Curriculum vitae
                Christopher Bystroff

        Date of birth:  2 January 1960
        Home address:   35 Pinewoods Ave
                        Troy, NY 12180
        Home phone:     518-272-7888
        Work address:   Dept of Biology, MRC 303
                        Rensselaer Polytechnic Institute
                        Troy, NY 12180
        Work phone:     518-276-3185
        fax:            518-276-2162
        Nationality:    USA
        email:          bystrc@rpi.edu
        website:        www.bioinfo.rpi.edu/bystrc


================== Higher Education
years           institution                     degree
-----           -----------                     ------
1978-1983       Carleton College, Minnesota     B.A., (chemistry) 
1983-1985       UCSD, La Jolla, CA              M.S. (chemistry)
1985-1988       UCSD, La Jolla, CA              Ph.D. (chemistry)


================== Employment

year            position/ P.I.           place
----            --------------           -----
1988            postdoc, Joseph Kraut     UCSD
1989-1992       postdoc, R.J.Fletterick   UCSF
1992-1994       Visiting professor        UNI, Managua 
1995-1999       senior research fellow    UW, Seattle
1999-present    Asst. Prof. of Biology    RPI, Troy NY

================== Awards
2002-2003 NSF SGER award
1993-1994 Fulbright research/teaching fellowship to Nicaragua 
1989-1992 NIH PHS post-doctoral training grant, UCSF

================== Memberships
Protein Society
American Peptide Society
American Crystallographic Association
US Society for Ecological Economics (USSEE)
AAAS

================== PUBLICATIONS (most recent first)
Yuan, X., Bystroff, C. (2004) Non-sequential Structure-Based Alignment of Proteins
Using Local Structure Motifs and Contact Maps. PNAS (submitted)

Yuan, X., Shao, Y., Bystroff, C. (2003) Ab initio Protein Structure Prediction Using Pathway 
Models (review). Comparative Functional Genomics (inpress).

Hou, Y., Hsu, W., Lee, M.L., Bystroff, C. (2003) Efficient Remote Homology Detection 
Using Local Structure. Bioinformatics 19(17):2294-301.

Shao, Y., Bystroff, C. (2003) Predicting inter-residue contact using templates and pathways.
Proteins, Structure, Function and Genetics, 53 Suppl 6:497-502.

Bystroff. C , Garde, S. (2003) Helix propensities of short peptides:  Molecular dynamics versus 
Bioinformatics. Proteins, Structure, Function and Genetics, 50(4):552-62.

Bystroff, C. (2002). MASKER: Improved solvent excluded molecular surface area 
estimations using Boolean masks. Protein Eng 15, 959-965.

Hu, J., Shen, X., Shao, Y., Bystroff, C. & Zaki, M. J. (2002). Mining Non-local Structural 
Motifs in Proteins. BIOKDD 2002, Edmonton, Canada.

Bystroff, C. & Shao, Y. (2002). Fully automated ab initio  protein structure prediction 
using I-SITES, HMMSTR and ROSETTA. Bioinformatics 18, S54-61.

Bystroff. C An alternative derivation of the equations of motion in torsion space for a 
branched linear chain.  Protein Engineering, 14(11):101-4, 2001. 

Zaki, M., Jin, C., Bystroff, C. Mining residue contacts in proteins 
using predicted local structure.  IEEE Symposium on Bioinformatics 
and Biomedical Engineering. Baltimore, MD. Nov 8-10, 2000. 

Bystroff, C., Thorsson, V., Baker, D.  HMMSTR: A hidden Markov model for 
sequence-structure correlations in proteins. J. Mol. Biol. 301(1):173-190, 2000.

Thayer, E., Bystroff, C., Baker, D. Detection of protein sequences using
a mixure model for local protein amino acid sequence. J. Comput. Biol. 7:317-27, 2000.

Simons, K.T., Ruczinski, I., Kooperberg, C., Fox, B.A., Bystroff, C.,
Baker, D.  Improved recognition of native-like protein structures using
a combination of sequence-dependent and sequence-independent features of
proteins.  Proteins, Structure, Function and Genetics 34(1):82-95, 1999.

Yi, Q., Bystroff, C., Rajagopal, P., Klevit, R.E., Baker, D.  Prediction
and structural characterization of an independently folding substructure
in the src SH3 domain.  J. Mol. Biol. 283(1):293-300, 1998. 

Bystroff, C., Baker, D.  Prediction of local structure in proteins using
a library of sequence-structure motifs.  J. Mol. Biol. 281:565-577,
1998.

Bystroff, C., Baker, D.  Blind ab initio local structure predictions
using a library of sequence-structure motifs.  Proteins: Structure,
Function, and Genetics, Suppl. 1:167-171, 1997.  

Han, K.F., Bystroff, C., Baker, D.  Three dimensional structures and
contexts associated with recurrent amino acid sequence patterns.
Protein Science 6:1587-1590, 1997.  

Bystroff, C., Simons, K.T., Han, K.F., Baker, D.  Local
sequence-structure correlations in proteins.  Curr Op Biotech 7:417-421,
1996.  

McGrath, M.E., Erpel, T., Bystroff, C., Fletterick, R.J.  Macromolecular
chelation as an improved mechanism of protease inhibition: structure of
the ecotin-trypsin complex.  Embo J 13:1502-1507, 1994.  

Bystroff, C., Baker, D., Fletterick, R.J., Agard, D.A.  PRISM:
application to the solution of two protein structures.  Acta
Crystallographica, Section D 5:440-448, 1993.  

Baker, D., Bystroff, C., Fletterick, R.J., Agard, D.A.  PRISM:
topologically constrained phase refinement for macromolecular
crystallography.  Acta Crystallographica, Section D 5:429-439, 1993.  

Goddette, D.W., Paech, C., Yang, S.S., Mielenz, J.R., Bystroff, C.,
Wilke, M.E., Fletterick, R.J.  The crystal structure of the Bacillus
lentus alkaline protease, subtilisin BL, at 1.4 A resolution.  J Mol
Biol 228:580-595, 1992.  

Bystroff, C., Kraut, J.  Crystal structure of unliganded Escherichia
coli dihydrofolate reductase. Ligand-induced conformational changes and
cooperativity in binding.  Biochemistry 30:2227-2239, 1991.  

Bystroff, C., Oatley, S.J., Kraut, J.  Crystal structures of Escherichia
coli dihydrofolate reductase: the NADP+ holoenzyme and the folate.NADP+
ternary complex. Substrate binding and a model for the transition state.
Biochemistry 29:3263-3277, 1990.