Germán Plata


Postdoctoral Research Scientist

As a postdoctoral research scientist in the laboratory of Dr. Dennis Vitkup, I am interested in developing methods for the annotation, reconstruction, and simulation of microbial metabolic networks. Working as a graduate student in the Vitkup Lab, this research led to the development of the Global Biochemical Reconstruction Using Sampling (GLOBUS) algorithm, a novel probabilistic method for the genome-wide annotation of metabolic genes. GLOBUS combines information about sequence homology with gene-gene context correlations such as phylogenetic profiles, chromosomal gene clustering, or mRNA co-expression to predict the probabilities of genes to display specific biochemical functions. We have applied our methods to the annotation and discovery of gene functions in bacteria such as B. subtilis, and to identify novel potential targets for malaria treatment. We are currently expanding the types of data used by GLOBUS, and anticipate this will greatly enhance its performance. Another central object of my research is the comparative analysis of metabolic phenotypes across bacterial phylogenetic space. The wealth of available sequence data and the advancement of computational tools for the modeling and simulation of metabolic networks are allowing us to trace phenotypic properties of bacteria across 4 billion years of evolution. 

Before arriving at Columbia University, I worked for three years in the Agrobiodiversity Research Area at the International Center for Tropical Agriculture in Cali, Colombia, where I received the 2008 Outstanding Young Scientist of the Year Award. After my PhD, I was awarded the Titus M. Coan Prize for Excellence in Research by Columbia University.

Education History

PhD, Columbia University                                                                                                                 Integrated Program in Cellular, Molecular, and Biomedical Studies

BSc, National University of Colombia                                                                                                 Biology


Plata G, Henry CS, Vitkup D. Long-term phenotypic evolution of bacteria. Nature. 2014 Oct 26.

Ballén-Taborda C, Plata G, Ayling S, Rodríguez-Zapata F, Becerra Lopez-Lavalle LA, Duitama J, Tohme J. Identification of Cassava MicroRNAs under Abiotic Stress. Int J Genomics. 2013;2013:857986.

Plata G, Vitkup D.  2013.  Genetic Robustness and Functional Evolution of Gene Duplicates. Nucleic Acids Res. 2014 Feb;42(4):2405-14.

Anton BP, Chang Y-C, Brown P, Choi H-P, Faller LL, Guleria J, Hu Z, Klitgord N, Levy-Moonshine A, Maksad A et al.  2013. The COMBREX project: design, methodology, and initial results. PLoS Biol. 11(8):e1001638.

Plata G, Fuhrer T, Hsiao T-L, Sauer U, Vitkup D.  2012.  Global probabilistic annotation of metabolic networks enables enzyme discovery. Nat Chem Biol. 8(10):848-54.

Plata G, Gottesman ME, Vitkup D. The rate of the molecular clock and the cost of gratuitous protein synthesis. Genome Biol. 2010;11(9):R98.

Plata G, Hsiao TL, Olszewski KL, Llinás M, Vitkup D. Reconstruction and flux-balance analysis of the Plasmodium falciparum metabolic network. Mol Syst Biol. 2010 Sep 7;6:408.

Sakurai T, Plata G, Rodríguez-Zapata F, Seki M, Salcedo A, Toyoda A, Ishiwata A, Tohme J, Sakaki Y, Shinozaki K, Ishitani M. Sequencing analysis of 20,000 full-length cDNA clones from cassava reveals lineage specific expansions in gene families related to stress response. BMC Plant Biol. 2007 Dec 20;7:66.