Timothy L. Bailey
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View article: XSTREME: Comprehensive motif analysis of biological sequence datasets
XSTREME: Comprehensive motif analysis of biological sequence datasets Open
XSTREME is a web-based tool for performing comprehensive motif discovery and analysis in DNA, RNA or protein sequences, as well as in sequences in user-defined alphabets. It is designed for both very large and very small datasets. XSTREME …
View article: SEA: Simple Enrichment Analysis of motifs
SEA: Simple Enrichment Analysis of motifs Open
Motif enrichment algorithms can identify known sequence motifs that are present to a statistically significant degree in DNA, RNA and protein sequences. Databases of such known motifs exist for DNA- and RNA-binding proteins, as well as for…
View article: STREME: accurate and versatile sequence motif discovery
STREME: accurate and versatile sequence motif discovery Open
Motivation Sequence motif discovery algorithms can identify novel sequence patterns that perform biological functions in DNA, RNA and protein sequences—for example, the binding site motifs of DNA- and RNA-binding proteins. Results The STRE…
View article: STREME: Accurate and versatile sequence motif discovery
STREME: Accurate and versatile sequence motif discovery Open
Sequence motif discovery algorithms can identify novel sequence patterns that perform biological functions in DNA, RNA and protein sequences—for example, the binding site motifs of DNA- and RNA-binding proteins. The STREME algorithm presen…
View article: T-Gene: improved target gene prediction
T-Gene: improved target gene prediction Open
Motivation Identifying the genes regulated by a given transcription factor (TF) (its ‘target genes’) is a key step in developing a comprehensive understanding of gene regulation. Previously, we developed a method (CisMapper) for predicting…
View article: T-Gene: Improved target gene prediction
T-Gene: Improved target gene prediction Open
Motivation Identifying the genes regulated by a given transcription factor (its “target genes”) is a key step in developing a comprehensive understanding of gene regulation. Previously we developed a method for predicting the target genes …
View article: PeaKO: MEME Suite CentriMo patch and binary
PeaKO: MEME Suite CentriMo patch and binary Open
patch_5.0.5_peaKO.txt: Patch file, against MEME Suite version 5.0.5, for our changes to centrimo.c revised_CentriMo_test_files.tar.gz: tarball, containing all revised CentriMo test files that differ after this patch (only those with differ…
View article: MoMo: discovery of statistically significant post-translational modification motifs
MoMo: discovery of statistically significant post-translational modification motifs Open
Motivation Post-translational modifications (PTMs) of proteins are associated with many significant biological functions and can be identified in high throughput using tandem mass spectrometry. Many PTMs are associated with short sequence …
View article: Homodimerization regulates an endothelial specific signature of the SOX18 transcription factor
Homodimerization regulates an endothelial specific signature of the SOX18 transcription factor Open
During embryogenesis, vascular development relies on a handful of transcription factors that instruct cell fate in a distinct sub-population of the endothelium (1). The SOXF proteins that comprise SOX7, 17 and 18, are molecular switches mo…
View article: MoMo: Discovery of statistically significant post-translational modification motifs
MoMo: Discovery of statistically significant post-translational modification motifs Open
Motivation Post-translational modifications (PTMs) of proteins are associated with many significant biological functions and can be identified in high throughput using tandem mass spectrometry. Many PTMs are associated with short sequence …
View article: MoMo: Discovery of post-translational modification motifs
MoMo: Discovery of post-translational modification motifs Open
Motivation Post-translational modifications (PTMs) of proteins are associated with many significant biological functions and can be identified in high throughput using tandem mass spectrometry. Many PTMs are associated with short sequence …
View article: Krüppel-like factors compete for promoters and enhancers to fine-tune transcription
Krüppel-like factors compete for promoters and enhancers to fine-tune transcription Open
Krüppel-like factors (KLFs) are a family of 17 transcription factors characterized by a conserved DNA-binding domain of three zinc fingers and a variable N-terminal domain responsible for recruiting cofactors. KLFs have diverse functions …
View article: Pharmacological targeting of the transcription factor SOX18 delays breast cancer in mice
Pharmacological targeting of the transcription factor SOX18 delays breast cancer in mice Open
Pharmacological targeting of transcription factors holds great promise for the development of new therapeutics, but strategies based on blockade of DNA binding, nuclear shuttling, or individual protein partner recruitment have yielded limi…
View article: Promiscuous DNA-binding of a mutant zinc finger protein corrupts the transcriptome and diminishes cell viability
Promiscuous DNA-binding of a mutant zinc finger protein corrupts the transcriptome and diminishes cell viability Open
The rules of engagement between zinc finger transcription factors and DNA have been partly defined by in vitro DNA-binding and structural studies, but less is known about how these rules apply in vivo. Here, we demonstrate how a missense m…
View article: CisMapper: predicting regulatory interactions from transcription factor ChIP-seq data
CisMapper: predicting regulatory interactions from transcription factor ChIP-seq data Open
Identifying the genomic regions and regulatory factors that control the transcription of genes is an important, unsolved problem. The current method of choice predicts transcription factor (TF) binding sites using chromatin immunoprecipita…
View article: Modeling methyl-sensitive transcription factor motifs with an expanded epigenetic alphabet
Modeling methyl-sensitive transcription factor motifs with an expanded epigenetic alphabet Open
Transcription factors bind DNA in specific sequence contexts. In addition to distinguishing one nucleobase from another, some transcription factors can distinguish between unmodified and modified bases. Current models of transcription fact…
View article: MCAST: scanning for <i>cis</i>-regulatory motif clusters
MCAST: scanning for <i>cis</i>-regulatory motif clusters Open
Summary: Precise regulatory control of genes, particularly in eukaryotes, frequently requires the joint action of multiple sequence-specific transcription factors. A cis-regulatory module (CRM) is a genomic locus that is responsible for ge…
View article: EMX1 regulates NRP1-mediated wiring of the mouse anterior cingulate cortex
EMX1 regulates NRP1-mediated wiring of the mouse anterior cingulate cortex Open
Transcription factors act during cortical development as master regulatory genes that specify cortical arealization and cellular identities. Although numerous transcription factors have been identified as being crucial for cortical develop…
View article: Conservation analysis of sequences flanking the testis-determining gene Sry in 17 mammalian species
Conservation analysis of sequences flanking the testis-determining gene Sry in 17 mammalian species Open
The unusually fast pace of sequence drift on the Y chromosome sharpens the likely functional significance of both the SPCI and the identified binding motifs, providing a basis for future studies of the role(s) of these elements in Sry regu…
View article: The MEME Suite
The MEME Suite Open
The MEME Suite is a powerful, integrated set of web-based tools for studying sequence motifs in proteins, DNA and RNA. Such motifs encode many biological functions, and their detection and characterization is important in the study of mole…
View article: Additional file 10: of Conservation analysis of sequences flanking the testis-determining gene Sry in 17 mammalian species
Additional file 10: of Conservation analysis of sequences flanking the testis-determining gene Sry in 17 mammalian species Open
Windowed FIMO results. Processed results of FIMO analysis with 10Â kb windows. (XLS 81Â kb)
View article: Additional file 2: of Conservation analysis of sequences flanking the testis-determining gene Sry in 17 mammalian species
Additional file 2: of Conservation analysis of sequences flanking the testis-determining gene Sry in 17 mammalian species Open
Sry 5’ flanking sequences. Repeat-masked 10 kb sequences from 5’ ofSry. (TXT 149 kb)
View article: Additional file 7: of Conservation analysis of sequences flanking the testis-determining gene Sry in 17 mammalian species
Additional file 7: of Conservation analysis of sequences flanking the testis-determining gene Sry in 17 mammalian species Open
Full CentriMo results. A single interactive HTML file containing all results from the CentriMo analysis. (HTML 795Â kb)
View article: Additional file 4: of Conservation analysis of sequences flanking the testis-determining gene Sry in 17 mammalian species
Additional file 4: of Conservation analysis of sequences flanking the testis-determining gene Sry in 17 mammalian species Open
Sequence of the SPCI. The sequence of the SPCI from human and mouse. (TXT 250 bytes)
View article: Additional file 1: of Conservation analysis of sequences flanking the testis-determining gene Sry in 17 mammalian species
Additional file 1: of Conservation analysis of sequences flanking the testis-determining gene Sry in 17 mammalian species Open
Sry coding sequences. (TXT 12Â kb)
View article: Additional file 9: of Conservation analysis of sequences flanking the testis-determining gene Sry in 17 mammalian species
Additional file 9: of Conservation analysis of sequences flanking the testis-determining gene Sry in 17 mammalian species Open
Windowed FIMO results. Processed results of FIMO analysis with 1Â kb windows. (XLS 39Â kb)