My Research Summary

in statistical and computational biology

by Alejandro Ochoa García

I've studied evolution in DNA and proteins, and malaria.

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My goal is to develop statistical methods, probabilistic models, and algorithms for problems in computational biology. I am particularly interested in human disease and evolution, including the study of population genetics and protein sequences. I analyze large datasets and tackle problems with a variety of tools from statistics and computer science, balancing accuracy with efficiency. Examples include properly accounting for genomic relatedness to better associate genotype to disease, improving remote homology prediction across large protein databases, modeling psychiatric scores in clinical trials, and expanding functional annotations in malaria parasites.

I am currently a Postdoctoral Reseach Associate in John D Storey's lab at Princeton University.

I received my PhD in Molecular Biology in 2013 from Princeton University, coadvised by Mona Singh and Manuel Llinás. In 2006 I earned a double-majored in Biology and Mathematics at the Massachusetts Institute of Technology. See my CV (PDF).

Population genetics

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Alejandro Ochoa, John D Storey. FST and kinship for arbitrary population structures II: Method of moments estimators. Submitted. bioRxiv 2016-10-27.

Software: popkin and bnpsd

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Alejandro Ochoa, John D Storey. FST and kinship for arbitrary population structures I: Generalized definitions. Submitted. bioRxiv 2016-10-27.

Protein domain prediction

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2017-04-12. Alejandro Ochoa, Mona Singh. Domain prediction with probabilistic directional context. Bioinf. 2017 btx221 Pubmed Article. bioRxiv 2016-12-14.

Software: dPUC2

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2015-11-17. Alejandro Ochoa, John D Storey, Manuel Llinás, Mona Singh. Beyond the E-value: stratified statistics for protein domain prediction. PLoS Comput Biol. 11 e1004509. Pubmed Article arXiv 2014-09-23.

Software: DomStratStats and RandProt

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2011-03-31. Alejandro Ochoa, Manuel Llinás, Mona Singh. Using context to improve protein domain identification. BMC Bioinformatics 12:90. Pubmed Article.

Software: dPUC1

Collaborative research

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2016-01-27. Simon A Cobbold, Joana M Santos, Alejandro Ochoa, David H Perlman, Manuel Llinás. Proteome-wide analysis reveals widespread lysine acetylation of major protein complexes in the malaria parasite. Sci Rep 2016;6:19722 Pubmed Article.

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2013-11-13. Moriah L. Szpara, Derek Gatherer, Alejandro Ochoa, Benjamin Greenbaum, Aidan Dolan, Rory J. Bowden, Lynn W. Enquist, Matthieu Legendre, Andrew J. Davison. Evolution and diversity in human herpes simplex virus genomes. J Virol 88:1209–1227. Pubmed Article

Computational protein design

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2007-11-01. Gevorg Grigoryan, Alejandro Ochoa, Amy E Keating. Computing van der Waals energies in the context of the rotamer approximation. Proteins 68 (4), 863-78. Pubmed Article

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VIIIA

History