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

Combinatorial Cis -regulation in Saccharomyces Species

(2016) Aaron T. Spivak et al.   G3-Genes Genomes Genetics

Low Affinity Binding Site Clusters Confer Hox Specificity and Regulatory Robustness

(2015) Justin Crocker et al.   CELL

Unraveling determinants of transcription factor binding outside the core binding site

(2015) Michal Levo et al.   GENOME RESEARCH

DNA-dependent formation of transcription factor pairs alters their binding specificity

(2015) Arttu Jolma et al.   NATURE

C2H2 zinc finger proteins greatly expand the human regulatory lexicon

(2015) Hamed S Najafabadi et al.   NATURE BIOTECHNOLOGY

Predicting the sequence specificities of DNA- and RNA-binding proteins by deep learning

(2015) Babak Alipanahi et al.   NATURE BIOTECHNOLOGY

Specificity and nonspecificity in RNA–protein interactions

(2015) Eckhard Jankowsky et al.   NATURE REVIEWS MOLECULAR CELL BIOLOGY

Varying levels of complexity in transcription factor binding motifs

(2015) Jens Keilwagen et al.   NUCLEIC ACIDS RESEARCH

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

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

JASPAR 2016: a major expansion and update of the open-access database of transcription factor binding profiles

(2015) Anthony Mathelier et al.   NUCLEIC ACIDS RESEARCH

Quantitative modeling of transcription factor binding specificities using DNA shape

(2015) Tianyin Zhou et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Application of experimentally verified transcription factor binding sites models for computational analysis of ChIP-Seq data

(2014) Victor G Levitsky et al.   BMC GENOMICS

High-Resolution Specificity from DNA Sequencing Highlights Alternative Modes of Lac Repressor Binding

(2014) Z. Zuo et al.   GENETICS

Transcriptome Maps of mRNP Biogenesis Factors Define Pre-mRNA Recognition

(2014) Carlo Baejen et al.   MOLECULAR CELL

Diversity and dynamics of the Drosophila transcriptome

(2014) James B. Brown et al.   NATURE

CTCF: an architectural protein bridging genome topology and function

(2014) Chin-Tong Ong et al.   NATURE REVIEWS GENETICS

Binding site discovery from nucleic acid sequences by discriminative learning of hidden Markov models

(2014) Jonas Maaskola et al.   NUCLEIC ACIDS RESEARCH

A pause sequence enriched at translation start sites drives transcription dynamics in vivo

(2014) M. H. Larson et al.   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

Transcriptome Surveillance by Selective Termination of Noncoding RNA Synthesis

(2013) Daniel Schulz et al.   CELL

Extensive transcriptional heterogeneity revealed by isoform profiling

(2013) Vicent Pelechano et al.   NATURE

Genome-wide probing of RNA structure reveals active unfolding of mRNA structures in vivo

(2013) Silvi Rouskin et al.   NATURE

Evaluation of methods for modeling transcription factor sequence specificity

(2013) Matthew T Weirauch et al.   NATURE BIOTECHNOLOGY

TherMos: Estimating protein–DNA binding energies from in vivo binding profiles

(2013) Wenjie Sun et al.   NUCLEIC ACIDS RESEARCH

Structural insights into the targeting of mRNA GU-rich elements by the three RRMs of CELF1

(2013) J. M. Edwards et al.   NUCLEIC ACIDS RESEARCH

Unravelling the hidden DNA structural/physical code provides novel insights on promoter location

(2013) Elisa Durán et al.   NUCLEIC ACIDS RESEARCH

JASPAR 2014: an extensively expanded and updated open-access database of transcription factor binding profiles

(2013) Anthony Mathelier et al.   NUCLEIC ACIDS RESEARCH

A Genome-wide Map of CTCF Multivalency Redefines the CTCF Code

(2013) Hirotaka Nakahashi et al.   Cell Reports

Genomic Regions Flanking E-Box Binding Sites Influence DNA Binding Specificity of bHLH Transcription Factors through DNA Shape

(2013) Raluca Gordân et al.   Cell Reports

The Next Generation of Transcription Factor Binding Site Prediction

(2013) Anthony Mathelier et al.   PLoS Computational Biology

FROM BINDING MOTIFS IN CHIP-SEQ DATA TO IMPROVED MODELS OF TRANSCRIPTION FACTOR BINDING SITES

(2013) IVAN KULAKOVSKIY et al.   Journal of Bioinformatics and Computational Biology

Improved Models for Transcription Factor Binding Site Identification Using Nonindependent Interactions

(2012) Yue Zhao et al.   GENETICS

P-value-based regulatory motif discovery using positional weight matrices

(2012) H. Hartmann et al.   GENOME RESEARCH

Sequence and chromatin determinants of cell-type-specific transcription factor binding

(2012) A. Arvey et al.   GENOME RESEARCH

An integrated encyclopedia of DNA elements in the human genome

(2012)   NATURE

SwissRegulon, a database of genome-wide annotations of regulatory sites: recent updates

(2012) Mikhail Pachkov et al.   NUCLEIC ACIDS RESEARCH

Basic leucine zipper transcription factor Hac1 binds DNA in two distinct modes as revealed by microfluidic analyses

(2012) P. M. Fordyce et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

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

(2011) Yue Zhao et al.   NATURE BIOTECHNOLOGY

Transcriptome-Wide Binding Sites for Components of the Saccharomyces cerevisiae Non-Poly(A) Termination Pathway: Nrd1, Nab3, and Sen1

(2011) Tyler J. Creamer et al.   PLoS Genetics

Signals for pre-mRNA cleavage and polyadenylation

(2011) Bin Tian et al.   Wiley Interdisciplinary Reviews-RNA

Origins of Specificity in Protein-DNA Recognition

(2010) Remo Rohs et al.   Annual Review of Biochemistry

Structural Basis of Alternative DNA Recognition by Maf Transcription Factors

(2009) H. Kurokawa et al.   MOLECULAR AND CELLULAR BIOLOGY

The role of DNA shape in protein–DNA recognition

(2009) Remo Rohs et al.   NATURE

A census of human transcription factors: function, expression and evolution

(2009) Juan M. Vaquerizas et al.   NATURE REVIEWS GENETICS

Diversity and Complexity in DNA Recognition by Transcription Factors

(2009) G. Badis et al.   SCIENCE

DNA Binding Site Sequence Directs Glucocorticoid Receptor Structure and Activity

(2009) S. H. Meijsing et al.   SCIENCE

Motif composition, conservation and condition-specificity of single and alternative transcription start sites in the Drosophila genome

(2009) Elizabeth A Rach et al.   GENOME BIOLOGY

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

(2008) Xi Chen et al.   CELL