-
1
-
-
0002003951
-
Linear time algorithms for NP-hard problems restricted to partial k-trees
-
S. Arnborg and A. Proskurowski, "Linear time algorithms for NP-hard problems restricted to partial k-trees", Discrete Applied Mathematics, 23: 11-24, 1989.
-
(1989)
Discrete Applied Mathematics
, vol.23
, pp. 11-24
-
-
Arnborg, S.1
Proskurowski, A.2
-
2
-
-
0000504885
-
Easy problems for tree-decomposable graphs
-
S. Arnborg, J. Lagergrcn, and D. Seese, "Easy problems for tree-decomposable graphs", Journal of Algorithms 12: 308-340, 1991.
-
(1991)
Journal of Algorithms
, vol.12
, pp. 308-340
-
-
Arnborg, S.1
Lagergrcn, J.2
Seese, D.3
-
3
-
-
0025830469
-
A method to identify protein sequences that fold into a known three-dimensional structure
-
J. Bowie, R. Luthy, and D. Eisenberg, "A method to identify protein sequences that fold into a known three-dimensional structure", Science 253: 164-170, 1991.
-
(1991)
Science
, vol.253
, pp. 164-170
-
-
Bowie, J.1
Luthy, R.2
Eisenberg, D.3
-
4
-
-
0001294529
-
A linear time algorithm for finding tree-decompositions of small trcewidlh
-
H. L. Bodlaender, "A linear time algorithm for finding tree-decompositions of small trcewidlh", SIAM Journal on Computing 25: 1305-1317, 1996.
-
(1996)
SIAM Journal on Computing
, vol.25
, pp. 1305-1317
-
-
Bodlaender, H.L.1
-
6
-
-
0030310297
-
UNA pseudoknot modeling using intersections of stochastic context free grammars with applications to database search
-
M. Brown and C. Wilson, "UNA pseudoknot modeling using intersections of stochastic context free grammars with applications to database search", Pacific Symposium on Biocomputing. 109-125, 1995.
-
(1995)
Pacific Symposium on Biocomputing
, pp. 109-125
-
-
Brown, M.1
Wilson, C.2
-
7
-
-
3543069105
-
Stochastic modeling of pseudoknot structures: A grammatical approach
-
L. Cai, R. Malmberg, and Y. Wu, "Stochastic Modeling of Pseudoknot Structures: A Grammatical Approach", Bioinformatics, 19, i66-i73, 2003.
-
(2003)
Bioinformatics
, vol.19
-
-
Cai, L.1
Malmberg, R.2
Wu, Y.3
-
8
-
-
0033215210
-
Pathway alignment: Application to the comparative analysis of glycolylic enzymes
-
T. Dandekar, S. Schuster S. B. Snel, M. Muynen, and P. Bork, "Pathway alignment: application to the comparative analysis of glycolylic enzymes", Hiochemical Journal. 1: 115-24, 1999.
-
(1999)
Hiochemical Journal
, vol.1
, pp. 115-124
-
-
Dandekar, T.1
Schuster, S.2
Snel, S.B.3
Muynen, M.4
Bork, P.5
-
9
-
-
3142532677
-
A phylogenetically based secondary structure for the yeast telomerase RNA
-
A. T. Dandjinou, N. Lévesque, S. Larose, J. Lucier, S. A. Elela, and R. J. Wellinger, "A phylogenetically based secondary structure for the yeast telomerase RNA.", Current Biology, 14: 1148-1158, 2004.
-
(2004)
Current Biology
, vol.14
, pp. 1148-1158
-
-
Dandjinou, A.T.1
Lévesque, N.2
Larose, S.3
Lucier, J.4
Elela, S.A.5
Wellinger, R.J.6
-
10
-
-
0033757940
-
Structural genomics of RNA
-
J.A. Doudna, "Structural genomics of RNA", Nature Structural Biology 7(11) supp. 954-956, 2000.
-
(2000)
Nature Structural Biology
, vol.7
, Issue.11 SUPPL.
, pp. 954-956
-
-
Doudna, J.A.1
-
12
-
-
0037133945
-
Computational genomtes of non-coding RNA genes
-
S.R. Eddy, "Computational genomtes of non-coding RNA genes", Cell 109:137-140, 2002.
-
(2002)
Cell
, vol.109
, pp. 137-140
-
-
Eddy, S.R.1
-
13
-
-
0028272315
-
RNA sequence analysis using covariance models
-
S. Eddy and R. Durbin, "RNA sequence analysis using covariance models", Nucleic Acids Research, 22: 2079-2088, 1994.
-
(1994)
Nucleic Acids Research
, vol.22
, pp. 2079-2088
-
-
Eddy, S.1
Durbin, R.2
-
14
-
-
85137859893
-
Subgraph isomorphism in planar graphs and related problems
-
3.3
-
D. Eppstein, "Subgraph isomorphism in planar graphs and related problems", Journal of Graph Algorithms and Applications, 3.3: 1-27, 1999.
-
(1999)
Journal of Graph Algorithms and Applications
, pp. 1-27
-
-
Eppstein, D.1
-
15
-
-
0346688645
-
Characterization of the RNA components of a putative molecular switch in the 3' untranslated region of the murine coronavirus genome
-
S. J. Geobel, B. Hsue, T. F. Dombrowski, and P. S. Masters, "Characterization of the RNA components of a Putative Molecular Switch in the 3' Untranslated Region of the Murine Coronavirus Genome.", Journal of Virology, 78: 669-682, 2004.
-
(2004)
Journal of Virology
, vol.78
, pp. 669-682
-
-
Geobel, S.J.1
Hsue, B.2
Dombrowski, T.F.3
Masters, P.S.4
-
16
-
-
0037252684
-
Rfam: An RNA family database
-
S. Griffiths-Jones, A. Bateman, M. Marshall, A. Khanna, and S. R. Eddy, "Rfam: an RNA family database", Nucleic Acids Research, 31: 439-441, 2003.
-
(2003)
Nucleic Acids Research
, vol.31
, pp. 439-441
-
-
Griffiths-Jones, S.1
Bateman, A.2
Marshall, M.3
Khanna, A.4
Eddy, S.R.5
-
17
-
-
2942544566
-
RSEARCH: Finding homologs of single structured RNA sequences
-
R. J. Klein and S. R. Eddy, "RSEARCH: Finding Homologs of Single Structured RNA Sequences.", BMC Bioinformatics, 4:44, 2003.
-
(2003)
BMC Bioinformatics
, vol.4
, pp. 44
-
-
Klein, R.J.1
Eddy, S.R.2
-
18
-
-
0028015988
-
The protein threading problem with sequence amino acid interaction preferences is NP-complete
-
R.H. Lathrop, "The protein threading problem with sequence amino acid interaction preferences is NP-complete", Protein Engineering 7: 1069-1068, 1994.
-
(1994)
Protein Engineering
, vol.7
, pp. 1069-11068
-
-
Lathrop, R.H.1
-
19
-
-
0002318812
-
Analysis and algorithms for protein sequence-structure alignment
-
Salzberg, Searls, and Kasifed., Elsevier
-
R.H. Lathrop, R.G. Rogers Jr, J. Bienkowska, B.K.M. Bryant, L. J. Buturovic, C. Gaitatzes, R.Nambudripad, J.V. White, and T.F. Smith, "Analysis and algorithms for protein sequence-structure alignment", in Computational Methods in Molecular Biology, Salzberg, Searls, and Kasifed., Elsevier, 1998.
-
(1998)
Computational Methods in Molecular Biology
-
-
Lathrop, R.H.1
Rogers Jr., R.G.2
Bienkowska, J.3
Bryant, B.K.M.4
Buturovic, L.J.5
Gaitatzes, C.6
Nambudripad, R.7
White, J.V.8
Smith, T.F.9
-
20
-
-
0031750905
-
A polyhedral approach to RNA sequence structure alignment
-
H-P. Lenhof, K. Reinert, and M. Vingron. "A polyhedral approach to RNA sequence structure alignment", Journal of Computational Biology 5(3): 517-530, 1998.
-
(1998)
Journal of Computational Biology
, vol.5
, Issue.3
, pp. 517-530
-
-
Lenhof, H.-P.1
Reinert, K.2
Vingron, M.3
-
21
-
-
25144471197
-
Profiling and searching for RNA pseudoknot structures in genomes
-
C. Liu, Y. Song, R. Malmberg, and L. Cai, "Profiling and searching for RNA pseudoknot structures in genomes", Lecture Notes in Computer Science 3515, 968-975, 2005.
-
(2005)
Lecture Notes in Computer Science
, vol.3515
, pp. 968-975
-
-
Liu, C.1
Song, Y.2
Malmberg, R.3
Cai, L.4
-
22
-
-
0030854739
-
TRNAscan-SE: A program for improved detection of transfer RNA genes in genomic sequence
-
T. M. Lowe and S. R. Eddy, "tRNAscan-SE: A Program for improved detection of transfer RNA genes in genomic sequence", Nucleic Acids Research, 25: 955-964, 1997.
-
(1997)
Nucleic Acids Research
, vol.25
, pp. 955-964
-
-
Lowe, T.M.1
Eddy, S.R.2
-
24
-
-
0346084492
-
On the complexity of finding iso- and other morphisms for partial k-trees
-
J. Matousek and R. Thomas, "On the complexity of finding iso- and other morphisms for partial k-trees", Discrete Mathematics, 108: 343-364, 1992.
-
(1992)
Discrete Mathematics
, vol.108
, pp. 343-364
-
-
Matousek, J.1
Thomas, R.2
-
25
-
-
0033618555
-
Detecting protein function and protein-protein interactions from genome sequences
-
E.M. Marcotte, P. Matteo, HL. Ng, D.W. Rice, TO. Yeates, and D. Eisenberg, "Detecting protein function and protein-protein interactions from genome sequences", Science 285: 751-753, 1999.
-
(1999)
Science
, vol.285
, pp. 751-753
-
-
Marcotte, E.M.1
Matteo, P.2
Ng, H.L.3
Rice, D.W.4
Yeates, T.O.5
Eisenberg, D.6
-
26
-
-
0033605218
-
Functional and structural analysis of a pseudoknot upstream of the tag-encoded sequence in E. coli tmRNA
-
N. Nameki, B. Felden, J. F Atkins, R. F. Gesteland, H. Himeno, and A. Muto, "Functional and structural analysis of a pseudoknot upstream of the tag-encoded sequence in E. coli tmRNA", Journal of Molecular Biology, 286(3): 733-744, 1999.
-
(1999)
Journal of Molecular Biology
, vol.286
, Issue.3
, pp. 733-744
-
-
Nameki, N.1
Felden, B.2
Atkins, J.F.3
Gesteland, R.F.4
Himeno, H.5
Muto, A.6
-
27
-
-
33644667975
-
IRIS: Intermolecular RNA interaction search
-
D.D. Pervouchine, "IRIS: Intermolecular RNA Interaction Search", Genome Informatics 15(2): 92-101, 2004.
-
(2004)
Genome Informatics
, vol.15
, Issue.2
, pp. 92-101
-
-
Pervouchine, D.D.1
-
28
-
-
0030697670
-
A branch-and-cut algorithm for multiple sequence alignment
-
K. Reinert, H-P. Lenhof, P. Mutzel, K. Mehlhorn, and J.D. Kececioglu, "A branch-and-cut algorithm for multiple sequence alignment", Proceedings of the first annual international conference on Computational molecular biology, 241-250, 1997.
-
(1997)
Proceedings of the First Annual International Conference on Computational Molecular Biology
, pp. 241-250
-
-
Reinert, K.1
Lenhof, H.-P.2
Mutzel, P.3
Mehlhorn, K.4
Kececioglu, J.D.5
-
29
-
-
0003157183
-
Noncoding RNA gene detection using comparative sequence analysis
-
E. Rivas and S. R. Eddy, "Noncoding RNA gene detection using comparative sequence analysis", BMC Bioinformatics, 2:8, 2001.
-
(2001)
BMC Bioinformatics
, vol.2
, pp. 8
-
-
Rivas, E.1
Eddy, S.R.2
-
30
-
-
0000673493
-
Graph minors II. Algorithmic aspects of tree-width
-
N. Robertson and P. D. Seymour, "Graph Minors II. Algorithmic aspects of tree-width", Journal of Algorithms 7: 309-322, 1986.
-
(1986)
Journal of Algorithms
, vol.7
, pp. 309-322
-
-
Robertson, N.1
Seymour, P.D.2
-
31
-
-
33646171538
-
Tree decomposition based fast search of RNA secondary structures in genomes
-
in press
-
Y. Song. C. Liu, R. Malmberg, F. Pan, and L. Cai, "Tree decomposition based fast search of RNA secondary structures in genomes", Proceedings of 2005 IEEE Computational Systems Biology Conference, in press.
-
Proceedings of 2005 IEEE Computational Systems Biology Conference
-
-
Song, Y.1
Liu, C.2
Malmberg, R.3
Pan, F.4
Cai, L.5
-
32
-
-
0001396964
-
Tree adjoining grammars for RNA structure prediction
-
Y. Uemura, A. Hasegawa, Y. Kobayashi, and T. Yokomori, "Tree adjoining grammars for RNA structure prediction", Theoretical Computer Science, 210: 277-303, 1999.
-
(1999)
Theoretical Computer Science
, vol.210
, pp. 277-303
-
-
Uemura, Y.1
Hasegawa, A.2
Kobayashi, Y.3
Yokomori, T.4
-
33
-
-
0043180474
-
PISCES: A protein sequence culling server
-
G. Wang and R.L. Dunbrack, Jr. "PISCES: a protein sequence culling server", Bioinformatics 19: 1589-1591, 2003.
-
(2003)
Bioinformatics
, vol.19
, pp. 1589-1591
-
-
Wang, G.1
Dunbrack Jr., R.L.2
-
34
-
-
0034088593
-
Sequence-structure specificity of a knowledge based energy function at the secondary structure level
-
D. Xu, M.A. Unseren, Y. Xu, and B.C. Uberbacher, "Sequence-structure specificity of a knowledge based energy function at the secondary structure level", Bioinformatics 16:257-268, 2000.
-
(2000)
Bioinformatics
, vol.16
, pp. 257-268
-
-
Xu, D.1
Unseren, M.A.2
Xu, Y.3
Uberbacher, B.C.4
-
36
-
-
0242369082
-
RAPTOR: Optimal protein threading by linear programming
-
J. Xu, M. Li, D. Kim, and Y. Xu. "RAPTOR: optimal protein threading by linear programming", Journal of Bioinformatics and Computational Biology, 1 (1):95-113, 2003.
-
(2003)
Journal of Bioinformatics and Computational Biology
, vol.1
, Issue.1
, pp. 95-113
-
-
Xu, J.1
Li, M.2
Kim, D.3
Xu, Y.4
-
37
-
-
0031750906
-
An efficient computational method for globally optimal threading
-
Y. Xu, D. Xu, and B.C. Uberbacher, "An efficient computational method for globally optimal threading", Journal of Computational Biology 5(3):597-614.
-
Journal of Computational Biology
, vol.5
, Issue.3
, pp. 597-614
-
-
Xu, Y.1
Xu, D.2
Uberbacher, B.C.3
|