Robert C. Edgar
Mill Valley, CA 94941
Phone (day / eve): (415) 389-6245
Experience
4/02–now Computational biologist
I am working on algorithm
development in computational biology, specializing in sequence
alignment and applications of hidden Markov models. Some of this work has been
pursued independently, and some in collaboration with scientists at UC Berkeley
and elsewhere. I have presented several seminars and invited talks and have
guest-lectured at undergraduate and post-graduate classes at UC Berkeley and UC
San Francisco. I have a Visiting Scholar appointment at the University of
California.
1989–3/02 CEO/Owner,
Parity Software, Sausalito, California; sold to Intel Corp.
Parity created and
sold software development tools for computer telephony applications. I was
chief architect and lead developer of Parity's core products, which won
numerous industry awards. I built the business to 30 employees and $10M/year
sales by 1999, then sold the company to Intel Corp.
1982–1988 CTO,
IDBS ApS, Copenhagen, Denmark.
At IDBS I designed
and implemented a database server and application development environment. The IDBS
software was based on a flexible, self-describing data format that was quite
different from traditional hierarchical and relational systems. Our platform
anticipated key features of XML as early as 1982.
1977–1982 PhD
research in theoretical particle physics at University College, London.
My research focused
on computer simulations of relativistic quantum gauge theories, in particular
Monte Carlo calculations of lattice gauge models. My PhD research was completed
in less than three years and led to five published papers. This was achieved
despite the lack of a thesis advisor (my designated supervisor could not find
funding to bring me to the United States).
Education
1976 to 1982 University
College, London.
PhD,
Theoretical High-Energy Physics (1982).
BSc (1st class honors), Physics (1977).
Peer-reviwed
publications
Edgar RC (2004),: MUSCLE:
a multiple sequence alignment method with reduced time and space complexity.
BMC Bioinformatics, 5(1):113.
Edgar RC (2004),: MUSCLE: Low-complexity multiple sequence alignment with
T-Coffee accuracy. ISMB2004 short paper.
Edgar,R.C. (2004), MUSCLE: multiple sequence alignment with high accuracy and high throughput
Nucleic Acids Research 32(5), 1792-97.
Edgar,R.C. (2003), Local homology detection and
distance measures in linear time using compressed amino acid alphabets Nucleic
Acids Res 32(1):
380-5.
Edgar,R.C. and Sjölander,K. (2004), COACH: profile-profile alignment
of protein families using hidden Markov models, Bioinformatics (in
press).
Edgar,R.C. and Sjölander,K.
(2004), A comparison of scoring
functions for protein sequence profile construction, Bioinformatics
(in press).
La,D., Silver,M., Edgar,R.C. and Livesay,D,R.
(2003), Using
motif-based methods in multiple genome analyses: a case study comparing orthologous mesophilic and thermophilic proteins, Biochemistry 42(10),
8988-8998.
Edgar,R.C. and Sjölander,K. (2003), SATCHMO: Simultaneous
alignment and tree construction using hidden Markov models, Bioinformatics
19(11), 1404-1411.
Edgar,R.C. and Sjölander,K.
(2003), Simultaneous sequence alignment
and tree construction using hidden Markov models, Proc. Pac. Symp. Biocomp . 2003, 180-191.
Edgar,R.C. (1985), Basic techniques of Euclidean lattice gauge theory, Fortschritte der Physik 33(2), 57-116.
Edgar,R.C. (1982), Generalized actions for lattice gauge models, Nucl . Phys. B 200(FS4), 345-354.
Edgar,R.C. (1981), A roughening effect in small Wilson loops, J. Phys. G 7(10), L215–219.
Edgar,R.C., McRossen,L.
and Moriarty,K J.M. (1981), The specific heat of
SU(3) lattice gauge theory, J. Phys. G 7(5), 85–88.
Edgar,R.C., McRossen,L. and Moriarty,K.J.M. (1981), Monte Carlo simulation of U(1) lattice gauge theory, Comp. Phys. Comm. 122(4), 433-437.
The VoiceXML Handbook, CMP Books (2001).
PC Telephony, CMP Books, 1st ed. (1992) through 4th ed. (1998).
Awards
ISMB/ECCB
2004 Best paper award.