Feature-based classification of human transcription factors into hypothetical sub-classes related to regulatory function

Role of Ets Proteins in Development, Differentiation, and Function of T-Cell Subsets

(2015) Mian Liu et al.   MEDICINAL RESEARCH REVIEWS

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

(2015) Arttu Jolma et al.   NATURE

Transcribed enhancers lead waves of coordinated transcription in transitioning mammalian cells

(2015) Erik Arner et al.   SCIENCE

Chromatin remodeling mediated by the FOXA1/A2 transcription factors activatesCFTRexpression in intestinal epithelial cells

(2014) Jenny L Kerschner et al.   Epigenetics

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

(2014) Richard I Sherwood et al.   NATURE BIOTECHNOLOGY

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

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

The Interplay between Chromatin and Transcription Factor Networks during B Cell Development: Who Pulls the Trigger First?

(2014) Mohamed Amin Choukrallah et al.   Frontiers in Immunology

KRAB-Zinc Finger Proteins: A Repressor Family Displaying Multiple Biological Functions

(2013) Angelo Lupo et al.   CURRENT GENOMICS

Pfam: the protein families database

(2013) Robert D. Finn et al.   NUCLEIC ACIDS RESEARCH

JASPAR 2014: an extensively expanded and updated open-access database of transcription factor binding profiles

(2013) Anthony Mathelier et al.   NUCLEIC ACIDS RESEARCH

Multi-class AdaBoost

(2013) Trevor Hastie et al.   Statistics and Its Interface

How to evaluate performance of prediction methods? Measures and their interpretation in variation effect analysis

(2012) Mauno Vihinen   BMC GENOMICS

Sequence features and chromatin structure around the genomic regions bound by 119 human transcription factors

(2012) J. Wang et al.   GENOME RESEARCH

An integrated encyclopedia of DNA elements in the human genome

(2012)   NATURE

TFClass: an expandable hierarchical classification of human transcription factors

(2012) Edgar Wingender et al.   NUCLEIC ACIDS RESEARCH

The BioGRID interaction database: 2013 update

(2012) Andrew Chatr-aryamontri et al.   NUCLEIC ACIDS RESEARCH

PhosphoSitePlus: a comprehensive resource for investigating the structure and function of experimentally determined post-translational modifications in man and mouse

(2011) P. V. Hornbeck et al.   NUCLEIC ACIDS RESEARCH

Pioneer factors: directing transcriptional regulators within the chromatin environment

(2011) Luca Magnani et al.   TRENDS IN GENETICS

An Atlas of Combinatorial Transcriptional Regulation in Mouse and Man

(2010) Timothy Ravasi et al.   CELL

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

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

GOrilla: a tool for discovery and visualization of enriched GO terms in ranked gene lists

(2009) Eran Eden et al.   BMC BIOINFORMATICS

Learning from Imbalanced Data

(2009) Haibo He et al.   IEEE TRANSACTIONS ON KNOWLEDGE AND DATA ENGINEERING

Systematic and integrative analysis of large gene lists using DAVID bioinformatics resources

(2009) Da Wei Huang et al.   Nature Protocols

Distinctive sequence patterns in metazoan and yeast nucleosomes: Implications for linker histone binding to AT-rich and methylated DNA

(2009) Feng Cui et al.   NUCLEIC ACIDS RESEARCH

Patterns of evolutionary constraints on genes in humans

(2008) Subhajyoti De et al.   BMC EVOLUTIONARY BIOLOGY

Human Protein Reference Database--2009 update

(2008) T. S. Keshava Prasad et al.   NUCLEIC ACIDS RESEARCH

Functional protein divergence in the evolution of Homo sapiens

(2008) Nuria Lopez-Bigas et al.   GENOME BIOLOGY