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Dipòsit Digital de Documents de la UAB 35 registres trobats  1 - 10següentfinal  anar al registre: La cerca s'ha fet en 0.01 segons. 
1.
20 p, 1.1 MB Comparative genomics of the DNA damage-inducible network in the Patescibacteria / Sánchez-Osuna, Miquel (Universitat Autònoma de Barcelona. Departament de Genètica i de Microbiologia) ; Barbé García, Jordi (Universitat Autònoma de Barcelona. Departament de Genètica i de Microbiologia) ; Erill, Ivan (University of Maryland Baltimore County. Department of Biological Sciences)
Metagenomics provide unprecedented insights into the genetic diversity of uncultivated bacteria inhabiting natural environments. Recent surveys have uncovered a major radiation of candidate phyla encompassing the Patescibacteria superphylum. [...]
2017 - 10.1111/1462-2920.13826
Environmental Microbiology, Vol. 19, issue 9 (Sep. 2017) , p. 3465-3474  
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2.
10 p, 1.4 MB Assessment of transfer methods for comparative genomics of regulatory networks in Bacteria / Kılıç, Sefa (University of Maryland Baltimore County. Department of Biological Sciences) ; Erill, Ivan (University of Maryland Baltimore County. Department of Biological Sciences)
Background: Comparative genomics can leverage the vast amount of available genomic sequences to reconstruct and analyze transcriptional regulatory networks in Bacteria, but the efficacy of this approach hinges on the ability to transfer regulatory network information from reference species to the genomes under analysis. [...]
2016 - 10.1186/s12859-016-1113-7
BMC bioinformatics, Vol. 17, Suppl. 8 (August 2016) , art. 277  
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3.
10 p, 992.7 KB From data repositories to submission portals: rethinking the role of domain-specific databases in CollecTF / Kılıç, Sefa (University of Maryland Baltimore County. Department of Biological Sciences) ; Sagitova, Dinara M. (University of Maryland Baltimore County. Department of Biological Sciences) ; Wolfish, Shoshannah (University of Maryland School ofMedicine) ; Bely, Benoit (European Bioinformatics Institute) ; Courtot, Mélanie (European Bioinformatics Institute) ; Ciufo, Stacy (National Institutes of Health (Bethesda, Estats Units d'Amèrica)) ; Tatusova, Tatiana (National Institutes of Health (Bethesda, Estats Units d'Amèrica)) ; O'Donovan Claire (European Bioinformatics Institute) ; Chibucos, Marcus C. (University of Maryland School of Medicine. Department of Microbiology and Immunology) ; Martin, Maria J. (European Bioinformatics Institute) ; Erill, Ivan (University of Maryland Baltimore County. Department of Biological Sciences)
Domain-specific databases are essential resources for the biomedical community, leveraging expert knowledge to curate published literature and provide access to referenced data and knowledge. The limited scope of these databases, however, poses important challenges on their infrastructure, visibility, funding and usefulness to the broader scientific community. [...]
2016 - 10.1093/database/baw055
Database, Vol. 2016 (April 2016) , art. baw055  
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4.
5 p, 395.9 KB Characterization of the SOS meta-regulon in the human gut microbiome / Cornish, Joseph P. (University of Maryland Baltimore County. Department of Biological Sciences) ; Sanchez-Alberola, Neus (University of Maryland Baltimore County. Department of Biological Sciences) ; O'Neill, Patrik K. (University of Maryland Baltimore County. Department of Biological Sciences) ; O'Keefe, Ronald (University of Maryland Baltimore County. Department of Biological Sciences) ; Gheba, Jameel (University of Maryland Baltimore County. Department of Biological Sciences) ; Erill, Ivan (University of Maryland Baltimore County. Department of Biological Sciences)
Motivation: Data from metagenomics projects remain largely untapped for the analysis of transcriptional regulatory networks. Here, we provide proof-of-concept that metagenomic data can be effectively leveraged to analyze regulatory networks by characterizing the SOS meta-regulon in the human gut microbiome. [...]
2014 - 10.1093/bioinformatics/btt753
Bioinformatics, Vol. 30, Issue 9 (May 2014) , p. 1193-1197  
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5.
5 p, 4.0 MB CollecTF : a database of experimentally-validated transcription factor-binding sites in Bacteria / Kılıç, Sefa (University of Maryland Baltimore County. Department of Biological Sciences) ; White, Elliot R. (University of Maryland Baltimore County. Department of Biological Sciences) ; Sagitova, Dinara M. (University of Maryland Baltimore County. Department of Biological Sciences) ; Cornish, Joseph P. (University of Maryland Baltimore County. Department of Biological Sciences) ; Erill, Ivan (University of Maryland Baltimore County. Department of Biological Sciences)
The influx of high-throughput data and the need for complex models to describe the interaction of prokaryotic transcription factors (TF) with their target sites pose new challenges for TF-binding site databases. [...]
2014 - 10.1093/nar/gkt1123
Nucleic Acids Research, Vol. 42, Issue D1 (January 2014) , p. D156-D160  
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6.
11 p, 865.3 KB scnRCA : a novel method to detect consistent patterns of translational selection in mutationally-biased genomes / O'Neill, Patrick K. (University of Maryland. Department of Biological Sciences) ; Or, Mindy (University of Maryland. Department of Biological Sciences) ; Erill, Ivan (University of Maryland Baltimore County. Department of Biological Sciences)
Codon usage bias (CUB) results from the complex interplay between translational selection and mutational biases. Current methods for CUB analysis apply heuristics to integrate both components, limiting the depth and scope of CUB analysis as a technique to probe into the evolution and optimization of protein-coding genes. [...]
2013 - 10.1371/journal.pone.0076177
PloS one, Vol. 8, Issue 10 (October 2013) , art. e76177  
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7.
7 p, 1.0 MB BioWord: a sequence manipulation suite for Microsoft Word / Anzaldi, Laura J. (University of Maryland Baltimore County. Department of Biological Sciences) ; Muñoz-Fernández, Daniel (Universitat Autònoma de Barcelona. Departament de Ciències de la Computació) ; Erill, Ivan (Universitat Autònoma de Barcelona. Departament de Ciències de la Computació)
Background: The ability to manipulate, edit and process DNA and protein sequences has rapidly become a necessary skill for practicing biologists across a wide swath of disciplines. In spite of this, most everyday sequence manipulation tools are distributed across several programs and web servers, sometimes requiring installation and typically involving frequent switching between applications. [...]
2012 - 10.1186/1471-2105-13-124
BMC bioinformatics, Vol. 13 (June 2012) , art. 124  
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8.
6 p, 470.1 KB The SOS response controls integron recombination / Guerin, Émilie (Université de Limoges. Faculté de Medicine) ; Cambray, Guillaume (Institut Pasteur) ; Sánchez Alberola, Neus (Universitat Autònoma de Barcelona. Departament de Genètica i de Microbiologia) ; Campoy Sánchez, Susana (Universitat Autònoma de Barcelona. Departament de Genètica i de Microbiologia) ; Erill, Ivan (Centro Nacional de Microelectrónica (Espanya)) ; Da Re, Sandra (Université de Limoges. Faculté de Médecine) ; González Zorn, Bruno (Universidad Complutense de Madrid. Departamento de Sanidad Animal) ; Barbé García, Jordi (Universitat Autònoma de Barcelona. Departament de Genètica i de Microbiologia) ; Ploy, Marie-Cécile (Université de Limoges. Faculté de Médecine) ; Mazel, Didier (Institut Pasteur)
Integrons are found in the genome of hundreds of environmental bacteria but are mainly known for their role in the capture and spread of antibiotic resistance determinants among Gram-negative pathogens. [...]
2009 - 10.1126/science.1172914
Science, Vol. 324, issue 5930 (May 2009) , p. 1034  
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9.
38 p, 1.3 MB Aeons of distress : an evolutionary perspective on the bacterial SOS response / Erill, Ivan (Centro Nacional de Microelectrónica (Espanya)) ; Campoy Sánchez, Susana (Institut de Recerca i Tecnologia Agroalimentàries. Centre de Recerca en Sanitat Animal) ; Barbé García, Jordi (Universitat Autònoma de Barcelona. Departament de Genètica i de Microbiologia)
The SOS response of bacteria is a global regulatory network targeted at addressing DNA damage. Governed by the products of the lexA and recA genes, it co-ordinates a comprehensive response against DNA lesions and its description in Escherichia coli has stood for years as a textbook paradigm of stress-response systems in bacteria. [...]
2007 - doi: 10.1111/j.1574-6976.2007.00082.x
FEMS Microbiology Reviews, Vol. 31, issue 6 (Nov. 2007) , p. 637-656  
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10.
12 p, 319.2 KB Relative Codon Adaptation : A Generic Codon Bias Index for Prediction of Gene Expression / Fox, Jesse M. (University of Maryland Baltimore County. Department of Biological Sciences) ; Erill, Ivan (University of Maryland Baltimore County. Department of Biological Sciences)
The development of codon bias indices (CBIs) remains an active field of research due to their myriad applications in computational biology. Recently, the relative codon usage bias (RCBS) was introduced as a novel CBI able to estimate codon bias without using a reference set. [...]
2010 - 10.1093/dnares/dsq012
DNA Research, Vol. 17, Issue 3 (June 2010) , p. 185-196  
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