Beyond Trees: Regulons and Regulatory Motif Characterization

Translation Control of HAC1 by Regulation of Splicing in Saccharomyces cerevisiae

(2019) Xuhua Xia   INTERNATIONAL JOURNAL OF MOLECULAR SCIENCES

Enhanced maps of transcription factor binding sites improve regulatory networks learned from accessible chromatin data

(2019) Shubhada R. Kulkarni et al.   PLANT PHYSIOLOGY

JASPAR 2020: update of the open-access database of transcription factor binding profiles

(2019) Oriol Fornes et al.   NUCLEIC ACIDS RESEARCH

Resolving noise–control conflict by gene duplication

(2019) Michal Chapal et al.   PLOS BIOLOGY

The AtHB1 Transcription Factor Controls the miR164-CUC2 Regulatory Node to Modulate Leaf Development

(2019) Virginia N Miguel et al.   PLANT AND CELL PHYSIOLOGY

Global Proteome Remodeling during ER Stress Involves Hac1-Driven Expression of Long Undecoded Transcript Isoforms

(2018) Kelsey Marie Van Dalfsen et al.   DEVELOPMENTAL CELL

DAMBE7: New and Improved Tools for Data Analysis in Molecular Biology and Evolution

(2018) Xuhua Xia   MOLECULAR BIOLOGY AND EVOLUTION

GIGANTEA- like genes control seasonal growth cessation in Populus

(2018) Jihua Ding et al.   NEW PHYTOLOGIST

Multiple Links between HD-Zip Proteins and Hormone Networks

(2018) Giovanna Sessa et al.   INTERNATIONAL JOURNAL OF MOLECULAR SCIENCES

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

DAMBE6: New Tools for Microbial Genomics, Phylogenetics, and Molecular Evolution

(2017) Xuhua Xia   JOURNAL OF HEREDITY

An atypical R2R3 MYB transcription factor increases cold hardiness by CBF-dependent and CBF-independent pathways in apple

(2017) Yinpeng Xie et al.   NEW PHYTOLOGIST

The G-box transcriptional regulatory code in Arabidopsis

(2017) Daphne Ezer et al.   PLANT PHYSIOLOGY

An efficient targeted nuclease strategy for high-resolution mapping of DNA binding sites

(2017) Peter J Skene et al.   eLife

Comparative transcriptomic analysis reveals the roles of overlapping heat-/drought-responsive genes in poplars exposed to high temperature and drought

(2017) Jingbo Jia et al.   Scientific Reports

Structure-based prediction of transcription factor binding specificity using an integrative energy function

(2016) Alvin Farrel et al.   BIOINFORMATICS

Cistrome and Epicistrome Features Shape the Regulatory DNA Landscape

(2016) Ronan C. O’Malley et al.   CELL

GTRD: a database of transcription factor binding sites identified by ChIP-seq experiments

(2016) Ivan Yevshin et al.   NUCLEIC ACIDS RESEARCH

ChIPBase v2.0: decoding transcriptional regulatory networks of non-coding RNAs and protein-coding genes from ChIP-seq data

(2016) Ke-Ren Zhou et al.   NUCLEIC ACIDS RESEARCH

Cistrome Data Browser: a data portal for ChIP-Seq and chromatin accessibility data in human and mouse

(2016) Shenglin Mei et al.   NUCLEIC ACIDS RESEARCH

PlantTFDB 4.0: toward a central hub for transcription factors and regulatory interactions in plants

(2016) Jinpu Jin et al.   NUCLEIC ACIDS RESEARCH

DamID-seq: Genome-wide Mapping of Protein-DNA Interactions by High Throughput Sequencing of Adenine-methylated DNA Fragments

(2016) Feinan Wu et al.   Jove-Journal of Visualized Experiments

Genome-wide transcriptional and physiological responses to drought stress in leaves and roots of two willow genotypes

(2015) Pascal Pucholt et al.   BMC PLANT BIOLOGY

ChIP-nexus enables improved detection of in vivo transcription factor binding footprints

(2015) Qiye He et al.   NATURE BIOTECHNOLOGY

Arabidopsis thalianaHomeoBox 1 (AtHB1), a Homedomain-Leucine Zipper I (HD-Zip I) transcription factor, is regulated by PHYTOCHROME-INTERACTING FACTOR 1 to promote hypocotyl elongation

(2015) Matías Capella et al.   NEW PHYTOLOGIST

The unfolded protein response: the dawn of a new field

(2015) Kazutoshi MORI   PROCEEDINGS OF THE JAPAN ACADEMY SERIES B-PHYSICAL AND BIOLOGICAL SCIENCES

ChEC-seq kinetics discriminates transcription factor binding sites by DNA sequence and shape in vivo

(2015) Gabriel E. Zentner et al.   Nature Communications

The UPR Branch IRE1-bZIP60 in Plants Plays an Essential Role in Viral Infection and Is Complementary to the Only UPR Pathway in Yeast

(2015) Lingrui Zhang et al.   PLoS Genetics

Determination and Inference of Eukaryotic Transcription Factor Sequence Specificity

(2014) Matthew T. Weirauch et al.   CELL

Protein-DNA binding: complexities and multi-protein codes

(2013) T. Siggers et al.   NUCLEIC ACIDS RESEARCH

CBF gene expression in peach leaf and bark tissues is gated by a circadian clock

(2013) T. S. Artlip et al.   TREE PHYSIOLOGY

Ribosome Deficiency Protects Against ER Stress in Saccharomyces cerevisiae

(2012) K. K. Steffen et al.   GENETICS

Identifying ChIP-seq enrichment using MACS

(2012) Jianxing Feng et al.   Nature Protocols

Basic leucine zipper transcription factor Hac1 binds DNA in two distinct modes as revealed by microfluidic analyses

(2012) P. M. Fordyce et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

AP2/ERF family transcription factors in plant abiotic stress responses

(2011) Junya Mizoi et al.   Biochimica et Biophysica Acta-Gene Regulatory Mechanisms

FIMO: scanning for occurrences of a given motif

(2011) Charles E. Grant et al.   BIOINFORMATICS

Comprehensive Genome-wide Protein-DNA Interactions Detected at Single-Nucleotide Resolution

(2011) Ho Sung Rhee et al.   CELL

Heat induces the splicing by IRE1 of a mRNA encoding a transcription factor involved in the unfolded protein response in Arabidopsis

(2011) Y. Deng et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Extracellular Secretion of Overexpressed Glycosylphosphatidylinositol-Linked Cell Wall Protein Utr2/Crh2p as a Novel Protein Quality Control Mechanism in Saccharomyces cerevisiae

(2010) Kelly A. Miller et al.   EUKARYOTIC CELL

Emerging Roles for XBP1, a sUPeR Transcription Factor

(2010) YIN HE et al.   GENE EXPRESSION

Walking Along the Serendipitous Path of Discovery

(2010) Peter Walter   MOLECULAR BIOLOGY OF THE CELL

Simple Combinations of Lineage-Determining Transcription Factors Prime cis-Regulatory Elements Required for Macrophage and B Cell Identities

(2010) Sven Heinz et al.   MOLECULAR CELL

A Library of Yeast Transcription Factor Motifs Reveals a Widespread Function for Rsc3 in Targeting Nucleosome Exclusion at Promoters

(2008) Gwenael Badis et al.   MOLECULAR CELL

Arabidopsis bZIP60 Is a Proteolysis-Activated Transcription Factor Involved in the Endoplasmic Reticulum Stress Response

(2008) Y. Iwata et al.   PLANT CELL