Genome-wide identification of binding sites for NAC and YABBY transcription factors and co-regulated genes during soybean seedling development by ChIP-Seq and RNA-Seq

Expression of fatty acid and lipid biosynthetic genes in developing endosperm of Jatropha curcas

(2012) Keyu Gu et al.   Biotechnology for Biofuels

Identification of soybean seed developmental stage-specific and tissue-specific miRNA targets by degradome sequencing

(2012) Md Shamimuzzaman et al.   BMC GENOMICS

Comprehensive Analysis of NAC Domain Transcription Factor Gene Family in Populus trichocarpa

(2012) Ruibo Hu et al.   BMC PLANT BIOLOGY

Divergent patterns of endogenous small RNA populations from seed and vegetative tissues of Glycine max

(2012) Gracia Zabala et al.   BMC PLANT BIOLOGY

Genome-wide binding-site analysis of REVOLUTA reveals a link between leaf patterning and light-mediated growth responses

(2012) Ronny Brandt et al.   PLANT JOURNAL

Characterization of SOC1's Central Role in Flowering by the Identification of Its Upstream and Downstream Regulators

(2012) R. G. H. Immink et al.   PLANT PHYSIOLOGY

Arabidopsis Fatty Acid Desaturase FAD2 Is Required for Salt Tolerance during Seed Germination and Early Seedling Growth

(2012) Jiantao Zhang et al.   PLoS One

Genome-Wide Analysis of the Complex Transcriptional Networks of Rice Developing Seeds

(2012) Liang-Jiao Xue et al.   PLoS One

Integrative genomics viewer

(2011) James T Robinson et al.   NATURE BIOTECHNOLOGY

Genome-Wide Binding Site Analysis of FAR-RED ELONGATED HYPOCOTYL3 Reveals Its Novel Function in Arabidopsis Development

(2011) X. Ouyang et al.   PLANT CELL

Flux of transcript patterns during soybean seed development

(2010) Sarah I Jones et al.   BMC GENOMICS

Pectin methylesterase and its proteinaceous inhibitor: a review

(2010) Ruben P. Jolie et al.   CARBOHYDRATE RESEARCH

Architectures of the unique domains associated with the DEAD-box helicase motif

(2010) Pavan Umate et al.   CELL CYCLE

Functional characterization of pectin methylesterase inhibitor (PMEI) in wheat

(2010) Min Jeong Hong et al.   GENES & GENETIC SYSTEMS

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

(2010) Martiniano M Ricardi et al.   Plant Methods

Arabidopsis EMBRYOMAKER encoding an AP2 domain transcription factor plays a key role in developmental change from vegetative to embryonic phase

(2010) Ryo Tsuwamoto et al.   PLANT MOLECULAR BIOLOGY

AP2/EREBP transcription factors are part of gene regulatory networks and integrate metabolic, hormonal and environmental signals in stress acclimation and retrograde signalling

(2010) Karl-Josef Dietz et al.   PROTOPLASMA

Differential expression analysis for sequence count data

(2010) Simon Anders et al.   GENOME BIOLOGY

A practical comparison of methods for detecting transcription factor binding sites in ChIP-seq experiments

(2009) Teemu D Laajala et al.   BMC GENOMICS

Arabidopsis WRKY2 transcription factor mediates seed germination and postgermination arrest of development by abscisic acid

(2009) Wenbo Jiang et al.   BMC PLANT BIOLOGY

Genomic location analysis by ChIP-Seq

(2009) Artem Barski et al.   JOURNAL OF CELLULAR BIOCHEMISTRY

ChIPing away at the genome: the new frontier travel guide

(2009) Jelena Aleksic et al.   Molecular BioSystems

Molecular characterization of stress-inducible GmNAC genes in soybean

(2009) Lam-Son Phan Tran et al.   MOLECULAR GENETICS AND GENOMICS

Computation for ChIP-seq and RNA-seq studies

(2009) Shirley Pepke et al.   NATURE METHODS

Genome-Wide Analysis of Genes Targeted by PHYTOCHROME INTERACTING FACTOR 3-LIKE5 during Seed Germination in Arabidopsis

(2009) E. Oh et al.   PLANT CELL

Unraveling Transcriptional Control in Arabidopsis Using cis-Regulatory Elements and Coexpression Networks

(2009) K. Vandepoele et al.   PLANT PHYSIOLOGY

Developmental roles of 21 Drosophila transcription factors are determined by quantitative differences in binding to an overlapping set of thousands of genomic regions

(2009) Stewart MacArthur et al.   GENOME BIOLOGY

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

(2009) Ben Langmead et al.   GENOME BIOLOGY

Genome-wide analysis of transcription factor binding sites based on ChIP-Seq data

(2008) Anton Valouev et al.   NATURE METHODS

Mapping and quantifying mammalian transcriptomes by RNA-Seq

(2008) Ali Mortazavi et al.   NATURE METHODS

Genome-wide identification of in vivo protein-DNA binding sites from ChIP-Seq data

(2008) R. Jothi et al.   NUCLEIC ACIDS RESEARCH

Signals Derived from YABBY Gene Activities in Organ Primordia Regulate Growth and Partitioning of Arabidopsis Shoot Apical Meristems

(2008) A. Goldshmidt et al.   PLANT CELL

Studies on DNA-binding selectivity of WRKY transcription factors lend structural clues into WRKY-domain function

(2008) Ingo Ciolkowski et al.   PLANT MOLECULAR BIOLOGY

Model-based Analysis of ChIP-Seq (MACS)

(2008) Yong Zhang et al.   GENOME BIOLOGY