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Melanie Nelson's Professional Summary

I'm interested in helping scientists better manage and exploit their data. It bothers me that it is easier to find a book on Amazon than it is to find reliable information about a particular protein in most biological databases. The complexity of biological data is only part of the reason for this discrepancy. The rest of the reason is incomplete implementation of good database design and data mining techniques in biology.

Since receiving my Ph.D. in 1999, I've worked in the biotechnology industry designing databases and developing repeatable and automatable processes for computational analysis of biological data. I also collaborated on the creation of CellML, an XML-based language for the specification and exchange of models of cells and cellular processes.

During my Ph.D. studies, I created a web-based resource about the family of proteins that I was studying. The EF-hand Calcium-Binding Data Library is now maintained by the lab of Walter Chazin (my thesis advisor).

My primary research project in graduate school was the design and study of mutants of calbindin D9k, with the goal of understanding which sequence differences are responsible for the differences in the response of calbindin D9k and calmodulin to calcium binding. I designed many mutants, generated and studied a few, and solved the solution structure of one using NMR methods (F36G, 1KCY).


1999, Ph.D., Macromolecular Structure and Chemistry, The Scripps Research Institute
Advisor: Walter Chazin
Thesis: A Rational Approach to Understanding the Relationship of Sequence, Structure, and Function in EF-Hand Calcium-Binding Proteins

1994, B.S., Biological Chemistry, The University of Chicago

Publication List


C. G. Bunick, M. R. Nelson, S. Mangahas, M. J. Hunter, J. H. Sheehan, L. S. Mizoue, G. J. Bunick, W. J. Chazin. Designing Sequence to Control Protein Function in an EF-Hand Protein. Submitted.

M.R. Nelson, S. J. Reisinger, S. G. Henry. Designing databases for biological information. (2003) BioSilico, 1: 134-142.

S.A. Cammer, B.T. Hoffman, J.A. Speir, M.A. Canady, M.R. Nelson, S. Knutson, M. Gallina, S.M. Baxter, J.S. Fetrow. Structure-based active site profiles for genome analysis and sub-family classification, (2003) J. Mol. Biol., 334:387-401. [ PubMed ]

S.M. Baxter, J. S. Rosenblum, S. Knutson, M.R. Nelson, J.S. Montimurro, J. Di Gennaro, J.A. Speir, J.S. Fetrow, J.J. Burbaum. Synergistic computational and experimental proteomics approaches for more accurate detection of active serine hydrolases in yeast. (2003) Mol. Cell Proteomics [ PubMed ]

W. J. Hedley, M. R. Nelson, D. P. Bullivant, and P. F. Nielsen. A short introduction to CellML. (2001) Phil. Trans. R. Soc. Lond. A, 359: 1073-1089.

M.R. Nelson, E. Thulin, P.A. Fagan, S. Forsen, W.J. Chazin. The EF-hand domain: A globally cooperative structural unit. (2002) Protein Sci., 11: 198-205. [ PubMed ]

M.R. Nelson and W.J. Chazin, An interaction-based analysis of calcium-induced conformational changes in Ca2+-sensor proteins. (1998) Protein Sci., 7, 270-282. [ PubMed ]

J. Li, M.R. Nelson, C.Y. Peng, D. Bashford, L. Noodleman, Incorporating protein environments in density functional theory: A self-consistent reaction field calculation of redox potentials of [2Fe-2S] clusters in ferredoxin and phthalate dioxygenase reductase. (1998) J. Phys. Chem. A, 102, 6311-6324.

Invited Reviews

B.T. Hoffman*, M.R. Nelson*, K. Burdick, S.M. Baxter, Protein tyrosine phosphatases: strategies for distinguishing proteins in a family containing multiple drug targets and anti-targets. Submitted. *These authors contributed equally

P. A. Fagan, M. R. Nelson, W. J. Chazin, "EF Hand" in The Wiley Encyclopedia of Molecular Medicine (2002).

M.R. Nelson and W.J. Chazin, "EF-Hand Calcium-Binding Proteins" in The Encyclopedia of Life Sciences (2001).

M.R. Nelson and W.J. Chazin, Structures of EF-hand Ca2+-binding proteins: diversity in the organization, packing and response to Ca2+ binding. (1998) Biometals, 11, 297-318. [ PubMed ]

M.R. Nelson and W.J. Chazin, "Calmodulin as a calcium sensor" in Calmodulin and Signal Transduction. L.J. Van Eldik and D.M. Watterson, eds. (1998) Academic Press, San Diego, pp. 17-64.

M.R. Nelson, C. Weber, and W.J. Chazin, in The Encyclopedia of Molecular Biology, T. Creighton, ed. John Wiley & Sons, New York (1999). "Calcium-binding proteins" 330-332, "Calmodulin" 332-334, "Parvalbumin" 1768-1770, "EF-hand motif" 784.

C. Weber, M.R. Nelson, and W.J. Chazin, in The Encyclopedia of Molecular Biology, T. Creighton, ed. John Wiley & Sons, New York,(1999). "EDTA" 782-783, "EGTA" 959.

Primary author: Melanie Nelson
Last edited: 1 February 2004