Ivan Erill

Summary

Affiliation: University of Maryland
Country: USA

Publications

  1. pmc Every Site Counts: Submitting Transcription Factor-Binding Site Information through the CollecTF Portal
    Ivan Erill
    Department of Biological Sciences, University of Maryland Baltimore County, Baltimore, Maryland, USA
    J Bacteriol 197:2454-7. 2015
  2. pmc xFITOM: a generic GUI tool to search for transcription factor binding sites
    Nidhi Bhargava
    Department of Biological Sciences, University of Maryland Baltimore County, 1000 Hilltop Circle, Baltimore, MD 21250, USA
    Bioinformation 5:49-51. 2010
  3. pmc Inference of self-regulated transcriptional networks by comparative genomics
    Joseph P Cornish
    Department of Biological Sciences, University of Maryland Baltimore County
    Evol Bioinform Online 8:449-61. 2012
  4. pmc Analysis of the SOS response of Vibrio and other bacteria with multiple chromosomes
    Neus Sanchez-Alberola
    Departament de Genetica i de Microbiologia, Universitat Autonoma de Barcelona, 08193 Bellaterra, Spain
    BMC Genomics 13:58. 2012
  5. pmc Prevalence of SOS-mediated control of integron integrase expression as an adaptive trait of chromosomal and mobile integrons
    Guillaume Cambray
    Institut Pasteur, Unité Plasticité du Génome Bactérien, CNRS URA 2171, 75015 Paris, France
    Mob DNA 2:6. 2011
  6. pmc A reexamination of information theory-based methods for DNA-binding site identification
    Ivan Erill
    Department of Biological Sciences, University of Maryland Baltimore County, Baltimore, MD, USA
    BMC Bioinformatics 10:57. 2009
  7. ncbi request reprint Identification of the Acidobacterium capsulatum LexA box reveals a lateral acquisition of the Alphaproteobacteria lexA gene
    Gerard Mazon
    Centre de Recerca en Sanitat Animal CReSA, Universitat Autonoma de Barcelona, 08193 Bellaterra, Spain
    Microbiology 152:1109-18. 2006
  8. pmc Dispersal and regulation of an adaptive mutagenesis cassette in the bacteria domain
    Ivan Erill
    Biomedical Applications Group, Centro Nacional de Microelectronica, 08193 Bellaterra, Spain
    Nucleic Acids Res 34:66-77. 2006
  9. ncbi request reprint Reconstruction of the evolutionary history of the LexA-binding sequence
    Gerard Mazon
    Departament de Genetica i Microbiologia, Universitat Autonoma de Barcelona, 08193 Bellaterra, Spain
    Microbiology 150:3783-95. 2004
  10. pmc Differences in LexA regulon structure among Proteobacteria through in vivo assisted comparative genomics
    Ivan Erill
    Biomedical Applications Group, Centro Nacional de Microelectronica, 08193 Bellaterra, Spain
    Nucleic Acids Res 32:6617-26. 2004

Collaborators

  • Antoni Ivorra
  • Rosa Villa
  • David Emerson
  • Neus Sanchez-Alberola
  • Laura J Anzaldi
  • Fernando Rojo
  • Rodrigo Gomez
  • Michael C O'Neill
  • Patrick K O'Neill
  • Joseph P Cornish
  • Susana Campoy
  • Jordi Barbe
  • Gerard Mazon
  • Marc Abella
  • Sefa Kiliç
  • Guillaume Cambray
  • Nidhi Bhargava
  • Jesse M Fox
  • Damià Parramón
  • Pilar Cortés
  • Elliot R White
  • Dinara M Sagitova
  • Robert Forder
  • Ronald O'Keefe
  • Jameel Gheba
  • Antonio R Fernández de Henestrosa
  • Mindy Or
  • Julien R Thomas
  • Fialelei Matthews
  • Sandra Da Re
  • Emilie Guerin
  • Bruno Gonzalez-Zorn
  • Didier Mazel
  • Marie Cecile Ploy
  • Constantino Fondevila
  • Ángeles Muñoz
  • Anton Guimerà
  • Anna Sola
  • Juan Carlos Garcia-Valdecasas
  • Noelia Salvador
  • Evelyne Forano
  • Mónica Jara
  • Jon K Magnuson
  • Jordi Cuñé

Detail Information

Publications24

  1. pmc Every Site Counts: Submitting Transcription Factor-Binding Site Information through the CollecTF Portal
    Ivan Erill
    Department of Biological Sciences, University of Maryland Baltimore County, Baltimore, Maryland, USA
    J Bacteriol 197:2454-7. 2015
    ..CollecTF provides the first standardized resource for submission and deposition of these data into the NCBI RefSeq database, maximizing its accessibility and prompting the community to adopt direct submission policies. ..
  2. pmc xFITOM: a generic GUI tool to search for transcription factor binding sites
    Nidhi Bhargava
    Department of Biological Sciences, University of Maryland Baltimore County, 1000 Hilltop Circle, Baltimore, MD 21250, USA
    Bioinformation 5:49-51. 2010
    ..AVAILABILITY: XFITOM IS AVAILABLE FOR DOWNLOAD AT: http://research.umbc.edu/˜erill...
  3. pmc Inference of self-regulated transcriptional networks by comparative genomics
    Joseph P Cornish
    Department of Biological Sciences, University of Maryland Baltimore County
    Evol Bioinform Online 8:449-61. 2012
    ....
  4. pmc Analysis of the SOS response of Vibrio and other bacteria with multiple chromosomes
    Neus Sanchez-Alberola
    Departament de Genetica i de Microbiologia, Universitat Autonoma de Barcelona, 08193 Bellaterra, Spain
    BMC Genomics 13:58. 2012
    ....
  5. pmc Prevalence of SOS-mediated control of integron integrase expression as an adaptive trait of chromosomal and mobile integrons
    Guillaume Cambray
    Institut Pasteur, Unité Plasticité du Génome Bactérien, CNRS URA 2171, 75015 Paris, France
    Mob DNA 2:6. 2011
    ..abstract:..
  6. pmc A reexamination of information theory-based methods for DNA-binding site identification
    Ivan Erill
    Department of Biological Sciences, University of Maryland Baltimore County, Baltimore, MD, USA
    BMC Bioinformatics 10:57. 2009
    ..Here we use newly available data on transcription factors from different bacterial genomes to make a more thorough assessment of information theory-based search methods...
  7. ncbi request reprint Identification of the Acidobacterium capsulatum LexA box reveals a lateral acquisition of the Alphaproteobacteria lexA gene
    Gerard Mazon
    Centre de Recerca en Sanitat Animal CReSA, Universitat Autonoma de Barcelona, 08193 Bellaterra, Spain
    Microbiology 152:1109-18. 2006
    ..Lastly, in vivo experiments demonstrate that the A. capsulatum recA gene is DNA-damage inducible, despite the fact that a LexA-binding sequence is not present in its promoter region...
  8. pmc Dispersal and regulation of an adaptive mutagenesis cassette in the bacteria domain
    Ivan Erill
    Biomedical Applications Group, Centro Nacional de Microelectronica, 08193 Bellaterra, Spain
    Nucleic Acids Res 34:66-77. 2006
    ....
  9. ncbi request reprint Reconstruction of the evolutionary history of the LexA-binding sequence
    Gerard Mazon
    Departament de Genetica i Microbiologia, Universitat Autonoma de Barcelona, 08193 Bellaterra, Spain
    Microbiology 150:3783-95. 2004
    ..This constitutes the first report based on experimental evidence of lateral gene transfer in the evolution of a gene governing such a complex regulatory network as the bacterial SOS system...
  10. pmc Differences in LexA regulon structure among Proteobacteria through in vivo assisted comparative genomics
    Ivan Erill
    Biomedical Applications Group, Centro Nacional de Microelectronica, 08193 Bellaterra, Spain
    Nucleic Acids Res 32:6617-26. 2004
    ....
  11. pmc Cohabitation of two different lexA regulons in Pseudomonas putida
    Marc Abella
    Departament de Genetica i Microbiologia, Ed Cn, Universitat Autonoma de Barcelona, 08193 Bellaterra, Spain
    J Bacteriol 189:8855-62. 2007
    ..In silico searches suggested that this marked asymmetry in regulon contents also occurs in other Pseudomonas species with two lexA genes, and the implications of this asymmetry in the evolution of the SOS network are discussed...
  12. pmc Expression of canonical SOS genes is not under LexA repression in Bdellovibrio bacteriovorus
    Susana Campoy
    Centre de Recerca en Sanitat Animal CReSA, 08193 Bellaterra, Spain
    J Bacteriol 187:5367-75. 2005
    ....
  13. ncbi request reprint In silico analysis reveals substantial variability in the gene contents of the gamma proteobacteria LexA-regulon
    Ivan Erill
    Biomedical Applications Group, Centro Nacional de Microelectronica, Universitat Autonoma de Barcelona, 08193 Bellaterra, Spain
    Bioinformatics 19:2225-36. 2003
    ....
  14. ncbi request reprint Widespread distribution of a lexA-regulated DNA damage-inducible multiple gene cassette in the Proteobacteria phylum
    Marc Abella
    Departament de Genetica i Microbiologia, Universitat Autonoma de Barcelona, 08193 Bellaterra, Spain
    Mol Microbiol 54:212-22. 2004
    ....
  15. pmc Characterization of the SOS meta-regulon in the human gut microbiome
    Joseph P Cornish
    Department of Biological Sciences, University of Maryland Baltimore County UMBC, Baltimore, MD 21250, USA
    Bioinformatics 30:1193-7. 2014
    ..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...
  16. pmc CollecTF: a database of experimentally validated transcription factor-binding sites in Bacteria
    Sefa Kiliç
    Department of Biological Sciences, University of Maryland Baltimore County UMBC, 1000 Hilltop Circle, Baltimore, MD 21250, USA
    Nucleic Acids Res 42:D156-60. 2014
    ....
  17. ncbi request reprint In vivo detection of liver steatosis in rats based on impedance spectroscopy
    Damià Parramón
    Biomedical Applications Group, Centro Nacional de Microelectronica, 08193 Bellaterra, Spain
    Physiol Meas 28:813-28. 2007
    ..7 kHz. We further support our findings on a theoretical model of tissue impedance, and the simulations carried out suggest a possible mechanism to expound the negative effect of steatosis in post-transplant graft function...
  18. pmc A green nonsulfur bacterium, Dehalococcoides ethenogenes, with the LexA binding sequence found in gram-positive organisms
    Antonio R Fernández de Henestrosa
    Departament Genètica i Microbiologia, Universitat Autonoma de Barcelona, Spain
    J Bacteriol 184:6073-80. 2002
    ..ethenogenes LexA operator. This constitutes the first non-gram-positive bacterium exhibiting a LexA binding site identical to that of B. subtilis...
  19. pmc An SOS Regulon under Control of a Noncanonical LexA-Binding Motif in the Betaproteobacteria
    Neus Sanchez-Alberola
    Departament de Genetica i de Microbiologia, Universitat Autonoma de Barcelona, Barcelona, Spain Department of Biological Sciences, University of Maryland Baltimore County, Baltimore, Maryland, USA
    J Bacteriol 197:2622-30. 2015
    ..subtilis-type motif an optimal interface for multiple LexA sequences...
  20. pmc scnRCA: a novel method to detect consistent patterns of translational selection in mutationally-biased genomes
    Patrick K O'Neill
    Department of Biological Sciences, University of Maryland Baltimore County UMBC, Baltimore, Maryland, United States of America
    PLoS ONE 8:e76177. 2013
    ..We generalize these results to other moderate and fast growing bacteria, hinting at selection for a universal pattern of gene expression that is conserved and detectable in conserved patterns of codon usage bias. ..
  21. pmc Informational requirements for transcriptional regulation
    Patrick K O'Neill
    1 Department of Biological Sciences, University of Maryland Baltimore County, Baltimore, Maryland
    J Comput Biol 21:373-84. 2014
    ....
  22. pmc BioWord: a sequence manipulation suite for Microsoft Word
    Laura J Anzaldi
    Department of Biological Sciences, University of Maryland Baltimore County, 1000 Hilltop Circle, Baltimore, MD 21250, USA
    BMC Bioinformatics 13:124. 2012
    ..To address this problem, here we have developed BioWord, a macro-enabled self-installing template for Microsoft Word documents that integrates an extensive suite of DNA and protein sequence manipulation tools...
  23. pmc Relative codon adaptation: a generic codon bias index for prediction of gene expression
    Jesse M Fox
    Department of Biological Sciences, University of Maryland Baltimore County UMBC, 1000 Hilltop Road, Baltimore, MD 21228, USA
    DNA Res 17:185-96. 2010
    ....
  24. ncbi request reprint A SiC microdevice for the minimally invasive monitoring of ischemia in living tissues
    Rodrigo Gomez
    Biomedical Applications Group, Centro Nacional de Microelectrónica CNM CSIC, Campus UAB s n, 08193 Bellaterra, Spain
    Biomed Microdevices 8:43-9. 2006
    ....