A deep learning approach to automate whole‐genome prediction of diverse epigenomic modifications in plants

A cost‐effective maize ear phenotyping platform enables rapid categorization and quantification of kernels

(2021) Cedar Warman et al.   PLANT JOURNAL

Deep6mA: A deep learning framework for exploring similar patterns in DNA N6-methyladenine sites across different species

(2021) Zutan Li et al.   PLoS Computational Biology

eRice: a refined epigenomic platform for japonica and indica rice

(2020) Pingxian Zhang et al.   PLANT BIOTECHNOLOGY JOURNAL

Deep learning for plant genomics and crop improvement

(2020) Hai Wang et al.   CURRENT OPINION IN PLANT BIOLOGY

Determinants of Base Editing Outcomes from Target Library Analysis and Machine Learning

(2020) Mandana Arbab et al.   CELL

RNA 5-Methylcytosine Controls Plant Development and Environmental Adaptation

(2020) Pingxian Zhang et al.   TRENDS IN PLANT SCIENCE

Predicting the efficiency of prime editing guide RNAs in human cells

(2020) Hui Kwon Kim et al.   NATURE BIOTECHNOLOGY

Pollen analysis using multispectral imaging flow cytometry and deep learning

(2020) Susanne Dunker et al.   NEW PHYTOLOGIST

i6mA-Pred: Identifying DNA N6-methyladenine sites in the rice genome

(2019) Wei Chen et al.   BIOINFORMATICS

Evolutionarily informed deep learning methods for predicting relative transcript abundance from DNA sequence

(2019) Jacob D. Washburn et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Deep learning: new computational modelling techniques for genomics

(2019) Gökcen Eraslan et al.   NATURE REVIEWS GENETICS

Messenger RNA Modifications in Plants

(2019) Lisha Shen et al.   TRENDS IN PLANT SCIENCE

Deep Learning: A Rapid and Efficient Route to Automatic Metasurface Design

(2019) Tianshuo Qiu et al.   Advanced Science

A Neuromorphic Device Implemented on a Salmon‐DNA Electrolyte and its Application to Artificial Neural Networks

(2019) Dong‐Ho Kang et al.   Advanced Science

Functional interpretation of genetic variants using deep learning predicts impact on chromatin accessibility and histone modification

(2019) Gabriel E Hoffman et al.   NUCLEIC ACIDS RESEARCH

Evolution of the RNA N6-methyladenosine methylome mediated by genomic duplication

(2019) Zhenyan Miao et al.   PLANT PHYSIOLOGY

iDNA6mA-Rice: A Computational Tool for Detecting N6-Methyladenine Sites in Rice

(2019) Hao Lv et al.   Frontiers in Genetics

SNNRice6mA: A Deep Learning Method for Predicting DNA N6-Methyladenine Sites in Rice Genome

(2019) Haitao Yu et al.   Frontiers in Genetics

Epigenetic Modifications of mRNA and DNA in Plants

(2019) Zhe Liang et al.   Molecular Plant

Learning from methylomes: epigenomic correlates of Populus balsamifera traits based on deep learning models of natural DNA methylation

(2019) Marc J. Champigny et al.   PLANT BIOTECHNOLOGY JOURNAL

DNA N 6 -Adenine Methylation in Arabidopsis thaliana

(2018) Zhe Liang et al.   DEVELOPMENTAL CELL

Enhancing Hi-C data resolution with deep convolutional neural network HiCPlus

(2018) Yan Zhang et al.   Nature Communications

Adenine Methylation: New Epigenetic Marker of DNA and mRNA

(2018) Zhe Liang et al.   Molecular Plant

Polycomb-mediated gene silencing by the BAH–EMF1 complex in plants

(2018) Zicong Li et al.   NATURE GENETICS

Epigenetic Environmental Memories in Plants: Establishment, Maintenance, and Reprogramming

(2018) Yuehui He et al.   TRENDS IN GENETICS

N6-Methyladenine DNA Methylation in Japonica and Indica Rice Genomes and Its Association with Gene Expression, Plant Development, and Stress Responses

(2018) Qian Zhang et al.   Molecular Plant

A deep learning approach to automate refinement of somatic variant calling from cancer sequencing data

(2018) Benjamin J. Ainscough et al.   NATURE GENETICS

A primer on deep learning in genomics

(2018) James Zou et al.   NATURE GENETICS

Machine learning for epigenetics and future medical applications

(2017) Lawrence B. Holder et al.   Epigenetics

TET-mediated active DNA demethylation: mechanism, function and beyond

(2017) Xiaoji Wu et al.   NATURE REVIEWS GENETICS

Deep learning of the splicing (epi)genetic code reveals a novel candidate mechanism linking histone modifications to ESC fate decision

(2017) Yungang Xu et al.   NUCLEIC ACIDS RESEARCH

Epigenomic Diversity in a Global Collection of Arabidopsis thaliana Accessions

(2016) Taiji Kawakatsu et al.   CELL

N 6 -Methyladenosine RNA Modification Regulates Shoot Stem Cell Fate in Arabidopsis

(2016) Lisha Shen et al.   DEVELOPMENTAL CELL

TensorFlow: Biology’s Gateway to Deep Learning?

(2016) Ladislav Rampasek et al.   Cell Systems

ChIPseeker: an R/Bioconductor package for ChIP peak annotation, comparison and visualization

(2015) Guangchuang Yu et al.   BIOINFORMATICS

Deep learning

(2015) Yann LeCun et al.   NATURE

Photosynthetic Genes and Genes Associated with the C4 Trait in Maize Are Characterized by a Unique Class of Highly Regulated Histone Acetylation Peaks on Upstream Promoters

(2015) Renke Perduns et al.   PLANT PHYSIOLOGY

RNA-directed DNA methylation enforces boundaries between heterochromatin and euchromatin in the maize genome

(2015) Qing Li et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

PcG and trxG in plants – friends or foes

(2015) Li Pu et al.   TRENDS IN GENETICS

Transcriptional Repression by Histone Deacetylases in Plants

(2014) Xuncheng Liu et al.   Molecular Plant

Transcriptome-wide N6-methyladenosine profiling of rice callus and leaf reveals the presence of tissue-specific competitors involved in selective mRNA modification

(2014) Yuli Li et al.   RNA Biology

CD-HIT: accelerated for clustering the next-generation sequencing data

(2012) Limin Fu et al.   BIOINFORMATICS

Differential gene and transcript expression analysis of RNA-seq experiments with TopHat and Cufflinks

(2012) Cole Trapnell et al.   Nature Protocols

Rice ABI5-Like1 Regulates Abscisic Acid and Auxin Responses by Affecting the Expression of ABRE-Containing Genes

(2011) X. Yang et al.   PLANT PHYSIOLOGY

Global Epigenetic and Transcriptional Trends among Two Rice Subspecies and Their Reciprocal Hybrids

(2010) G. He et al.   PLANT CELL

Model-based Analysis of ChIP-Seq (MACS)

(2008) Yong Zhang et al.   GENOME BIOLOGY