Fast motif matching revisited: high-order PWMs, SNPs and indels

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

(2016) Matthias Siebert et al.   NUCLEIC ACIDS RESEARCH

atSNP: transcription factor binding affinity testing for regulatory SNP detection

(2015) Chandler Zuo et al.   BIOINFORMATICS

A global reference for human genetic variation

(2015) Richard A. Gibbs et al.   NATURE

HOCOMOCO: expansion and enhancement of the collection of transcription factor binding sites models

(2015) Ivan V. Kulakovskiy et al.   NUCLEIC ACIDS RESEARCH

Structural insights into the DNA-binding specificity of E2F family transcription factors

(2015) Ekaterina Morgunova et al.   Nature Communications

Conservation of transcription factor binding specificities across 600 million years of bilateria evolution

(2015) Kazuhiro R Nitta et al.   eLife

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

(2014) Marc Santolini et al.   PLoS One

Motif matching using gapped patterns

(2014) Emanuele Giaquinta et al.   THEORETICAL COMPUTER SCIENCE

Stability selection for regression-based models of transcription factor-DNA binding specificity

(2013) F. Mordelet et al.   BIOINFORMATICS

DNA-Binding Specificities of Human Transcription Factors

(2013) Arttu Jolma et al.   CELL

Fast Matching of Transcription Factor Motifs Using Generalized Position Weight Matrix Models

(2013) Emanuele Giaquinta et al.   JOURNAL OF COMPUTATIONAL BIOLOGY

Evaluation of methods for modeling transcription factor sequence specificity

(2013) Matthew T Weirauch et al.   NATURE BIOTECHNOLOGY

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

E2F1 Regulates Cellular Growth by mTORC1 Signaling

(2011) Sebastian Real et al.   PLoS One

is-rSNP: a novel technique for in silico regulatory SNP detection

(2010) Geoff Macintyre et al.   BIOINFORMATICS

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

(2010) Rahul Siddharthan   PLoS One

MOODS: fast search for position weight matrix matches in DNA sequences

(2009) J. Korhonen et al.   BIOINFORMATICS

Finding Significant Matches of Position Weight Matrices in Linear Time

(2009) Cinzia Pizzi et al.   IEEE-ACM Transactions on Computational Biology and Bioinformatics

The common colorectal cancer predisposition SNP rs6983267 at chromosome 8q24 confers potential to enhanced Wnt signaling

(2009) Sari Tuupanen et al.   NATURE GENETICS

In Silico Detection of Sequence Variations Modifying Transcriptional Regulation

(2008) Malin C. Andersen et al.   PLoS Computational Biology

Fast profile matching algorithms — A survey

(2008) Cinzia Pizzi et al.   THEORETICAL COMPUTER SCIENCE

A Feature-Based Approach to Modeling Protein–DNA Interactions

(2008) Eilon Sharon et al.   PLoS Computational Biology