A General Pairwise Interaction Model Provides an Accurate Description of In Vivo Transcription Factor Binding Sites

Searching for Collective Behavior in a Large Network of Sensory Neurons

(2014) Gašper Tkačik et al.   PLoS Computational Biology

DNA-Binding Specificities of Human Transcription Factors

(2013) Arttu Jolma et al.   CELL

Elements of Coevolution in Biological Sequences

(2013) Olivier Rivoire   PHYSICAL REVIEW LETTERS

From Principal Component to Direct Coupling Analysis of Coevolution in Proteins: Low-Eigenvalue Modes are Needed for Structure Prediction

(2013) Simona Cocco et al.   PLoS Computational Biology

The Next Generation of Transcription Factor Binding Site Prediction

(2013) Anthony Mathelier et al.   PLoS Computational Biology

Improved Models for Transcription Factor Binding Site Identification Using Nonindependent Interactions

(2012) Yue Zhao et al.   GENETICS

What does our genome encode?

(2012) J. A. Stamatoyannopoulos   GENOME RESEARCH

An integrated encyclopedia of DNA elements in the human genome

(2012)   NATURE

Transcription factors: from enhancer binding to developmental control

(2012) François Spitz et al.   NATURE REVIEWS GENETICS

Statistical mechanics for natural flocks of birds

(2012) W. Bialek et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

High-dimensional inference with the generalized Hopfield model: Principal component analysis and corrections

(2011) S. Cocco et al.   PHYSICAL REVIEW E

Direct-coupling analysis of residue coevolution captures native contacts across many protein families

(2011) F. Morcos et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Genome-wide MyoD Binding in Skeletal Muscle Cells: A Potential for Broad Cellular Reprogramming

(2010) Yi Cao et al.   DEVELOPMENTAL CELL

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

On the detection and refinement of transcription factor binding sites using ChIP-Seq data

(2010) Ming Hu et al.   NUCLEIC ACIDS RESEARCH

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

(2010) Rahul Siddharthan   PLoS One

Maximum entropy models for antibody diversity

(2010) T. Mora et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Genome-wide identification of cis-regulatory motifs and modules underlying gene coregulation using statistics and phylogeny

(2010) H. Rouault et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Combinatorial binding predicts spatio-temporal cis-regulatory activity

(2009) Robert P. Zinzen et al.   NATURE

JASPAR 2010: the greatly expanded open-access database of transcription factor binding profiles

(2009) Elodie Portales-Casamar et al.   NUCLEIC ACIDS RESEARCH

Diversity and Complexity in DNA Recognition by Transcription Factors

(2009) G. Badis et al.   SCIENCE

The TRANSFAC project as an example of framework technology that supports the analysis of genomic regulation

(2008) E. Wingender   BRIEFINGS IN BIOINFORMATICS

Integration of External Signaling Pathways with the Core Transcriptional Network in Embryonic Stem Cells

(2008) Xi Chen et al.   CELL

The Statistics of Repeating Patterns of Cortical Activity Can Be Reproduced by a Model Network of Stochastic Binary Neurons

(2008) A. Roxin et al.   JOURNAL OF NEUROSCIENCE

Identification of direct residue contacts in protein-protein interaction by message passing

(2008) M. Weigt 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