Related references
Note: Only part of the references are listed.H3K27me3-rich genomic regions can function as silencers to repress gene expression via chromatin interactions
Yichao Cai et al.
NATURE COMMUNICATIONS (2021)
Enhancing grain-yield-related traits by CRISPR-Cas9 promoter editing of maize CLE genes
Lei Liu et al.
NATURE PLANTS (2021)
Chromatin accessibility profiling methods
Liesbeth Minnoye et al.
NATURE REVIEWS METHODS PRIMERS (2021)
Determinants of enhancer and promoter activities of regulatory elements
Robin Andersson et al.
NATURE REVIEWS GENETICS (2020)
Chromatin interaction analyses elucidate the roles of PRC2-bound silencers in mouse development
Chew Yee Ngan et al.
NATURE GENETICS (2020)
Mechanisms of tissue and cell-type specificity in heritable traits and diseases
Idan Hekselman et al.
NATURE REVIEWS GENETICS (2020)
Genome-wide selection and genetic improvement during modern maize breeding
Baobao Wang et al.
NATURE GENETICS (2020)
Stable unmethylated DNA demarcates expressed genes and their cis-regulatory space in plant genomes
Peter A. Crisp et al.
PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA (2020)
MarchantiaTCP transcription factor activity correlates with three-dimensional chromatin structure
Ezgi Suheyla Karaaslan et al.
NATURE PLANTS (2020)
3D genome architecture coordinates trans and cis regulation of differentially expressed ear and tassel genes in maize
Yonghao Sun et al.
GENOME BIOLOGY (2020)
Defining the developmental program leading to meiosis in maize
Brad Nelms et al.
SCIENCE (2019)
Comprehensive Integration of Single-Cell Data
Tim Stuart et al.
CELL (2019)
Single-Cell Multi-omic Integration Compares and Contrasts Features of Brain Cell Identity
Joshua D. Welch et al.
CELL (2019)
Chromatin interaction maps reveal genetic regulation for quantitative traits in maize
Yong Peng et al.
NATURE COMMUNICATIONS (2019)
Massively parallel single-cell chromatin landscapes of human immune cell development and intratumoral T cell exhaustion
Ansuman T. Satpathy et al.
NATURE BIOTECHNOLOGY (2019)
Fast, sensitive and accurate integration of single-cell data with Harmony
Ilya Korsunsky et al.
NATURE METHODS (2019)
Mobile PEAR transcription factors integrate positional cues to prime cambial growth
Shunsuke Miyashima et al.
NATURE (2019)
Phloem Companion Cell-Specific Transcriptomic and Epigenomic Analyses Identify MRF1, a Regulator of Flowering
Yuan You et al.
PLANT CELL (2019)
OrthoFinder: phylogenetic orthology inference for comparative genomics
David M. Emms et al.
GENOME BIOLOGY (2019)
Widespread long-range cis-regulatory elements in the maize genome
William A. Ricci et al.
NATURE PLANTS (2019)
Normalization and variance stabilization of single-cell RNA-seq data using regularized negative binomial regression
Christoph Hafemeister et al.
GENOME BIOLOGY (2019)
fastp: an ultra-fast all-in-one FASTQ preprocessor
Shifu Chen et al.
BIOINFORMATICS (2018)
Enhanced JBrowse plugins for epigenomics data visualization
Brigitte T. Hofmeister et al.
BMC BIOINFORMATICS (2018)
Recovering Gene Interactions from Single-Cell Data Using Data Diffusion
David van Dijk et al.
CELL (2018)
Genetic determinants of co-accessible chromatin regions in activated T cells across humans
Rachel E. Gate et al.
NATURE GENETICS (2018)
Alignment of single-cell trajectories to compare cellular expression dynamics
Ayelet Alpert et al.
NATURE METHODS (2018)
Proliferation of Regulatory DNA Elements Derived from Transposable Elements in the Maize Genome
Hainan Zhao et al.
PLANT PHYSIOLOGY (2018)
A Single-Cell Atlas of In Vivo Mammalian Chromatin Accessibility
Darren A. Cusanovich et al.
CELL (2018)
Selection Signatures Underlying Dramatic Male Inflorescence Transformation During Modern Hybrid Maize Breeding
Joseph L. Gage et al.
GENETICS (2018)
Cicero Predicts cis-Regulatory DNA Interactions from Single-Cell Chromatin Accessibility Data
Hannah A. Pliner et al.
MOLECULAR CELL (2018)
The chromatin accessibility landscape of primary human cancers
M. Ryan Corces et al.
SCIENCE (2018)
The DNA binding landscape of the maize AUXIN RESPONSE FACTOR family
Mary Galli et al.
NATURE COMMUNICATIONS (2018)
3D Chromatin Architecture of Large Plant Genomes Determined by Local A/B Compartments
Pengfei Dong et al.
MOLECULAR PLANT (2017)
Improved maize reference genome with single-molecule technologies
Yinping Jiao et al.
NATURE (2017)
Cis and trans determinants of epigenetic silencing by Polycomb repressive complex 2 in Arabidopsis
Jun Xiao et al.
NATURE GENETICS (2017)
chromVAR : inferring transcription-factor-associated accessibility from single-cell epigenomic data
Alicia N. Schep et al.
NATURE METHODS (2017)
Towards genome-wide prediction and characterization of enhancers in plants
Alexandre P. Marand et al.
BIOCHIMICA ET BIOPHYSICA ACTA-GENE REGULATORY MECHANISMS (2017)
Engineering Quantitative Trait Variation for Crop Improvement by Genome Editing
Daniel Rodriguez-Leal et al.
CELL (2017)
Prominent topologically associated domains differentiate global chromatin packing in rice from Arabidopsis
Chang Liu et al.
NATURE PLANTS (2017)
Genome-wide mapping of transcriptional enhancer candidates using DNA and chromatin features in maize
Rurika Oka et al.
GENOME BIOLOGY (2017)
Enhancer evolution and the origins of morphological novelty
Mark Rebeiz et al.
CURRENT OPINION IN GENETICS & DEVELOPMENT (2017)
Strigolactone- and Karrikin-Independent SMXL Proteins Are Central Regulators of Phloem Formation
Eva-Sophie Wallner et al.
CURRENT BIOLOGY (2017)
Cistrome and Epicistrome Features Shape the Regulatory DNA Landscape (vol 165, pg 1280, 2016)
Ronan C. O'Malley et al.
CELL (2016)
Genome-wide analysis of chromatin packing in Arabidopsis thaliana at single-gene resolution
Chang Liu et al.
GENOME RESEARCH (2016)
Functionally Similar WRKY Proteins Regulate Vacuolar Acidification in Petunia and Hair Development in Arabidopsis
Walter Verweij et al.
PLANT CELL (2016)
Sucrose Transporter ZmSut1 Expression and Localization Uncover New Insights into Sucrose Phloem Loading
R. Frank Baker et al.
PLANT PHYSIOLOGY (2016)
Enhancer Evolution across 20 Mammalian Species
Diego Villar et al.
CELL (2015)
Prolonged expression of the BX1 signature enzyme is associated with a recombination hotspot in the benzoxazinoid gene cluster in Zea mays
Linlin Zheng et al.
JOURNAL OF EXPERIMENTAL BOTANY (2015)
Single-cell chromatin accessibility reveals principles of regulatory variation
Jason D. Buenostro et al.
NATURE (2015)
Maize SBP-box transcription factors unbranched2 and unbranched3 affect yield traits by regulating the rate of lateral primordia initiation
George S. Chuck et al.
PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA (2014)
Association Mapping across Numerous Traits Reveals Patterns of Functional Variation in Maize
Jason G. Wallace et al.
PLOS GENETICS (2014)
Architecture of the human regulatory network derived from ENCODE data
Mark B. Gerstein et al.
NATURE (2012)
Characterizing Regulatory and Functional Differentiation between Maize Mesophyll and Bundle Sheath Cells by Transcriptomic Analysis
Yao-Ming Chang et al.
PLANT PHYSIOLOGY (2012)
The chromatin insulator CTCF and the emergence of metazoan diversity
Peter Heger et al.
PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA (2012)
MEME-ChIP: motif analysis of large DNA datasets
Philip Machanick et al.
BIOINFORMATICS (2011)
FIMO: scanning for occurrences of a given motif
Charles E. Grant et al.
BIOINFORMATICS (2011)
The INTACT method for cell type-specific gene expression and chromatin profiling in Arabidopsis thaliana
Roger B. Deal et al.
NATURE PROTOCOLS (2011)
edgeR: a Bioconductor package for differential expression analysis of digital gene expression data
Mark D. Robinson et al.
BIOINFORMATICS (2010)
BEDTools: a flexible suite of utilities for comparing genomic features
Aaron R. Quinlan et al.
BIOINFORMATICS (2010)
An Atlas of Combinatorial Transcriptional Regulation in Mouse and Man
Timothy Ravasi et al.
CELL (2010)
VND-INTERACTING2, a NAC Domain Transcription Factor, Negatively Regulates Xylem Vessel Formation in Arabidopsis
Masatoshi Yamaguchi et al.
PLANT CELL (2010)
The maize root stem cell niche: a partnership between two sister cell populations
Keni Jiang et al.
PLANTA (2010)
The Sequence Alignment/Map format and SAMtools
Heng Li et al.
BIOINFORMATICS (2009)
A penalized matrix decomposition, with applications to sparse principal components and canonical correlation analysis
Daniela M. Witten et al.
BIOSTATISTICS (2009)
BLAST plus : architecture and applications
Christiam Camacho et al.
BMC BIOINFORMATICS (2009)
CTCF: Master Weaver of the Genome
Jennifer E. Phillips et al.
CELL (2009)
miR319a targeting of TCP4 is critical for petal growth and development in Arabidopsis
Anwesha Nag et al.
PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA (2009)
The RHA2a-interacting proteins ANAC019 and ANAC055 may play a dual role in regulating ABA response and jasmonate response
Hongling Jiang et al.
PLANT SIGNALING & BEHAVIOR (2009)
Who begets whom? Plant cell fate determination by asymmetric cell division
Colette A. ten Hove et al.
CURRENT OPINION IN PLANT BIOLOGY (2008)
Transcription factor AtTCP14 regulates embryonic growth potential during seed germination in Arabidopsis thaliana
Kiyoshi Tatematsu et al.
PLANT JOURNAL (2008)
Model-based Analysis of ChIP-Seq (MACS)
Yong Zhang et al.
GENOME BIOLOGY (2008)
A high-resolution root spatiotemporal map reveals dominant expression patterns
Siobhan M. Brady et al.
SCIENCE (2007)
Conserved noncoding genomic sequences associated with a flowering-time quantitative trait locus m maize
Silvio Salvi et al.
PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA (2007)
The epidermis both drives and restricts plant shoot growth
Sigal Savaldi-Goldstein et al.
NATURE (2007)
Quantifying similarity between motifs
Shobhit Gupta et al.
GENOME BIOLOGY (2007)
A distant upstream enhancer at the maize domestication gene tb1 has pleiotropic effects on plant and inflorescent architecture
RM Clark et al.
NATURE GENETICS (2006)
A gene expression map of the Arabidopsis root
K Birnbaum et al.
SCIENCE (2003)
Share Paper
