Research

Our research focuses on the analysis of biological sequences and how these are regulated in the context of an entire system. We conduct experimental and computational research by collecting and integrating Genome-Wide Measurements (Genomics, Transcriptomic and Proteomics) to derive and test models and behaviors of complex biological systems. These are the main research areas we are exploring at the Integrative Systems Biology Laboratory.

Current Research

Coral reefs are complex and dynamic systems that are geologically robust and have persisted through major climactic shifts, yet they are highly sensitive to environmental perturbations on ecological timescales. The Earth’s climate is changing rapidly mostly due to anthropogenic disturbances. The average temperature of the ocean is projected to increase at least 3°C by the end of the century, and there is a progressive oceans acidification (cecrising pH) due to increasing atmospheric CO2, with potentially serious effects on the structure and function of coral reef systems. It is unclear if and how reef species, such as tropical fishes, will adapt to these rapid changes in ocean temperature. In particular, tropical species may be more vulnerable to rising temperatures and decrising pH than species from cooler climates, because they are already living close to their thermal limits. Transgenerational acclimation is a form of non-genetic inheritance in which the environmental conditions experienced by one-generation influences the performance of future generations in that environment. New studies show that the performance of juvenile fish at higher water temperatures is significantly improved when their parents also experienced the warmer temperature. The molecular mechanisms responsible for transgenerational thermal acclimation, and how it is controlled, are currently unknown. Genomic DNA methylation is a form of epigenetic inheritance that cells use to control gene expression, and recent evidence suggests that genome methylation can be driven by external signals in cells after birth as well as in adult cells. This raises the intriguing possibility that DNA methylation can serve as a mechanism for genomes to rapidly adapt to changing environments. Here we propose a unique multi-generational manipulative experiment for a common coral reef fish, Acanthochromis polyacanthus, with genome-wide measurements of gene expression and DNA methylation. Using an integrative analysis, we seek to identify molecular pathways responsible for transgenerational acclimation to rising ocean temperatures and to test the hypothesis that genomic DNA methylation serves as a central mechanism mediating transgenerational acclimation to climate change.
Mathematical modeling has been an important component of several biological disciplines for many decades. One of the earliest quantitative biological models involved ecology: the Lotka-Volterra model of species competition and predator-prey relationships In the context of cell biology, models and simulations are used to examine the structure and dynamics of a cell, rather than the characteristics of isolated parts of a cell or organism
Every molecular process occurring in a living cell is a concerted activity of numerous players. Networks defined by the interactions between genes and proteins perform specific cellular functions. A great challenge of modern biology is to elucidate these mechanisms and to decipher the dominant actors in these molecular networks.
Translational genomics is the integrated application of innovative functional genomic tools and modern biophysical and clinical technologies to leverage maximum benefit out of vast amount of genome-scale datasets that are available in many experimental system including model organisms. ​