Conserved pleiotropy of an ancient plant homeobox gene uncovered by cis-regulatory dissection

A WOX/Auxin Biosynthesis Module Controls Growth to Shape Leaf Form

(2020) Zhongjuan Zhang et al.   CURRENT BIOLOGY

Dense and pleiotropic regulatory information in a developmental enhancer

(2020) Timothy Fuqua et al.   NATURE

Development of plant regeneration and Agrobacterium tumefaciens-mediated transformation methodology for Physalis pruinosa

(2019) Kerry Swartwood et al.   PLANT CELL TISSUE AND ORGAN CULTURE

CRISPR/Cas Genome Editing and Precision Plant Breeding in Agriculture

(2019) Kunling Chen et al.   Annual Review of Plant Biology

Genome-wide identification and analysis of the WUSCHEL-related homeobox (WOX) gene family in allotetraploid Brassica napus reveals changes in WOX genes during polyploidization

(2019) Mengdi Li et al.   BMC GENOMICS

Base Editing in Crops: Current Advances, Limitations, and Future Implications

(2019) Rukmini Mishra et al.   PLANT BIOTECHNOLOGY JOURNAL

Challenges of Translating Gene Regulatory Information into Agronomic Improvements

(2019) Nathan Springer et al.   TRENDS IN PLANT SCIENCE

Arabidopsis SWR1-associated protein methyl-CpG-binding domain 9 is required for histone H2A.Z deposition

(2019) Magdalena E. Potok et al.   Nature Communications

Evolution, Initiation, and Diversity in Early Plant Embryogenesis

(2019) Tatyana Radoeva et al.   DEVELOPMENTAL CELL

Revolutions in agriculture chart a course for targeted breeding of old and new crops

(2019) Yuval Eshed et al.   SCIENCE

Large-scale phylogenomic analysis suggests three ancient superclades of the WUSCHEL-RELATED HOMEOBOX transcription factor family in plants

(2019) Cheng-Chiang Wu et al.   PLoS One

ape 5.0: an environment for modern phylogenetics and evolutionary analyses in R

(2018) Emmanuel Paradis et al.   BIOINFORMATICS

Towards a more predictable plant breeding pipeline with CRISPR/Cas-induced allelic series to optimize quantitative and qualitative traits

(2018) Armin Scheben et al.   CURRENT OPINION IN PLANT BIOLOGY

Renewing Felsenstein’s phylogenetic bootstrap in the era of big data

(2018) F. Lemoine et al.   NATURE

Genome sequence of M6, a diploid inbred clone of the high-glycoalkaloid-producing tuber-bearing potato species Solanum chacoense , reveals residual heterozygosity

(2018) Courtney P. Leisner et al.   PLANT JOURNAL

HEAD LESS, a WUSCHEL homologue, uncovers novel aspects of shoot meristem regulation and leaf blade development in Medicago truncatula

(2018) Yingying Meng et al.   JOURNAL OF EXPERIMENTAL BOTANY

PlantPAN3.0: a new and updated resource for reconstructing transcriptional regulatory networks from ChIP-seq experiments in plants

(2018) Chi-Nga Chow et al.   NUCLEIC ACIDS RESEARCH

LEAF LATERAL SYMMETRY1, a Member of the WUSCHEL-RELATED HOMEOBOX3 Gene Family, Regulates Lateral Organ Development Differentially from Other Paralogs, NARROW LEAF2 and NARROW LEAF3 in Rice

(2017) Eriko Honda et al.   PLANT AND CELL PHYSIOLOGY

Increased efficiency of targeted mutagenesis by CRISPR/Cas9 in plants using heat stress

(2017) Chantal LeBlanc et al.   PLANT JOURNAL

Estimating the Effective Sample Size of Tree Topologies from Bayesian Phylogenetic Analyses

(2016) Robert Lanfear et al.   Genome Biology and Evolution

The evolution of inflorescence diversity in the nightshades and heterochrony during meristem maturation

(2016) Zachary H. Lemmon et al.   GENOME RESEARCH

Stem Cell Regulation by Arabidopsis WOX Genes

(2016) Alicja Dolzblasz et al.   Molecular Plant

A plethora of pleiotropy across complex traits

(2016) Peter M Visscher et al.   NATURE GENETICS

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

(2016) Fidel Ramírez et al.   NUCLEIC ACIDS RESEARCH

New genes from old: asymmetric divergence of gene duplicates and the evolution of development

(2016) Peter W. H. Holland et al.   PHILOSOPHICAL TRANSACTIONS OF THE ROYAL SOCIETY B-BIOLOGICAL SCIENCES

A Collection of Conserved Non-Coding Sequences to Study Gene Regulation in Flowering Plants

(2016) Jan Van de Velde et al.   PLANT PHYSIOLOGY

Evolution of gene duplication in plants

(2016) Nicholas Panchy et al.   PLANT PHYSIOLOGY

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

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

The detection and characterization of pleiotropy: discovery, progress, and promise

(2015) Anna L. Tyler et al.   BRIEFINGS IN BIOINFORMATICS

The WRKY Transcription Factor WRKY71/EXB1 Controls Shoot Branching by Transcriptionally RegulatingRAXGenes in Arabidopsis

(2015) Dongshu Guo et al.   PLANT CELL

Axillary Meristem Formation in Rice Requires theWUSCHELOrthologTILLERS ABSENT1

(2015) Wakana Tanaka et al.   PLANT CELL

The role of WOX genes in flower development

(2014) Enrico Costanzo et al.   ANNALS OF BOTANY

Trimmomatic: a flexible trimmer for Illumina sequence data

(2014) Anthony M. Bolger et al.   BIOINFORMATICS

MafFilter: a highly flexible and extensible multiple genome alignment files processor

(2014) Julien Y Dutheil et al.   BMC GENOMICS

The architecture of gene expression: integrating dispersed cis-regulatory modules into coherent regulatory domains

(2014) Wibke Schwarzer et al.   CURRENT OPINION IN GENETICS & DEVELOPMENT

WUSCHEL-RELATED HOMEOBOX 8/9 is important for proper embryo patterning in the gymnosperm Norway spruce

(2014) Tianqing Zhu et al.   JOURNAL OF EXPERIMENTAL BOTANY

Capsicum annuum S(CaS) promotes reproductive transition and is required for flower formation in pepper (Capsicum annuum)

(2014) Oded Cohen et al.   NEW PHYTOLOGIST

Efficient Gene Editing in Tomato in the First Generation Using the Clustered Regularly Interspaced Short Palindromic Repeats/CRISPR-Associated9 System

(2014) C. Brooks et al.   PLANT PHYSIOLOGY

Origins and Evolution of WUSCHEL-Related Homeobox Protein Family in Plant Kingdom

(2014) Gaibin Lian et al.   TheScientificWorldJOURNAL

DWARF TILLER1, a WUSCHEL-Related Homeobox Transcription Factor, Is Required for Tiller Growth in Rice

(2014) Wenfei Wang et al.   PLoS Genetics

Meristem maturation and inflorescence architecture—lessons from the Solanaceae

(2013) Soon Ju Park et al.   CURRENT OPINION IN PLANT BIOLOGY

Control of grass inflorescence form by the fine-tuning of meristem phase change

(2013) Junko Kyozuka et al.   CURRENT OPINION IN PLANT BIOLOGY

Conserved non-coding elements and cis regulation: actions speak louder than words

(2013) A. C. Nelson et al.   DEVELOPMENT

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

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

Evaluation of methods for modeling transcription factor sequence specificity

(2013) Matthew T Weirauch et al.   NATURE BIOTECHNOLOGY

Evolution of crop species: genetics of domestication and diversification

(2013) Rachel S. Meyer et al.   NATURE REVIEWS GENETICS

Pleiotropy in complex traits: challenges and strategies

(2013) Nadia Solovieff et al.   NATURE REVIEWS GENETICS

Plant genome editing made easy: targeted mutagenesis in model and crop plants using the CRISPR/Cas system

(2013) Khaoula Belhaj et al.   Plant Methods

STAR: ultrafast universal RNA-seq aligner

(2012) Alexander Dobin et al.   BIOINFORMATICS

Evolutionarily conserved repressive activity of WOX proteins mediates leaf blade outgrowth and floral organ development in plants

(2012) H. Lin et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

The many faces of pleiotropy

(2012) Annalise B. Paaby et al.   TRENDS IN GENETICS

FIMO: scanning for occurrences of a given motif

(2011) Charles E. Grant et al.   BIOINFORMATICS

THE QTN PROGRAM AND THE ALLELES THAT MATTER FOR EVOLUTION: ALL THAT'S GOLD DOES NOT GLITTER

(2011) Matthew V. Rockman   EVOLUTION

The pleiotropic structure of the genotype–phenotype map: the evolvability of complex organisms

(2011) Günter P. Wagner et al.   NATURE REVIEWS GENETICS

Cis-regulatory elements: molecular mechanisms and evolutionary processes underlying divergence

(2011) Patricia J. Wittkopp et al.   NATURE REVIEWS GENETICS

A Modular Cloning System for Standardized Assembly of Multigene Constructs

(2011) Ernst Weber et al.   PLoS One

Rate of meristem maturation determines inflorescence architecture in tomato

(2011) S. J. Park et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

BEDTools: a flexible suite of utilities for comparing genomic features

(2010) Aaron R. Quinlan et al.   BIOINFORMATICS

One Hundred Years of Pleiotropy: A Retrospective

(2010) F. W. Stearns   GENETICS

Genomic patterns of pleiotropy and the evolution of complexity

(2010) Z. Wang et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

WRKY transcription factors

(2010) Paul J. Rushton et al.   TRENDS IN PLANT SCIENCE

The Sequence Alignment/Map format and SAMtools

(2009) H. Li et al.   BIOINFORMATICS

cis-Regulatory elements in plant cell signaling

(2009) Henry D Priest et al.   CURRENT OPINION IN PLANT BIOLOGY

Flexibility of transcription factor target site position in conserved cis-regulatory modules

(2009) R. Andrew Cameron et al.   DEVELOPMENTAL BIOLOGY

Twenty years on: The inner workings of the shoot apical meristem, a developmental dynamo

(2009) M.K. Barton   DEVELOPMENTAL BIOLOGY

Detection of nonneutral substitution rates on mammalian phylogenies

(2009) K. S. Pollard et al.   GENOME RESEARCH

Deep homology and the origins of evolutionary novelty

(2009) Neil Shubin et al.   NATURE

MEME SUITE: tools for motif discovery and searching

(2009) T. L. Bailey et al.   NUCLEIC ACIDS RESEARCH

Genes of the most conserved WOX clade in plants affect root and flower development in Arabidopsis

(2008) Yves Deveaux et al.   BMC EVOLUTIONARY BIOLOGY

Role of EVERGREEN in the Development of the Cymose Petunia Inflorescence

(2008) Alexandra B. Rebocho et al.   DEVELOPMENTAL CELL

Differential Expression of WOX Genes Mediates Apical-Basal Axis Formation in the Arabidopsis Embryo

(2008) Holger Breuninger et al.   DEVELOPMENTAL CELL

The Making of a Compound Inflorescence in Tomato and Related Nightshades

(2008) Zachary B Lippman et al.   PLOS BIOLOGY