Tuesday, February 10, 2015

Group member profile - Brandon Invergo

I had mentioned previously that we should do a better job of using the web to describe our group and work. As part of this effort I will try to have a recurrent blog post series to introduce the lab members more extensively. The first group member to give this a try is Brandon Invergo (website, twitter, GScholar) who is currently doing a postdoc in the group with an ESPOD fellowship. Here follows Brandon's answers to a few questions I asked him.

What was the path the brought you to the group? Where are you from and what did you work on before arriving in the group?

I originally studied Computer Science, but by the time I was finishing my degree, I was more interested in doing something Biology-related than in working for a software company. Not sure yet what I wanted to do specifically, after receiving my degree I was fortunate to get a job working in the lab of Lawrence H. Pinto at Northwestern University (Evanston, IL, USA). There, I performed electrophysiological and behavioral assays of the mouse visual system, in the context of a functional genomics program. After a few years, I decided that it was time to go back to school and to start on the path towards a career in academic research. So, I moved to the Netherlands to pursue a master's degree in Biology at Leiden University. I specialized in evolutionary and ecological sciences and I did my primary research project under the supervision of Bas Zwaan. I investigated how the dynamics of hormonal signaling during pupal development of a tropical butterfly change in response to environmental conditions (temperature) and how those changes give rise to distinct adult phenotypes (polyphenism).

For my PhD, I wanted to perform research where I could combine my backgrounds in computer science and evolution and a nascent interest in systems biology (bonus points if I could also tie in my background in vision research). For this, I moved to the Institute of Evolutionary Biology (Pompeu Fabra University / Spanish National Research Council) in Barcelona, Spain, where I joined the group of Jaume Bertranpetit and worked under his supervision with the co-supervision of Ludovica Montanucci. My thesis, which I successfully defended in November 2013, was entitled "A system-level, molecular evolutionary analysis of mammalian phototransduction". In it, I combined techniques from bioinformatics and computational biology for molecular evolution with network- and modelling-based tools from systems biology. I sought to uncover the influence of the structure and dynamics of the visual phototransduction pathway on the evolution of the proteins that comprise it. The work also resulted in the improvement of the most comprehensive mathematical model of the system produced to date (currently under review at Biomodels), as well as a Biopython module for working with codeml and other programs from the PAML package (which are notoriously annoying to work with in analysis pipelines).

What are you currently working on?

I joined the EBI and the Sanger Institute in December 2013 as an ESPOD fellow, one week after my thesis defense. Here, I am continuing to explore how complex signaling systems function and evolve, except now I'm working in the context of malarial parasites (Plasmodium spp.).

In particular, I'm studying post-translational modifications (PTMs) on a proteome scale in the parasites, with an eye towards how the parasite uses reversible PTMs (mainly phosphorylation) for cellular signaling during key transitions in its complex lifecycle. This work involves performing both the mass-spectrometry experiments to collect the data and the computational analyses on these and other datasets. I'm finishing up a rather big experiment now and in a few weeks I expect to be neck-deep in data.

What are some of the areas of research that excite you right now?

Really anything at the intersection (well, more generally, the union) of molecular evolution and systems biology immediately catches my attention, such as the evolvability of pathways or the patterning of natural selection across systems. Of course, I'm reading a lot right now about detecting and describing PTMs at the proteomic scale. I'm also excited by developments in biochemical system modelling, particularly right now in methods for bayesian inference of parameters from large-scale datasets. Finally, though it's not directly my field, I like to keep an eye on what's happening in complexity research at the most fundamental, mathematical level.

What sort of things do you like outside of the science?

I'm very active in the Free Software community and within GNU in particular. I help out a lot behind the scenes: working with (read: pestering) GNU software maintainers, evaluating new software that has been offered to us, and being on the advisory board. I also maintain some GNU packages (GSRC & pyconfigure) and some of my own software projects in my free time. My other main passion is music. I have written many mediocre electronic music songs over the years, some of which have even been released, and I was a moderately successful DJ for nearly a decade. Sadly, my music-writing died off as my PhD thesis gained steam and I haven't written anything recently. When I decide to take a break from all that or to be social, I like to play boardgames.