Author details

Full Name

Timothy L Bailey

Affiliation

ORCID

Career Start Year

1994

Papers

H Index

Expertise

CM4AI Collaborator

PMID	Paper Title	Journal Title	Published Year
37551662	Correction: Pharmacological targeting of the transcription factor SOX18 delays breast cancer in mice.	Elife	2023
33760053	STREME: accurate and versatile sequence motif discovery.		2021
32246829	T-Gene: improved target gene prediction.		2020
30596994	MoMo: discovery of statistically significant post-translational modification motifs.		2019
30335167	HomodimerizationÂ regulates an endothelial specific signature of the SOX18 transcription factor.	Nucleic Acids Research	2018
28180284	Promiscuous DNA-binding of a mutant zinc finger protein corrupts the transcriptome and diminishes cell viability.	Nucleic Acids Research	2017
28541545	KrÃ¼ppel-like factors compete for promoters and enhancers to fine-tune transcription.	Nucleic Acids Research	2017
28204599	CisMapper: predicting regulatory interactions from transcription factor ChIP-seq data.	Nucleic Acids Research	2017
26704599	MCAST: scanning for cis-regulatory motif clusters.		2016
26534986	EMX1 regulates NRP1-mediated wiring of the mouse anterior cingulate cortex.	Development	2015
25331604	NFIX Regulates Proliferation and Migration Within the Murine SVZ Neurogenic Niche.	Cereb Cortex	2015
25960350	Expansion of the lateral ventricles and ependymal deficits underlie the hydrocephalus evident in mice lacking the transcription factor NFIX.	Brain Res	2015
25953851	The MEME Suite.	Nucleic Acids Research	2015
26444262	Conservation analysis of sequences flanking the testis-determining gene Sry in 17 mammalian species.	BMC Developmental Biology	2015
25179504	Differential motif enrichment analysis of paired ChIP-seq experiments.	BMC Genomics	2014
24501021	Statistical confidence estimation for Hi-C data reveals regulatory chromatin contacts.	Genome Research	2014
23042739	NFIX regulates neural progenitor cell differentiation during hippocampal morphogenesis.	Cereb Cortex	2014
24866114	Switching on sex: transcriptional regulation of the testis-determining gene Sry.	Development (Cambridge)	2014
24860161	GT-Scan: identifying unique genomic targets.		2014
24532840	Predicting the dynamics of protein abundance.	Molecular and Cellular Proteomics	2014
25200088	Creating and validating cis-regulatory maps of tissue-specific gene expression regulation.	Nucleic Acids Research	2014
24853928	Motif-based analysis of large nucleotide data sets using MEME-ChIP.		2014
24665130	Improving MEME via a two-tiered significance analysis.		2014
24661679	An overlapping set of genes is regulated by both NFIB and the glucocorticoid receptor during lung maturation.	BMC Genomics	2014
24553933	NFIB-mediated repression of the epigenetic factor Ezh2 regulates cortical development.	J Neurosci	2014
23142965	DLocalMotif: a discriminative approach for discovering local motifs in protein sequences.		2013
23852417	Nuclear factor one X regulates Bobby sox during development of the mouse forebrain.	Cell Mol Neurobiol	2013
23894279	SVM-based prediction of propeptide cleavage sites in spider toxins identifies toxin innovation in an Australian tarantula.	PLoS ONE	2013
24244136	Practical guidelines for the comprehensive analysis of ChIP-seq data.	PLoS Comput Biol	2013
23746349	Defining the RGG/RG motif.	Molecular Cell	2013
23740745	Triplex-Inspector: an analysis tool for triplex-mediated targeting of genomic loci.	Bioinformatics	2013
22072382	Epigenetic priors for identifying active transcription factor binding sites.		2012
22510988	Identification of molecular compartments and genetic circuitry in the developing mammalian kidney.	Development	2012
22753024	An in-depth map of polyadenylation sites in cancer.	Nucleic Acids Res	2012
22550012	Triplexator: detecting nucleic acid triple helices in genomic and transcriptomic data.	Genome Res	2012
22835905	Novel roles for KLF1 in erythropoiesis revealed by mRNA-seq.	Genome Research	2012
22954627	Genome-wide in silico prediction of gene expression.		2012
22822203	Cyclic peptides arising by evolutionary parallelism via asparaginyl-endopeptidase-mediated biosynthesis.	Plant Cell	2012
22610855	Inferring direct DNA binding from ChIP-seq.	Nucleic Acids Research	2012
23237380	Prediction of novel long non-coding RNAs based on RNA-Seq data of mouse Klf1 knockout study.	BMC Bioinformatics	2012
23249739	Neural-specific Sox2 input and differential Gli-binding affinity provide context and positional information in Shh-directed neural patterning.	Genes Dev	2012
21685104	Sorting the nuclear proteome.	Bioinformatics	2011
21486936	MEME-ChIP: motif analysis of large DNA datasets.		2011
21330290	FIMO: scanning for occurrences of a given motif.		2011
21372083	A probabilistic model of nuclear import of proteins.		2011
21525785	Potential in vivo roles of nucleic acid triple-helices.	RNA Biol	2011
21724591	Tissue-specific prediction of directly regulated genes.		2011
21602262	Inferring transcription factor complexes from ChIP-seq data.	Nucleic Acids Res	2011
21543443	Improved similarity scores for comparing motifs.		2011
21543442	DREME: motif discovery in transcription factor ChIP-seq data.		2011