Related references
Note: Only part of the references are listed.Quantitative modeling of transcription factor binding specificities using DNA shape
Tianyin Zhou et al.
PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA (2015)
Systematic discovery and characterization of regulatory motifs in ENCODE TF binding experiments
Pouya Kheradpour et al.
NUCLEIC ACIDS RESEARCH (2014)
c-Jun/c-Fos heterodimers regulate cellular genes via a newly identified class of methylated DNA sequence motifs
Montse Gustems et al.
NUCLEIC ACIDS RESEARCH (2014)
TFBSshape: a motif database for DNA shape features of transcription factor binding sites
Lin Yang et al.
NUCLEIC ACIDS RESEARCH (2014)
On the Value of Intra-Motif Dependencies of Human Insulator Protein CTCF
Ralf Eggeling et al.
PLOS ONE (2014)
Absence of a simple code: how transcription factors read the genome
Matthew Slattery et al.
TRENDS IN BIOCHEMICAL SCIENCES (2014)
Stability selection for regression-based models of transcription factor-DNA binding specificity
Fantine Mordelet et al.
BIOINFORMATICS (2013)
DNA-Binding Specificities of Human Transcription Factors
Arttu Jolma et al.
CELL (2013)
Evaluation of methods for modeling transcription factor sequence specificity
Matthew T. Weirauch et al.
NATURE BIOTECHNOLOGY (2013)
A general approach for discriminative de novo motif discovery from high-throughput data
Jan Grau et al.
NUCLEIC ACIDS RESEARCH (2013)
A Genome-wide Map of CTCF Multivalency Redefines the CTCF Code
Hirotaka Nakahashi et al.
CELL REPORTS (2013)
Genomic Regions Flanking E-Box Binding Sites Influence DNA Binding Specificity of bHLH Transcription Factors through DNA Shape
Raluca Gordan et al.
CELL REPORTS (2013)
The Next Generation of Transcription Factor Binding Site Prediction
Anthony Mathelier et al.
PLOS COMPUTATIONAL BIOLOGY (2013)
FROM BINDING MOTIFS IN CHIP-SEQ DATA TO IMPROVED MODELS OF TRANSCRIPTION FACTOR BINDING SITES
Ivan Kulakovskiy et al.
JOURNAL OF BIOINFORMATICS AND COMPUTATIONAL BIOLOGY (2013)
Improved Models for Transcription Factor Binding Site Identification Using Nonindependent Interactions
Yue Zhao et al.
GENETICS (2012)
An integrated encyclopedia of DNA elements in the human genome
Ian Dunham et al.
NATURE (2012)
DECOD: fast and accurate discriminative DNA motif finding
Peter Huggins et al.
BIOINFORMATICS (2011)
DREME: motif discovery in transcription factor ChIP-seq data
Timothy L. Bailey
BIOINFORMATICS (2011)
Coassembly of REST and its cofactors at sites of gene repression in embryonic stem cells
Hong-Bing Yu et al.
GENOME RESEARCH (2011)
Jury remains out on simple models of transcription factor specificity
Quaid Morris et al.
NATURE BIOTECHNOLOGY (2011)
Quantitative analysis demonstrates most transcription factors require only simple models of specificity
Yue Zhao et al.
NATURE BIOTECHNOLOGY (2011)
Systems Analysis of ATF3 in Stress Response and Cancer Reveals Opposing Effects on Pro-Apoptotic Genes in p53 Pathway
Yujiro Tanaka et al.
PLOS ONE (2011)
ATF3, an HTLV-1 bZip factor binding protein, promotes proliferation of adult T-cell leukemia cells
Keita Hagiya et al.
RETROVIROLOGY (2011)
De-Novo Discovery of Differentially Abundant Transcription Factor Binding Sites Including Their Positional Preference
Jens Keilwagen et al.
PLOS COMPUTATIONAL BIOLOGY (2011)
Unifying generative and discriminative learning principles
Jens Keilwagen et al.
BMC BIOINFORMATICS (2010)
Apples and oranges: avoiding different priors in Bayesian DNA sequence analysis
Jens Keilwagen et al.
BMC BIOINFORMATICS (2010)
Inclusion of neighboring base interdependencies substantially improves genome-wide prokaryotic transcription factor binding site prediction
Rafik A. Salama et al.
NUCLEIC ACIDS RESEARCH (2010)
Galaxy: a comprehensive approach for supporting accessible, reproducible, and transparent computational research in the life sciences
Jeremy Goecks et al.
GENOME BIOLOGY (2010)
Functional diversity for REST (NRSF) is defined by in vivo binding affinity hierarchies at the DNA sequence level
Alexander W. Bruce et al.
GENOME RESEARCH (2009)
Diversity and Complexity in DNA Recognition by Transcription Factors
Gwenael Badis et al.
SCIENCE (2009)
A Feature-Based Approach to Modeling Protein-DNA Interactions
Eilon Sharon et al.
PLOS COMPUTATIONAL BIOLOGY (2008)
A potential dichotomous role of ATF3, an adaptive-response gene, in cancer development
X. Yin et al.
ONCOGENE (2008)
STAMP: a web tool for exploring DNA-binding motif similarities
Shaun Mahony et al.
NUCLEIC ACIDS RESEARCH (2007)
Position dependencies in transcription factor binding sites
Andrija Tomovic et al.
BIOINFORMATICS (2007)
ARTS:: accurate recognition of transcription starts in human
Soeren Sonnenburg et al.
BIOINFORMATICS (2006)
MEME: discovering and analyzing DNA and protein sequence motifs
Timothy L. Bailey et al.
NUCLEIC ACIDS RESEARCH (2006)
Identification of transcription factor binding sites with variable-order Bayesian networks
I Ben-Gal et al.
BIOINFORMATICS (2005)
Analysis and recognition of 5′ UTR intron splice sites in human pre-mRNA
E Eden et al.
NUCLEIC ACIDS RESEARCH (2004)
Environmentally induced foregut remodeling by PHA-4/FoxA and DAF-12/NHR
W Ao et al.
SCIENCE (2004)
Maximum entropy modeling of short sequence motifs with applications to RNA splicing signals
G Yeo et al.
JOURNAL OF COMPUTATIONAL BIOLOGY (2004)
Additivity in protein-DNA interactions: how good an approximation is it?
PV Benos et al.
NUCLEIC ACIDS RESEARCH (2002)
Activating transcription factor 3 induces DNA synthesis and expression of cyclin D1 in hepatocytes
AL Allan et al.
JOURNAL OF BIOLOGICAL CHEMISTRY (2001)