Pablo's research and teaching areas Anaga mountains in Tenerife, Canary Islands
Pablo Vinuesa at Chichenitza


Pablo Vinuesa, PhD
Tutor of the PhD Program in Biomedical Sciences
Centro de Ciencias Genómicas, UNAM
A.P. 565-A
Av. Universidad s/n, Col. Chamilpa,
C.P. 62210, Cuernavaca, Morelos

Tel(s). (777) 317 5867,(55) 5622 7691
Fax. (777) 317 5581
Red UNAM: 27691
Int. 125


April 19th, 2013 - present. Professor of Environmental and Evolutionary Microbiology at the Center for Genomic Sciences (CCG-UNAM) in Cuernavaca, Mexico.
2005 - 2013. Associate Professor of environmental and evolutionary microbiology at the Center for Genomic Sciences (CCG-UNAM) in Cuernavaca, Mexico.
2001 - 2004. Assistant Professor at the Center for Genomic Sciences (CCG-UNAM) in Cuernavaca, Mexico.
1999 - 2001. EU-Training and Mobility of Researchers Postdoctoral Fellow in Bacterial Molecular Genetics in the group of Prof. Dietrich Werner, at the Philipps-Universität-Marburg, Germany.
Research (Google Scholar)
I'm a microbiologist interested in host-microbe interactions, microbial ecology, genomics and evolution. In collaboration with Dr. Bruno Contreras-Moreira, head of the Laboratory of Computational Biology at EEAD-CSIC, we are developing bioinformatics tools and genomic analysis strategies to identify highly informative molecular markers in genome sequences. The students in my group use these and other markers in diverse microbial molecular ecology and evolutionary genetic studies. We focus on communities and populations of the Rhizobiales, environmental mycobactera and Escherichia spp. in contrasting habitats (perturbed vs. conserved Mexican rivers and forests) ( »read more)
I'm actively involved in different teaching activities at the graduate and undergratuate levels. The most noteworthy are the Latin American Workshop on Molecular Evolution (TLEM), the International Workshops on Bioinformatics (TIB), and my regular course on Molecular Phylogenetics and Evolutionary Genomics, taught every second semester, at the Undergraduate Program in Genomic Sciences (LCG-UNAM), as well as the courses on bioinformatics (Intro2Bioinfo) and Perl programming for bioinformatics (Perl4bioinfo) I regularly teach for the PhD Program in Biomedical sciences. ( »more English; »más - Español).

( »detailed biosketch)

Academic information and resources on this site:

1) Research projects with an introduction to the students, friends and colleagues involved in them.
2) Publications and article downloads.
3) Hands-on tutorials on how to perform phylogenetic analyses using sequence data, from SSU rRNA sequence alignment and model fitting, up to ML tree searches and hypothesis testing. Many other tutorials and full-length course materials are provided as PDF files (tutoriales y cursos de bioinformática y filogenética en español), available only in Spanish at the present time.
4) Information on current issues in rhizobial taxonomy, systematics and genomics.
5) Links to bioinformatic data mining, programming and analysis tools, including our recent primers4clades web server
primers4clades (primers for clades) is an easy-to-use and interactive web server for the automatic design of degenerate PCR primers from multiple sequence alignments of protein-coding sequences. The resulting primers are suited for for cross-species amplification of novel sequences from metagenomic DNA, or from uncharacterized organisms belonging to user-specified phylogenetic lineages or taxa. The system is therefore ideal for the development of novel molecular markers (PCR amplicons) for MLSA and MLST studies. It implements an extended CODEHOP primer design strategy, based on both DNA and protein multiple sequence alignments of coding sequences. It evaluates a comprehensive set of thermodynamic parameters of the oligonucleotide pairs, as well as the phylogenetic information content of the theoretical amplicons, which is computed from the branch support values of maximum likelihood phylogenies estimated for each molecular marker. Phylogenetic trees displayed on screen make it easy to target the primer design for particular species groups or sequence clusters selected by the user. A detailed documentation and tutorial can be found here.
Mirror sites: primers4clades - Mexico and primers4clades - Spain. We would appreciate your feedback!
Citing primers4clades