Automated incorporation of pairwise dependency in transcription factor binding site prediction using dinucleotide weight tensors

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

(2016) Matthias Siebert et al.   NUCLEIC ACIDS RESEARCH

DNA-Binding Specificities of Human Transcription Factors

(2013) Arttu Jolma et al.   CELL

The Next Generation of Transcription Factor Binding Site Prediction

(2013) Anthony Mathelier et al.   PLoS Computational Biology

MotEvo: integrated Bayesian probabilistic methods for inferring regulatory sites and motifs on multiple alignments of DNA sequences

(2012) Phil Arnold et al.   BIOINFORMATICS

Improved Models for Transcription Factor Binding Site Identification Using Nonindependent Interactions

(2012) Yue Zhao et al.   GENETICS

An integrated encyclopedia of DNA elements in the human genome

(2012)   NATURE

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

(2011) Razvan Nutiu et al.   NATURE BIOTECHNOLOGY

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

(2010) A. Jolma et al.   GENOME RESEARCH

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

(2010) Rahul Siddharthan   PLoS One

Disentangling Direct from Indirect Co-Evolution of Residues in Protein Alignments

(2010) Lukas Burger et al.   PLoS Computational Biology

Diversity and Complexity in DNA Recognition by Transcription Factors

(2009) G. Badis et al.   SCIENCE

A Feature-Based Approach to Modeling Protein–DNA Interactions

(2008) Eilon Sharon et al.   PLoS Computational Biology