CharPlant: A De Novo Open Chromatin Region Prediction Tool for Plant Genomes

Chromatin accessibility and the regulatory epigenome

(2019) Sandy L. Klemm et al.   NATURE REVIEWS GENETICS

Selene: a PyTorch-based deep learning library for sequence data

(2019) Kathleen M. Chen et al.   NATURE METHODS

FOXA 2 controls the cis ‐regulatory networks of pancreatic cancer cells in a differentiation grade‐specific manner

(2019) Marta Milan et al.   EMBO JOURNAL

Chromatin-informed inference of transcriptional programs in gynecologic and basal breast cancers

(2019) Hatice U. Osmanbeyoglu et al.   Nature Communications

Tet inactivation disrupts YY1 binding and long-range chromatin interactions during embryonic heart development

(2019) Shaohai Fang et al.   Nature Communications

Chromatin Accessibility Landscape in Human Early Embryos and Its Association with Evolution

(2018) Lei Gao et al.   CELL

Recent Trends in Deep Learning Based Natural Language Processing [Review Article]

(2018) Tom Young et al.   IEEE Computational Intelligence Magazine

The cis-regulatory dynamics of embryonic development at single-cell resolution

(2018) Darren A. Cusanovich et al.   NATURE

PCSD: a plant chromatin state database

(2017) Yue Liu et al.   NUCLEIC ACIDS RESEARCH

Profiling of Accessible Chromatin Regions across Multiple Plant Species and Cell Types Reveals Common Gene Regulatory Principles and New Control Modules

(2017) Kelsey A. Maher et al.   PLANT CELL

Nfib Promotes Metastasis through a Widespread Increase in Chromatin Accessibility

(2016) Sarah K. Denny et al.   CELL

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

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

Combining ATAC-seq with nuclei sorting for discovery of cis-regulatory regions in plant genomes

(2016) Zefu Lu et al.   NUCLEIC ACIDS RESEARCH

The epigenetic landscape of T cell exhaustion

(2016) D. R. Sen et al.   SCIENCE

Single-cell chromatin accessibility reveals principles of regulatory variation

(2015) Jason D. Buenrostro et al.   NATURE

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

PlantDHS: a database for DNase I hypersensitive sites in plants

(2015) Tao Zhang et al.   NUCLEIC ACIDS RESEARCH

Meiotic Chromosome Structure and Function in Plants

(2014) Samantha Mainiero et al.   CYTOGENETIC AND GENOME RESEARCH

DNase Footprint Signatures Are Dictated by Factor Dynamics and DNA Sequence

(2014) Myong-Hee Sung et al.   MOLECULAR CELL

Chromatin accessibility: a window into the genome

(2014) Maria Tsompana et al.   Epigenetics & Chromatin

Representation Learning: A Review and New Perspectives

(2013) Y. Bengio et al.   IEEE TRANSACTIONS ON PATTERN ANALYSIS AND MACHINE INTELLIGENCE

Refined DNase-seq protocol and data analysis reveals intrinsic bias in transcription factor footprint identification

(2013) Housheng Hansen He et al.   NATURE METHODS

Dynamic regulation of transcriptional states by chromatin and transcription factors

(2013) Ty C. Voss et al.   NATURE REVIEWS GENETICS

JASPAR 2014: an extensively expanded and updated open-access database of transcription factor binding profiles

(2013) Anthony Mathelier et al.   NUCLEIC ACIDS RESEARCH

Snakemake--a scalable bioinformatics workflow engine

(2012) J. Koster et al.   BIOINFORMATICS

The accessible chromatin landscape of the human genome

(2012) Robert E. Thurman et al.   NATURE

Perceiving the epigenetic landscape through histone readers

(2012) Catherine A Musselman et al.   NATURE STRUCTURAL & MOLECULAR BIOLOGY

Genome-Wide Identification of Regulatory DNA Elements and Protein-Binding Footprints Using Signatures of Open Chromatin in Arabidopsis

(2012) W. Zhang et al.   PLANT CELL

High-resolution mapping of open chromatin in the rice genome

(2011) W. Zhang et al.   GENOME RESEARCH

MEME SUITE: tools for motif discovery and searching

(2009) T. L. Bailey et al.   NUCLEIC ACIDS RESEARCH

Model-based Analysis of ChIP-Seq (MACS)

(2008) Yong Zhang et al.   GENOME BIOLOGY