Years Experience Design

Robert G. Rogers Jr

Resume (summary)

[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version had fallen out of date.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 ExpertiseSoftware 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 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

$Id: resume.html 94 2004-12-26 03:47:08Z rogers $

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