相关参考文献
注意:仅列出部分参考文献,下载原文获取全部文献信息。PlantTFDB 4.0: toward a central hub for transcription factors and regulatory interactions in plants
Jinpu Jin et al.
NUCLEIC ACIDS RESEARCH (2017)
Combining ATAC-seq with nuclei sorting for discovery of cis-regulatory regions in plant genomes
Zefu Lu et al.
NUCLEIC ACIDS RESEARCH (2017)
A high quality Arabidopsis transcriptome for accurate transcript-level analysis of alternative splicing
Runxuan Zhang et al.
NUCLEIC ACIDS RESEARCH (2017)
Phylogenomic analysis of gene co-expression networks reveals the evolution of functional modules
Colin Ruprecht et al.
PLANT JOURNAL (2017)
Genome-wide characterization of differential transcript usage in Arabidopsis thaliana
Dries Vaneechoutte et al.
PLANT JOURNAL (2017)
Predictive Models of Spatial Transcriptional Response to High Salinity1[OPEN]
Sahra Uygun et al.
PLANT PHYSIOLOGY (2017)
Cross-Family Transcription Factor Interactions: An Accitional Layer of Gene Reculation
Marian Bemer et al.
TRENDS IN PLANT SCIENCE (2017)
Identification of plant transcription factor target sequences
Jose M. Franco-Zorrilla et al.
BIOCHIMICA ET BIOPHYSICA ACTA-GENE REGULATORY MECHANISMS (2017)
Plant Stress Tolerance Requires Auxin-Sensitive Aux/IAA Transcriptional Repressors
Eilon Shani et al.
CURRENT BIOLOGY (2017)
PlantPAN 2.0: an update of plant promoter analysis navigator for reconstructing transcriptional regulatory networks in plants
Chi-Nga Chow et al.
NUCLEIC ACIDS RESEARCH (2016)
Transcriptional regulatory networks in Arabidopsis thaliana during single and combined stresses
Pankaj Barah et al.
NUCLEIC ACIDS RESEARCH (2016)
JASPAR 2016: a major expansion and update of the open-access database of transcription factor binding profiles
Anthony Mathelier et al.
NUCLEIC ACIDS RESEARCH (2016)
Cistrome and Epicistrome Features Shape the Regulatory DNA Landscape
Ronan C. O'Malley et al.
CELL (2016)
Establishment of Expression in the SHORTROOT-SCARECROW Transcriptional Cascade through Opposing Activities of Both Activators and Repressors
Erin E. Sparks et al.
DEVELOPMENTAL CELL (2016)
Near-optimal probabilistic RNA-seq quantification
Nicolas L. Bray et al.
NATURE BIOTECHNOLOGY (2016)
Transcriptional Regulation of Arabidopsis Polycomb Repressive Complex 2 Coordinates Cell-Type Proliferation and Differentiation
Miguel de Lucas et al.
PLANT CELL (2016)
A high resolution map of the Arabidopsis thaliana developmental transcriptome based on RNA-seq profiling
Anna V. Klepikova et al.
PLANT JOURNAL (2016)
New BAR tools for mining expression data and exploring Cis-elements in Arabidopsis thaliana
Ryan S. Austin et al.
PLANT JOURNAL (2016)
A transcription factor hierarchy defines an environmental stress response network
Liang Song et al.
SCIENCE (2016)
Positional distribution of transcription factor binding sites in Arabidopsis thaliana
Chun-Ping Yu et al.
SCIENTIFIC REPORTS (2016)
Advances in understanding cis regulation of the plant gene with an emphasis on comparative genomics
Diane G. Burgess et al.
CURRENT OPINION IN PLANT BIOLOGY (2015)
Reassessing the Duon Hypothesis of Protein Evolution
Ke Xing et al.
MOLECULAR BIOLOGY AND EVOLUTION (2015)
From milliseconds to lifetimes: tracking the dynamic behavior of transcription factors in gene networks
Ying Li et al.
TRENDS IN GENETICS (2015)
An Arabidopsis gene regulatory network for secondary cell wall synthesis
M. Taylor-Teeples et al.
NATURE (2015)
PLAZA 3.0: an access point for plant comparative genomics
Sebastian Proost et al.
NUCLEIC ACIDS RESEARCH (2015)
Determination and Inference of Eukaryotic Transcription Factor Sequence Specificity
Matthew T. Weirauch et al.
CELL (2014)
Gene networks controlling Arabidopsis thaliana flower development
Diarmuid Seosamh O'Maoileidigh et al.
NEW PHYTOLOGIST (2014)
Combinatorial Complexity in a Transcriptionally Centered Signaling Hub in Arabidopsis
Anne Pfeiffer et al.
MOLECULAR PLANT (2014)
An organ boundary-enriched gene regulatory network uncovers regulatory hierarchies underlying axillary meristem initiation
Caihuan Tian et al.
MOLECULAR SYSTEMS BIOLOGY (2014)
Inference of Transcriptional Networks in Arabidopsis through Conserved Noncoding Sequence Analysis
Jan Van de Velde et al.
PLANT CELL (2014)
A Functional and Evolutionary Perspective on Transcription Factor Binding in Arabidopsis thaliana
Ken S. Heyndrickx et al.
PLANT CELL (2014)
Promoter-Based Integration in Plant Defense Regulation
Baohua Li et al.
PLANT PHYSIOLOGY (2014)
Hit-and-run transcriptional control by bZIP1 mediates rapid nutrient signaling in Arabidopsis
Alessia Para et al.
PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA (2014)
DNA-binding specificities of plant transcription factors and their potential to define target genes
Jose M. Franco-Zorrilla et al.
PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA (2014)
Mapping and Dynamics of Regulatory DNA and Transcription Factor Networks in A-thaliana
Alessandra M. Sullivan et al.
CELL REPORTS (2014)
Dynamics of chromatin accessibility and gene regulation by MADS-domain transcription factors in flower development
Alice Pajoro et al.
GENOME BIOLOGY (2014)
An atlas of over 90,000 conserved noncoding sequences provides insight into crucifer regulatory regions
Annabelle Haudry et al.
NATURE GENETICS (2013)
From plant gene regulatory grids to network dynamics
Maria Katherine Mejia-Guerra et al.
BIOCHIMICA ET BIOPHYSICA ACTA-GENE REGULATORY MECHANISMS (2012)
Fast gapped-read alignment with Bowtie 2
Ben Langmead et al.
NATURE METHODS (2012)
CORNET 2.0: integrating plant coexpression, protein-protein interactions, regulatory interactions, gene associations and functional annotations
Stefanie De Bodt et al.
NEW PHYTOLOGIST (2012)
The sequence read archive: explosive growth of sequencing data
Yuichi Kodama et al.
NUCLEIC ACIDS RESEARCH (2012)
The Arabidopsis Information Resource (TAIR): improved gene annotation and new tools
Philippe Lamesch et al.
NUCLEIC ACIDS RESEARCH (2012)
Genome-Wide Identification of Regulatory DNA Elements and Protein-Binding Footprints Using Signatures of Open Chromatin in Arabidopsis
Wenli Zhang et al.
PLANT CELL (2012)
Conserved Noncoding Sequences Highlight Shared Components of Regulatory Networks in Dicotyledonous Plants
Laura Baxter et al.
PLANT CELL (2012)
Genome-Wide Analysis Uncovers Regulation of Long Intergenic Noncoding RNAs in Arabidopsis
Jun Liu et al.
PLANT CELL (2012)
Systematic Identification of Functional Plant Modules through the Integration of Complementary Data Sources
Ken S. Heyndrickx et al.
PLANT PHYSIOLOGY (2012)
Arabidopsis paves the way: genomic and network analyses in crops
Thilia Ferrier et al.
CURRENT OPINION IN BIOTECHNOLOGY (2011)
A stele-enriched gene regulatory network in the Arabidopsis root
Siobhan M. Brady et al.
MOLECULAR SYSTEMS BIOLOGY (2011)
PInTFDB: updated content and new features of the plant transcription factor database
Paulino Perez-Rodriguez et al.
NUCLEIC ACIDS RESEARCH (2010)
CORNET: A User-Friendly Tool for Data Mining and Integration
Stefanie De Bodt et al.
PLANT PHYSIOLOGY (2010)
The 5′ untranslated region of the FAD3 mRNA is required for its translational enhancement at low temperature in Arabidopsis roots
Chun-Tao Wang et al.
PLANT SCIENCE (2010)
Evaluation of seed storage-protein gene 5' untranslated regions in enhancing gene expression in transgenic rice seed
Wen Xian Liu et al.
THEORETICAL AND APPLIED GENETICS (2010)
UniPROBE: an online database of protein binding microarray data on protein-DNA interactions
Daniel E. Newburger et al.
NUCLEIC ACIDS RESEARCH (2009)
Unraveling Transcriptional Control in Arabidopsis Using cis-Regulatory Elements and Coexpression Networks
Klaas Vandepoele et al.
PLANT PHYSIOLOGY (2009)
PlantPAN: Plant promoter analysis navigator, for identifying combinatorial cis-regulatory elements with distance constraint in plant gene groups
Wen-Chi Chang et al.
BMC GENOMICS (2008)
Model-based Analysis of ChIP-Seq (MACS)
Yong Zhang et al.
GENOME BIOLOGY (2008)
Networks of WRKY transcription factors in defense signaling
Thomas Eulgem et al.
CURRENT OPINION IN PLANT BIOLOGY (2007)
AGRIS and AtRegNet. A platform to link cis-regulatory elements and transcription factors into regulatory networks
SK Palaniswamy et al.
PLANT PHYSIOLOGY (2006)
Identification of novel regulatory modules in dicotyledonous plants using expression data and comparative genomics
Klaas Vandepoele et al.
GENOME BIOLOGY (2006)
Athena:: a resource for rapid visualization and systematic analysis of Arabidopsis promoter sequences
TR O'Connor et al.
BIOINFORMATICS (2005)
Assessing computational tools for the discovery of transcription factor binding sites
M Tompa et al.
NATURE BIOTECHNOLOGY (2005)
AthaMap: an online resource for in silico transcription factor binding sites in the Arabidopsis thaliana genome
NO Steffens et al.
NUCLEIC ACIDS RESEARCH (2004)
Cluster-Buster: finding dense clusters of motifs in DNA sequences
MC Frith et al.
NUCLEIC ACIDS RESEARCH (2003)
S phase and weristem-specific expression of the tobacco RNR1b gene is mediated by an E2F element located in the 5′ leader sequence
ME Chabouté et al.
JOURNAL OF BIOLOGICAL CHEMISTRY (2002)
PlantCARE, a database of plant cis-acting regulatory elements and a portal to tools for in silico analysis of promoter sequences
M Lescot et al.
NUCLEIC ACIDS RESEARCH (2002)