Bayesian methods in bioinformatics and computational systems biology
DJ Wilkinson - Briefings in bioinformatics, 2007 - academic.oup.com
Bayesian methods are valuable, inter alia, whenever there is a need to extract information
from data that are uncertain or subject to any kind of error or noise (including measurement …
from data that are uncertain or subject to any kind of error or noise (including measurement …
Identifying regulatory elements in eukaryotic genomes
L Narlikar, I Ovcharenko - Briefings in functional genomics and …, 2009 - academic.oup.com
Proper development and functioning of an organism depends on precise spatial and
temporal expression of all its genes. These coordinated expression-patterns are maintained …
temporal expression of all its genes. These coordinated expression-patterns are maintained …
The MEME suite
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 …
motifs in proteins, DNA and RNA. Such motifs encode many biological functions, and their …
The TRANSFAC project as an example of framework technology that supports the analysis of genomic regulation
E Wingender - Briefings in bioinformatics, 2008 - academic.oup.com
Since its beginning as a data collection more than 20 years ago, the TRANSFAC project
underwent an evolution to become the basis for a complex platform for the description and …
underwent an evolution to become the basis for a complex platform for the description and …
High resolution genome wide binding event finding and motif discovery reveals transcription factor spatial binding constraints
An essential component of genome function is the syntax of genomic regulatory elements
that determine how diverse transcription factors interact to orchestrate a program of …
that determine how diverse transcription factors interact to orchestrate a program of …
Curated collection of yeast transcription factor DNA binding specificity data reveals novel structural and gene regulatory insights
Abstract Background Transcription factors (TFs) play a central role in regulating gene
expression by interacting with cis-regulatory DNA elements associated with their target …
expression by interacting with cis-regulatory DNA elements associated with their target …
Epigenetic priors for identifying active transcription factor binding sites
G Cuellar-Partida, FA Buske, RC McLeay… - …, 2012 - academic.oup.com
Motivation Accurate knowledge of the genome-wide binding of transcription factors in a
particular cell type or under a particular condition is necessary for understanding …
particular cell type or under a particular condition is necessary for understanding …
Integrating multiple evidence sources to predict transcription factor binding in the human genome
Information about the binding preferences of many transcription factors is known and
characterized by a sequence binding motif. However, determining regions of the genome in …
characterized by a sequence binding motif. However, determining regions of the genome in …
A nucleosome-guided map of transcription factor binding sites in yeast
Finding functional DNA binding sites of transcription factors (TFs) throughout the genome is
a crucial step in understanding transcriptional regulation. Unfortunately, these binding sites …
a crucial step in understanding transcriptional regulation. Unfortunately, these binding sites …
P-value-based regulatory motif discovery using positional weight matrices
H Hartmann, EW Guthöhrlein, M Siebert… - Genome …, 2013 - genome.cshlp.org
To analyze gene regulatory networks, the sequence-dependent DNA/RNA binding affinities
of proteins and noncoding RNAs are crucial. Often, these are deduced from sets of …
of proteins and noncoding RNAs are crucial. Often, these are deduced from sets of …