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Deep Learning and Its Applications in Biomedicine

Genomics, proteomics & bioinformatics, 2018-02, Vol.16 (1), p.17-32

2018

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Comprehensive identification and annotation of cell type-specific and ubiquitous CTCF-binding sites in the human genome

PloS one, 2012-07, Vol.7 (7), p.e41374-e41374

2012

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Oocyte competence is maintained by m6A methyltransferase KIAA1429-mediated RNA metabolism during mouse follicular development

Cell death and differentiation, 2020-08, Vol.27 (8), p.2468-2483

2020

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Characterization of Metabolic Patterns in Mouse Oocytes during Meiotic Maturation

Molecular cell, 2020-11, Vol.80 (3), p.525-540.e9

2020

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Embryonic defects induced by maternal obesity in mice derive from Stella insufficiency in oocytes

Nature genetics, 2018-03, Vol.50 (3), p.432-442

2018

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High-resolution annotation of the mouse preimplantation embryo transcriptome using long-read sequencing

Nature communications, 2020-05, Vol.11 (1), p.2653-2653, Article 2653

2020

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Author Correction: High-resolution annotation of the mouse preimplantation embryo transcriptome using long-read sequencing

Nature communications, 2021-03, Vol.12 (1), p.1767-1767, Article 1767

2021

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Editorial: Reproductive genomics

Frontiers in genetics, 2022-08, Vol.13, p.1002458-1002458

2022

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Differential roles of Stella in the modulation of DNA methylation during oocyte and zygotic development

Cell discovery, 2019-01, Vol.5 (1), p.9-9, Article 9

2019

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Application of machine learning to associative scRNA-seq data gene expression and alternative polyadenylation sites clustering

BIO web of conferences, 2023-01, Vol.59, p.3004

2023

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Functional annotation of structural ncRNAs within enhancer RNAs in the human genome: implications for human disease

Scientific reports, 2017-11, Vol.7 (1), p.15518-15, Article 15518

2017

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A guidebook of spatial transcriptomic technologies, data resources and analysis approaches

Computational and structural biotechnology journal, 2023-01, Vol.21, p.940-955

2023

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Cytosine and adenine deaminase base-editors induce broad and nonspecific changes in gene expression and splicing

Communications biology, 2021-07, Vol.4 (1), p.882-882, Article 882

2021

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iFORM: Incorporating Find Occurrence of Regulatory Motifs

PloS one, 2016-12, Vol.11 (12), p.e0168607-e0168607

2016

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PEDLA: predicting enhancers with a deep learning-based algorithmic framework

Scientific reports, 2016-06, Vol.6 (1), p.28517-28517, Article 28517

2016

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BiRen: predicting enhancers with a deep-learning-based model using the DNA sequence alone

Bioinformatics (Oxford, England), 2017-07, Vol.33 (13), p.1930-1936

2017

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RDMAS: a web server for RNA deleterious mutation analysis

BMC bioinformatics, 2006-09, Vol.7 (1), p.404-404, Article 404

2006

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A novel representation of RNA secondary structure based on element-contact graphs

BMC bioinformatics, 2008-04, Vol.9 (1), p.188-188, Article 188

2008

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METTL3-mediated m6A is required for murine oocyte maturation and maternal-to-zygotic transition

Cell cycle (Georgetown, Tex.), 2020-02, Vol.19 (4), p.391-404

2020

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Nuezhenoside G13 from Osmanthus fragrans fruit ameliorates Concanavalin A-induced autoimmune hepatitis by regulating the NF-κB/MAPK pathway

Journal of ethnopharmacology, 2024-01, Vol.319 (Pt 3), p.117257-117257, Article 117257

2024

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Engineering Synthetic CopT/A-Based Genetic Biosensors for miRNA Imaging and Functional Gene Regulation

Analytical chemistry (Washington), 2023-04, Vol.95 (16), p.6748-6756

2023

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Liver Fibrosis Amelioration by Macrophage-Biomimetic Polydopamine Nanoparticles via Synergistically Alleviating Inflammation and Scavenging ROS

Molecular pharmaceutics, 2024-06, Vol.21 (6), p.3040-3052

2024

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EvoRSR: an integrated system for exploring evolution of RNA structural robustness

BMC bioinformatics, 2009-08, Vol.10 (1), p.249-249, Article 249

2009

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In silico genetic robustness analysis of microRNA secondary structures: potential evidence of congruent evolution in microRNA

BMC evolutionary biology, 2007-11, Vol.7 (1), p.223, Article 223

2007

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A DddA ortholog-based and transactivator-assisted nuclear and mitochondrial cytosine base editors with expanded target compatibility

Molecular cell, 2023-05, Vol.83 (10), p.1710-1724.e7

2023

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Deep Learning and Its Applications in Biomedicine

Comprehensive identification and annotation of cell type-specific and ubiquitous CTCF-binding sites in the human genome

Oocyte competence is maintained by m6A methyltransferase KIAA1429-mediated RNA metabolism during mouse follicular development

Characterization of Metabolic Patterns in Mouse Oocytes during Meiotic Maturation

Embryonic defects induced by maternal obesity in mice derive from Stella insufficiency in oocytes

High-resolution annotation of the mouse preimplantation embryo transcriptome using long-read sequencing

Author Correction: High-resolution annotation of the mouse preimplantation embryo transcriptome using long-read sequencing

Editorial: Reproductive genomics

Differential roles of Stella in the modulation of DNA methylation during oocyte and zygotic development

Application of machine learning to associative scRNA-seq data gene expression and alternative polyadenylation sites clustering

Functional annotation of structural ncRNAs within enhancer RNAs in the human genome: implications for human disease

A guidebook of spatial transcriptomic technologies, data resources and analysis approaches

Cytosine and adenine deaminase base-editors induce broad and nonspecific changes in gene expression and splicing

iFORM: Incorporating Find Occurrence of Regulatory Motifs

PEDLA: predicting enhancers with a deep learning-based algorithmic framework

BiRen: predicting enhancers with a deep-learning-based model using the DNA sequence alone

RDMAS: a web server for RNA deleterious mutation analysis

A novel representation of RNA secondary structure based on element-contact graphs

METTL3-mediated m6A is required for murine oocyte maturation and maternal-to-zygotic transition

Nuezhenoside G13 from Osmanthus fragrans fruit ameliorates Concanavalin A-induced autoimmune hepatitis by regulating the NF-κB/MAPK pathway

Engineering Synthetic CopT/A-Based Genetic Biosensors for miRNA Imaging and Functional Gene Regulation

Liver Fibrosis Amelioration by Macrophage-Biomimetic Polydopamine Nanoparticles via Synergistically Alleviating Inflammation and Scavenging ROS

EvoRSR: an integrated system for exploring evolution of RNA structural robustness

In silico genetic robustness analysis of microRNA secondary structures: potential evidence of congruent evolution in microRNA

A DddA ortholog-based and transactivator-assisted nuclear and mitochondrial cytosine base editors with expanded target compatibility

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