Transcriptional and temporal response of Populus stems to gravi-stimulation

Identifying gene coexpression networks underlying the dynamic regulation of wood-forming tissues in Populus under diverse environmental conditions

(2017) Matthew Zinkgraf et al.   NEW PHYTOLOGIST

Gravitropisms and reaction woods of forest trees - evolution, functions and mechanisms

(2016) Andrew Groover   NEW PHYTOLOGIST

Natural Cubic Spline Regression Modeling Followed by Dynamic Network Reconstruction for the Identification of Radiation-Sensitivity Gene Association Networks from Time-Course Transcriptome Data

(2016) Agata Michna et al.   PLoS One

Transcript profiling of Populus tomentosa genes in normal, tension, and opposite wood by RNA-seq

(2015) Jinhui Chen et al.   BMC GENOMICS

RNA-seq analysis of an apical meristem time series reveals a critical point in Arabidopsis thaliana flower initiation

(2015) Anna V. Klepikova et al.   BMC GENOMICS

Patterns of gene expression during Arabidopsis flower development from the time of initiation to maturation

(2015) Patrick T. Ryan et al.   BMC GENOMICS

Molecular control of wood formation in trees

(2015) Zheng-Hua Ye et al.   JOURNAL OF EXPERIMENTAL BOTANY

Combinatorial gene regulation by modulation of relative pulse timing

(2015) Yihan Lin et al.   NATURE

HISAT: a fast spliced aligner with low memory requirements

(2015) Daehwan Kim et al.   NATURE METHODS

Transcriptional Dynamics Driving MAMP-Triggered Immunity and Pathogen Effector-Mediated Immunosuppression in Arabidopsis Leaves Following Infection withPseudomonas syringaepv tomato DC3000

(2015) Laura A. Lewis et al.   PLANT CELL

A resource for characterizing genome-wide binding and putative target genes of transcription factors expressed during secondary growth and wood formation inPopulus

(2015) Lijun Liu et al.   PLANT JOURNAL

Acclimation of mechanical and hydraulic functions in trees: impact of the thigmomorphogenetic process

(2015) Eric Badel et al.   Frontiers in Plant Science

NAC-MYB-based transcriptional regulation of secondary cell wall biosynthesis in land plants

(2015) Yoshimi Nakano et al.   Frontiers in Plant Science

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

(2014) S. Anders et al.   BIOINFORMATICS

Evaluation of experimental design and computational parameter choices affecting analyses of ChIP-seq and RNA-seq data in undomesticated poplar trees

(2014) Lijun Liu et al.   BMC GENOMICS

Antisense expression of the fasciclin-like arabinogalactan protein FLA6 gene in Populus inhibits expression of its homologous genes and alters stem biomechanics and cell wall composition in transgenic trees

(2014) Haihai Wang et al.   JOURNAL OF EXPERIMENTAL BOTANY

Slow, fast and furious: understanding the physics of plant movements

(2013) Yoël Forterre   JOURNAL OF EXPERIMENTAL BOTANY

Amyloplast displacement is necessary for gravisensing in Arabidopsis shoots as revealed by a centrifuge microscope

(2013) Masatsugu Toyota et al.   PLANT JOURNAL

Functional Roles of Pulsing in Genetic Circuits

(2013) J. H. Levine et al.   SCIENCE

Navigating the transcriptional roadmap regulating plant secondary cell wall deposition

(2013) Steven G. Hussey et al.   Frontiers in Plant Science

Studying and modelling dynamic biological processes using time-series gene expression data

(2012) Ziv Bar-Joseph et al.   NATURE REVIEWS GENETICS

An integrative clustering and modeling algorithm for dynamical gene expression data

(2011) J. Sivriver et al.   BIOINFORMATICS

Impulse Control: Temporal Dynamics in Gene Transcription

(2011) Nir Yosef et al.   CELL

Tensional stress generation in gelatinous fibres: a review and possible mechanism based on cell-wall structure and composition

(2011) E. J. Mellerowicz et al.   JOURNAL OF EXPERIMENTAL BOTANY

Salt stress induces the formation of a novel type of ‘pressure wood’ in two Populus species

(2011) Dennis Janz et al.   NEW PHYTOLOGIST

Transcription Dynamics in Plant Immunity

(2011) John W. Moore et al.   PLANT CELL

EST analysis of functional genes associated with cell wall biosynthesis and modification in the secondary xylem of the yellow poplar (Liriodendron tulipifera) stem during early stage of tension wood formation

(2011) Hyunjung Jin et al.   PLANTA

Emerging properties of animal gene regulatory networks

(2010) Eric H. Davidson   NATURE

Fasciclin-like arabinogalactan proteins: specialization for stem biomechanics and cell wall architecture in Arabidopsis and Eucalyptus

(2010) Colleen P. MacMillan et al.   PLANT JOURNAL

edgeR: a Bioconductor package for differential expression analysis of digital gene expression data

(2009) M. D. Robinson et al.   BIOINFORMATICS

The transcriptional network that controls growth arrest and differentiation in a human myeloid leukemia cell line

(2009) Harukazu Suzuki et al.   NATURE GENETICS

Functional Characterization of Poplar Wood-Associated NAC Domain Transcription Factors

(2009) R. Zhong et al.   PLANT PHYSIOLOGY

How confident can we be that orthologs are similar, but paralogs differ?

(2009) Romain A. Studer et al.   TRENDS IN GENETICS

Global regulatory logic for specification of an embryonic cell lineage

(2008) P. Oliveri et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA