GTRD: an integrated view of transcription regulation

BioUML: an integrated environment for systems biology and collaborative analysis of biomedical data

(2019) Fedor Kolpakov et al.   NUCLEIC ACIDS RESEARCH

Population size estimation for quality control of ChIP-Seq datasets

(2019) Semyon K. Kolmykov et al.   PLoS One

KnockTF: a comprehensive human gene expression profile database with knockdown/knockout of transcription factors

(2019) Chenchen Feng et al.   NUCLEIC ACIDS RESEARCH

New developments on the Encyclopedia of DNA Elements (ENCODE) data portal

(2019) Yunhai Luo et al.   NUCLEIC ACIDS RESEARCH

The BaMM web server for de-novo motif discovery and regulatory sequence analysis

(2018) Anja Kiesel et al.   NUCLEIC ACIDS RESEARCH

MethMotif: an integrative cell specific database of transcription factor binding motifs coupled with DNA methylation profiles

(2018) Quy Xiao Xuan Lin et al.   NUCLEIC ACIDS RESEARCH

BRENDA in 2019: a European ELIXIR core data resource

(2018) Lisa Jeske et al.   NUCLEIC ACIDS RESEARCH

GTRD: a database on gene transcription regulation—2019 update

(2018) Ivan Yevshin et al.   NUCLEIC ACIDS RESEARCH

Update of the FANTOM web resource: expansion to provide additional transcriptome atlases

(2018) Marina Lizio 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

HOCOMOCO: towards a complete collection of transcription factor binding models for human and mouse via large-scale ChIP-Seq analysis

(2017) Ivan V Kulakovskiy et al.   NUCLEIC ACIDS RESEARCH

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

(2016) Ivan Yevshin et al.   NUCLEIC ACIDS RESEARCH

Bayesian Markov models consistently outperform PWMs at predicting motifs in nucleotide sequences

(2016) Matthias Siebert et al.   NUCLEIC ACIDS RESEARCH

The Cell Ontology 2016: enhanced content, modularization, and ontology interoperability

(2016) Alexander D. Diehl et al.   Journal of Biomedical Semantics

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

(2015) Qiye He et al.   NATURE BIOTECHNOLOGY

The Molecular Signatures Database Hallmark Gene Set Collection

(2015) Arthur Liberzon et al.   Cell Systems

Determination and Inference of Eukaryotic Transcription Factor Sequence Specificity

(2014) Matthew T. Weirauch et al.   CELL

A promoter-level mammalian expression atlas

(2014)   NATURE

In pursuit of design principles of regulatory sequences

(2014) Michal Levo et al.   NATURE REVIEWS GENETICS

Track data hubs enable visualization of user-defined genome-wide annotations on the UCSC Genome Browser

(2013) B. J. Raney et al.   BIOINFORMATICS

The Genotype-Tissue Expression (GTEx) project

(2013) John Lonsdale et al.   NATURE GENETICS

Transposition of native chromatin for fast and sensitive epigenomic profiling of open chromatin, DNA-binding proteins and nucleosome position

(2013) Jason D Buenrostro et al.   NATURE METHODS

ChIP-seq guidelines and practices of the ENCODE and modENCODE consortia

(2012) S. G. Landt et al.   GENOME RESEARCH

NCBI GEO: archive for functional genomics data sets—update

(2012) Tanya Barrett et al.   NUCLEIC ACIDS RESEARCH

The Plant Ontology as a Tool for Comparative Plant Anatomy and Genomic Analyses

(2012) Laurel Cooper et al.   PLANT AND CELL PHYSIOLOGY

Deciphering the transcriptional cis-regulatory code

(2012) J. Omar Yáñez-Cuna et al.   TRENDS IN GENETICS

Uberon, an integrative multi-species anatomy ontology

(2012) Christopher J Mungall et al.   GENOME BIOLOGY

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

(2011) Ho Sung Rhee et al.   CELL

The sequence read archive: explosive growth of sequencing data

(2011) Y. Kodama et al.   NUCLEIC ACIDS RESEARCH

BigWig and BigBed: enabling browsing of large distributed datasets

(2010) W. J. Kent et al.   BIOINFORMATICS

Modeling sample variables with an Experimental Factor Ontology

(2010) James Malone et al.   BIOINFORMATICS

A map of open chromatin in human pancreatic islets

(2010) Kyle J Gaulton et al.   NATURE GENETICS

A Non-Homogeneous Hidden-State Model on First Order Differences for Automatic Detection of Nucleosome Positions

(2009) Pei Fen Kuan et al.   Statistical Applications in Genetics and Molecular Biology