Genome-wide data (ChIP-seq) enabled identification of cell wall-related and aquaporin genes as targets of tomato ASR1, a drought stress-responsive transcription factor

Unique genome-wide map of TCF4 and STAT3 targets using ChIP-seq reveals their association with new molecular subtypes of glioblastoma

(2013) Jun-Xia Zhang et al.   NEURO-ONCOLOGY

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

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

Pitx1 broadly associates with limb enhancers and is enriched on hindlimb cis-regulatory elements

(2012) Carlos R. Infante et al.   DEVELOPMENTAL BIOLOGY

Insights into Populus XIP aquaporins: evolutionary expansion, protein functionality, and environmental regulation

(2012) D. Lopez et al.   JOURNAL OF EXPERIMENTAL BOTANY

The tomato genome sequence provides insights into fleshy fruit evolution

(2012)   NATURE

Identifying ChIP-seq enrichment using MACS

(2012) Jianxing Feng et al.   Nature Protocols

Challenges and perspectives to improve crop drought and salinity tolerance

(2012) Eleonora Cominelli et al.   New Biotechnology

Transcriptional Enhancers in Protein-Coding Exons of Vertebrate Developmental Genes

(2012) Deborah I. Ritter et al.   PLoS One

ChIP-seq Analysis in R (CSAR): An R package for the statistical detection of protein-bound genomic regions

(2011) Jose M Muiño et al.   Plant Methods

GimmeMotifs: a de novo motif prediction pipeline for ChIP-sequencing experiments

(2010) Simon J. van Heeringen et al.   BIOINFORMATICS

Large-scale analysis of full-length cDNAs from the tomato (Solanum lycopersicum) cultivar Micro-Tom, a reference system for the Solanaceae genomics

(2010) Koh Aoki et al.   BMC GENOMICS

Protocol: fine-tuning of a Chromatin Immunoprecipitation (ChIP) protocol in tomato

(2010) Martiniano M Ricardi et al.   Plant Methods

Mechanics and modeling of plant cell growth

(2009) Anja Geitmann et al.   TRENDS IN PLANT SCIENCE

Ultrafast and memory-efficient alignment of short DNA sequences to the human genome

(2009) Ben Langmead et al.   GENOME BIOLOGY

Plant Aquaporins: Membrane Channels with Multiple Integrated Functions

(2008) Christophe Maurel et al.   Annual Review of Plant Biology

Analysis of 90 Mb of the potato genome reveals conservation of gene structures and order with tomato but divergence in repetitive sequence composition

(2008) Wei Zhu et al.   BMC GENOMICS

Unexpected complexity of the Aquaporin gene family in the moss Physcomitrella patens

(2008) Jonas ÅH Danielson et al.   BMC PLANT BIOLOGY

Nucleotide polymorphism in the drought responsive gene Asr2 in wild populations of tomato

(2008) Mariano I. Giombini et al.   GENETICA

Transport functions and expression analysis of vacuolar membrane aquaporins in response to various stresses in rice

(2008) Guo-Wei Li et al.   JOURNAL OF PLANT PHYSIOLOGY

An integrated software system for analyzing ChIP-chip and ChIP-seq data

(2008) Hongkai Ji et al.   NATURE BIOTECHNOLOGY

Adaptations of higher plant cell walls to water loss: drought vs desiccation

(2008) John P. Moore et al.   PHYSIOLOGIA PLANTARUM

Tomato ASR1 abrogates the response to abscisic acid and glucose in Arabidopsis by competing with ABI4 for DNA binding

(2008) Doron Shkolnik et al.   PLANT BIOTECHNOLOGY JOURNAL

Arabidopsis PPR40 Connects Abiotic Stress Responses to Mitochondrial Electron Transport

(2008) L. Zsigmond et al.   PLANT PHYSIOLOGY

The Enigmatic LEA Proteins and Other Hydrophilins

(2008) M. Battaglia et al.   PLANT PHYSIOLOGY

In Vivo Interference with AtTCP20 Function Induces Severe Plant Growth Alterations and Deregulates the Expression of Many Genes Important for Development

(2008) C. Herve et al.   PLANT PHYSIOLOGY

Synergism between the chaperone-like activity of the stress regulated ASR1 protein and the osmolyte glycine-betaine

(2008) Zvia Konrad et al.   PLANTA

When cells lose water: Lessons from biophysics and molecular biology

(2008) Julio J. Caramelo et al.   PROGRESS IN BIOPHYSICS & MOLECULAR BIOLOGY

Model-based Analysis of ChIP-Seq (MACS)

(2008) Yong Zhang et al.   GENOME BIOLOGY