer against SARS-CoV-2 Spike Protein.

Published by

Biochemistry

Summary

journal-article

Deep generative design of RNA family sequences

Published by

Nature Methods

Summary

journal-article

Comparison of early clinical outcome in carpal tunnel release - mini-open technique with palmar incision vs. endoscopic technique with wrist crease incision.

Published by

BMC musculoskeletal disorders

Summary

journal-article

Hidden Challenges in Evaluating Spillover Risk of Zoonotic Viruses using Machine Learning Models

Summary

preprint

Transposons contribute to the acquisition of cell type-specific cis-elements in the brain

Published by

Communications Biology

Summary

journal-article

Landscape of semi-extractable RNAs across five human cell lines

Published by

Nucleic Acids Research

Summary

journal-article

Mobile element variation contributes to population-specific genome diversification, gene regulation and disease risk.

Published by

Nature genetics

Summary

journal-article

Recent trends in RNA informatics: a review of machine learning and deep learning for RNA secondary structure prediction and RNA drug discovery.

Published by

Briefings in bioinformatics

Summary

journal-article

Fast RNA-RNA Interaction Prediction Methods for Interaction Analysis of Transcriptome-Scale Large Datasets.

Published by

Methods in molecular biology (Clifton, N.J.)

Summary

journal-article

Web Services for RNA-RNA Interaction Prediction.

Published by

Methods in molecular biology (Clifton, N.J.)

Summary

journal-article

Bioinformatics approaches for unveiling virus-host interactions

Published by

Computational and Structural Biotechnology Journal

Summary

journal-article

Probiotic responder identification in cross-over trials for constipation using a Bayesian statistical model considering lags between intake and effect periods

Published by

Computational and Structural Biotechnology Journal

Summary

journal-article

DeepRaccess: High-speed RNA accessibility prediction using deep learning

Summary

preprint

LinAliFold and CentroidLinAliFold: fast RNA consensus secondary structure prediction for aligned sequences using beam search methods

Published by

Bioinformatics Advances

Summary

journal-article

Structure-based screening for functional non-coding RNAs in fission yeast identifies a factor repressing untimely initiation of sexual differentiation

Published by

Nucleic Acids Research

Summary

journal-article

PBSIM3: a simulator for all types of PacBio and ONT long reads

Published by

NAR Genomics and Bioinformatics

Summary

journal-article

Landscape of semi-extractable RNAs across five human cell lines

Summary

preprint

Generative aptamer discovery using RaptGen

Published by

Nature Computational Science

Summary

journal-article

LinAliFold and CentroidLinAliFold: Fast RNA consensus secondary structure prediction for aligned sequences using beam search methods

Summary

preprint

Probiotic responder identification in cross-over trials for constipation using a Bayesian statistical model considering lags between intake and effect periods

Summary

preprint

Author Correction: Discovery of widespread transcription initiation at microsatellites predictable by sequence-based deep neural network.

Published by

Nature communications

Summary

journal-article

G0S2 regulates innate immunity in Kawasaki disease via lncRNA HSD11B1-AS1.

Published by

Pediatric research

Summary

journal-article

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

Published by

Molecular Therapy Nucleic Acids

Summary

journal-article

Mobile elements in human population-specific genome and phenotype divergence

Summary

preprint

Prediction of RNA–protein interactions using a nucleotide language model

Published by

Bioinformatics Advances

Summary

journal-article

Bioinformatics Approaches for Determining the Functional Impact of Repetitive Elements on Non-coding RNAs.

Published by

Methods in molecular biology (Clifton, N.J.)

Summary

journal-article

Binding patterns of RNA binding proteins to repeat-derived RNA sequences reveal putative functional RNA elements

Published by

bioRxiv

Summary

other

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

Published by

Frontiers in Genetics

Summary

journal-article

Clone decomposition based on mutation signatures provides novel insights into mutational processes

Published by

NAR Genomics and Bioinformatics

Summary

journal-article

Impact of human gene annotations on RNA-seq differential expression analysis.

Published by

BMC genomics

Summary

journal-article

Binding patterns of RNA-binding proteins to repeat-derived RNA sequences reveal putative functional RNA elements

Published by

NAR Genomics and Bioinformatics

Summary

journal-article

Clone decomposition based on mutation signatures provides novel insights into mutational processes

Summary

preprint

Bioinformatics Approaches for Determining the Functional Impact of Repetitive Elements on Non-coding RNAs

Summary

other

Umibato: Estimation of time-varying microbial interaction using continuous-time regression hidden Markov model

Published by

Bioinformatics

Summary

journal-article

Multi-resBind: a residual network-based multi-label classifier for in vivo RNA binding prediction and preference visualization.

Published by

BMC bioinformatics

Summary

journal-article

PBSIM2: a simulator for long-read sequencers with a novel generative model of quality scores

Published by

Bioinformatics

Summary

journal-article

PBSIM2: A simulator for long-read sequencers with a novel generative model of quality scores

Published by

Bioinformatics

Summary

journal-article

Prediction of RNA-protein interactions using a nucleotide language model

Summary

preprint

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

Published by

International Journal of Molecular Sciences

Summary

journal-article

Long non-coding RNA CRNDE is involved in resistance to EGFR tyrosine kinase inhibitor in EGFR-mutant lung cancer via eIF4A3/MUC1/EGFR signaling

Published by

International Journal of Molecular Sciences

Summary

journal-article

Representation learning applications in biological sequence analysis

Summary

preprint

RaptGen: A variational autoencoder with profile hidden Markov model for generative aptamer discovery

Summary

preprint

RaptGen: A variational autoencoder with profile hidden Markov model for generative aptamer discovery

Published by

bioRxiv

Summary

other

Umibato: estimation of time-varying microbial interaction using continuous-time regression hidden Markov model

Summary

preprint

Association analysis of repetitive elements and R-loop formation across species

Published by

Mobile DNA

Summary

journal-article

Association analysis of repetitive elements and R-loop formation across species

Published by

Mobile DNA

Summary

journal-article

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

Published by

NAR Genomics and Bioinformatics

Summary

journal-article

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

Published by

Microbiome

Summary

journal-article

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

Published by

BMC Bioinformatics

Summary

journal-article

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

Published by

Genes

Summary

journal-article

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

Published by

Genes

Summary

journal-article

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

Published by

Nucleic Acids Research

Summary

journal-article

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

Published by

Genes

Summary

journal-article

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

Published by

Genes

Summary

journal-article

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

Published by

IEEE/ACM Transactions on Computational Biology and Bioinformatics

Summary

journal-article

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

Summary

preprint

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

Published by

Frontiers in genetics

Summary

journal-article

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

Summary

other

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

Published by

Bioinformatics

Summary

journal-article

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

Published by

Oncogene

Summary

journal-article

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

Summary

other

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

Published by

Life science alliance

Summary

journal-article

Computational approaches for alternative and transient secondary structures of ribonucleic acids

Published by

Briefings in Functional Genomics

Summary

journal-article

Estimating energy parameters for RNA secondary structure predictions using both experimental and computational data.

Published by

IEEE/ACM transactions on computational biology and bioinformatics

Summary

journal-article

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

Published by

Bioinformatics

Summary

journal-article

In silico approaches to RNA aptamer design

Published by

Biochimie

Summary

journal-article

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

Published by

Genes

Summary

journal-article

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

Published by

BMC bioinformatics

Summary

journal-article

Nearest-neighbor parameter for inosine-cytosine pairs through a combined experimental and computational approach

Summary

other

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

Published by

Journal of computational biology : a journal of computational molecular cell biology

Summary

journal-article

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

Published by

BMC genomics

Summary

journal-article

Identifying sequence features that drive ribosomal association for lncRNA.

Published by

BMC genomics

Summary

journal-article

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

Published by

Biochemical and biophysical research communications

Summary

journal-article

The hominoid-specific gene DSCR4 is involved in regulation of human leukocyte migration

Summary

journal-article

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

Published by

Bioinformatics (Oxford, England)

Summary

journal-article

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

Published by

Biology Direct

Summary

journal-article

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

Summary

journal-article

Bioinformatics tools for lncRNA research.

Summary

journal-article

Training alignment parameters for arbitrary sequencers with LAST-TRAIN.

Summary

journal-article

Comprehensive prediction of lncRNA-RNA interactions in human transcriptome.

Summary

journal-article

RIblast: An ultrafast RNA-RNA interaction prediction system for comprehensive lncRNA interaction analysis

Summary

journal-article

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

Summary

journal-article

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

Summary

journal-article

A semi-supervised learning approach for RNA secondary structure prediction

Published by

Computational Biology and Chemistry

Summary

journal-article

RNA secondary structure prediction from multi-aligned sequences.

Summary

journal-article

Privacy-preserving search for chemical compound databases.

Summary

journal-article

Privacy-preserving search for chemical compound databases

Summary

journal-article

Learning chromatin states with factorized information criteria.

Summary

journal-article

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

Summary

journal-article

Reference-free prediction of rearrangement breakpoint reads.

Summary

journal-article

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

Summary

journal-article

CentroidAlign-Web: A Fast and Accurate Multiple Aligner for Long Non-Coding RNAs.

Summary

journal-article

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

Summary

journal-article

Fighting against uncertainty: an essential issue in bioinformatics.

Summary

journal-article

PBSIM: PacBio reads simulator--toward accurate genome assembly.

Summary

journal-article

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

Summary

journal-article

Direct updating of an RNA base-pairing probability matrix with marginal probability constraints.

Summary

journal-article

A classification of bioinformatics algorithms from the viewpoint of maximizing expected accuracy (MEA).

Summary

journal-article

Generalized centroid estimators in bioinformatics.

Summary

journal-article

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

Summary

journal-article

Improving the accuracy of predicting secondary structure for aligned RNA sequences.

Summary

journal-article

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

Summary

journal-article

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

Summary

journal-article

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

Summary

journal-article

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

Summary

journal-article

Parameters for accurate genome alignment.

Summary

journal-article

Prediction of RNA secondary structure by maximizing pseudo-expected accuracy.

Summary

journal-article

CENTROIDFOLD: a web server for RNA secondary structure prediction.

Summary

journal-article

Predictions of RNA secondary structure by combining homologous sequence information.

Summary

journal-article

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

Summary

journal-article

Prediction of RNA secondary structure using generalized centroid estimators.

Summary

journal-article

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

Summary

journal-article

Mining frequent stem patterns from unaligned RNA sequences.

Summary

journal-article

Michiaki Hamada