Innovation, conservation, and repurposing of gene function in root cell type development

An importin‐beta‐like protein mediates lignin‐modification‐induced dwarfism in Arabidopsis

(2020) Chinmayee Panda et al.   PLANT JOURNAL

Exodermis and Endodermis Respond to Nutrient Deficiency in Nutrient-Specific and Localized Manner

(2020) Jiří Namyslov et al.   Plants-Basel

Protein Phosphorylation Dynamics Under Carbon/Nitrogen-Nutrient Stress and Identification of a Cell Death-Related Receptor-Like Kinase in Arabidopsis

(2020) Xingwen Li et al.   Frontiers in Plant Science

Comparative transcriptomics of primary cells in vertebrates

(2020) Tanvir Alam et al.   GENOME RESEARCH

Necrotic upper tips1 mimics heat and drought stress and encodes a protoxylem-specific transcription factor in maize

(2020) Zhaobin Dong et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Single-cell RNA sequencing resolves molecular relationships among individual plant cells

(2019) Kook Hui Ryu et al.   PLANT PHYSIOLOGY

Dynamics of gene expression in single root cells of A. thaliana

(2019) Ken Jean-Baptiste et al.   PLANT CELL

Spatiotemporal Developmental Trajectories in the Arabidopsis Root Revealed Using High-Throughput Single-Cell RNA Sequencing

(2019) Tom Denyer et al.   DEVELOPMENTAL CELL

High-Throughput Single-Cell Transcriptome Profiling of Plant Cell Types

(2019) Christine N. Shulse et al.   Cell Reports

Molecular Mechanisms Driving Switch Behavior in Xylem Cell Differentiation

(2019) Gina M. Turco et al.   Cell Reports

Lignin‐based barrier restricts pathogens to the infection site and confers resistance in plants

(2019) Myoung‐Hoon Lee et al.   EMBO JOURNAL

Evolutionary flexibility in flooding response circuitry in angiosperms

(2019) Mauricio A. Reynoso et al.   SCIENCE

Pervasive Correlated Evolution in Gene Expression Shapes Cell and Tissue Type Transcriptomes

(2018) Cong Liang et al.   Genome Biology and Evolution

A Role for MINIYO and QUATRE-QUART2 in the Assembly of RNA Polymerases II, IV, and V in Arabidopsis

(2018) Yaoxi Li et al.   PLANT CELL

A protocol for combining fluorescent proteins with histological stains for diverse cell wall components

(2018) Robertas Ursache et al.   PLANT JOURNAL

A quantitative framework for characterizing the evolutionary history of mammalian gene expression

(2018) Jenny Chen et al.   GENOME RESEARCH

Transcriptional regulation of nitrogen-associated metabolism and growth

(2018) Allison Gaudinier et al.   NATURE

Regulation of Root Angle and Gravitropism

(2018) Ted W. Toal et al.   G3-Genes Genomes Genetics

Dehydration responsive element binding transcription factors and their applications for the engineering of stress tolerance

(2017) Pradeep K. Agarwal et al.   JOURNAL OF EXPERIMENTAL BOTANY

Complex Relationships between Chromatin Accessibility, Sequence Divergence, and Gene Expression in Arabidopsis thaliana

(2017) Cristina M Alexandre et al.   MOLECULAR BIOLOGY AND EVOLUTION

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

Nuclear Transcriptomes at High Resolution Using Retooled INTACT

(2017) Mauricio A. Reynoso et al.   PLANT PHYSIOLOGY

Repression of BLADE-ON-PETIOLE genes by KNOX homeodomain protein BREVIPEDICELLUS is essential for differentiation of secondary xylem in Arabidopsis root

(2017) Natalie Woerlen et al.   PLANTA

Convergent occurrence of the developmental hourglass in plant and animal embryogenesis?

(2016) Andrew G. Cridge et al.   ANNALS OF BOTANY

Adaptation of Root Function by Nutrient-Induced Plasticity of Endodermal Differentiation

(2016) Marie Barberon et al.   CELL

Cistrome and Epicistrome Features Shape the Regulatory DNA Landscape

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

RGF1 INSENSITIVE 1 to 5, a group of LRR receptor-like kinases, are essential for the perception of root meristem growth factor 1 in Arabidopsis thaliana

(2016) Yang Ou et al.   CELL RESEARCH

High-Resolution Expression Map of the Arabidopsis Root Reveals Alternative Splicing and lincRNA Regulation

(2016) Song Li et al.   DEVELOPMENTAL CELL

Near-optimal probabilistic RNA-seq quantification

(2016) Nicolas L Bray et al.   NATURE BIOTECHNOLOGY

Analysis of Ribosome-Associated mRNAs in Rice Reveals the Importance of Transcript Size and GC Content in Translation

(2016) Dongyan Zhao et al.   G3-Genes Genomes Genetics

Immunoprofiling of Rice Root Cortex Reveals Two Cortical Subdomains

(2016) Sophia Henry et al.   Frontiers in Plant Science

Evidence for Active Maintenance of Phylotranscriptomic Hourglass Patterns in Animal and Plant Embryogenesis

(2015) Hajk-Georg Drost et al.   MOLECULAR BIOLOGY AND EVOLUTION

limma powers differential expression analyses for RNA-sequencing and microarray studies

(2015) Matthew E. Ritchie et al.   NUCLEIC ACIDS RESEARCH

FunRich: An open access standalone functional enrichment and interaction network analysis tool

(2015) Mohashin Pathan et al.   PROTEOMICS

BrAD-seq: Breath Adapter Directional sequencing: a streamlined, ultra-simple and fast library preparation protocol for strand specific mRNA library construction

(2015) Brad T. Townsley et al.   Frontiers in Plant Science

The Evolutionary History of R2R3-MYB Proteins Across 50 Eukaryotes: New Insights Into Subfamily Classification and Expansion

(2015) Hai Du et al.   Scientific Reports

Determination and Inference of Eukaryotic Transcription Factor Sequence Specificity

(2014) Matthew T. Weirauch et al.   CELL

The genome of the stress-tolerant wild tomato species Solanum pennellii

(2014) Anthony Bolger et al.   NATURE GENETICS

deepTools: a flexible platform for exploring deep-sequencing data

(2014) Fidel Ramírez et al.   NUCLEIC ACIDS RESEARCH

InParanoid 8: orthology analysis between 273 proteomes, mostly eukaryotic

(2014) Erik L.L. Sonnhammer et al.   NUCLEIC ACIDS RESEARCH

Multiple Classes of Transcription Factors Regulate the Expression of VASCULAR-RELATED NAC-DOMAIN7, a Master Switch of Xylem Vessel Differentiation

(2014) Hitoshi Endo et al.   PLANT AND CELL PHYSIOLOGY

The TRANSPLANTA collection of Arabidopsis lines: a resource for functional analysis of transcription factors based on their conditional overexpression

(2014) Alberto Coego et al.   PLANT JOURNAL

AtMYB41 activates ectopic suberin synthesis and assembly in multiple plant species and cell types

(2014) Dylan K. Kosma et al.   PLANT JOURNAL

Identification of direct targets of transcription factor MYB46 provides insights into the transcriptional regulation of secondary wall biosynthesis

(2014) Won-Chan Kim et al.   PLANT MOLECULAR BIOLOGY

Hairy Root Transformation Using Agrobacterium rhizogenes as a Tool for Exploring Cell Type-Specific Gene Expression and Function Using Tomato as a Model

(2014) M. Ron et al.   PLANT PHYSIOLOGY

Non-Cell-Autonomous Regulation of Root Hair Patterning Genes by WRKY75 in Arabidopsis

(2014) L. Rishmawi et al.   PLANT PHYSIOLOGY

Beyond the Barrier: Communication in the Root through the Endodermis

(2014) N. E. Robbins et al.   PLANT PHYSIOLOGY

The Origin and Early Evolution of Roots

(2014) P. Kenrick et al.   PLANT PHYSIOLOGY

Mapping and Dynamics of Regulatory DNA and Transcription Factor Networks in A. thaliana

(2014) Alessandra M. Sullivan et al.   Cell Reports

voom: precision weights unlock linear model analysis tools for RNA-seq read counts

(2014) Charity W Law et al.   GENOME BIOLOGY

MAFFT Multiple Sequence Alignment Software Version 7: Improvements in Performance and Usability

(2013) K. Katoh et al.   MOLECULAR BIOLOGY AND EVOLUTION

Identification of Novel Loci Regulating Interspecific Variation in Root Morphology and Cellular Development in Tomato

(2013) M. Ron et al.   PLANT PHYSIOLOGY

Arabidopsis NIN-like transcription factors have a central role in nitrate signalling

(2013) Mineko Konishi et al.   Nature Communications

BEDOPS: high-performance genomic feature operations

(2012) Shane Neph et al.   BIOINFORMATICS

A comprehensive evaluation of normalization methods for Illumina high-throughput RNA sequencing data analysis

(2012) M.-A. Dillies et al.   BRIEFINGS IN BIOINFORMATICS

Assessing the function of the plant nuclear pore complex and the search for specificity

(2012) Geraint Parry   JOURNAL OF EXPERIMENTAL BOTANY

A transcriptomic hourglass in plant embryogenesis

(2012) Marcel Quint et al.   NATURE

The tomato genome sequence provides insights into fleshy fruit evolution

(2012)   NATURE

Fast gapped-read alignment with Bowtie 2

(2012) Ben Langmead et al.   NATURE METHODS

Primer3—new capabilities and interfaces

(2012) Andreas Untergasser et al.   NUCLEIC ACIDS RESEARCH

BAR expressolog identification: expression profile similarity ranking of homologous genes in plant species

(2012) Rohan V. Patel et al.   PLANT JOURNAL

Length Bias Correction in Gene Ontology Enrichment Analysis Using Logistic Regression

(2012) Gu Mi et al.   PLoS One

Measurement of mRNA abundance using RNA-seq data: RPKM measure is inconsistent among samples

(2012) Günter P. Wagner et al.   THEORY IN BIOSCIENCES

The Choice between MapMan and Gene Ontology for Automated Gene Function Prediction in Plant Science

(2012) Sebastian Klie et al.   Frontiers in Genetics

False positive peaks in ChIP-seq and other sequencing-based functional assays caused by unannotated high copy number regions

(2011) Joseph K. Pickrell et al.   BIOINFORMATICS

Non-cell-autonomous microRNA165 acts in a dose-dependent manner to regulate multiple differentiation status in the Arabidopsis root

(2011) S. Miyashima et al.   DEVELOPMENT

Cell Identity Regulators Link Development and Stress Responses in the Arabidopsis Root

(2011) Anjali S. Iyer-Pascuzzi et al.   DEVELOPMENTAL CELL

A NAC domain protein family contributing to the regulation of wood formation in poplar

(2011) Misato Ohtani et al.   PLANT JOURNAL

RSS1 regulates the cell cycle and maintains meristematic activity under stress conditions in rice

(2011) Daisuke Ogawa et al.   Nature Communications

BEDTools: a flexible suite of utilities for comparing genomic features

(2010) Aaron R. Quinlan et al.   BIOINFORMATICS

Motif Enrichment Analysis: a unified framework and an evaluation on ChIP data

(2010) Robert C McLeay et al.   BMC BIOINFORMATICS

A Simple Method for Gene Expression and Chromatin Profiling of Individual Cell Types within a Tissue

(2010) Roger B. Deal et al.   DEVELOPMENTAL CELL

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

Cell signalling by microRNA165/6 directs gene dose-dependent root cell fate

(2010) Annelie Carlsbecker et al.   NATURE

The Populus Class III HD ZIP, popREVOLUTA, Influences Cambium Initiation and Patterning of Woody Stems

(2010) M. Robischon et al.   PLANT PHYSIOLOGY

FastTree 2 – Approximately Maximum-Likelihood Trees for Large Alignments

(2010) Morgan N. Price et al.   PLoS One

Gene ontology analysis for RNA-seq: accounting for selection bias

(2010) Matthew D Young et al.   GENOME BIOLOGY

trimAl: a tool for automated alignment trimming in large-scale phylogenetic analyses

(2009) S. Capella-Gutierrez et al.   BIOINFORMATICS

The Sequence Alignment/Map format and SAMtools

(2009) H. Li et al.   BIOINFORMATICS

Fast and accurate short read alignment with Burrows-Wheeler transform

(2009) H. Li et al.   BIOINFORMATICS

Circos: An information aesthetic for comparative genomics

(2009) M. Krzywinski et al.   GENOME RESEARCH

Mapping identifiers for the integration of genomic datasets with the R/Bioconductor package biomaRt

(2009) Steffen Durinck et al.   Nature Protocols

Profiling translatomes of discrete cell populations resolves altered cellular priorities during hypoxia in Arabidopsis

(2009) A. Mustroph et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Root Suberin Forms an Extracellular Barrier That Affects Water Relations and Mineral Nutrition in Arabidopsis

(2009) Ivan Baxter et al.   PLoS Genetics

WGCNA: an R package for weighted correlation network analysis

(2008) Peter Langfelder et al.   BMC BIOINFORMATICS

Microevolutionary support for a developmental hourglass: gene expression patterns shape sequence variation and divergence inDrosophila

(2008) Tami Cruickshank et al.   EVOLUTION & DEVELOPMENT

VASCULAR-RELATED NAC-DOMAIN7 is involved in the differentiation of all types of xylem vessels in Arabidopsis roots and shoots

(2008) Masatoshi Yamaguchi et al.   PLANT JOURNAL

Cell-specific nitrogen responses mediate developmental plasticity

(2008) M. L. Gifford et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Cell Identity Mediates the Response of Arabidopsis Roots to Abiotic Stress

(2008) J. R. Dinneny et al.   SCIENCE

Control of Jasmonate Biosynthesis and Senescence by miR319 Targets

(2008) Carla Schommer et al.   PLOS BIOLOGY