Noteworthy
New stuff on the site
Bioinformatics
Cursos y tutoriales
Rhizobial taxonomy
Biosketch
- Appointments
-
2005 - present. Associate Professor in 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
-
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)
- Teaching
-
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),
and my regular course on Molecular Phylogenetics and Evolutionary Genomics,
taught every second semester, at the Undergraduate Program in Genomic Sciences
(LCG-UNAM).
( »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
