bacterial genomics

Bacterial genomics is one of the fundamental research lines of Era7 Bioinformatics Unit. Era7 participates actively in this research area.


Within this line, we focus on


transcriptional regulation
We have developed ExtraTrain, a database focused on bacterial transcriptional factors and we have research interests in specific features of the different families of regulators and their DNA-binding sites.  We also are working in new paradigms to represent and analyze transcriptional networks from a systems biology point of view.
extragenic space: palindromes and repeats
Within bacterial genomics and related to transcriptional regulation we are studying the extragenic space of bacterial genomes, since within non-coding sequences are included the most important regulatory signals. Palindromicity is one feature of DNA binding-sites and other repetitive extragenic sequences that we are paying attention to.


Characterization of a Listeria monocytogenes protein interfering with Rab5a.
Alvarez-Dominguez C, Madrazo-Toca F, Fernandez-Prieto L, Vandekerckhove J, Pareja E, Tobes R, Gomez-Lopez MT, Del Cerro-Vadillo E, Fresno M, Leyva-Cobián F, Carrasco-Marín E.
Traffic. 2008 Mar;9(3):325-37.
Cutting edge: natural DNA repetitive extragenic sequences from gram-negative pathogens strongly stimulate TLR9.
Magnusson M, Tobes R, Sancho J, Pareja E.
J Immunol. 2007 Jul 1;179(1):31-5.
Bacterial repetitive extragenic palindromic sequences are DNA targets for Insertion Sequence elements.
Tobes R, Pareja E.
BMC Genomics. 2006 Mar 24;7:62. Review.
ExtraTrain: a database of Extragenic regions and Transcriptional information in prokaryotic organisms.
Pareja E, Pareja-Tobes P, Manrique M, Pareja-Tobes E, Bonal J, Tobes R.
BMC Microbiol. 2006 Mar 15;6:29.
Repetitive extragenic palindromic sequences in the Pseudomonas syringae pv. tomato DC3000 genome: extragenic signals for genome reannotation.
Tobes R, Pareja E.
Res Microbiol. 2005 Apr;156(3):424-33. Epub 2005 Jan 28.