Gabriel Moreno-Hagelsieb
Group of Computational Genomics
Wilfrid Laurier University

Publications:

• Gonzalez, V., Santamaria, R.I., Bustos, P., Hernandez-Gonzalez, I., Medrano-Soto, A., Moreno-Hagelsieb, G., Janga, S.C., Ramirez, M.A., Jimenez-Jacinto, V., Collado-Vides, J. et al. (2006) The partitioned Rhizobium etli genome: Genetic and metabolic redundancy in seven interacting replicons. Proc Natl Acad Sci U S A. Reprint
• Janga, S.C., Collado-Vides, J. and 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, 2521-30. Reprint
• 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. Mol Biol Evol, 21, 1884-1894. Reprint
• Lamboy, W.F. and Moreno-Hagelsieb, G. (2004) A new method of solution for the occupancy problem and its application to operon size prediction. J Theor Biol, 227, 315-322. Reprint
• Janga, S.C. and Moreno-Hagelsieb, G. (2004) Conservation of adjacency as evidence of paralogous operons. Nucleic Acids Res, 32, 5392-5397. Reprint
• Jauregui, R., Abreu-Goodger, C., Moreno-Hagelsieb, G., Collado-Vides, J. and Merino, E. (2003) Conservation of DNA curvature signals in regulatory regions of prokaryotic genes. Nucleic Acids Res, 31, 6770-6777. Reprint
• Gonzalez, V., Bustos, P., Ramirez-Romero, M.A., Medrano-Soto, A., Salgado, H., Hernandez-Gonzalez, I., Hernandez-Celis, J.C., Quintero, V., Moreno-Hagelsieb, G., Girard, L. et al. (2003) The mosaic structure of the symbiotic plasmid of Rhizobium etli CFN42 and its relation to other symbiotic genome compartments. Genome Biol, 4, R36. Reprint
• Moreno-Hagelsieb, G. and Collado-Vides, J. (2002) A powerful non-homology method for the prediction of operons in prokaryotes. Bioinformatics, 18 Suppl 1, S329-336. Reprint
• Moreno-Hagelsieb, G. and Collado-Vides, J. (2002) Operon conservation from the point of view of Escherichia coli, and inference of functional interdependence of gene products from genome context. In Silico Biol, 2, 87-95. Reprint
• Benitez-Bellon, E., Moreno-Hagelsieb, G. and Collado-Vides, J. (2002) Evaluation of thresholds for the detection of binding sites for regulatory proteins in Escherichia coli K12 DNA. Genome Biol, 3, RESEARCH0013. Reprint
• Tan, K., Moreno-Hagelsieb, G., Collado-Vides, J. and Stormo, G.D. (2001) A comparative genomics approach to prediction of new members of regulons. Genome Res, 11, 566-584. Reprint
• Ramirez-Benitez Mdel, C., Moreno-Hagelsieb, G. and Almagro, J.C. (2001) VIR.II: a new interface with the antibody sequences in the Kabat database. Biosystems, 61, 125-131. Reprint
• Moreno-Hagelsieb, G., Trevino, V., Perez-Rueda, E., Smith, T.F. and Collado-Vides, J. (2001) Transcription unit conservation in the three domains of life: a perspective from Escherichia coli. Trends Genet, 17, 175-177. Reprint
• 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 U S A, 97, 6652-6657. Reprint
• Moreno-Hagelsieb, G., Gomez-Puyou, A. and Soberon, X. (1999) Escherichia coli TEM1 beta-lactamase in CTAB reverse micelles: exchange/diffusion-limited catalysis. FEBS Lett, 459, 111-114. Reprint
• Moreno-Hagelsieb, G. and Soberon, X. (1996) Protein engineering as a powerful tool for the chemical modification of enzymes. Biol Res, 29, 127-140. Reprint
• Gurrola, G.B., Moreno-Hagelsieb, G., Zamudio, F.Z., Garcia, M., Soberon, X. and Possani, L.D. (1994) The disulfide bridges of toxin 2 from the scorpion Centruroides noxius Hoffmann and its three-dimensional structure calculated using the coordinates of variant 3 from Centruroides sculpturatus. FEBS Lett, 347, 59-62. Reprint

Research Interests:

Functional and Comparative Genomics (a bit outdated)
Biological Plasticity

I am currently working on comparative genomics. Mainly on prokaryotic microorganisms. My interests are varied, but I might say that my main motivation is on the understanding of functional plasticity.

For the moment my main research has been concentrated on genome organization, or re-organization. The first emphasis has been the development of a transcription unit prediction tool based on information about transcription units of Escherichia coli found in RegulonDB (yes, I mean operons). After this, we studied operon conservation across genomes, showing them to be the main reason for conservation of gene order. Being ambitious, we sought for evidence that we could predict operons in any prokaryote, and finally demonstrated, by the use of functional inference by genomic context (see references in paper), and other analyses, that we could.

Now, I have also participated in the search for signals in DNA, first referring to DNA sequences bound by transcriptional regulators. This is a very interesting area, and, though much work and most of the main ideas are already there, there is a lot of work to do at the global and specific levels. The main problem is the accurate identification, by computational methods of the DNA sequences themselves, since these are in general semi-conserved short sequences (generally 20 bases long), and most computer algorithms produce many false positives (again, see references everywhere, as I said, the ideas are out there already). To help the correct identification there are several proposals, semi-tested here and there, but not completely exhausted, that use comparative genomics tools (see Tan et al 2001). This is an area that I am currently developing by using the information, again, gathered in RegulonDB, about regulons (see Benitez et al 2002), and lots of sequence comparisons, and runs of motif search programs. Identification of regulons by computational methods requires a lot of work along several lines of research, and tests to be performed.

I was talking about biological plasticity, right? Well, I have also started some work on compositional analyses of genomic, or genomic-derived sequences (with a lot of help from my friends). Of course, this means codon usage, and also oligo-nucleotide compositions. Since this part is rather embryonic, I talk to you about it later. Just one important remark here, there is no such thing as "optimization". You can talk about "tendencies", but not optimization. The only one rule in Evolution is "whatever works" (this is not mine, I have heard it twice in conferences, but, sorry, I do not remember by whom).