DynaMIT: the dynamic motif integration toolkit

SeAMotE: a method for high-throughput motif discovery in nucleic acid sequences

(2014) Federico Agostini et al.   BMC GENOMICS

CTCF: an architectural protein bridging genome topology and function

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

GraphProt: modeling binding preferences of RNA-binding proteins

(2014) Daniel Maticzka et al.   GENOME BIOLOGY

Global target mRNA specification and regulation by the RNA-binding protein ZFP36

(2014) Neelanjan Mukherjee et al.   GENOME BIOLOGY

An integrated toolkit for accurate prediction and analysis of cis-regulatory motifs at a genome scale

(2013) Qin Ma et al.   BIOINFORMATICS

MotifLab: a tools and data integration workbench for motif discovery and regulatory sequence analysis

(2013) Kjetil Klepper et al.   BMC BIOINFORMATICS

A compendium of RNA-binding motifs for decoding gene regulation

(2013) Debashish Ray et al.   NATURE

Evaluation of methods for modeling transcription factor sequence specificity

(2013) Matthew T Weirauch et al.   NATURE BIOTECHNOLOGY

Hyper conserved elements in vertebrate mRNA 3′-UTRs reveal a translational network of RNA-binding proteins controlled by HuR

(2013) Erik Dassi et al.   NUCLEIC ACIDS RESEARCH

A Discriminative Approach for Unsupervised Clustering of DNA Sequence Motifs

(2013) Philip Stegmaier et al.   PLoS Computational Biology

Sequence features and chromatin structure around the genomic regions bound by 119 human transcription factors

(2012) J. Wang et al.   GENOME RESEARCH

Systematic discovery of structural elements governing stability of mammalian messenger RNAs

(2012) Hani Goodarzi et al.   NATURE

Integrative Regulatory Mapping Indicates that the RNA-Binding Protein HuR Couples Pre-mRNA Processing and mRNA Stability

(2011) Neelanjan Mukherjee et al.   MOLECULAR CELL

RSAT 2011: regulatory sequence analysis tools

(2011) M. Thomas-Chollier et al.   NUCLEIC ACIDS RESEARCH

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

AREsite: a database for the comprehensive investigation of AU-rich elements

(2010) A. R. Gruber et al.   NUCLEIC ACIDS RESEARCH

RBPDB: a database of RNA-binding specificities

(2010) K. B. Cook et al.   NUCLEIC ACIDS RESEARCH

Biopython: freely available Python tools for computational molecular biology and bioinformatics

(2009) P. J. A. Cock et al.   BIOINFORMATICS

Circos: An information aesthetic for comparative genomics

(2009) M. Krzywinski et al.   GENOME RESEARCH

MEME SUITE: tools for motif discovery and searching

(2009) T. L. Bailey et al.   NUCLEIC ACIDS RESEARCH

Regulatory element identification in subsets of transcripts: Comparison and integration of current computational methods

(2009) D. Fan et al.   RNA