Robert G. Rogers Jr

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[This is the abbreviated version; I got tired of getting spammed by head-hunters who couldn't be bothered even to skim it well enough to know that I wasn't at all what they were looking for. Besides, the full version had fallen out of date. -- rgr, 25-Dec-04.]

Summary of Expertise

Software Engineering
Interests
  • Applying object-oriented technology to rationalize the design of large software systems.
  • System and network security.
Systems
Linux, Solaris, SunOS, Tru64 Unix.
Five years sysadmin experience with Linux, and a smattering with the others.
Languages (fluent)
Fluent: Common Lisp, Perl, emacs lisp.
Proficient: C, SQL, Unix shell.
Historic: Basic, Fortran, PL/1, COBOL, various assemblers.
Bioinformatics
Interests
  • Protein structure modeling.
  • I have long been fascinated by evolution, particularly early molecular evolution and the emergence of life.
Experience
Two years experience in writing software to automate oligo design for PCR of various sorts.
Experienced with manipulation of the Protein Data Bank format for publishing protein structures (see the http://bmerc-www.bu.edu/needle-doc/new/atom-format.html page, for example).
Experienced with using and extending sequence data manipulation tools (e.g. search and alignment).

Publications

[1]
M. Cline, K. Karplus, R. H. Lathrop, T. F. Smith, R. G. Rogers Jr., D. Haussler. Information-theoretic dissection of pairwise contact potentials. Proteins: Structure, Function and Genetics. [Revised draft submitted.]
[2]
J. Bienkowska, H. He, R. G. Rogers Jr., and L. Yu. Bayesian approach to protein fold recognition: building protein structural models from bits and pieces. Chapter in Igor Tsigelny, editor, Protein Structure Prediction: Bioinformatics approach, 2002, pages 43-84. [In press.]
[3]
J. R. Bienkowska, L. H. Yu, R. G. Rogers Jr., S. Zarakhovich, and T. F. Smith. Protein fold recognition by total alignment probability. Proteins: Structure, Function and Genetics, 40:451-462, 2000.
[4]
J. R. Bienkowska, R. G. Rogers Jr., and T. F. Smith. Eliminating superfluous neighbor pairs while threading fold models. In Pacific Symposium on Biocomputing 2000, January 2000.
[5]
J. R. Bienkowska, R. G. Rogers Jr., and T. F. Smith. A method for optimal design of a threading scoring function. In S. Istrail, P. Pevzner, and M. Waterman, editors, RECOMB99 Proceedings of the Third Annual International Conference on Computational Molecular Biology, pages 25-32, Lyon, France, April 1999. ACM Press New York NY.
[6]
J. R. Bienkowska, R. G. Rogers Jr., and T. F. Smith. Performance of threading scoring function designed using a new optimization method. Journal of Computational Biology, 6(3):299-311, 1999.
[7]
J. R. Bienkowska, R. G. Rogers Jr., and T. F. Smith. Filtered neighbors threading. Proteins: Structure, Function and Genetics, 1999.
[8]
R. H. Lathrop, R. G. Rogers Jr., J. R. Bienkowska, B. K. M. Bryant, L. J. Buturovic, C. Gaitatzes, R. Nambudripad, J. V. White, and T. F. Smith. "Analysis and Algorithms for Protein Sequence-Structure Alignment," chapter in Computational Methods in Molecular Biology, Elsevier Press, Amsterdam, Netherlands, 227-283, 1998.
[9]
R. H. Lathrop, R. G. Rogers Jr., T. F. Smith, and J. V. White. A bayes-optimal sequence-structure theory that unifies protein sequence-structure recognition and alignment. Bull. Math. Biol., 60:1039-1071, 1998.
[10]
T. F. Smith, L. Lo Conte, J. Bienkowska, C. Gaitatzes, R. G. Rogers Jr., and R. H. Lathrop. Current limitations to protein threading approaches. J. Comp. Biol., 4:217-225, 1997.
[11]
S. Das, L. H. Yu, C. Gaitatzes, R. Rogers, J. Freeman, J. Bienkowska, R. M. Adams, T. F. Smith, and J. Lindellen. Biology's new rosetta stone. Nature, 385:29-30, 1997.
[12]
T. F. Smith, L. Lo Conte, J. R. Bienkowska, R. G. Rogers Jr., C. Gaitatzes, and R. H. Lathrop. The threading approach to the inverse protein folding problem. In S. Istrail, P. Pevzner, and M. Waterman, editors, RECOMB97 Proceedings of the First Annual International Conference on Computational Molecular Biology, New York, NY, January 1997. ACM Press.


Bob Rogers <rogers@rgrjr.dyndns.org>
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