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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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Mirage 2.0: fast and memory-efficient reconstruction of gene-content evolution considering heterogeneous evolutionary patterns among gene families

Bioinformatics, 2022-08, Vol.38 (16), p.4039-4041

2022

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Inverse Potts model improves accuracy of phylogenetic profiling

Bioinformatics, 2022-03, Vol.38 (7), p.1794-1800

2022

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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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Logicome Profiler: Exhaustive detection of statistically significant logic relationships from comparative omics data

PloS one, 2020-05, Vol.15 (5), p.e0232106-e0232106

2020

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

Journal of computational biology, 2018-09, Vol.25 (9), p.976-986

2018

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Inactivity periods and postural change speed can explain atypical postural change patterns of Caenorhabditis elegans mutants

BMC bioinformatics, 2017-01, Vol.18 (1), p.46-46, Article 46

2017

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

Microbiome, 2020-06, Vol.8 (1), p.95-95, Article 95

2020

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

Bioinformatics advances, 2022, Vol.2 (1), p.vbac078-vbac078

2022

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Evolutionary origin of the Scombridae (tunas and mackerels): members of a paleogene adaptive radiation with 14 other pelagic fish families

PloS one, 2013-09, Vol.8 (9), p.e73535-e73535

2013

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Neat1 lncRNA organizes the inflammatory gene expressions in the dorsal root ganglion in neuropathic pain caused by nerve injury

Frontiers in immunology, 2023-08, Vol.14, p.1185322-1185322

2023

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Mirage: estimation of ancestral gene-copy numbers by considering different evolutionary patterns among gene families

Bioinformatics advances, 2021, Vol.1 (1), p.vbab014-vbab014

2021

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DeepRaccess: high-speed RNA accessibility prediction using deep learning

Frontiers in bioinformatics, 2023-10, Vol.3, p.1275787-1275787

2023

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Computational approaches for alternative and transient secondary structures of ribonucleic acids

Briefings in functional genomics, 2018-06, Vol.18 (3), p.182-191

2018

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GroupTracker: Video tracking system for multiple animals under severe occlusion

Computational biology and chemistry, 2015-08, Vol.57, p.39-45

2015

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Representation learning applications in biological sequence analysis

Computational and structural biotechnology journal, 2021-01, Vol.19, p.3198-3208

2021

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Bioinformatics approaches for unveiling virus-host interactions

Computational and structural biotechnology journal, 2023-01, Vol.21, p.1774-1784

2023

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Solar-panel and parasol strategies shape the proteorhodopsin distribution pattern in marine Flavobacteriia

The ISME Journal, 2018-05, Vol.12 (5), p.1329-1343

2018

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MitoFish and MiFish Pipeline: A Mitochondrial Genome Database of Fish with an Analysis Pipeline for Environmental DNA Metabarcoding

Molecular biology and evolution, 2018-06, Vol.35 (6), p.1553-1555

2018

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

Bioinformatics, 2019-11, Vol.35 (22), p.4543-4552

2019

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

Mirage 2.0: fast and memory-efficient reconstruction of gene-content evolution considering heterogeneous evolutionary patterns among gene families

Inverse Potts model improves accuracy of phylogenetic profiling

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

Logicome Profiler: Exhaustive detection of statistically significant logic relationships from comparative omics data

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

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

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

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

Inactivity periods and postural change speed can explain atypical postural change patterns of Caenorhabditis elegans mutants

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

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

Evolutionary origin of the Scombridae (tunas and mackerels): members of a paleogene adaptive radiation with 14 other pelagic fish families

Neat1 lncRNA organizes the inflammatory gene expressions in the dorsal root ganglion in neuropathic pain caused by nerve injury

Mirage: estimation of ancestral gene-copy numbers by considering different evolutionary patterns among gene families

DeepRaccess: high-speed RNA accessibility prediction using deep learning

Computational approaches for alternative and transient secondary structures of ribonucleic acids

GroupTracker: Video tracking system for multiple animals under severe occlusion

Representation learning applications in biological sequence analysis

Bioinformatics approaches for unveiling virus-host interactions

Solar-panel and parasol strategies shape the proteorhodopsin distribution pattern in marine Flavobacteriia

MitoFish and MiFish Pipeline: A Mitochondrial Genome Database of Fish with an Analysis Pipeline for Environmental DNA Metabarcoding

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

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