Absence of a simple code: how transcription factors read the genome
Transcription factors (TFs) influence cell fate by interpreting the regulatory DNA within a
genome. TFs recognize DNA in a specific manner; the mechanisms underlying this …
genome. TFs recognize DNA in a specific manner; the mechanisms underlying this …
Transcriptional control of human p53-regulated genes
The p53 protein regulates the transcription of many different genes in response to a wide
variety of stress signals. Following DNA damage, p53 regulates key processes, including …
variety of stress signals. Following DNA damage, p53 regulates key processes, including …
JASPAR: an open‐access database for eukaryotic transcription factor binding profiles
The analysis of regulatory regions in genome sequences is strongly based on the detection
of potential transcription factor binding sites. The preferred models for representation of …
of potential transcription factor binding sites. The preferred models for representation of …
Discovering motifs in ranked lists of DNA sequences
Computational methods for discovery of sequence elements that are enriched in a target set
compared with a background set are fundamental in molecular biology research. One …
compared with a background set are fundamental in molecular biology research. One …
Zelda Binding in the Early Drosophila melanogaster Embryo Marks Regions Subsequently Activated at the Maternal-to-Zygotic Transition
The earliest stages of development in most metazoans are driven by maternally deposited
proteins and mRNAs, with widespread transcriptional activation of the zygotic genome …
proteins and mRNAs, with widespread transcriptional activation of the zygotic genome …
Analysis of genomic sequence motifs for deciphering transcription factor binding and transcriptional regulation in eukaryotic cells
V Boeva - Frontiers in genetics, 2016 - frontiersin.org
Eukaryotic genomes contain a variety of structured patterns: repetitive elements, binding
sites of DNA and RNA associated proteins, splice sites, and so on. Often, these structured …
sites of DNA and RNA associated proteins, splice sites, and so on. Often, these structured …
The next generation of transcription factor binding site prediction
A Mathelier, WW Wasserman - PLoS computational biology, 2013 - journals.plos.org
Finding where transcription factors (TFs) bind to the DNA is of key importance to decipher
gene regulation at a transcriptional level. Classically, computational prediction of TF binding …
gene regulation at a transcriptional level. Classically, computational prediction of TF binding …
Nonparametric Bayes modeling of multivariate categorical data
Modeling of multivariate unordered categorical (nominal) data is a challenging problem,
particularly in high dimensions and cases in which one wishes to avoid strong assumptions …
particularly in high dimensions and cases in which one wishes to avoid strong assumptions …
Quantitative analysis demonstrates most transcription factors require only simple models of specificity
To the Editor: In his News Feature published in the February issue, Michael Eisenstein
outlines several alternative methods of drug delivery1 and discusses how several targets in …
outlines several alternative methods of drug delivery1 and discusses how several targets in …
Quantitative Models of the Mechanisms That Control Genome-Wide Patterns of Transcription Factor Binding during Early Drosophila Development
Transcription factors that drive complex patterns of gene expression during animal
development bind to thousands of genomic regions, with quantitative differences in binding …
development bind to thousands of genomic regions, with quantitative differences in binding …