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Inference of splicing regulatory activities by sequence neighborhood analysis. [PDF]
PLoS Genetics, 2006 Sequence-specific recognition of nucleic-acid motifs is critical to many cellular processes. We have developed a new and general method called Neighborhood Inference (NI) that predicts sequences with activity in regulating a biochemical process based on ...
Michael B Stadler +5 more
doaj +1 more source
Multigenome DNA sequence conservation identifies Hox cis-regulatory elements [PDF]
, 2008 To learn how well ungapped sequence comparisons of multiple species can predict cis-regulatory elements in Caenorhabditis elegans, we made such predictions across the large, complex ceh-13/lin-39 locus and tested them transgenically. We also examined how
De Buysscher, Tristan +7 more
core +3 more sources
Prediction accuracy of regulatory elements from sequence varies by functional sequencing technique
Frontiers in Cellular and Infection Microbiology, 2023 IntroductionVarious sequencing based approaches are used to identify and characterize the activities of cis-regulatory elements in a genome-wide fashion.
Ronald J. Nowling +3 more
doaj +1 more source
Expand+Functional selection and systematic analysis of intronic splicing elements identify active sequence motifs and associated splicing factors [PDF]
, 2010 Despite the critical role of pre-mRNA splicing in generating proteomic diversity and regulating gene expression, the sequence composition and function of intronic splicing regulatory elements (ISREs) have not been well elucidated.
Berglund, J. Andrew +4 more
core +4 more sources
Dynamics of transcription factor binding site evolution [PDF]
, 2015 Evolution of gene regulation is crucial for our understanding of the phenotypic differences between species, populations and individuals. Sequence-specific binding of transcription factors to the regulatory regions on the DNA is a key regulatory ...
Barton, Nicholas H. +3 more
core +11 more sources
Waiting for regulatory sequences to appear
The Annals of Applied Probability, 2007 Published at http://dx.doi.org/10.1214/105051606000000619 in the Annals of Applied Probability (http://www.imstat.org/aap/) by the Institute of Mathematical Statistics (http://www.imstat.org)
Durrett, Richard, Schmidt, Deena
openaire +5 more sources
A regulatory code for neurogenic gene expression in the Drosophila embryo [PDF]
, 2004 Bioinformatics methods have identified enhancers that mediate restricted expression in the Drosophila embryo. However, only a small fraction of the predicted enhancers actually work when tested in vivo.
Erives, Albert +6 more
core +2 more sources
Regulatory Sequence Analysis Tools [PDF]
Nucleic Acids Research, 2003 The web resource Regulatory Sequence Analysis Tools (RSAT) (http://rsat.ulb.ac.be/rsat) offers a collection of software tools dedicated to the prediction of regulatory sites in non-coding DNA sequences. These tools include sequence retrieval, pattern discovery, pattern matching, genome-scale pattern matching, feature-map drawing, random sequence ...
openaire +4 more sources
Design principles for riboswitch function [PDF]
, 2009 Scientific and technological advances that enable the tuning of integrated regulatory components to match network and system requirements are critical to reliably control the function of biological systems. RNA provides a promising building block for the
A Belle +62 more
core +4 more sources
RSAT 2011: regulatory sequence analysis tools [PDF]
Nucleic Acids Research, 2011 RSAT (Regulatory Sequence Analysis Tools) comprises a wide collection of modular tools for the detection of cis-regulatory elements in genome sequences. Thirteen new programs have been added to the 30 described in the 2008 NAR Web Software Issue, including an automated sequence retrieval from EnsEMBL (retrieve-ensembl-seq), two novel motif discovery ...
Thomas-Chollier, Morgane +7 more
openaire +5 more sources