BIOCOMPLEXITY

In the past decade, bioinformatics has become an integral part of research and development in the biomedical sciences. Bioinformatics now has an essential role both in deciphering genomic, transcriptomic and proteomic data generated by high-throughput experimental technologies and in organizing information gathered from traditional biology.

Sequence-based methods of analyzing individual genes or proteins have been elaborated and expanded, and methods have been developed for analyzing large numbers of genes or proteins simultaneously, such as in the identification of clusters of related genes and networks of interacting proteins. With the complete genome sequences for an increasing number of organisms at hand, bioinformatics is beginning to provide both conceptual bases and practical methods for detecting systemic functional behaviors of the cell and the organism.

From: Kanehisha and Bork, Bioinformatics in the post-sequence era, Nature Genetics 33, 305-310 (2002).

 

Biochemical networks

Guimerà, Sales-Pardo, Amaral, A network-based method for target selection in metabolic networks, Bioinformatics 23, 1616-1622 (2007).

Guimerà, Sales-Pardo, Amaral, Classes of complex networks defined by role-to-role connectivity profiles, Nature Physics 3, 63-69 (2007).

Guimerà, Sales-Pardo, Form follows function: the architecture of complex networks, Molecular Systems Biology 2, art. no. 42 (2006).

Guimerà, Amaral, Functional cartography of complex metabolic networks, Nature 433, 895-900 (2005).

Evolution

Sales-Pardo, Chan, Amaral, Guimerà, Evolution of protein families: Is it possible to distinguish between domains of life?, Gene 402, 81-93 (2007).

Molecular biophysics

Sales-Pardo, Guimerà, Moreira, Widom, Amaral, Mesoscopic modeling for nucleic acid chain dynamics, Physical Review E 71, 051902 (2005).