JASPAR 2022: the 9th release of the open-access database of transcription factor binding profiles

A high-resolution protein architecture of the budding yeast genome

(2021) Matthew J. Rossi et al.   NATURE

Base-resolution models of transcription-factor binding reveal soft motif syntax

(2021) Žiga Avsec et al.   NATURE GENETICS

UniBind: maps of high-confidence direct TF-DNA interactions across nine species

(2021) Rafael Riudavets Puig et al.   BMC GENOMICS

Transcription factors: Bridge between cell signaling and gene regulation

(2021) Paula Weidemüller et al.   PROTEOMICS

ReMap 2022: a database of Human, Mouse, Drosophila and Arabidopsis regulatory regions from an integrative analysis of DNA-binding sequencing experiments

(2021) Fayrouz Hammal et al.   NUCLEIC ACIDS RESEARCH

SlGRAS4 mediates a novel regulatory pathway promoting chilling tolerance in tomato

(2020) Yudong Liu et al.   PLANT BIOTECHNOLOGY JOURNAL

MAGIC: A tool for predicting transcription factors and cofactors driving gene sets using ENCODE data

(2020) Avtar Roopra   PLoS Computational Biology

Cross-species analysis of enhancer logic using deep learning

(2020) Liesbeth Minnoye et al.   GENOME RESEARCH

Global reference mapping of human transcription factor footprints

(2020) Jeff Vierstra et al.   NATURE

Database resources of the National Center for Biotechnology Information

(2020) Eric W Sayers et al.   NUCLEIC ACIDS RESEARCH

ZNF410 Uniquely Activates the NuRD Component CHD4 to Silence Fetal Hemoglobin Expression

(2020) Xianjiang Lan et al.   MOLECULAR CELL

UniProt: the universal protein knowledgebase in 2021

(2020) et al.   NUCLEIC ACIDS RESEARCH

The UCSC Genome Browser database: 2021 update

(2020) Jairo Navarro Gonzalez et al.   NUCLEIC ACIDS RESEARCH

The Kipoi repository accelerates community exchange and reuse of predictive models for genomics

(2019) Žiga Avsec et al.   NATURE BIOTECHNOLOGY

Similarity regression predicts evolution of transcription factor sequence specificity

(2019) Samuel A. Lambert et al.   NATURE GENETICS

TFEA.ChIP: A tool kit for transcription factor binding site enrichment analysis capitalizing on ChIP-seq datasets

(2019) Laura Puente-Santamaria et al.   BIOINFORMATICS

CUT&Tag for efficient epigenomic profiling of small samples and single cells

(2019) Hatice S. Kaya-Okur et al.   Nature Communications

CiiiDER: A tool for predicting and analysing transcription factor binding sites

(2019) Linden J. Gearing et al.   PLoS One

DNA Readout Viewer (DRV): visualization of specificity determining patterns of protein-binding DNA segments

(2019) Krisztian Adam et al.   BIOINFORMATICS

The Human Transcription Factors

(2018) Samuel A. Lambert et al.   CELL

Bioconda: sustainable and comprehensive software distribution for the life sciences

(2018) Björn Grüning et al.   NATURE METHODS

RSAT 2018: regulatory sequence analysis tools 20th anniversary

(2018) Nga Thi Thuy Nguyen et al.   NUCLEIC ACIDS RESEARCH

The interaction landscape between transcription factors and the nucleosome

(2018) Fangjie Zhu et al.   NATURE

A Transcription Factor Addiction in Leukemia Imposed by the MLL Promoter Sequence

(2018) Bin Lu et al.   CANCER CELL

A map of direct TF–DNA interactions in the human genome

(2018) Marius Gheorghe et al.   NUCLEIC ACIDS RESEARCH

TFClass: expanding the classification of human transcription factors to their mammalian orthologs

(2017) Edgar Wingender et al.   NUCLEIC ACIDS RESEARCH

RSAT matrix-clustering: dynamic exploration and redundancy reduction of transcription factor binding motif collections

(2017) Jaime Abraham Castro-Mondragon et al.   NUCLEIC ACIDS RESEARCH

ANISEED 2017: extending the integrated ascidian database to the exploration and evolutionary comparison of genome-scale datasets

(2017) Matija Brozovic et al.   NUCLEIC ACIDS RESEARCH

MYC2 Orchestrates a Hierarchical Transcriptional Cascade That Regulates Jasmonate-Mediated Plant Immunity in Tomato

(2017) Minmin Du et al.   PLANT CELL

A placental growth factor is silenced in mouse embryos by the zinc finger protein ZFP568

(2017) Peng Yang et al.   SCIENCE

DNA methylation at enhancers identifies distinct breast cancer lineages

(2017) Thomas Fleischer et al.   Nature Communications

CAGEd-oPOSSUM: motif enrichment analysis from CAGE-derived TSSs

(2016) David J. Arenillas et al.   BIOINFORMATICS

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

(2016) Jinpu Jin et al.   NUCLEIC ACIDS RESEARCH

How eukaryotic genes are transcribed

(2016) Bryan J. Venters et al.   CRITICAL REVIEWS IN BIOCHEMISTRY AND MOLECULAR BIOLOGY

LOLA: enrichment analysis for genomic region sets and regulatory elements in R and Bioconductor

(2015) Nathan C. Sheffield et al.   BIOINFORMATICS

DNA-dependent formation of transcription factor pairs alters their binding specificity

(2015) Arttu Jolma et al.   NATURE

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

(2015) Qiye He et al.   NATURE BIOTECHNOLOGY

i-cisTarget 2015 update: generalized cis-regulatory enrichment analysis in human, mouse and fly

(2015) Hana Imrichová et al.   NUCLEIC ACIDS RESEARCH

The MEME Suite

(2015) Timothy L. Bailey et al.   NUCLEIC ACIDS RESEARCH

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

(2014) Martiniano M Ricardi et al.   BMC PLANT BIOLOGY

Determination and Inference of Eukaryotic Transcription Factor Sequence Specificity

(2014) Matthew T. Weirauch et al.   CELL

Absence of a simple code: how transcription factors read the genome

(2014) Matthew Slattery et al.   TRENDS IN BIOCHEMICAL SCIENCES

TFBSshape: a motif database for DNA shape features of transcription factor binding sites

(2013) Lin Yang et al.   NUCLEIC ACIDS RESEARCH

oPOSSUM-3: Advanced Analysis of Regulatory Motif Over-Representation Across Genes or ChIP-Seq Datasets

(2013) Andrew T. Kwon et al.   G3-Genes Genomes Genetics

The Next Generation of Transcription Factor Binding Site Prediction

(2013) Anthony Mathelier et al.   PLoS Computational Biology

i-cisTarget: an integrative genomics method for the prediction of regulatory features and cis-regulatory modules

(2012) Carl Herrmann et al.   NUCLEIC ACIDS RESEARCH

NCBI GEO: archive for functional genomics data sets—update

(2012) Tanya Barrett et al.   NUCLEIC ACIDS RESEARCH

Multiplexed massively parallel SELEX for characterization of human transcription factor binding specificities

(2010) A. Jolma et al.   GENOME RESEARCH

Biopython: freely available Python tools for computational molecular biology and bioinformatics

(2009) P. J. A. Cock et al.   BIOINFORMATICS

JASPAR 2010: the greatly expanded open-access database of transcription factor binding profiles

(2009) Elodie Portales-Casamar et al.   NUCLEIC ACIDS RESEARCH