Context and History
Pérez-Rueda brought evolutionary analyses of gene regulation to this
lab, when he expanded the repertoire of transcription factors of E.coli
(Pérez-Rueda and Collado-Vides, 2000) to all the bacterial and archeal
genomes (Pérez-Rueda and Collado-Vides, 2001), showing that in fact
some ancient families are shared between bacteria and archea.
In a similar transition, based on the high capacity to predict operons initially in E.coli (Salgado et al., 2000),
analyzed the conservation and flexibility in the organization of
operons across all bacteria (Moreno-Hagelsieb et al., 2001). This
provided the basis for a non-orthologous comprehensive method to
predict operons in bacteria (Moreno-Hagelsieb and Collado-Vides 2002).
Nebulon: Predicting Functionally associated genes
flexibility in operon organization and rearrangement across Prokaryotes
is the basis for a method to predict functionally associated genes in
bacteria that we named Nebulon (Janga et al., 2005).
A radical new type of bioinformatic studies enriched our laboratory with the Ph.D. thesis of Arturo Medrano-Soto,
who, while working with Gabriel Moreno-Hagelsieb, got interested in
horizontal gene transfer in association with his studies in
collaboration with Andrés Christen
on clustering methods of heterogeneous variables (Medrano-Soto et al.,
2005). Arturo's paper challenges the view that successfully transferred
genes have a poor codon usage within the recipient genome (Medrano-Soto
et al., 2004).
Janga SC , Collado-Vides J., Moreno-Hagelsieb G. (2005) "Nebulon: a system for the inference of functional relationships of gene products from the rearrangement of predicted operons" Nucleic Acids Res. 33 : 2521-2530.
Medrano-Soto A., Moreno-Hagelsieb G , Vinuesa P., Christen J.A. and Collado-Vides J. (2004) "Successful Lateral Transfer Requires Codon Usage Compatibility Between Foreign Genes and Recipient Genomes" Molecular Biology and Evolution 21 :1884-1894
Medrano-Soto, A. Christen, J.A. and Collado-Vides, J. (2005) "BClass: A Bayesian Approach Based on Mixture Models for Clustering and Classification of Heterogeneous Biological Data" Journal of Statistical Software 13 (2):1-18.
Moreno-Hagelsieb, G., Treviño, V., Pérez-Rueda, E., Smith, T.E., and Collado-Vides, J. (2001) "Transcription unit conservation in the three domains of life: a perspective from Escherichia coli " Trends in Genetics , 17 : 175-177.
Moreno-Hagelsieb G. and Collado-Vides J. (2002) "A powerful non-homology method for the prediction of operons in prokaryotes" Bioinformatics (ISMB-02) 18: Suppl.1 S329-S336
Pérez-Rueda E., and Collado-Vides J. (2000) "The Repertoire of DNA-Binding Transcriptional Regulators in Escherichia coli" Nucleic Acids Research 28 : 1838-1847
Pérez-Rueda E., and Collado-Vides J. (2001) "Common History at the Origin of the Position-Function Correlation in Transcriptional Regulators in Archaea and Bacteria" J. Mol. Evol . 53 : 172-179
Salgado H., Moreno-Hagelsieb G., Smith T.F., and Collado-Vides J. (2000) "Operons in Escherichia coli : Genomic Analyses and Predictions" Proc.Natl.Acad.Sci.USA 97 : 6652-6657