Luís A. Nunes Amaral Integrative approach to modeling cellular signaling pathways

Research Interests

The Amaral lab conducts research on complex biological and social systems across a wide variety of disciplines. Gene regulators network, metabolic pathways, ecosystems, and the Internet are all examples of complex systems. These systems typically have a large number of components that act according to rules that may change over time and that may not be well understood. Moreover, the connectivity of the components may be quite plastic and their roles may be fluid. Because of such adaptability, one frequently observes the emergence of novel structures that could not be predicted from the individual characteristics of the components.

Our goal is to develop mechanistic models that provide insight into the emergence, evolution, and stability of complex systems. We pursue approaches that emphasize a holistic view of the system instead of focusing on the details of the components. The recent focus of our research includes studying stress response and aging in C. elegans, gene regulation networks in eye development in Drosophila, and evolutionary signatures in the codon utilization rates of different microbes. 

Selected Publications

A network approach to discerning the identities of C. elegans in a free moving population. Winter PB, Brielmann RM, Timkovich NP, Navarro HT, Teixeira-Castro A, Morimoto RI, and Amaral LAN. Scientific Reports. 2016 October 11;6:34859.

Dynamics and heterogeneity of a fate determinant during transition towards cell differentiation. Peláez N, Gavalda-Miralles A, Wang B, Tejedor Navarro H, Gudjonson H, Rebay I, Dinner AR, Katsaggelos AK, Amaral LAN, and Carthew RW. eLife. 2015;4:e08924.

Quantifying Position-Dependent Codon Usage Bias. Hockenberry AJ, Sirer MI, Amaral LAN, and Jewett MC. Molecular Biology and Evolution. 2014 July;31(7):1880-1893.

Phenomenological Model for Predicting the Catabolic Potential of an Arbitrary Nutrient. Seaver SMD, Sales-Pardo M, Guimerà R, and Amaral LAN. PLoS Computational Biology. 2012 November 1;8(11):e1002762.

Macro-level Modeling of the Response of C. elegans Reproduction to Chronic Heat Stress. McMullen PD, Aprison EZ, Winter PB, Amaral LAN, Morimoto RI, and Ruvinsky I. PLoS Computational Biology. 2012 January 26;8(1):e1002338.

View all publications by Luís A. Nunes Amaral listed in the National Library of Medicine (PubMed). Current and former IBiS students in blue.