Chromatin and regulatory differentiation between bundle sheath and mesophyll cells in maize

Single-cell RNA sequencing of developing maize ears facilitates functional analysis and trait candidate gene discovery

(2021) Xiaosa Xu et al.   DEVELOPMENTAL CELL

Twelve years of SAMtools and BCFtools

(2021) Petr Danecek et al.   GigaScience

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

(2021) Alexandre P. Marand et al.   CELL

ZmOrphan94 Transcription Factor Downregulates ZmPEPC1 Gene Expression in Maize Bundle Sheath Cells

(2021) Alicja M. Górska et al.   Frontiers in Plant Science

Genome-wide Characterization of DNase I-hypersensitive Sites and Cold Response Regulatory Landscapes in Grasses

(2020) Jinlei Han et al.   PLANT CELL

Installation of C 4 photosynthetic pathway enzymes in rice using a single construct

(2020) Maria Ermakova et al.   PLANT BIOTECHNOLOGY JOURNAL

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

Reconstructing the maize leaf regulatory network using ChIP-seq data of 104 transcription factors

(2020) Xiaoyu Tu et al.   Nature Communications

ATAC-seq footprinting unravels kinetics of transcription factor binding during zygotic genome activation

(2020) Mette Bentsen et al.   Nature Communications

MapMan4: a refined protein classification and annotation framework applicable to multi-omics data analysis

(2019) Rainer Schwacke et al.   Molecular Plant

Tissue‐specific Hi‐C analyses of rice, foxtail millet and maize suggest non‐canonical function of plant chromatin domains

(2019) Pengfei Dong et al.   Journal of Integrative Plant Biology

Genome-Wide Transcription Factor Binding in Leaves from C3 and C4 Grasses

(2019) Steven J. Burgess et al.   PLANT CELL

3D extruded composite thermoelectric threads for flexible energy harvesting

(2019) J. Peng et al.   Nature Communications

Identification of cis -regulatory elements by chromatin structure

(2018) Zefu Lu et al.   CURRENT OPINION IN PLANT BIOLOGY

Synergistic Binding of bHLH Transcription Factors to the Promoter of the Maize NADP-ME Gene Used in C4 Photosynthesis Is Based on an Ancient Code Found in the Ancestral C3 State

(2018) Ana Rita Borba et al.   MOLECULAR BIOLOGY AND EVOLUTION

Ancient duons may underpin spatial patterning of gene expression in C4leaves

(2018) Ivan Reyna-Llorens et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Understanding the Genetic Basis of C4 Kranz Anatomy with a View to Engineering C3 Crops

(2018) Olga V. Sedelnikova et al.   Annual Review of Genetics

Getting closer: vein density in C4 leaves

(2018) Dhinesh Kumar et al.   NEW PHYTOLOGIST

WRKY transcription factors in plant responses to stresses

(2017) Jingjing Jiang et al.   Journal of Integrative Plant Biology

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

Differential methylation analysis for BS-seq data under general experimental design

(2016) Yongseok Park et al.   BIOINFORMATICS

Cistrome and Epicistrome Features Shape the Regulatory DNA Landscape

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

Regulatory gateways for cell-specific gene expression in C4leaves with Kranz anatomy

(2016) Gregory Reeves et al.   JOURNAL OF EXPERIMENTAL BOTANY

A MEM1-like motif directs mesophyll cell-specific expression of the gene encoding the C4carbonic anhydrase inFlaveria

(2016) Udo Gowik et al.   JOURNAL OF EXPERIMENTAL BOTANY

deepTools2: a next generation web server for deep-sequencing data analysis

(2016) Fidel Ramírez et al.   NUCLEIC ACIDS RESEARCH

An Untranslated cis -Element Regulates the Accumulation of Multiple C 4 Enzymes in Gynandropsis gynandra Mesophyll Cells

(2016) Ben P. Williams et al.   PLANT CELL

Engineering C4photosynthesis into C3chassis in the synthetic biology age

(2016) Mara L. Schuler et al.   PLANT JOURNAL

Open chromatin reveals the functional maize genome

(2016) Eli Rodgers-Melnick et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Lessons from Domestication: Targeting Cis -Regulatory Elements for Crop Improvement

(2016) Gwen Swinnen et al.   TRENDS IN PLANT SCIENCE

The MEME Suite

(2015) Timothy L. Bailey et al.   NUCLEIC ACIDS RESEARCH

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

HTSeq--a Python framework to work with high-throughput sequencing data

(2014) S. Anders et al.   BIOINFORMATICS

Trimmomatic: a flexible trimmer for Illumina sequence data

(2014) Anthony M. Bolger et al.   BIOINFORMATICS

Determination and Inference of Eukaryotic Transcription Factor Sequence Specificity

(2014) Matthew T. Weirauch et al.   CELL

Developmental dynamics of Kranz cell transcriptional specificity in maize leaf reveals early onset of C4-related processes

(2014) S. Lori Tausta et al.   JOURNAL OF EXPERIMENTAL BOTANY

Deconstructing Kranz anatomy to understand C4 evolution

(2014) Marjorie R. Lundgren et al.   JOURNAL OF EXPERIMENTAL BOTANY

From proto-Kranz to C4 Kranz: building the bridge to C4 photosynthesis

(2014) Rowan F. Sage et al.   JOURNAL OF EXPERIMENTAL BOTANY

Comparative analyses of C4 and C3 photosynthesis in developing leaves of maize and rice

(2014) Lin Wang et al.   NATURE BIOTECHNOLOGY

Epigenetic regulation of gene responsiveness in Arabidopsis

(2014) Taiko K. To et al.   Frontiers in Plant Science

bZIPs and WRKYs: two large transcription factor families executing two different functional strategies

(2014) Carles M. Llorca et al.   Frontiers in Plant Science

Photorespiration and the Evolution of C4Photosynthesis

(2012) Rowan F. Sage et al.   Annual Review of Plant Biology

Integrative Genomics Viewer (IGV): high-performance genomics data visualization and exploration

(2012) H. Thorvaldsdottir et al.   BRIEFINGS IN BIOINFORMATICS

Engineering C4 photosynthetic regulatory networks

(2012) Sarit Weissmann et al.   CURRENT OPINION IN BIOTECHNOLOGY

Fast gapped-read alignment with Bowtie 2

(2012) Ben Langmead et al.   NATURE METHODS

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

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

methylKit: a comprehensive R package for the analysis of genome-wide DNA methylation profiles

(2012) Altuna Akalin et al.   GENOME BIOLOGY

Bismark: a flexible aligner and methylation caller for Bisulfite-Seq applications

(2011) Felix Krueger et al.   BIOINFORMATICS

Exploiting the engine of C4 photosynthesis

(2011) R. F. Sage et al.   JOURNAL OF EXPERIMENTAL BOTANY

The role of proteins in C3 plants prior to their recruitment into the C4 pathway

(2011) Sylvain Aubry et al.   JOURNAL OF EXPERIMENTAL BOTANY

Identification of a functional transposon insertion in the maize domestication gene tb1

(2011) Anthony Studer et al.   NATURE GENETICS

Independent and Parallel Recruitment of Preexisting Mechanisms Underlying C4 Photosynthesis

(2011) N. J. Brown et al.   SCIENCE

The Regulation of Gene Expression Required for C4Photosynthesis

(2010) Julian M. Hibberd et al.   Annual Review of Plant Biology

BEDTools: a flexible suite of utilities for comparing genomic features

(2010) Aaron R. Quinlan et al.   BIOINFORMATICS

Simple Combinations of Lineage-Determining Transcription Factors Prime cis-Regulatory Elements Required for Macrophage and B Cell Identities

(2010) Sven Heinz et al.   MOLECULAR CELL

Transcript assembly and quantification by RNA-Seq reveals unannotated transcripts and isoform switching during cell differentiation

(2010) Cole Trapnell et al.   NATURE BIOTECHNOLOGY

The developmental dynamics of the maize leaf transcriptome

(2010) Pinghua Li et al.   NATURE GENETICS

Histone H3K27ac separates active from poised enhancers and predicts developmental state

(2010) M. P. Creyghton et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Genome-Wide and Organ-Specific Landscapes of Epigenetic Modifications and Their Relationships to mRNA and Small RNA Transcriptomes in Maize

(2009) X. Wang et al.   PLANT CELL

What is the maximum efficiency with which photosynthesis can convert solar energy into biomass?

(2008) Xin-Guang Zhu et al.   CURRENT OPINION IN BIOTECHNOLOGY

Model-based Analysis of ChIP-Seq (MACS)

(2008) Yong Zhang et al.   GENOME BIOLOGY