Selected Publications
- 1
- Steven A. Benner. Predicting de novo the folded structure of
proteins. Current Opinion in Structural Biology, 2:402-412,
1992.
- 2
- Steven A. Benner, Ian Badcoe, Mark A. Cohen, and Dietlind L.
Gerloff. Bona fide prediction of aspects of protein conformation:
Assigning interior and surface residues from patterns of variation
and conservation in homologous protein sequences. Journal
of Molecular Biology, 235:926-958, 1994.
- 3
- Steven A. Benner, Mark A. Cohen, and Dietlind L. Gerloff. A
predicted secondary structure for the src homology domain 3. Journal
of Molecular Biology, 229:295-305, 1993.
- 4
- Steven A. Benner and Dietlind L. Gerloff. Patterns of divergence
in homologous proteins as indicators of tertiary and quaternary
structure: The catalytic domain of protein kinases. Advances
in Enzyme Regulation, 31:121-181, 1991.
- 5
- Steven A. Benner, Thomas F. Jenny, Mark A. Cohen, and Gaston
H. Gonnet. Predicting the conformation of proteins from sequences.
progress and future progress. Advances in Enzyme Regulation,
34:269-353, 1994.
- 6
- Mark A. Cohen, Steven A. Benner, and Gaston H. Gonnet. Analysis
of mutation during divergent evolution: The 400 by 400 dipeptide
mutation matrix. Biochem. Biophys. Res. Commun., 199:489-496,
1994.
- 7
- Dietlind L. Gerloff, Thomas F. Jenny, Lukas J. Knecht, and
Steven A. Benner. A secondary structure prediction of the hemorrhagic
metalloprotease family. Biochem. Biophys. Res. Commun.,
194:560-565, 1993.
- 8
- Dietlind L. Gerloff, Thomas F. Jenny, Lukas J. Knecht, Gaston
H. Gonnet, and Steven A. Benner. The nitrogenase MoFe protein
- a secondary structure prediction. FEBS Letters, 318:118-224,
1993.
- 9
- Gaston H. Gonnet. New algorithms for the computation of evolutionary
phylogenetic trees. In S. Suhai, editor, Computational methods
in genome research. Plenum Press, New York, 1994.
- 10
- Gaston H. Gonnet and Steven A. Benner. Computational biochemistry
research at eth. Technical Report 154, Institute for Scientific
Computing, E.T.H. Zurich, Switzerland, March 1991.
- 11
- Gaston. H. Gonnet, Mark A. Cohen, and Steven A. Benner. Exhaustive
matching of the entire protein sequence database. Science,
256:1443-1445, June 1992.
- 12
- Gaston. H. Gonnet, Mark A. Cohen, and Steven A. Benner. Empirical
and structural models for insertions and deletions in the divergent
evolution of proteins. Journal of Molecular Biology,
229:1065-1082, 1993.
- 13
- Thomas F. Jenny and Steven A. Benner. Evaluating predictions
of secondary structure in proteins. Biochem. Biophys. Res.
Commun., 200:149-155, 1994.
- 14
- Lukas J. Knecht and Gaston H. Gonnet. Alignment of nucleotide
with peptide sequences. Technical Report 184, Institute for Scientific
Computing, E.T.H. Zurich, Switzerland, September 1992.
- Hallett, M., Gonnet, G., Korostensky, C., Bernardin L. "Darwin
v. 2.0. An interpreted computer language for the biosciences".
Bioinformatics (1999) (accepted)
- Korostensky, C. Chapter "Evolution of Comics Faces" in the
book "Projekterfahrungen in Java" (in print) Verlag dPunkt,
ISBN 3-932588-33-9. Silvano; Maffeis, Fridtjof Toenniessen, Christian
Zeidler (Hrsg.) (1999)
- Stagljar, I., Korostenky, C., Johnsson, N., and te Heesen,
S. (1998)."A new genetic system for the analysis of interactions
between membrane proteins in vivo". Proc. Natl. Acad. Sci.
USA 95, 5187-5192.
- M. Fellows, M. Hallett, Ch. Korostensky, and U. Stege. Analogs
& Duals of the MAST Problem for Sequences & Trees, Proceedings
of the 6th Annual European Sympoium, Venice, Italy, August
1998 (ESA'98)
- Korostensky, C., Staudenmann, W., Dainese, P., Hoving, S.,
Gonnet, G., and James, P."An algorithm for the identification
of proteins in sequence databases using peptides with ragged N-
or C- termini generated by sequential endo- and exopeptidase digestions".
Electrophoresis, 19, 1933-1940 (1998)
- Dainese, P., Staudenmann, W., Quadroni, M., Korostensky, C.,
Gonnet, G., Kertesz, M., and James, P. "Probing protein function
using a combination of gene knockout and proteome analysis by
mass spectrometry".Electrophoresis, 18:432--442. (1997).
- Gerloff, D.L., Cohen, F.E., Korostensky, C., Turcotte, M.,
Gonnet, G., and Benner, S.A. "A predicted consensus structure
for the n-terminal fragment of the heat shock protein hsp90 family".
Proteins: Struct. Funct. Genet., 27:450--458. (1997)
M. T. Hallett and J. Lagergren. (1999)
Accepted to RECOMB '00, Tokyo, Japan. (ETH
Tech. Report given here)
M. T. Hallett and J. Lagergren (1999)
Submitted to ESA '00 (ETH Tech. Report given
here)
H. L. Bodlaender, M. R. Fellows, M. T. Hallett, H. T. Wareham, T.
J. Warnow (1999)
Accepted to Theoretical Computer Science, to appear.
Parts of this paper appeared in STOC '94, Montreal, Canada.
G. Gonnet, M. T. Hallett, C. Korostensky, L. Bernardin. (1999)
Accepted to Bioinformatics.
M. R. Fellows, M. T. Hallett, C. Korostensky, U. Stege (1998)
Appeared in 6th Annual European Symposium on Algorithms
(ESA '98), Venice.
LNCS 1461, pp. 103-114.
M. R. Fellows, M. T. Hallett, and U. Stege. (1998)
Proceedings of the 9th International Symposium on Algorithms
and Computation (ISAAC'98), Taejon, Korea, LNCS 1533, pp. 347-356.
- DNA Physical Mapping: 3 Ways Difficult
M. R. Fellows, M. T. Hallett and H. T. Wareham (1993),
Appeared in European Symposium on Algorithms (ESA '93), pp.157-168
- Parameterized complexity analysis in computational biology.
H. L. Bodlaender, R. G. Downey, M. R. Fellows, M. T. Hallett, H.
T. Wareham. (1995)
Bioinformatics (formerly Computer Applications in
the Biosciences) 11, 49-57.
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