Deep learning for DNase I hypersensitive sites identification

Exploring the relationship between intron retention and chromatin accessibility in plants

(2018) Fahad Ullah et al.   BMC GENOMICS

ProLanGO: Protein Function Prediction Using Neural Machine Translation Based on a Recurrent Neural Network

(2017) Renzhi Cao et al.   MOLECULES

Genome-wide mapping of DNase I hypersensitive sites in rare cell populations using single-cell DNase sequencing

(2017) James Cooper et al.   Nature Protocols

Genome-wide prediction of DNase I hypersensitivity using gene expression

(2017) Weiqiang Zhou et al.   Nature Communications

DeepNano: Deep recurrent neural networks for base calling in MinION nanopore reads

(2017) Vladimír Boža et al.   PLoS One

Basset: learning the regulatory code of the accessible genome with deep convolutional neural networks

(2016) David R. Kelley et al.   GENOME RESEARCH

DanQ: a hybrid convolutional and recurrent deep neural network for quantifying the function of DNA sequences

(2016) Daniel Quang et al.   NUCLEIC ACIDS RESEARCH

Spatial Pyramid Pooling in Deep Convolutional Networks for Visual Recognition

(2015) Kaiming He et al.   IEEE TRANSACTIONS ON PATTERN ANALYSIS AND MACHINE INTELLIGENCE

Deep learning

(2015) Yann LeCun et al.   NATURE

Predicting the sequence specificities of DNA- and RNA-binding proteins by deep learning

(2015) Babak Alipanahi et al.   NATURE BIOTECHNOLOGY

A method to predict the impact of regulatory variants from DNA sequence

(2015) Dongwon Lee et al.   NATURE GENETICS

PlantDHS: a database for DNase I hypersensitive sites in plants

(2015) Tao Zhang et al.   NUCLEIC ACIDS RESEARCH

A deep learning framework for modeling structural features of RNA-binding protein targets

(2015) Sai Zhang et al.   NUCLEIC ACIDS RESEARCH

Predicting pupylation sites in prokaryotic proteins using pseudo-amino acid composition and extreme learning machine

(2013) Yong-Xian Fan et al.   NEUROCOMPUTING

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

(2012) Limin Fu et al.   BIOINFORMATICS

The accessible chromatin landscape of the human genome

(2012) Robert E. Thurman et al.   NATURE

ARTADE2DB: Improved Statistical Inferences for Arabidopsis Gene Functions and Structure Predictions by Dynamic Structure-Based Dynamic Expression (DSDE) Analyses

(2011) Kei Iida et al.   PLANT AND CELL PHYSIOLOGY

Genome-wide analysis of endogenous abscisic acid-mediated transcription in dry and imbibed seeds of Arabidopsis using tiling arrays

(2010) Masanori Okamoto et al.   PLANT JOURNAL

Genome-wide profiling of histone H3 lysine 9 acetylation and dimethylation in Arabidopsis reveals correlation between multiple histone marks and gene expression

(2010) Junli Zhou et al.   PLANT MOLECULAR BIOLOGY

Genome-wide analysis of mono-, di- and trimethylation of histone H3 lysine 4 in Arabidopsis thaliana

(2009) Xiaoyu Zhang et al.   GENOME BIOLOGY

High-Resolution Mapping and Characterization of Open Chromatin across the Genome

(2008) Alan P. Boyle et al.   CELL

Histone H2A.Z and DNA methylation are mutually antagonistic chromatin marks

(2008) Daniel Zilberman et al.   NATURE