The Latinamerican bioinformatics force

20140619_145020

The Latin-American conSequences force

Since Julie was leaving on Saturday, those present in the lab last Thursday had lunch together.

Julie is a PhD student co-supervised by me and Dr. Santoyo. She came from Mexico for a few months to learn some bioinformatics that she will apply to her PhD project on the rhizospheric microbiome associated to a few crops.

See ya later Julie!

Three-minute thesis 2014

Today, Scott Dobson-Mitchell was the runner up at the three-minute thesis competition (3MT) at Laurier. image

Marc is done with the M.Sc.!

undergrads_fall2013Marc presented his thesis defense last Wednesday (Oct 30). All is well. Some corrections to make, but that’s that. Anyway, the photo presents the undergrad force of the lab of Computational conSequences (Brigitte, Erum, and Thomas), plus Marc. Taken that very day.

Congrats Marc!

Nobel 2013

I reacted too late. Maybe because I was at a conference:

http://smb-bacterias.org/images/POSTER_tabloide.pdf

In any event, the Nobel prizes! Take a look:

http://www.nobelprize.org/

The laureates in chemistry! I used to read several articles by Martin Karplus and by Michael Levitt when I was a grad student.

Have fun!

–Gabo

CSM 2013

Several members of The Lab of Computational conSequences went to the Canadian Society of Microbiologists conference in Ottawa last week: Lisa, Jenny, Marc, Scott, and honorary members Mike Lynch, and Laura (Lisa’s sister). All of them presented posters, Jenny gave her first talk in a scientific conference, and Mike gave a talk that I missed on exploring “the rare biosphere” (your homework to figure out what that means).

Posters were successful, Marc, who is working on the evolution of regulation of transcription by, ahem, transcription factors, had lots of visitors, the twins (Lisa and Laura) presented work on the gene cluster for cellulose biosynthesis in Bacteria, Jenny talked about 16S rRNA genes, and Scott presented a bit about phage and horizontal gene transfer.

We shall talk about these projects some time soon. We are preparing several articles and will post something about them as they are finished and submitted.

Have fun!

Visitors this summer

We have two visitors this summer to the lab of Computational conSequences:

  1. Karla Valenzuela, originally Chilean, working for her master’s at Dalhousie in Halifax (NS, Canada). Karla is doing some analyses I always was curious to do: evolutionary trace analyses, plus a few other, related, thingies. This means going back to my structural biology roots.
  2. Ismael Hernández, originally from Mexico, working for his PhD in CINVESTAV-Irapuato. Ismael is analyzing several strains of Bacillus isolated from Cuatro Ciénegas, Coahuila, Mexico.

We are talking a lot in Spanish, which is inspiring the Canadian Students in the lab to keep learning the language. Of course, we have had to explain differences between Chilean Spanish and Mexican Spanish, and it’s been fun.

Non-redundant prokaryotic genomes

We just had an Applications Note accepted in Bioinformatics. The little note presents a tool we develped to choose sets of non-redundant prokaryotic genomes (see Research-Genome Clusters too).

The tool derives from previous work where we selected sets of non-redundant prokaryotic genomes filtered at different levels of similarity for such tasks as displaying results on operon predictions, to finding the level of filtering out redundancy to maximize the number of high-quality predicted associations by phylogenetic profiles. Other groups have been using our non-redundant sets. Thus, we thought it was better to share to the wider community and we developed this tool. If you have suggestions for improvements, please let us know. We cannot promise to implement all suggestions, but we will try to make the tool very useful. Also note that the R-scripts used to produce these datasets are provided (as is). These might help you develop your own datasets if so you require.

-SuperGabo

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