Publications

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