Results 21 to 30 of about 1,518,123 (337)

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, Noam Shomron, Gene W Yeo, Aniket Schneider, Xinshu Xiao, Christopher B Burge   +5 more
doaj   +1 more source

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, Kimani Njoya, John G. Peters, Michelle M. Riehle   +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, Culler, Stephanie J., Hoff, Kevin G., Smolke, Christina D., Voelker, Rodger B.   +4 more
core   +4 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, Levine, Michael, Markstein, Michele, Markstein, Peter, Stathopoulos, Angela, Yee, Ka Ping, Zinzen, Robert   +6 more
core   +2 more sources

Sequence determinants of human gene regulatory elements [PDF]

Nature Genetics, 2021
Abstract DNA can determine where and when genes are expressed, but the full set of sequence determinants that control gene expression is unknown. Here, we measured the transcriptional activity of DNA sequences that represent an ~100 times larger sequence space than the human genome using massively parallel reporter assays (MPRAs ...
Sahu, Biswajyoti, Hartonen, Tuomo, Pihlajamaa, Päivi, Wei, Bei, Dave, Kashyap, Zhu, Fangjie, Kaasinen, Eevi, Lidschreiber, Katja, Lidschreiber, Michael, Daub, Carsten O, Cramer, Patrick, Kivioja, Teemu, Taipale, Jussi   +12 more
openaire   +7 more sources

RSAT 2018: regulatory sequence analysis tools 20th anniversary. [PDF]

Nucleic Acids Res, 2018
RSAT (Regulatory Sequence Analysis Tools) is a suite of modular tools for the detection and the analysis of cis-regulatory elements in genome sequences. Its main applications are (i) motif discovery, including from genome-wide datasets like ChIP-seq/ATAC-seq, (ii) motif scanning, (iii) motif analysis (quality assessment, comparisons and clustering ...
Nguyen NTT, Contreras-Moreira B, Castro-Mondragon JA, Santana-Garcia W, Ossio R, Robles-Espinoza CD, Bahin M, Collombet S, Vincens P, Thieffry D, van Helden J, Medina-Rivera A, Thomas-Chollier M.   +12 more
europepmc   +7 more sources

Predictive analyses of regulatory sequences with EUGENe [PDF]

Nature Computational Science, 2023
AbstractDeep learning has become a popular tool to study cis-regulatory function. Yet efforts to design software for deep-learning analyses in regulatory genomics that are findable, accessible, interoperable and reusable (FAIR) have fallen short of fully meeting these criteria.
Adam Klie, David Laub, James V. Talwar, Hayden Stites, Tobias Jores, Joe J. Solvason, Emma K. Farley, Hannah Carter   +7 more
openaire   +3 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   +3 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, Sand, Olivier, Turatsinze, Jean-Valery, Janky, Rekin'S, Defrance, Matthieu, Vervisch, Eric, Brohee, Sylvain, Helden, Jacques   +7 more
openaire   +5 more sources

Phylum-Level Conservation of Regulatory Information in Nematodes despite Extensive Non-coding Sequence Divergence. [PDF]

PLoS Genetics, 2015
Gene regulatory information guides development and shapes the course of evolution. To test conservation of gene regulation within the phylum Nematoda, we compared the functions of putative cis-regulatory sequences of four sets of orthologs (unc-47, unc ...
Kacy L Gordon, Robert K Arthur, Ilya Ruvinsky   +2 more
doaj   +1 more source