Integrated analysis of motif activity and gene expression changes of transcription factors

Dynamic Rewiring of Promoter-Anchored Chromatin Loops during Adipocyte Differentiation

(2017) Rasmus Siersbæk et al.   MOLECULAR CELL

Predicting transcription factor binding motifs from DNA-binding domains, chromatin accessibility and gene expression data

(2017) Mahdi Zamanighomi et al.   NUCLEIC ACIDS RESEARCH

Mocap: large-scale inference of transcription factor binding sites from chromatin accessibility

(2017) Xi Chen et al.   NUCLEIC ACIDS RESEARCH

TFBSTools: an R/bioconductor package for transcription factor binding site analysis

(2016) Ge Tan et al.   BIOINFORMATICS

Romulus: robust multi-state identification of transcription factor binding sites from DNase-seq data

(2016) Aleksander Jankowski et al.   BIOINFORMATICS

Modelingcis-regulation with a compendium of genome-wide histone H3K27ac profiles

(2016) Su Wang et al.   GENOME RESEARCH

Integrative Genomics Outlines a Biphasic Glucose Response and a ChREBP-RORγ Axis Regulating Proliferation in β Cells

(2016) Søren Fisker Schmidt et al.   Cell Reports

E-Flux2 and SPOT: Validated Methods for Inferring Intracellular Metabolic Flux Distributions from Transcriptomic Data

(2016) Min Kyung Kim et al.   PLoS One

BinDNase: a discriminatory approach for transcription factor binding prediction using DNase I hypersensitivity data

(2015) Juhani Kähärä et al.   BIOINFORMATICS

Optimally choosing PWM motif databases and sequence scanning approaches based on ChIP-seq data

(2015) Michal Dabrowski et al.   BMC BIOINFORMATICS

C2H2 zinc finger proteins greatly expand the human regulatory lexicon

(2015) Hamed S Najafabadi et al.   NATURE BIOTECHNOLOGY

iRNA-seq: computational method for genome-wide assessment of acute transcriptional regulation from total RNA-seq data

(2015) Jesper Grud Skat Madsen et al.   NUCLEIC ACIDS RESEARCH

KEGG as a reference resource for gene and protein annotation

(2015) Minoru Kanehisa et al.   NUCLEIC ACIDS RESEARCH

HOCOMOCO: expansion and enhancement of the collection of transcription factor binding sites models

(2015) Ivan V. Kulakovskiy et al.   NUCLEIC ACIDS RESEARCH

RegulonDB version 9.0: high-level integration of gene regulation, coexpression, motif clustering and beyond

(2015) Socorro Gama-Castro et al.   NUCLEIC ACIDS RESEARCH

Determination and Inference of Eukaryotic Transcription Factor Sequence Specificity

(2014) Matthew T. Weirauch et al.   CELL

ISMARA: automated modeling of genomic signals as a democracy of regulatory motifs

(2014) P. J. Balwierz et al.   GENOME RESEARCH

Discovery of directional and nondirectional pioneer transcription factors by modeling DNase profile magnitude and shape

(2014) Richard I Sherwood et al.   NATURE BIOTECHNOLOGY

Gene Ontology Consortium: going forward

(2014)   NUCLEIC ACIDS RESEARCH

AnimalTFDB 2.0: a resource for expression, prediction and functional study of animal transcription factors

(2014) Hong-Mei Zhang et al.   NUCLEIC ACIDS RESEARCH

Transcription Factor Cooperativity in Early Adipogenic Hotspots and Super-Enhancers

(2014) Rasmus Siersbæk et al.   Cell Reports

Identification of the transcription factor ZEB1 as a central component of the adipogenic gene regulatory network

(2014) Carine Gubelmann et al.   eLife

Predicting tissue specific transcription factor binding sites

(2013) Shan Zhong et al.   BMC GENOMICS

A community-driven global reconstruction of human metabolism

(2013) Ines Thiele et al.   NATURE BIOTECHNOLOGY

Target analysis by integration of transcriptome and ChIP-seq data with BETA

(2013) Su Wang et al.   Nature Protocols

Systematic discovery and characterization of regulatory motifs in ENCODE TF binding experiments

(2013) P. Kheradpour et al.   NUCLEIC ACIDS RESEARCH

The Reactome pathway knowledgebase

(2013) David Croft et al.   NUCLEIC ACIDS RESEARCH

STAR: ultrafast universal RNA-seq aligner

(2012) Alexander Dobin et al.   BIOINFORMATICS

Uncovering cis-regulatory sequence requirements for context-specific transcription factor binding

(2012) J. O. Yanez-Cuna et al.   GENOME RESEARCH

Sequence and chromatin determinants of cell-type-specific transcription factor binding

(2012) A. Arvey et al.   GENOME RESEARCH

Genome-Wide Profiling of Peroxisome Proliferator-Activated Receptor   in Primary Epididymal, Inguinal, and Brown Adipocytes Reveals Depot-Selective Binding Correlated with Gene Expression

(2012) M. S. Siersbaek et al.   MOLECULAR AND CELLULAR BIOLOGY

An integrated encyclopedia of DNA elements in the human genome

(2012)   NATURE

Fiji: an open-source platform for biological-image analysis

(2012) Johannes Schindelin et al.   NATURE METHODS

TFClass: an expandable hierarchical classification of human transcription factors

(2012) Edgar Wingender et al.   NUCLEIC ACIDS RESEARCH

Identification of New Genes Involved in Human Adipogenesis and Fat Storage

(2012) Jörn Söhle et al.   PLoS One

Increasing Coverage of Transcription Factor Position Weight Matrices through Domain-level Homology

(2012) Brady Bernard et al.   PLoS One

FIMO: scanning for occurrences of a given motif

(2011) Charles E. Grant et al.   BIOINFORMATICS

Cofactor Binding Evokes Latent Differences in DNA Binding Specificity between Hox Proteins

(2011) Matthew Slattery et al.   CELL

Extensive chromatin remodelling and establishment of transcription factor ‘hotspots’ during early adipogenesis

(2011) Rasmus Siersbaek et al.   EMBO JOURNAL

An Integrated Pipeline for the Genome-Wide Analysis of Transcription Factor Binding Sites from ChIP-Seq

(2011) Eloi Mercier et al.   PLoS One

Gene-chip studies of adipogenesis-regulated microRNAs in mouse primary adipocytes and human obesity

(2011) Pernille Keller et al.   BMC Endocrine Disorders

Propagation of adipogenic signals through an epigenomic transition state

(2010) D. J. Steger et al.   GENES & DEVELOPMENT

Accurate inference of transcription factor binding from DNA sequence and chromatin accessibility data

(2010) R. Pique-Regi et al.   GENOME RESEARCH

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

Gene ontology analysis for RNA-seq: accounting for selection bias

(2010) Matthew D Young et al.   GENOME BIOLOGY

edgeR: a Bioconductor package for differential expression analysis of digital gene expression data

(2009) M. D. Robinson et al.   BIOINFORMATICS

BLAST+: architecture and applications

(2009) Christiam Camacho et al.   BMC BIOINFORMATICS

Re-expression of GATA2 Cooperates with Peroxisome Proliferator-activated Receptor-γ Depletion to Revert the Adipocyte Phenotype

(2009) Michael Schupp et al.   JOURNAL OF BIOLOGICAL CHEMISTRY

The transcriptional network that controls growth arrest and differentiation in a human myeloid leukemia cell line

(2009) Harukazu Suzuki et al.   NATURE GENETICS

Adaptive Evolution in Zinc Finger Transcription Factors

(2009) Ryan O. Emerson et al.   PLoS Genetics

Predicting the binding preference of transcription factors to individual DNA k-mers

(2008) T. M. Alleyne et al.   BIOINFORMATICS

Variation in Homeodomain DNA Binding Revealed by High-Resolution Analysis of Sequence Preferences

(2008) Michael F. Berger et al.   CELL

Analysis of Homeodomain Specificities Allows the Family-wide Prediction of Preferred Recognition Sites

(2008) Marcus B. Noyes et al.   CELL