Title
|
Journal/Proceedings/Report
|
Volume
|
Year
|
Pages
|
Co-authors
|
Ranking Beta Sheet Topologies with Applications to Protein Structure Prediction
|
accepted for publication in Journal of Mathematical Modelling and Algorithms
|
|
2011
|
|
R. Fonseca, G. Helles
|
Protein Packing Quality Using Delaunay Complexes
|
Proc. of the 8-th Int. Symp.
on Voronoi Diagrams in Science and Engineering, ISVD 2011,
Qingdao, China
|
|
2011
|
117-122
|
R. Fonseca, K. Karplus
|
Adjustable Chain Trees for Proteins
|
accepted for publication in Journal of Computational Biology
|
|
2011
|
|
R. Fonseca
|
Ranking Beta Sheet Topologies of Proteins
|
Proc. og the Int. Conf. on Computational Biology, ICCB'10, San Francisco, USA, October 2010
|
|
2010
|
624-628
|
R. Hansen, G. Helles
|
Protein Structure Prediction Using Bee Colony Optimization Metaheuristic
|
J. of Math. Modeling and Algorithms
|
10
|
2010
|
181-194
|
R. Hansen, M. Paluszewski
|
| Alpha Shapes and Proteins
|
Proc. of 6-th Int. Symp. on Voronoi Diagrams in
Science and Engineering, ISVD 2009, Lyngby Denmark
|
|
2009
|
217-224
|
H. Sterner, P. Sterner
|
| A Novel Approach to Phylogenetic Tress: d-Dimensional Geometric Steiner Trees [pdf] [doi]
|
Networks
|
53
|
2009
|
104-111
|
M. Brazil, B.K. Nielsen, D.A. Thomas, M. Zachariasen
|
Protein Structure Prediction Using Bee Colony Optimization Metaheuristic
|
Tech. Report 08-12, Dept. of Computer Science, Univ. of Copenhagen
|
|
2008
|
|
R. Hansen, M. Paluszewski
|
Protein Structure Prediction Using Bee Colony Optimization Metaheuristic: Extended Abstract
|
Presented at META (2008)
|
|
2008
|
|
R. Hansen, M. Paluszewski
|
Protein Decoy Generation using Branch and Bound with Efficient Bounding
|
Proc. of 8-th Int. Workshop on Algorithms in Bioinformatics, WABI (2008), Karlsruhe, Germany
|
LNBI 5251
|
2008
|
382-393
|
M. Paluszewski
|
Bounding Component Sizes of Two-Connected Steiner Networks
|
Information Processing Letters
|
104
|
2007
|
159-163
|
K.L. Hvam, L.B. Reinhardt, M. Zachariasen
|
Branch and Bound Algorithm for Protein Structure Prediction Using Efficient Bounding: Poster
|
RECOMB, San Francisco, USA
|
|
2007
|
|
M. Paluszewski
|
Reconstructing protein structure
from solvent exposure using
tabu search
|
Algorithms for Molecular Biology
|
1:20
|
2006
|
|
M. Paluszewski, T. Hamelryck
|
Some structural and geometric properties of two-connected Steiner networks
|
Proc. of the 13. Computing: The Australasian Theory Symposium (CATS2007), Ballarat, Australia
|
65
|
2007
|
85-90
|
K.L. Hvam, L.B. Reinhardt, M. Zachariasen
|
Protein structure prediction using tabu search and half-sphere exposure measure - Poster
|
RECOMB, Venice, Italy
|
|
2006
|
|
M. Paluszewski, T. Hamelryck
|
Deferred path heuristic for phylogenetic trees revisited
|
Proc. of CompBioNets05, Lyon, France
|
|
2005
|
75-92
|
B.K. Nielsen, S. Lindgren, M. Zachariasen
|
Flexibility of Steiner trees in uniform orientation metrics
|
Networks
|
46
|
2005
|
142-153
|
M. Brazil, M. Zachariasen
|
Euclidaen TSP between two nested convex obstacles
|
Information Processing Letters
|
95
|
2005
|
370-375
|
J. Abrahamson, A. Shokoufandeh
|
The Structure and Flexibility of Steiner Trees
in Uniform Orientation Metrics
|
Proceedings of 6-th Int. Conference on Optimization:
Techniques and Applications, Ballarat, Australia
|
|
2004
|
11 pages
|
M. Brazil, D.A. Thomas, J.F. Weng, M. Zachariasen
|
Flexibility of Steiner trees in uniform orientation
metrics
|
Proc. of the 15-th Int. Symp., ISAAC 2004, Hong Kong, China, LNCS 3341
|
|
2004
|
196-208
|
M. Brazil, M. Zachariasen
|
Two-connected Steiner networks: structural
properties
|
Operations Research Letters |
33
|
2005
|
395-402
|
M. Zachariasen
|
Rotationally optimal spanning and Steiner
trees in uniform orientation metrics
|
Computational Geometry: Theory and Applications
|
29
|
2004
|
251-263
|
M. Brazil, B.K. Nielsen and M. Zachariasen
|
A New Paradigm for General Architecture Routing
|
Proc. of the 14th ACM Great Lakes Symposium on VLSI, Boston, USA
|
|
2004
|
202-207
|
M. Paluszewski, M. Zachariasen
|
Geometric Steiner tree problems
|
Proceedings of 4-th ALIO/EURO Workshop on
Applied Combinatorial Optimization, Pucon, Chile
|
|
2002
|
137-140
|
M. Zachariasen
|
An exact algorithm for the uniformly-oriented
Steiner tree problem
|
Proceedings of 10-th European Symposium on
Algorithms, ESA, Rome, Italy, LNCS 2461
|
|
2002
|
760-771
|
B. K. Nielsen and
M. Zachariasen
|
On the location of Steiner points in uniformly-oriented
Steiner trees
|
Information Processing Letters
|
83
|
2002
|
237-241
|
B. K. Nielsen and
M. Zachariasen
|
Optimal Steiner hull algorithm
|
Computational Geometry: Theory and Applications
|
23
|
2002
|
163-169
|
|
Rectilinear trees under rotation, Abstract
|
Proceedings of 12-th Int. Symp. on Combinatorial
Optimization, CO'02, Paris, France
|
|
2002
|
101
|
B. K. Nielsen and
M. Zachariasen
|
Rectilinear trees under rotation and related
problems, Extended Abstract
|
Proceedings of 18-th European Workshop on Computational
Geometry, Warszawa, Poland
|
|
2002
|
18-22
|
B. K. Nielsen and
M. Zachariasen
|
Short trees in polygons
|
Discrete Applied Mathematics
|
118
|
2002
|
55-72
|
M. Zachariasen and
J. Nielsen
|
Exact algorithms for
plane Steiner tree problems: A computational study
|
D.-Z. Du, J.M. Smith, and J.H. Rubinstein (eds.),
Advances in Steiner Trees, Kluwer Academic Publishers
|
|
2000
|
81-116
|
M. Zachariasen and D. Warme
|
Obstacle-avoiding Euclidean
Steiner trees in the plane: an exact algorithm
|
M.T. Goodrich and C.C. McGeoch (Eds.), Algorithm
Engineering and Experimentation, LNCS 1619
|
|
1999
|
282-295
|
M. Zachariasen
|
Exact solutions to large-scale
plane Steiner tree problems
|
Proc. of the 10-th Ann. ACM-SIAM Symp. on Discrete
Algorithms (SODA-99
), Baltimore, Maryland, U.S.A.
|
|
1999
|
979-980
|
D.M. Warme and M.
Zachariasen
|
Distance-based
classification methods
|
INFOR
|
37
|
1999
|
337-352
|
O. Ekin, P.L. Hammer
and A. Kogan
|
Concatenation-based greedy heuristics for the Euclidean Steiner tree
problem
|
Algorithmica
|
25
|
1999
|
418-437
|
M. Zachariasen
|
Euclidean Steiner minimum trees: an improved exact algorithm
|
Networks
|
30
|
1997
|
149-166
|
M. Zachariasen
|
Plane embeddings of 2-trees
and biconnected partial 2-trees
|
SIAM J. on Discr.
Math
|
9
|
1996
|
277-296
|
A. Proskurowski
and M.M. Syslo
|
Steiner minimal trees in simple polygons
|
Tech. Report 95-43 , DIMACS
, Rutgers Univ.
, Piscataway, NJ, U.S.A.
|
|
1995
|
|
|
Reductions for the rectilinear
Steiner tree problem
|
Networks
|
26
|
1995
|
187-198
|
|
Euclidean Steiner minimal
trees for 3 terminals in simple polygons
|
Proc. of the 7-th Canadian Conference on Computational
Geometry, Univ. Laval , Quebec
City, Quebec, Canada
|
|
1995
|
247-253
|
|
Maximal outerplanar graphs
with perfect face-independent vertex covers
|
Discrete
Applied Mathematics
|
54
|
1994
|
267-280
|
M.M. Syslo
|
Euclidean Steiner minimal
trees with obstacles and Steiner visibility graphs
|
Discrete
Applied Mathematics
|
47
|
1993
|
187-206
|
|
The Steiner Tree Problem
|
North-Holland (1992), Annals of Discrete
Mathematics 53
|
|
1992
|
|
F.K. Hwang and D.S.
Richards
|
Computational geometry
and topological network design
|
D.Z. Du and F.K. Hwang (eds.)
Computing in Euclidean Geometry , World Scientific Publishing
Co.
|
|
1992
|
287-385
|
J. MacGregor Smith
|
Euclidean Steiner minimal
trees with obstacles and Steiner visibility graphs: Extended abstract
|
M. Akgul, H.W. Hamacher and
S. Tufekci (eds.) Combinatorial Optimization: New Frontiers in the Theory
and Practice, NATO ASI Series, Springer-Verlag, Berlin
|
|
1992
|
313-315
|
|
Steiner minimal trees for
three points and one convex polygonal obstacle
|
Annals of Operations Research
|
|
1991
|
577-599
|
J. MacGregor Smith
|
Path-distance heuristics
for the Steiner problem in undirected networks
|
Algorithmica
|
7
|
1992
|
309-327
|
J. MacGregor Smith
|
Proceedings of NATO Advanced
Research Workshop on Topological Network Design: Analysis and Synthesiss, June 1989, Copenhagen,
|
Annals of Operations Research
|
|
1991
|
|
J. MacGregor Smith
|
In-trees and plane embeddings
of outerplanar graphs
|
BIT
|
30
|
1990
|
83-90
|
M.M. Syslo
|
Topological network synthesis
|
B. Simeone (ed.) Combinatorial Optimization,
Como, Italy 1986, Lecture Notes in Mathematics 1403, Springer-Verlag, Berlin-Heidelberg
|
|
1989
|
282-303
|
|
Independent covers in outerplanar
graphs
|
R. Karlsson and A. Lingas (eds.) SWAT 88:
Proceedings of the 1-st Scandinavian Workshop on Algorithm Theory Halmstad,
Sweden, July 1989, LNCS 318
|
|
1988
|
243-254
|
M.M. Syslo
|
Steiner problem in Halin
networks
|
Discrete
Applied Mathematics
|
17
|
1987
|
281-294
|
|
Steiner problem in networks
- A survey
|
Networks
|
17
|
1987
|
129-167
|
|
An algorithm for the enumeration
of spanning trees [pdf]
[doi]/
|
BIT
|
26
|
1986
|
46-55
|
|
Generalized Steiner problem
in series-parallel networks [pdf]
[doi]
|
J. of Algorithms
|
7
|
1986
|
549-566
|
|
An algorithm of the Steiner
problem in the Euclidean plane [pdf]
[doi]
|
Networks
|
15
|
1985
|
323-345
|
|
Generalized Steiner problem
in outerplanar networks [pdf]
[doi]
|
BIT
|
25
|
1985
|
485-496
|
|
