A cis-regulatory atlas in maize at single-cell resolution

H3K27me3-rich genomic regions can function as silencers to repress gene expression via chromatin interactions

(2021) Yichao Cai et al.   Nature Communications

Chromatin interaction analyses elucidate the roles of PRC2-bound silencers in mouse development

(2020) Chew Yee Ngan et al.   NATURE GENETICS

Mechanisms of tissue and cell-type specificity in heritable traits and diseases

(2020) Idan Hekselman et al.   NATURE REVIEWS GENETICS

Genome-wide selection and genetic improvement during modern maize breeding

(2020) Baobao Wang et al.   NATURE GENETICS

Stable unmethylated DNA demarcates expressed genes and their cis-regulatory space in plant genomes

(2020) Peter A. Crisp et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Mobile PEAR transcription factors integrate positional cues to prime cambial growth

(2019) Shunsuke Miyashima et al.   NATURE

Phloem companion cell-specific transcriptomic and epigenomic analyses identify MRF1, a novel regulator of flowering

(2019) Yuan You et al.   PLANT CELL

Defining the developmental program leading to meiosis in maize

(2019) Brad Nelms et al.   SCIENCE

Comprehensive Integration of Single-Cell Data

(2019) Tim Stuart et al.   CELL

Single-Cell Multi-omic Integration Compares and Contrasts Features of Brain Cell Identity

(2019) Joshua D. Welch et al.   CELL

Chromatin interaction maps reveal genetic regulation for quantitative traits in maize

(2019) Yong Peng et al.   Nature Communications

Massively parallel single-cell chromatin landscapes of human immune cell development and intratumoral T cell exhaustion

(2019) Ansuman T. Satpathy et al.   NATURE BIOTECHNOLOGY

Fast, sensitive and accurate integration of single-cell data with Harmony

(2019) Ilya Korsunsky et al.   NATURE METHODS

Determinants of enhancer and promoter activities of regulatory elements

(2019) Robin Andersson et al.   NATURE REVIEWS GENETICS

OUP accepted manuscript

(2018)   BIOINFORMATICS

Enhanced JBrowse plugins for epigenomics data visualization

(2018) Brigitte T. Hofmeister et al.   BMC BIOINFORMATICS

Recovering Gene Interactions from Single-Cell Data Using Data Diffusion

(2018) David van Dijk et al.   CELL

Genetic determinants of co-accessible chromatin regions in activated T cells across humans

(2018) Rachel E. Gate et al.   NATURE GENETICS

Alignment of single-cell trajectories to compare cellular expression dynamics

(2018) Ayelet Alpert et al.   NATURE METHODS

Proliferation of Regulatory DNA Elements Derived from Transposable Elements in the Maize Genome

(2018) Hainan Zhao et al.   PLANT PHYSIOLOGY

A Single-Cell Atlas of In Vivo Mammalian Chromatin Accessibility

(2018) Darren A. Cusanovich et al.   CELL

Selection Signatures Underlying Dramatic Male Inflorescence Transformation During Modern Hybrid Maize Breeding

(2018) Joseph L. Gage et al.   GENETICS

Cicero Predicts cis-Regulatory DNA Interactions from Single-Cell Chromatin Accessibility Data

(2018) Hannah A. Pliner et al.   MOLECULAR CELL

The chromatin accessibility landscape of primary human cancers

(2018) M. Ryan Corces et al.   SCIENCE

The DNA binding landscape of the maize AUXIN RESPONSE FACTOR family

(2018) Mary Galli et al.   Nature Communications

3D Chromatin Architecture of Large Plant Genomes Determined by Local A/B Compartments

(2017) Pengfei Dong et al.   Molecular Plant

Improved maize reference genome with single-molecule technologies

(2017) Yinping Jiao et al.   NATURE

Cis and trans determinants of epigenetic silencing by Polycomb repressive complex 2 in Arabidopsis

(2017) Jun Xiao et al.   NATURE GENETICS

chromVAR: inferring transcription-factor-associated accessibility from single-cell epigenomic data

(2017) Alicia N Schep et al.   NATURE METHODS

Cistrome and Epicistrome Features Shape the Regulatory DNA Landscape

(2016) Ronan C. O’Malley et al.   CELL

Genome-wide analysis of chromatin packing inArabidopsis thalianaat single-gene resolution

(2016) Chang Liu et al.   GENOME RESEARCH

Functionally Similar WRKY Proteins Regulate Vacuolar Acidification in Petunia and Hair Development in Arabidopsis

(2016) Walter Verweij et al.   PLANT CELL

Sucrose Transporter ZmSut1 Expression and Localization Uncover New Insights into Sucrose Phloem Loading

(2016) R. Frank Baker et al.   PLANT PHYSIOLOGY

Enhancer Evolution across 20 Mammalian Species

(2015) Diego Villar et al.   CELL

Prolonged expression of the BX1 signature enzyme is associated with a recombination hotspot in the benzoxazinoid gene cluster in Zea mays

(2015) Linlin Zheng et al.   JOURNAL OF EXPERIMENTAL BOTANY

Single-cell chromatin accessibility reveals principles of regulatory variation

(2015) Jason D. Buenrostro et al.   NATURE

MaizeSBP-boxtranscription factorsunbranched2andunbranched3affect yield traits by regulating the rate of lateral primordia initiation

(2014) George S. Chuck et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Association Mapping across Numerous Traits Reveals Patterns of Functional Variation in Maize

(2014) Jason G. Wallace et al.   PLoS Genetics

Architecture of the human regulatory network derived from ENCODE data

(2012) Mark B. Gerstein et al.   NATURE

Characterizing Regulatory and Functional Differentiation between Maize Mesophyll and Bundle Sheath Cells by Transcriptomic Analysis

(2012) Y.-M. Chang et al.   PLANT PHYSIOLOGY

The chromatin insulator CTCF and the emergence of metazoan diversity

(2012) P. Heger et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

MEME-ChIP: motif analysis of large DNA datasets

(2011) Philip Machanick et al.   BIOINFORMATICS

FIMO: scanning for occurrences of a given motif

(2011) Charles E. Grant et al.   BIOINFORMATICS

BEDTools: a flexible suite of utilities for comparing genomic features

(2010) Aaron R. Quinlan et al.   BIOINFORMATICS

An Atlas of Combinatorial Transcriptional Regulation in Mouse and Man

(2010) Timothy Ravasi et al.   CELL

The INTACT method for cell type–specific gene expression and chromatin profiling in Arabidopsis thaliana

(2010) Roger B Deal et al.   Nature Protocols

VND-INTERACTING2, a NAC Domain Transcription Factor, Negatively Regulates Xylem Vessel Formation inArabidopsis

(2010) Masatoshi Yamaguchi et al.   PLANT CELL

The Sequence Alignment/Map format and SAMtools

(2009) H. Li et al.   BIOINFORMATICS

edgeR: a Bioconductor package for differential expression analysis of digital gene expression data

(2009) M. D. Robinson et al.   BIOINFORMATICS

A penalized matrix decomposition, with applications to sparse principal components and canonical correlation analysis

(2009) D. M. Witten et al.   BIOSTATISTICS

BLAST+: architecture and applications

(2009) Christiam Camacho et al.   BMC BIOINFORMATICS

CTCF: Master Weaver of the Genome

(2009) Jennifer E. Phillips et al.   CELL

The maize root stem cell niche: a partnership between two sister cell populations

(2009) Keni Jiang et al.   PLANTA

miR319a targeting ofTCP4is critical for petal growth and development inArabidopsis

(2009) Anwesha Nag et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Who begets whom? Plant cell fate determination by asymmetric cell division

(2008) Colette A ten Hove et al.   CURRENT OPINION IN PLANT BIOLOGY

Model-based Analysis of ChIP-Seq (MACS)

(2008) Yong Zhang et al.   GENOME BIOLOGY

Transcription factor AtTCP14 regulates embryonic growth potential during seed germination inArabidopsis thaliana

(2007) Kiyoshi Tatematsu et al.   PLANT JOURNAL