Research interests

Nothing in biology makes sense except in the light of evolution.
Theodosius Dobzhansky, American Biology Teacher, 1973

My research interests can be mainly (but not exclusively!) grouped into the three following categories:

Evolutionary thermal biology

Temperature is a major driver of the performance of physiological and ecological traits (e.g., growth rate, escape body velocity) of all organisms, but especially of ectotherms. It is becoming increasingly clear that the shape of the thermal response curve (shown on the right) varies considerably across different traits, species, or thermal environments. I am interested in identifying processes that generate variation in the shape of the response, and factors that constrain it. Understanding these should improve our ability to predict the impacts of climate change on biological systems.

Relevant skills:
Fitting thermal response curves, phylogeny reconstruction and chronogram estimation, phylogenetic comparative methods, machine learning, some experience in fitting multivariate mixed-effects models, some experience in handling datasets of environmental variables, basic experience in mathematical modelling.

Relevant publications:
* Adaptive evolution shapes the present-day distribution of the thermal sensitivity of population growth rate.
* Phytoplankton thermal responses adapt in the absence of hard thermodynamic constraints.
* Use and misuse of temperature normalisation in meta-analyses of thermal responses of biological traits.

Evolution of genes and genomes

How do different genes and gene products (co-)evolve during adaptation, especially to extreme environments? What can we deduce from the size of a gene family across multiple species? Which gene expression alterations allow an organism to respond to changes in its local environment? These are some of the questions that I am interested in answering using comparative genomic and molecular approaches.

Relevant skills:
Gene tree inference, analysis of sequence conservation, Gene Ontology term enrichment, homology modelling, protein structure comparisons, some experience in performing and analysing molecular dynamics simulations, basic experience in identifying coevolving protein families, basic experience in gene set enrichment analysis.

Relevant publications:
* Higher temperatures worsen the effects of mutations on protein stability.
* Pinda: A Web service for detection and analysis of intraspecies gene duplication events.
* Recruitment of ubiquitin-activating enzyme UBA1 to DNA by poly(ADP-ribose) promotes ATR signalling.

Software development for computational biology

The breadth of available datasets (molecular, ecological, environmental, or others) continuously expands the range of questions that we can address to understand the structure and functioning of biological systems. To facilitate answering such questions, I am particularly interested in developing new software tools, or combining pre-existing ones into pipelines.

Relevant skills:
* Programming experience in Perl 5 (extensive), R (extensive), Python 2/3 (good), Common Lisp (basic), C (basic), and Shell (basic).
* Good experience with SQL databases (SQLite, MySQL).
* Can work on any major Operating System, including GNU/Linux distributions (e.g., Debian, Gentoo) and Mac OS X.

Relevant publications:
* Structuprint: a scalable and extensible tool for two-dimensional representation of protein surfaces.
* Space Constrained Homology Modelling: The Paradigm of the RNA-Dependent RNA Polymerase of Dengue (Type II) Virus.
* Pinda: A Web service for detection and analysis of intraspecies gene duplication events.