The analysis of Gene Regulatory Networks in plant evo-devo

Genome-wide identification of the Phaseolus vulgaris sRNAome using small RNA and degradome sequencing

(2015) Damien Formey et al.   BMC GENOMICS

Genome-wide histone acetylation correlates with active transcription in maize

(2015) Wei Zhang et al.   GENOMICS

Evolution of DNA-Binding Sites of a Floral Master Regulatory Transcription Factor

(2015) Jose M. Muiño et al.   MOLECULAR BIOLOGY AND EVOLUTION

The expanding world of small RNAs in plants

(2015) Filipe Borges et al.   NATURE REVIEWS MOLECULAR CELL BIOLOGY

RSAT 2015: Regulatory Sequence Analysis Tools

(2015) Alejandra Medina-Rivera et al.   NUCLEIC ACIDS RESEARCH

JASPAR 2016: a major expansion and update of the open-access database of transcription factor binding profiles

(2015) Anthony Mathelier et al.   NUCLEIC ACIDS RESEARCH

The early evolution of land plants, from fossils to genomics: a commentary on Lang (1937) ‘On the plant-remains from the Downtonian of England and Wales'

(2015) Dianne Edwards et al.   PHILOSOPHICAL TRANSACTIONS OF THE ROYAL SOCIETY B-BIOLOGICAL SCIENCES

MORPHEUS, a Webtool for Transcription Factor Binding Analysis Using Position Weight Matrices with Dependency

(2015) Eugenio Gómez Minguet et al.   PLoS One

Analysis of Histones H3 and H4 Reveals Novel and Conserved Post-Translational Modifications in Sugarcane

(2015) Izabel Moraes et al.   PLoS One

Importance of Mediator complex in the regulation and integration of diverse signaling pathways in plants

(2015) Subhasis Samanta et al.   Frontiers in Plant Science

An integrative analysis of post-translational histone modifications in the marine diatom Phaeodactylum tricornutum

(2015) Alaguraj Veluchamy et al.   GENOME BIOLOGY

Evolution of DNA Specificity in a Transcription Factor Family Produced a New Gene Regulatory Module

(2014) Alesia N. McKeown et al.   CELL

Structural Basis for DNA Binding Specificity by the Auxin-Dependent ARF Transcription Factors

(2014) D. Roeland Boer et al.   CELL

Gene activation and cell fate control in plants: a chromatin perspective

(2014) Julia Engelhorn et al.   CELLULAR AND MOLECULAR LIFE SCIENCES

Transcriptomics of developing embryos and organs: A raising tool for evo-devo

(2014) Sophie Pantalacci et al.   JOURNAL OF EXPERIMENTAL ZOOLOGY PART B-MOLECULAR AND DEVELOPMENTAL EVOLUTION

Toward More Accurate Ancestral Protein Genotype–Phenotype Reconstructions with the Use of Species Tree-Aware Gene Trees

(2014) Mathieu Groussin et al.   MOLECULAR BIOLOGY AND EVOLUTION

A comparative encyclopedia of DNA elements in the mouse genome

(2014) Feng Yue et al.   NATURE

Historical contingency and its biophysical basis in glucocorticoid receptor evolution

(2014) Michael J. Harms et al.   NATURE

Spatially resolved transcriptomics and beyond

(2014) Nicola Crosetto et al.   NATURE REVIEWS GENETICS

Cardamine hirsuta: a versatile genetic system for comparative studies

(2014) Angela S. Hay et al.   PLANT JOURNAL

Strepsiptera, Phylogenomics and the Long Branch Attraction Problem

(2014) Bastien Boussau et al.   PLoS One

Phylotranscriptomic analysis of the origin and early diversification of land plants

(2014) Norman J. Wickett et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Hit-and-run transcriptional control by bZIP1 mediates rapid nutrient signaling in Arabidopsis

(2014) A. Para et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

DNA-binding specificities of plant transcription factors and their potential to define target genes

(2014) José M. Franco-Zorrilla et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

The new frontier of genome engineering with CRISPR-Cas9

(2014) J. A. Doudna et al.   SCIENCE

Evolutionary history of plant microRNAs

(2014) Richard S. Taylor et al.   TRENDS IN PLANT SCIENCE

Evolution of DNA Methylation Patterns in the Brassicaceae is Driven by Differences in Genome Organization

(2014) Danelle K. Seymour et al.   PLoS Genetics

Data access for the 1,000 Plants (1KP) project

(2014) Naim Matasci et al.   GigaScience

TPMS: a set of utilities for querying collections of gene trees

(2013) Thomas Bigot et al.   BMC BIOINFORMATICS

DNA-Binding Specificities of Human Transcription Factors

(2013) Arttu Jolma et al.   CELL

A step-by-step protocol for formaldehyde-assisted isolation of regulatory elements fromArabidopsis thaliana

(2013) Mohammad Amin Omidbakhshfard et al.   Journal of Integrative Plant Biology

Genome-Wide Analysis of Histone Modifications: H3K4me2, H3K4me3, H3K9ac, and H3K27ac in Oryza sativa L. Japonica

(2013) Zhou Du et al.   Molecular Plant

RNA interference in the nucleus: roles for small RNAs in transcription, epigenetics and beyond

(2013) Stephane E. Castel et al.   NATURE REVIEWS GENETICS

Lessons on RNA Silencing Mechanisms in Plants from Eukaryotic Argonaute Structures

(2013) Christian Poulsen et al.   PLANT CELL

The Next Generation of Transcription Factor Binding Site Prediction

(2013) Anthony Mathelier et al.   PLoS Computational Biology

Dynamics and Adaptive Benefits of Protein Domain Emergence and Arrangements during Plant Genome Evolution

(2012) Anna R. Kersting et al.   Genome Biology and Evolution

An integrated encyclopedia of DNA elements in the human genome

(2012)   NATURE

A Light-Regulated Genetic Module Was Recruited to Carpel Development in Arabidopsis following a Structural Change to SPATULA

(2012) M. C. Reymond et al.   PLANT CELL

Mutations in two non-canonical Arabidopsis SWI2/SNF2 chromatin remodeling ATPases cause embryogenesis and stem cell maintenance defects

(2012) Yi Sang et al.   PLANT JOURNAL

Distinct modes of DNA accessibility in plant chromatin

(2012) Huan Shu et al.   Nature Communications

H2A.Z landscapes and dual modifications in pluripotent and multipotent stem cells underlie complex genome regulatory functions

(2012) Manching Ku et al.   GENOME BIOLOGY

Signals and Combinatorial Functions of Histone Modifications

(2011) Tamaki Suganuma et al.   Annual Review of Biochemistry

Histone modifications in transcriptional activation during plant development

(2011) Alexandre Berr et al.   Biochimica et Biophysica Acta-Gene Regulatory Mechanisms

FIMO: scanning for occurrences of a given motif

(2011) Charles E. Grant et al.   BIOINFORMATICS

Ultra-fast sequence clustering from similarity networks with SiLiX

(2011) Vincent Miele et al.   BMC BIOINFORMATICS

Comprehensive Genome-wide Protein-DNA Interactions Detected at Single-Nucleotide Resolution

(2011) Ho Sung Rhee et al.   CELL

Integrative epigenomic mapping defines four main chromatin states in Arabidopsis

(2011) François Roudier et al.   EMBO JOURNAL

Chromatin: constructing the big picture

(2011) Bas van Steensel   EMBO JOURNAL

Coordinated histone modifications are associated with gene expression variation within and between species

(2011) M. Ha et al.   GENOME RESEARCH

Ancestral polyploidy in seed plants and angiosperms

(2011) Yuannian Jiao et al.   NATURE

Transcription factor binding predictions using TRAP for the analysis of ChIP-seq data and regulatory SNPs

(2011) Morgane Thomas-Chollier et al.   Nature Protocols

Preparation of reduced representation bisulfite sequencing libraries for genome-scale DNA methylation profiling

(2011) Hongcang Gu et al.   Nature Protocols

The CHD3 Chromatin Remodeler PICKLE and Polycomb Group Proteins Antagonistically Regulate Meristem Activity in the Arabidopsis Root

(2011) E. Aichinger et al.   PLANT CELL

Improved protein-binding microarrays for the identification of DNA-binding specificities of transcription factors

(2011) Marta Godoy et al.   PLANT JOURNAL

Multigene Phylogeny of the Green Lineage Reveals the Origin and Diversification of Land Plants

(2010) Cédric Finet et al.   CURRENT BIOLOGY

Regulation of transcription in plants: mechanisms controlling developmental switches

(2010) Kerstin Kaufmann et al.   NATURE REVIEWS GENETICS

The evolutionary-developmental analysis of plant microRNAs

(2010) S. Jasinski et al.   PHILOSOPHICAL TRANSACTIONS OF THE ROYAL SOCIETY B-BIOLOGICAL SCIENCES

Parallel structural evolution of auxin response factors in the angiosperms

(2010) Cédric Finet et al.   PLANT JOURNAL

Identification of Functional Elements and Regulatory Circuits by Drosophila modENCODE

(2010) et al.   SCIENCE

MOODS: fast search for position weight matrix matches in DNA sequences

(2009) J. Korhonen et al.   BIOINFORMATICS

An update of the Angiosperm Phylogeny Group classification for the orders and families of flowering plants: APG III

(2009)   BOTANICAL JOURNAL OF THE LINNEAN SOCIETY

FastTree: Computing Large Minimum Evolution Trees with Profiles instead of a Distance Matrix

(2009) M. N. Price et al.   MOLECULAR BIOLOGY AND EVOLUTION

Universal protein-binding microarrays for the comprehensive characterization of the DNA-binding specificities of transcription factors

(2009) Michael F Berger et al.   Nature Protocols

The analysis of entire gene promoters by surface plasmon resonance

(2009) Edwige Moyroud et al.   PLANT JOURNAL

Target Genes of the MADS Transcription Factor SEPALLATA3: Integration of Developmental and Hormonal Pathways in the Arabidopsis Flower

(2009) Kerstin Kaufmann et al.   PLOS BIOLOGY

Evo-Devo and an Expanding Evolutionary Synthesis: A Genetic Theory of Morphological Evolution

(2008) Sean B. Carroll   CELL

Identification of conserved microRNAs and their target genes in tomato (Lycopersicon esculentum)

(2008) Zujun Yin et al.   GENE

Unraveling ancient hexaploidy through multiply-aligned angiosperm gene maps

(2008) H. Tang et al.   GENOME RESEARCH

Using RSAT to scan genome sequences for transcription factor binding sites and cis-regulatory modules

(2008) Jean-Valery Turatsinze et al.   Nature Protocols

The class E floral homeotic protein SEPALLATA3 is sufficient to loop DNA in ‘floral quartet’-like complexes in vitro

(2008) Rainer Melzer et al.   NUCLEIC ACIDS RESEARCH