Evaluation of methods for modeling transcription factor sequence specificity

Improved Models for Transcription Factor Binding Site Identification Using Nonindependent Interactions

(2012) Yue Zhao et al.   GENETICS

hmChIP: a database and web server for exploring publicly available human and mouse ChIP-seq and ChIP-chip data

(2011) Li Chen et al.   BIOINFORMATICS

MEME-ChIP: motif analysis of large DNA datasets

(2011) Philip Machanick et al.   BIOINFORMATICS

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

(2011) Matthew Slattery et al.   CELL

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

(2011) Ho Sung Rhee et al.   CELL

Direct measurement of DNA affinity landscapes on a high-throughput sequencing instrument

(2011) Razvan Nutiu et al.   NATURE BIOTECHNOLOGY

Quantitative analysis demonstrates most transcription factors require only simple models of specificity

(2011) Yue Zhao et al.   NATURE BIOTECHNOLOGY

Sequence specificity is obtained from the majority of modular C2H2 zinc-finger arrays

(2011) Kathy N. Lam et al.   NUCLEIC ACIDS RESEARCH

The UCSC Genome Browser database: extensions and updates 2011

(2011) T. R. Dreszer et al.   NUCLEIC ACIDS RESEARCH

YeTFaSCo: a database of evaluated yeast transcription factor sequence specificities

(2011) C. G. de Boer et al.   NUCLEIC ACIDS RESEARCH

A Linear Model for Transcription Factor Binding Affinity Prediction in Protein Binding Microarrays

(2011) Matti Annala et al.   PLoS One

De-Novo Discovery of Differentially Abundant Transcription Factor Binding Sites Including Their Positional Preference

(2011) Jens Keilwagen et al.   PLoS Computational Biology

Deep and wide digging for binding motifs in ChIP-Seq data

(2010) I. V. Kulakovskiy et al.   BIOINFORMATICS

Genome-wide analysis of ETS-family DNA-binding in vitro and in vivo

(2010) Gong-Hong Wei et al.   EMBO JOURNAL

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

(2010) A. Jolma et al.   GENOME RESEARCH

Conservation and regulatory associations of a wide affinity range of mouse transcription factor binding sites

(2010) Savina A. Jaeger et al.   GENOMICS

De novo identification and biophysical characterization of transcription-factor binding sites with microfluidic affinity analysis

(2010) Polly M Fordyce et al.   NATURE BIOTECHNOLOGY

From the editors

(2010)   NATURE REVIEWS MOLECULAR CELL BIOLOGY

ArrayExpress update--an archive of microarray and high-throughput sequencing-based functional genomics experiments

(2010) H. Parkinson et al.   NUCLEIC ACIDS RESEARCH

NCBI GEO: archive for functional genomics data sets--10 years on

(2010) T. Barrett et al.   NUCLEIC ACIDS RESEARCH

Towards a Rigorous Assessment of Systems Biology Models: The DREAM3 Challenges

(2010) Robert J. Prill et al.   PLoS One

Dinucleotide Weight Matrices for Predicting Transcription Factor Binding Sites: Generalizing the Position Weight Matrix

(2010) Rahul Siddharthan   PLoS One

Using deep sequencing to characterize the biophysical mechanism of a transcriptional regulatory sequence

(2010) J. B. Kinney et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

High Resolution Models of Transcription Factor-DNA Affinities Improve In Vitro and In Vivo Binding Predictions

(2010) Phaedra Agius et al.   PLoS Computational Biology

Lessons from the DREAM2 Challenges

(2009) Gustavo Stolovitzky et al.   Annals of the New York Academy of Sciences

High-resolution DNA-binding specificity analysis of yeast transcription factors

(2009) C. Zhu et al.   GENOME RESEARCH

Bind-n-Seq: high-throughput analysis of in vitro protein–DNA interactions using massively parallel sequencing

(2009) Artem Zykovich et al.   NUCLEIC ACIDS RESEARCH

The Pfam protein families database

(2009) Robert D. Finn et al.   NUCLEIC ACIDS RESEARCH

Diversity and Complexity in DNA Recognition by Transcription Factors

(2009) G. Badis et al.   SCIENCE

Inferring Binding Energies from Selected Binding Sites

(2009) Yue Zhao et al.   PLoS Computational Biology

MAMOT: hidden Markov modeling tool

(2008) Frédéric Schütz et al.   BIOINFORMATICS

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

(2008) Michael F. Berger et al.   CELL

Transcription factor and microRNA motif discovery: The Amadeus platform and a compendium of metazoan target sets

(2008) C. Linhart et al.   GENOME RESEARCH

Design of Compact, Universal DNA Microarrays for Protein Binding Microarray Experiments

(2008) Anthony A. Philippakis et al.   JOURNAL OF COMPUTATIONAL BIOLOGY

Predicting expression patterns from regulatory sequence in Drosophila segmentation

(2008) Eran Segal et al.   NATURE

Discovering gapped binding sites of yeast transcription factors

(2008) C.-Y. Chen et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

A Feature-Based Approach to Modeling Protein–DNA Interactions

(2008) Eilon Sharon et al.   PLoS Computational Biology