John Stephen Garavelli
Professional Synopsis
More than twenty-five years experience in research and administration in the biochemical
sciences, especially biotechnology database operation, bioinformatics, proteomics,
molecular modeling, molecular evolution, and information theory emphasizing organization
and management, research and analysis, problem solving and theory development
Organization and Management
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Secured funding for and managed components of a major biotechnology database, bringing
three components for proteomics into international then web distribution, and coordinated
information exchange with other major biotechnology databases
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Associate Director of an international protein sequence database, responsible for automated
annotation, quality control, genome database cross-referencing, and human entry annotation
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Participant in international efforts including the ASTM, CODATA, the IUBMB Enzyme Commission,
and the Gene Ontology Consortium to establish formats and standards for interchange of
biomolecular sequence, model, crystallographic and function data
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Experience leading programming staff efforts with Alpha UNIX, IBM PC Windows, and VAX VMS
operating systems, in Perl, C, C++, PASCAL and FORTRAN applications for XML, SQL, and Oracle
database projects
Research and Analysis
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Developed and maintained innovative chemical modification and 3-dimensional structure
biotechnology databases both in the public domain
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Assigned more than 3600 human gene identifications for protein sequences prior to reporting of
the Human Genome Project preliminary results
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Using advanced techniques of protein sequence comparison and data mining, initiated development
of a method for protein function assignment of genomic sequences based on multi-scale
Hidden Markov Modeling (HMM)
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With expertise in post-translational modifications, predicted a novel nickel-containing enzyme
cofactor structure, later experimentally confirmed
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Helped develop computer programs to implement advanced molecular modeling techniques
including molecular orbital calculations, conformation analysis, energy minimization,
drug design and x-ray and electron diffraction analysis
Problem Solving and Theory Development
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Developed and implemented procedures for automated rule-based annotation and correction of sequence
database information utilizing a variety of classification schemes
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Found a combinatoric solution for a statistical problem arising in biopolymer sequence
comparisons and developed special computer methods for calculating the results
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Developed an algorithm for multiplication of symmetric polynomials enabling practical solutions
for Pólya enumeration problems such as counting chemical isomers or phylogenetic trees