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

BMC bioinformatics, 2018-12, Vol.19 (Suppl 19), p.524-524, Article 524

2018

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

Bioinformatics (Oxford, England), 2017-09, Vol.33 (17), p.2666-2674

2017

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PBSIM: PacBio reads simulator--toward accurate genome assembly

Bioinformatics, 2013-01, Vol.29 (1), p.119-121

2013

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RNA secondary structure prediction from multi-aligned sequences

Methods in molecular biology (Clifton, N.J.), 2015-01, Vol.1269, p.17

Hamada, Michiaki

2015

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

BMC bioinformatics, 2021-11, Vol.22 (1), p.1-554, Article 554

2021

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

BMC bioinformatics, 2020-03, Vol.21 (1), p.103-103, Article 103

2020

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

Methods in molecular biology (Clifton, N.J.), 2023, Vol.2586, p.163

2023

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

Frontiers in genetics, 2019-05, Vol.10, p.462-462

2019

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

BMC genomics, 2018-05, Vol.19 (1), p.414-414, Article 414

2018

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Landscape of evolutionary arms races between transposable elements and KRAB-ZFP family

Scientific reports, 2024-10, Vol.14 (1), p.23358-13, Article 23358

2024

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Identifying sequence features that drive ribosomal association for lncRNA

BMC genomics, 2018-12, Vol.19 (Suppl 10), p.906-906, Article 906

2018

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Fighting against uncertainty: an essential issue in bioinformatics

Briefings in bioinformatics, 2014-09, Vol.15 (5), p.748-767

Hamada, Michiaki

2014

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Screening of Key Transcripts from Expression Data Using Applied Artificial Intelligence for Cancer Prediction

International journal of computational intelligence systems, 2024-09, Vol.17 (1), p.1-8, Article 252

2024

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Detection and Characterization of Ribosome-Associated Long Noncoding RNAs

Methods in molecular biology (Clifton, N.J.), 2021, Vol.2254, p.179

2021

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

Nucleic acids research, 2020-08, Vol.48 (14), p.e82-e82

2020

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

Bioinformatics, 2021-07, Vol.37 (Supplement_1), p.i16-i24

2021

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Prediction of RNA-protein interactions using a nucleotide language model

Bioinformatics advances, 2022, Vol.2 (1), p.vbac023

2022

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

BMC genomics, 2021-10, Vol.22 (1), p.1-730, Article 730

2021

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Web Services for RNA-RNA Interaction Prediction

Methods in molecular biology (Clifton, N.J.), 2023, Vol.2586, p.175

2023

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

Oncogene, 2020-01, Vol.39 (3), p.530-545

2020

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Identification of m6A-Associated RNA Binding Proteins Using an Integrative Computational Framework

Frontiers in genetics, 2021-03, Vol.12, p.625797-625797

2021

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Comprehensive prediction of lncRNA-RNA interactions in human transcriptome

BMC genomics, 2016-01, Vol.17 Suppl 1 (7), p.12-12, Article 12

2016

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

Bioinformatics, 2018-02, Vol.34 (4), p.576-584

2018

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Prediction of RNA secondary structure using generalized centroid estimators

Bioinformatics, 2009-02, Vol.25 (4), p.465-473

2009

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

Nucleic acids research, 2022-10, Vol.50 (19), p.11229-11242

2022

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

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

PBSIM: PacBio reads simulator--toward accurate genome assembly

RNA secondary structure prediction from multi-aligned sequences

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

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

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

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

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

Landscape of evolutionary arms races between transposable elements and KRAB-ZFP family

Identifying sequence features that drive ribosomal association for lncRNA

Fighting against uncertainty: an essential issue in bioinformatics

Screening of Key Transcripts from Expression Data Using Applied Artificial Intelligence for Cancer Prediction

Detection and Characterization of Ribosome-Associated Long Noncoding RNAs

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

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

Prediction of RNA-protein interactions using a nucleotide language model

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

Web Services for RNA-RNA Interaction Prediction

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

Identification of m6A-Associated RNA Binding Proteins Using an Integrative Computational Framework

Comprehensive prediction of lncRNA-RNA interactions in human transcriptome

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

Prediction of RNA secondary structure using generalized centroid estimators

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

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