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RNA secondary structure prediction using deep learning with thermodynamic integration

Nature communications, 2021-02, Vol.12 (1), p.941-941, Article 941

2021

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Convolutional neural networks for classification of alignments of non-coding RNA sequences

Bioinformatics, 2018-07, Vol.34 (13), p.i237-i244

2018

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MetaVelvet: an extension of Velvet assembler to de novo metagenome assembly from short sequence reads

Nucleic acids research, 2012-11, Vol.40 (20), p.e155-e155

2012

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Comprehensive evaluation of non-hybrid genome assembly tools for third-generation PacBio long-read sequence data

Briefings in bioinformatics, 2019-05, Vol.20 (3), p.866-876

2019

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Convolutional neural network based on SMILES representation of compounds for detecting chemical motif

BMC bioinformatics, 2018-12, Vol.19 (Suppl 19), p.526-526, Article 526

2018

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MetaVelvet-DL: a MetaVelvet deep learning extension for de novo metagenome assembly

BMC bioinformatics, 2021-06, Vol.22 (S6), p.1-427, Article 427

2021

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Deep learning integration of molecular and interactome data for protein–compound interaction prediction

Journal of cheminformatics, 2021-05, Vol.13 (1), p.36-36, Article 36

2021

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Informative RNA base embedding for RNA structural alignment and clustering by deep representation learning

NAR genomics and bioinformatics, 2022-03, Vol.4 (1)

2022

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Deep learning of multimodal networks with topological regularization for drug repositioning

Journal of cheminformatics, 2024-08, Vol.16 (1), p.103-12

2024

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Performance of a deep learning-based identification system for esophageal cancer from CT images

Esophagus : official journal of the Japan Esophageal Society, 2021-07, Vol.18 (3), p.612-620

2021

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Statistical prediction of protein–chemical interactions based on chemical structure and mass spectrometry data

Bioinformatics, 2007-08, Vol.23 (15), p.2004-2012

2007

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Generation of a Nonhuman Primate Model of Severe Combined Immunodeficiency Using Highly Efficient Genome Editing

Cell stem cell, 2016-07, Vol.19 (1), p.127-138

2016

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Direct Inference of Base-Pairing Probabilities with Neural Networks Improves Prediction of RNA Secondary Structures with Pseudoknots

Genes, 2022-11, Vol.13 (11), p.2155

2022

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Genome sequence and analysis of the Japanese morning glory Ipomoea nil

Nature communications, 2016-11, Vol.7 (1), p.13295-13295, Article 13295

2016

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Efficient generation of Knock-in/Knock-out marmoset embryo via CRISPR/Cas9 gene editing

Scientific reports, 2019-09, Vol.9 (1), p.12719-13, Article 12719

2019

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Grammatical Inference: Algorithms and Applications: 7th International Colloquium, ICGI 2004, Athens, Greece, October 11-13, 2004. Proceedings

2004

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Whole-Genome Sequencing and Comparative Genome Analysis of Bacillus subtilis Strains Isolated from Non-Salted Fermented Soybean Foods

PloS one, 2015-10, Vol.10 (10), p.e0141369

2015

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Poly-γ-glutamic acid production of Bacillus subtilis (natto) in the absence of DegQ: A gain-of-function mutation in yabJ gene

Journal of bioscience and bioengineering, 2019-12, Vol.128 (6), p.690-696

2019

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Whole genome complete resequencing of Bacillus subtilis natto by combining long reads with high-quality short reads

PloS one, 2014-10, Vol.9 (10), p.e109999-e109999

2014

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An improved de novo genome assembly of the common marmoset genome yields improved contiguity and increased mapping rates of sequence data

BMC genomics, 2020-04, Vol.21 (Suppl 3), p.243-243, Article 243

2020

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Whole genome assembly of a natto production strain Bacillus subtilis natto from very short read data

BMC genomics, 2010-04, Vol.11 (1), p.243-243, Article 243

2010

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Decoding host-microbiome interactions through co-expression network analysis within the non-human primate intestine

mSystems, 2024-05, Vol.9 (5), p.e0140523-e0140523

2024

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A Max-Margin Model for Predicting Residue-Base Contacts in Protein-RNA Interactions

Life (Basel, Switzerland), 2021-10, Vol.11 (11), p.1135

2021

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Quantum Algorithm for Position Weight Matrix Matching

IEEE transactions on quantum engineering, 2023, Vol.4, p.1-14

2023

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Time-Series Analysis of Tumorigenesis in a Murine Skin Carcinogenesis Model

Scientific reports, 2018-08, Vol.8 (1), p.12994-11, Article 12994

2018

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RNA secondary structure prediction using deep learning with thermodynamic integration

Convolutional neural networks for classification of alignments of non-coding RNA sequences

MetaVelvet: an extension of Velvet assembler to de novo metagenome assembly from short sequence reads

Comprehensive evaluation of non-hybrid genome assembly tools for third-generation PacBio long-read sequence data

Convolutional neural network based on SMILES representation of compounds for detecting chemical motif

MetaVelvet-DL: a MetaVelvet deep learning extension for de novo metagenome assembly

Deep learning integration of molecular and interactome data for protein–compound interaction prediction

Informative RNA base embedding for RNA structural alignment and clustering by deep representation learning

Deep learning of multimodal networks with topological regularization for drug repositioning

Performance of a deep learning-based identification system for esophageal cancer from CT images

Statistical prediction of protein–chemical interactions based on chemical structure and mass spectrometry data

Generation of a Nonhuman Primate Model of Severe Combined Immunodeficiency Using Highly Efficient Genome Editing

Direct Inference of Base-Pairing Probabilities with Neural Networks Improves Prediction of RNA Secondary Structures with Pseudoknots

Genome sequence and analysis of the Japanese morning glory Ipomoea nil

Efficient generation of Knock-in/Knock-out marmoset embryo via CRISPR/Cas9 gene editing

Grammatical Inference: Algorithms and Applications: 7th International Colloquium, ICGI 2004, Athens, Greece, October 11-13, 2004. Proceedings

Whole-Genome Sequencing and Comparative Genome Analysis of Bacillus subtilis Strains Isolated from Non-Salted Fermented Soybean Foods

Poly-γ-glutamic acid production of Bacillus subtilis (natto) in the absence of DegQ: A gain-of-function mutation in yabJ gene

Whole genome complete resequencing of Bacillus subtilis natto by combining long reads with high-quality short reads

An improved de novo genome assembly of the common marmoset genome yields improved contiguity and increased mapping rates of sequence data

Whole genome assembly of a natto production strain Bacillus subtilis natto from very short read data

Decoding host-microbiome interactions through co-expression network analysis within the non-human primate intestine

A Max-Margin Model for Predicting Residue-Base Contacts in Protein-RNA Interactions

Quantum Algorithm for Position Weight Matrix Matching

Time-Series Analysis of Tumorigenesis in a Murine Skin Carcinogenesis Model

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