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Fernando J. Pineda, PhD

  • Associate Professor

Departmental Affiliations

Contact Information

615 N. Wolfe Street
Room E3626
Baltimore, Maryland 21205


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PhD, University of Maryland, 1986
MS, University of Maryland, 1981
BS, Massachusetts Institute of Technology, 1977



My group applies advanced computational and mathematical techniques to problems in modern biology and public health. We develop analysis algorithms, software tools and models that help biologists to characterize biological systems. For example consider the Plasmodium falciparum parasite, which is responsible for an estimated 350–500 million annual episodes of clinical malaria, with more than 1 million deaths per year. The life cycle of this parasite is extraordinarily complex and exhibits stage-specific regulation of nearly all its genes. The regulatory mechanisms of gene expression, if they can be identified and characterized, are a potentially rich source of targets for drugs and vaccines.



How the parasite performs such extensive regulation remains largely unknown, and may be quite unconventional. Several lines of evidence suggest that non-coding RNAs (ncRNAs) may play a significant role in regulating genome-wide expression patterns in this parasite. With funding from a Malaria Research Institute pilot grant, our group is developing an ab initio computational strategy for detecting rapidly evolving ncRNA genes.

Toxoplasma gondii is an obligate intracellular parasite that causes encephalitis, pneumonia, myocarditis, ocular disease, and congenital birth defects. We have collaborated with the Carruthers lab to develop mathematical models of the host-parasite interaction during the host-cell invasion stage.












  • Bioinformatics Computational Biology Mass Spectrometry Protein Identification Proteomics Neural Networks Machine Learning Signal Processing Statistical Physics
  • Sarah B. Berman, Ying-bei Chen, Bing Qi, J. Michael McCaffery, Edmund B. Rucker III, Sandra Goebbels, Klaus-Armin Nave, Beth A. Arnold, Elizabeth Jonas, Fernando J. Pineda and J. Marie Hardwick, Bcl-xL Increases Mitochondrial Fission, Fusion and Biomass in Neurons, Journal of Cell Biology, 184(5), 707-719, (2009)

  • Sarah B. Berman, Fernando J. Pineda, and J. Marie Hardwick, Mitochondrial Fission and Fusion Dynamics: the Long and Short of It, Cell Death and Differentiation, 15, pp. 1147-1152, (2008)

  • Syversen E, Pineda F.J., Watson J., Temperature variations recorded during inter-institutional air shipments of laboratory mice, J Am Assoc Lab Animal Sci., 47(1), pp. 31-36, (2008)

  • Kafsack BF, Carruthers VB, Pineda F.J., Kinetic modeling of Toxoplasma gondii invasion, Journal of Theoretical Biology, 249(4), pp. 817-825, (2007)

  • Cheng, W. C., Berman, S. B., Ivanovska, I., Jonas, E. A., Lee, S. J., Chen, Y., Kaczmarek, L. K., Pineda, F., Hardwick, J. M., Mitochondrial factors with dual roles in death and survival, Oncogene, 25, pp. 4697-4705, (2006)