Results 11 to 20 of about 1,421,598 (316)

RSAT 2022: regulatory sequence analysis tools. [PDF]

Nucleic Acids Res, 2022
Abstract RSAT (Regulatory Sequence Analysis Tools) enables the detection and the analysis of cis-regulatory elements in genomic sequences. This software suite performs (i) de novo motif discovery (including from genome-wide datasets like ChIP-seq/ATAC-seq) (ii) genomic sequences scanning with known motifs, (iii) motif analysis (quality ...
Santana-Garcia W, Castro-Mondragon JA, Padilla-Gálvez M, Nguyen NTT, Elizondo-Salas A, Ksouri N, Gerbes F, Thieffry D, Vincens P, Contreras-Moreira B, van Helden J, Thomas-Chollier M, Medina-Rivera A.   +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

RSAT 2015: Regulatory Sequence Analysis Tools. [PDF]

Nucleic Acids Res, 2015
RSAT (Regulatory Sequence Analysis Tools) is a modular software suite for the analysis of cis-regulatory elements in genome sequences. Its main applications are (i) motif discovery, appropriate to genome-wide data sets like ChIP-seq, (ii) transcription factor binding motif analysis (quality assessment, comparisons and clustering), (iii) comparative ...
Medina-Rivera A, Defrance M, Sand O, Herrmann C, Castro-Mondragon JA, Delerce J, Jaeger S, Blanchet C, Vincens P, Caron C, Staines DM, Contreras-Moreira B, Artufel M, Charbonnier-Khamvongsa L, Hernandez C, Thieffry D, Thomas-Chollier M, van Helden J.   +17 more
europepmc   +8 more sources

Sequencing the regulatory genome [PDF]

Genome Biology, 2008
A report on the Cold Spring Harbor Laboratory meeting 'Systems Biology: Global Regulation of Gene Expression', Cold Spring Harbor, USA, 27-30 March 2008.
Stefanie L. Butland, Stein Aerts
openaire   +2 more sources

Functional conservation of sequence determinants at rapidly evolving regulatory regions across mammals. [PDF]

PLoS Computational Biology, 2018
Recent advances in epigenomics have made it possible to map genome-wide regulatory regions using empirical methods. Subsequent comparative epigenomic studies have revealed that regulatory regions diverge rapidly between genome of different species, and ...
Iksoo Huh, Isabel Mendizabal, Taesung Park, Soojin V Yi   +3 more
doaj   +1 more source

Sequence determinants of human gene regulatory elements [PDF]

Nature Genetics, 2021
AbstractDNA 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).
Biswajyoti Sahu, Carsten O. Daub, Carsten O. Daub, Patrick Cramer, Patrick Cramer, Tuomo Hartonen, Michael Lidschreiber, Michael Lidschreiber, Bei Wei, Katja Lidschreiber, Katja Lidschreiber, Kashyap Dave, Teemu Kivioja, Eevi Kaasinen, Eevi Kaasinen, Jussi Taipale, Jussi Taipale, Jussi Taipale, Päivi Pihlajamaa, Fangjie Zhu   +19 more
openaire   +8 more sources

RSAT: regulatory sequence analysis tools [PDF]

Nucleic Acids Research, 2008
The regulatory sequence analysis tools (RSAT, http://rsat.ulb.ac.be/rsat/) is a software suite that integrates a wide collection of modular tools for the detection of cis-regulatory elements in genome sequences. The suite includes programs for sequence retrieval, pattern discovery, phylogenetic footprint detection, pattern matching, genome scanning and
Thomas-Chollier, M., Sand, Olivier, Turatsinze, J. V., Janky, R., Defrance, M., Vervisch, E., Brohee, S., Helden, J.   +7 more
openaire   +4 more sources

Discovering sequences with potential regulatory characteristics [PDF]

Genomics, 2009
We developed a computational model to explore the hypothesis that regulatory instructions are context dependent and conveyed through specific 'codes' in human genomic DNA. We provide examples of correlation of computational predictions to reported mapped DNase I hypersensitive segments in the HOXA locus in human chromosome 7.
Gregory E. Crawford, Syed Rehan Shah, Xiaohui C. Song, Minou Bina, Sheryl A. Lazarus, Sang P. Park, Wenhui Ren, Wojciech Szpankowski, Phillip J. Wyss   +8 more
openaire   +2 more sources

Global properties of regulatory sequences are predicted by transcription factor recognition mechanisms

Genome Biology, 2021
Background Mammalian genomes contain millions of putative regulatory sequences, which are delineated by binding of multiple transcription factors. The degree to which spacing and orientation constraints among transcription factor binding sites contribute
Zain M. Patel, Timothy R. Hughes
doaj   +1 more source

MapGL: inferring evolutionary gain and loss of short genomic sequence features by phylogenetic maximum parsimony

BMC Bioinformatics, 2020
Background Comparative genomics studies are growing in number partly because of their unique ability to provide insight into shared and divergent biology between species. Of particular interest is the use of phylogenetic methods to infer the evolutionary
Adam G. Diehl, Alan P. Boyle
doaj   +1 more source