Jonas S. Almeida, Ph.D. 1995, University of Lisbon UT M. D. Anderson Cancer Center Bioinformatics and Computational Biology Contact Information Biographical Sketch

Research Interests: Integrative Bioinformatics; systems biology; biomarker identification; drug/target discovery; statistical mechanics

"Mathematics is the language of nature" famously said Galileo Galilei, and four centuries later, through computational biology, it is indeed becoming a central tool for experimentation and discovery in the life sciences. Two central problems limit the quest for a systemic understanding and manipulation of living systems. The first is the identification of molecular patterns that reliably diagnose the present status and future developments.  This pursuit has direct relevance to the identification of biomarkers for disease diagnosis and for the prediction of responses to alternative treatments. The second problem is that of inferring a causal mechanism from its observed consequences, a process that is much harder for complex, systemic conditions like cancer, but which is also potentially much more rewarding. My research interests are directed towards the computational and mathematical tools and mathematical formalisms needed to tackle the twin challenges of identifying biomarkers and targets for drug discovery. These two goals are pursued in tandem through close collaboration with clinical and molecular biology experimentalists working with a diverse range of problems.  These collaborations provide opportunities to find novel quantitative solutions to facilitate our representation and manipulation of living systems. In this context, the identification of an informatic mediator for the interaction between computational and experimental Biology has become a central topic of my research. As Molecular Biology, also integrative Computational Biology and Bioinformatics requires a set of experimental tools to develop and validate novel approaches to probe complex behaviors and achieve deeper insight into the underlying systemic phenomena. To know more about this research see the web-page of the Integrative Bioinformatics Laboratory (http://integrativebioinformatics.org/).
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Almeida JS, C Chen, R Gorlitsky, R Stanislaus, M Aires-de-Sousa, P Eleutério, JA Carriço, A Maretzek, A Bohn, A Chang, F Zhang, R Mitra, GB Mills, X Wang, HF Deus (2006) Data integration gets 'Sloppy'. Nature Biotechnology 24(9):1070-1071.

Almeida, J.S., S.Vinga (2006) Computing distribution of scale independent motifs in biological sequences. Algorithms for Molecular Biology. 1:18.

Chen YA, Chou CC, Lu X, Slate EH, Peck K, Xu W, Voit EO, Almeida JS (2006) A multivariate prediction model for microarray cross-hybridization BMC Bioinformatics 7:101.

Wang X, Gorlitsky R, Almeida JS (2005) From XML to RDF: How semantic Web technologies will change the design of "omic" standards. Nature Biotechnology. 23(9):1099-1103.

Almeida JS, Stanislaus R, Krug E, Arthur J (2005) Normalization and analysis of residual variation in 2D gel electrophoresis for quantitative differential proteomics. Proteomics. 5(5):1242-1249.

Mikhitarian K, Gillanders WE, Almeida JS, Hebert Martin R, Varela JC, Metcalf JS, Cole DJ, Mitas M (2005) An innovative microarray strategy identities informative molecular markers for the detection of micrometastatic breast cancer. Clinical Cancer Research. 11(10):3697-3704.

Oates JC, Varghese S, Bland AM, Taylor TP, Self SE, Stanislaus R, Almeida JS, Arthur JM (2005) Prediction of urinary protein markers in lupus nephritis. Kidney International. 68(6):2588-2592.

Stanislaus R, Chen C, Franklin J, Arthur J, Almeida JS (2005) AGML Central: AGML Compatible proteomic database. Bioinformatics. 21(9):1754-1757.

Program Affiliation:
Program in Biomathematics & Biostatistics