Classified References on Computational Biology
R. C. T. Lee
On Books
On Classification of Protein Folds
On Evolutionary Trees
On Divide-and-Conquer
On Genome Rearrangement
On LCS
On Miscellaneous
On Nearest Neighbor Search
On Pattern Discovery
On Physical Mapping
On Protein Structure
On RNA Structures
On Sequence Alignment
On Sequence Assembly Problem
On Sorting by Reversal
On String Matching
On Structure Alignment
On Superstrings
On Superstructures
On Visual Display
On NP-Complete Problems and Approximation Algorithms
1
On Sequence Assembly Problem
[CFM80] The k best spanning arborescences of a network, Camperini, P., Fratta,
L. and Maffioli, F., Networks, Vol. 10, 1980, pp. 91-110.
[DS1991]
A Sequence Assembly and Editing Program for Efficient
Management of Large Projects, Dean, S. and Staden, R., Nucleic Acids Research,
Vol. 19, 1991, pp. 3901-3917.
[GMSR79] Computer Problems for the Assembly of DNA Sequences, Gingeras,
T. R., Milao, J. P., Sciaky, P. and Roberts, R. J., Nucleic Acid Res, Vol. 7, 1979, pp.
529-545.
[H92] A Contig Assembly Program Based on Sensitive Detection of Fragments
Overlap, Huang, X., Genomics, Vol. 14, 1992, pp. 18-25.
[HGST86] Efficient algorithms for finding minimum spanning trees in
undirected and directed graphs, Harold, G., Galil, Z., Spencer, T. and Tarjan, R.,
Combinatorial, Vol. 6, 1986, pp. 109-122.
[KE95] Combinational Algorithms for DNA Sequence Assembly, Kececioglu, D.
J. and Myers, W. E., Algorithmica, Vol. 13, 1995, 7-51.
[KLT2001] A Probabilistic Approach to Sequence Assembly Validation, Kim, S.,
Liao, L. and Tomb, J. F., Workshop on Data Mining in Bioinformatics, 2001
[KM89] A Procedural Interface for a Fragment Assembly Tool, Kececioglu, D. J.
and Myers, W. E., Technical Reports 89-5, Department of Computer Science, The
University of Arizona,1989
[M93] Rethinking the DNA Fragment Assembly Problem, Meidanis, J., 1993.
[M95] Towards Simplifying and Accurately Formulating Fragment Assembly,
E. W. Myers, J. Comput. Biology, Vol. 2, 1995, pp. 275-290
[PTW2001] A New Approach to Fragment Assembly in DNA Sequencing,
Pevzner, P. A., Tang, H. and Waterman, M. S., RECOMB, Montreal, Canada, 2001,
pp. 256-267.
2
3
On Sequence Alignment
[AAS2000] On Approximation Algorithms for Local Multiple Alignment,
Akutsu, T., Arimura, H. and Shimozono, S., RECOMB, TOKYO, 2000, pp. 1-7.
[AKMSW87]
Geometric applications of a matrix-searching algorithm,
Aggarwal, A., Klawe, M., Moran. S., Shor, P. and Wilber, R., Algorithmica, Vol. 2,
1987, pp. 195-208.
[AL89] Trees, Stars, and Multiple Biological Sequence Aligment, Altschul, S. F.
and Lipman, D. J., SIAM J. Appl. Math.,Vol. 49, 1989, pp.197-209.
[B95] A space efficient algorithm for finding the best nonoverlapping
alignment score, Benson, G., Theoret. Comput. Sci., Vol. 145, 1995, pp. 357-369.
[BLP97] Approximation Algorithms for Multiple Sequence Alignment, Bafna,
V., Lawler, E. and Pevzner, P., Theoretical Computer Science, Vol. 182, 1997, pp.
233-244.
[BM98] Discovering internet marketing intelligence through online analytical
web usage mining, Buechner, A. and Mulvenna, M., SIGMOD Record, Vol. 27,
1998, pp. 54-61.
[BV2001] The Complexity of Multiple Sequence Alignment with SP-Score that
is a Metric, Bonizzoni, P. and Vedova, G. D. Theoretical Computer Science, Vol.
259, 2001, pp. 63-79.
[CHM92] Recent Developments in Linear-Space Alignment Methods: A Survey,
Chao, K. M, Hardison, R. C., and Miller, W., J. Comput. Biol., Vol. 1, 1992, pp.
271-291.
[CL88] The Multiple Sequence Alignment Problem in Biology, Carrillo,H. and
Lipman, D, SIAM J. Appl. Math, Vol. 48, 1988, pp.1073-1082.
[CL92] Theoretical and Empirical Comparisons of Approximate String
Matching Algorithms, Chang, W. I. and Lampe, J., In Proceedings of the 3rd
Symposium on Combinatorial Pattern Matching, Lecture Notes in Computer
Science, Vol. 644, 1992, pp. 172-181.
4
[CPM92] Aligning Two Sequences within a Specified Diagonal Band, Chao, K.
M., Pearson, W. R. and Miller, W., Comput. Appl. BioSciences, Vol. 8, 1992, pp.
481-487.
[CWC92] A survey of Multiple Sequence Comparison Methods, Chan, S. C.,
Wong, A. K. C. and Chiu, D. K.Y. Bull. Math. Biol. Vol. 54, 1992, pp. 563-598.
[DH75] Sequence Comparison by Dynamic Programming ,Delcoigne, A. and
Hansen, P., Biometrika, Vol. 62, 1975, pp. 661-664.
[FD87] Progressive Sequence Aligment as a Prerequisite to Correct Phylogenetic
Trees, Feng, D. and Doolittle, R., J. Molec. Evol. Vol. 25, 1987, pp. 351-360.
[FFB2000] A task-based architecture for application-aware adjuncts, Farrell, R.,
Fairweather, P. and Breimer, E., Proceedings of the 2000 International Conference
on Intelligent User Interfaces, 2000, pp. 82-85.
[G91] Efficient Methods for Multiple Sequence Alignment with Guaranteed
Error Bounds, Gusfield, D., Tech. Report, Computer Science Division, University
of California, Davis, CSE-91-4, 1991.
[G93] Efficient Methods for Multiple Sequence Alignment with Guaranteed
Error Bounds, Gusfield, D., Bull. Mathematics Biology. Vol. 55, 1993, pp. 141-154.
[GBN94] Parametric Optimization of Sequence Alignment, Gusfield, D.,
Balasubramanian, K. and Naor, D., Algorithmica, Vol.12, No. 4-5, Oct-Nov. 1994,
pp.312-326.
[GCS2000] Evaluation Measures of Multiple Sequence Alignments, Gonnet, G.
H., Korostensky, C. and Benner,S., Journal of Computational Biology, Vol. 7, No.
1-2, 2000, pp. 261-276.
[GG89] Speeding up dynamic programming with applications to molecular
biology, Galil, Z. and Giancarlo, R., Theoret. Comput. Sci., Vol. 64, 1989, pp.
107-118.
[GMP96]
Gene recognition via spliced sequence alignment, Gelfand, M.,
5
Mironov, A. and Pevzner, P., Proc. Natl. Acad. Sci. USA, Vol. 93, 1996, pp.
9061-9066.
[J99] Reducing Gap-0 Multiple Alignment to Multiple Alignment, Just, W.,
Manuscript, 1999.
[K93] The Maximun Weight Trace Alignment Problem in Multiple Sequence
Aligment, Kececioglu, J., A. Apostolico, M Crochemore, Z. Galil, U. Manber
(Eds.), Combinatorial Pattern Maching 93, Padova, Italy, June, 1993, Vol. 684,
pp.106-119.
[KM96] An algorithm for locating non-overlapping regions of maximum
alignment score, Kannan, S. and Myers, E., SIAM J. Comput., Vol. 25, No. 3, 1996,
pp. 648-662.
[KRGS2001] Gene Structure Prediction and Alternative Splicing Analysis
Using Genomically Aligned ESTs, Kan, Z., Rouchka, E. C., Gish, W. R. and States,
D. J., Genome Research, Vol. 11, 2001, pp. 889 –900.
[L88] Computational Molecular Biology, Sources and Methods for Sequence
Analysis, A. Lesk, ED., Oxford University Press, 1988.
[LAK89] A Tool for Multiple Sequence Aligment, Lipman, D. J., Altschul, S. F.
and Kececioglu, J. D., Proc. Nat. Acad Sci., Vol. 86, 1989, pp. 4412-4415.
[LMW99] Finding Similar Regions in Many Sequences, Li, M., Ma, B. and
Wang, L., Proc. 31st ACM Symp. Theory of Computing (STOC 99) , 1999.
[LP2000] RNA Pseudoknot Prediction in Energy Based Models, Lyngso, R. B.
and Pedersen, C. N. S., Journal of Computational biology, Vol. 7, 2000,
pp.409-427.
[LPSH2001] Visualization and analysis of clickstream data of online stores for
understanding web merchandising, Lee, J., Podlaseck, M., Schonberg, E. and Hoch,
R., J. Data Mining Knowledge Discovery, Vol. 5, Nos. 1/2, 2001, pp. 59-84.
[LR99] Local Multiple Sequence Alignment Using Dead-End Elimination,
Lukashin, A. V. and Rosa, J. J., Biogen, Inc, Cambridge Center, USA, Vol. 15, No.
11, 1999, pp. 947-953.
6
[LU2001] On the Common Substring Alignment Problem, Landau, G. and
Ukelson, M., Journal of Algorithms, Vol. 41, 2001, pp. 338-359.
[M88] A Flexible Multiple Sequence Alignment Program, Martinez, M, Nucleic
Acids Res, Vol. 16, 1988, pp. 1683-1691.
[MFDW97] DIALIGN: Finding Local Similarities by Multiple Sequence
Alignment, Morgenstern, B., Frech, K., Dress, A. and Werner, T., GSF-National
Research Center for Environment and Health, 1997.
[MRPG98] Performance-guarantee gene predictions via spliced alignment,
Mironov, A., Roytberg, M., Pevzner, P. and Gelfand, M., Genomics 51 A.N.
GE985251, 1998, pp. 332-339.
[MW97] Near Optimal Multiple Alignment within a Band in Polynomial Time,
Ma, B. and Wang, L., in the Proc. 32nd ACM, pp. 1-23.
[NW70] A General Method Applicable to the Search for Similarities in the
Amino Acid Sequence of Two Proteins, Neddleman, S. B. and Wunsch, C. D., J.
Mol. Biol., Vol. 48, 1970, pp. 443-453.
[P92] Multiple Alignment, Communication Cost, and Graph Matching, Pevzner,
P. A., SIAM Journal on Applied Mathematics, Vol. 52, No. 6, Dec. 1992, pp.
1763-1779.
[S80] The Theory and Computations of Evolutionary Distances: Pattern
Recognition, Sellers, P. H., J. Algorithms, Vol. 1, 1980, pp. 359-154.
[S2001] Non-Approximability of Weighted Multiple Sequence Alignment,
Siebert, B., COCOON, 2001, PP. 75-85.
[SBDGGHHLKMPS91] A system for distributed intrusion detection, Snapp, S.,
Brentano, J., Dias, G., Goan, T., Grance, T., Heberlein, L., Ho, C., Levitt, K.,
Mukerjee, B., Mansur, D., Pon, K. and Smaha, S., COMPCON Spring 91, the 36th
IEEE International Computer Conference, 1991, pp. 170-176.
7
[SM86] A Multiple Sequence Aligment Program, Sobel, E. And Martinez, M.,
Nucleic Acids Res., Vol. 14, 1986, pp. 363-374.
[SP97]
Las Vegas algorithms for gene recognition: Suboptimal and
error-tolerant spliced alignment, Sze, S. and Pevzner, P., J. Comp. Biol., Vol. 4, No.
3, 1997, pp. 297-309.
[SYYH02] Super Pairwise Alignment (SPA): An Efficient Approach to Global
Alignment for Homologous Sequence, Shen, S. Y., Yang, J., Yao, A., and Hwang, P.
I., Journal of Computational Biology, Vol.9, 2002, pp. 477-486.
[SZ90] Fast Algorithm for the Unit Cost Editing Distance between Trees,
Shasha, D. and Zhang, K., J. Algorithms, Vol. 11, 1990, pp. 581-621.
[T90] Hierarchical Method to Align Large Numbers of Biological Sequences,
Taylor, W. R., Mothods Enzymol. Vol. 183, 1990, pp. 456-474.
[UHLU]
Using repeats to speedup DNA sequence alignment, private
communication, Ukelson, M., Horesh, Y., Landau, G. and Unger, R.
[VLP94] Approximation Algorithms for Multiple Sequence Alignment, Bafna, V.,
Lawler, E. L. and Pevzner, P., Proc. of the 5th Annual Symp. on Combin. Pattern
Matching(CPM'94). Lecture Notes in Computer Science, Vol. 807, 1974, pp.
43-53.
[WJ94] On the Complexity of Multiple Sequence Alignment, Wang, L. and Jiang,
T., Journal of Computation Biology, Vol. 1, 1994, pp. 337-348.
[W95] A Simplified Proof of the NP- and MAX SNP-Hardness of Multiple
Sequence Tree Alignments, Wareham, H. T., J. Comput. Biol., Vol. 2, No. 4., 1995,
pp. 509-514.
[WJ94] On the Complexity of Multiple Sequence Aligment , Wang, L. and Jiang,
T., J. Comput. Biol., Vol. 1, 1994, pp. 337-348.
[WSB76] Some Biological Sequence Metrics, Waterman, M. S., Smith, T. F. and
Beyer, W. A., Adv. In Math. Vol. 20, 1976, pp. 367-378.
8
[Z96] A Constrained Edit Distance between Unordered Labeled Trees, Zhang,
K., Algorithmica, Vol. 15, 1996, pp. 205-222.
[ZSS92] On the Editing Distance between unordered Labeled Trees, Zhang, K.,
Statman, R. and Shasha, D., Information Processing Letters, Vol. 42, 1992, pp.
133-139.
9
On Evolutionary Trees
[AG83] Human Mitochondrial DNA Variation and Evolution: Analysis of
Nucleotide Sequences from Seven Individuals, Aquadro, C. F. and Greenberg, B. D.,
Genetics, Vol. 103, 1983, pp. 287-312.
[AK97] Maximun Agreement Subtree in a Set of Evolutionary Trees: Metrics
and Efficient Algorithms, Amir, A and Keselman, D., SIAM J. Comput., Vol. 26,
1997, pp. 1656-1669.
[B71]
The Recovery of Trees from Measures of Dissimilarity, Buneman, P.,
Mathematics in the Archaeological and Historical Sciences, 1971 , pp. 387-395.
[BBJKLWZ2000] Practical Algorithm for Recovering the Best Supported
Edges in an Evolutionary Tree, Berry, V., Bryant, D., Jiang, T., Kearney, P., Li, M.,
Wareham, T., and Zhang, H., Proc. 11th Annual ACM-SIAM Symp. on Discrete
Algorithms, Jan. 2000.
[BPWW82] Mitochondrial DNA Sequences of Primates: Tempo and Mode of
Evolution, Brown, W. M., Prager, E. M., Wang, A. and Wilson, A. C., Journal of
Molecular Evolution, Vol.18, 1982, pp.225-239.
[BSLGDV98] The Discovery of Two New Divergent STLVs has Implications for
the Evolution and Epidemiology of HTLVs, Brussel, M. V., Salemi, M., Liu, H. F.,
Goubau, P., Desmyter, J. and Vandamme, A. M., Rev. Med. Virol., Vol. 9, 1999, pp.
155-170.
[CBW84] Polymorphic Sites and the Mechanism of Evolution in Human
Mitochondrial DNA, Cann, R. L., Brown, W. M. and Wilson, A. C., Genetics, Vol.
106, , 1984, pp. 479-499.
[CR89] A Fast Algorithm for Constructing Trees from Distance Matrices,
Culbertson, J. C. and Rudnicki, P., Inform. Process. Lett., Vol. 30, No. 4., 1989, pp.
215-220.
[CSW87] Mitochondrial DNA and Human Evolution, Cann, R. L., Stoneking, M.
and Wilson, A. C., Nature, Vol. 325, 1987, pp. 31-36.
10
[F81] Evolutionary Trees from DNA sequences: A Maximum Likelihood
Approach, Felsenstein, J., J. Molecular Evolution, Vol. 17, 1981.
[F88] Phylogenies from Molecular Sequences: Inference and Reliability,
Felsenstein, J., Annu. Rev. Genet, Vol. 22, 1988, pp. 521-565.
[FKW95] A Robust Model for Finding Optimal Evolutionary Trees, Farach, M.,
Kannan, S. and Warnow, T., Algorithmica, Vol. 13, No. 1-2, Jan-Feb. 1995, pp.
155-179.
[FM67] Construction of Phylogenetic Trees, Fitch, W. M. and Margoliash, E.,
Science, Vol.155, No. 20, Jan.1967, pp. 279-284.
[FT97] Sparse Dynamic Programming for Evolutionary Tree Comparison,
Farach, M. and Thorup, M., SIAM J. Comput., Vol. 26, 1997, pp. 210-230.
[HH90] Intraspecific Nucleotide Sequence Differences in the Major Noncoding
Region of Human Mitochondrial DNA, Horai, S. and Hayasaka, Am. J. Hum
Genet., Vol. 46, No. 828, 1990.
[HH91] Time of the Deepest Root for Polymorphism in Human Mitochondrial
DNA, Hasegawa, M. and Horai, S., Journal of Molecular Evolution, Vol. 32, 1991,
pp. 37-42.
[HT84] Fast Algorithms for Finding Nearest Common Ancestors, D. Harel and R.
E. Tarjan, SIAM J. Comp, Vol. 13, No.2, 1984, pp.338-355.
[JKL2001]
A Polynomial Time Approximation Scheme For Inferring
Evolutionary Trees From Quartet Topologies and Its Application, Jiang, T.,
Kearney, P. and Li, M., SIAM Journal Comput. Vol. 30, No. 6, pp. 1942-1961.
[JLW94] Aligning Sequences via an Evolutionary Tree, Jiang, T., Lawler, E. L.
and Wang, L., Conference Proceedings of the Annual ACM Symposium on
Theory of Computing, May 23-25, 1994, pp. 760-769.
[KG98] Reconstructing a History of Recombination from a Set of Sequences,
Kececioglu, J. and Gusfield, D., Discrete Applied Mathematics, Vol. 88, 1998, pp.
239-260.
11
[KHM97] Inferring Evolutionary Trees from Ordinal Data, Kearney, P.,
Hayward, R. B. and Meijer, H. Proc. 8th Annual ACM-SIAM Symposium on
Discrete Algorithms, 1997, pp. 418-426.
[KLW96] Determining the Evolutionary Tree Using Experiments, Kannan, S. K.,
Lawler, E. L. and Warnow, T. J., J. Algorithms, Vol. 21, 1996, pp. 26-50.
[KW94] Inferring Evolutionary History from DNA Sequences, Kannan, S. K.
and Warnow, T. J., SIAM Journal on Computing, Vol. 23, No. 4, Aug. 1994, pp.
713-737.
[KW95] Tree Reconstruction from Partial Orders, Kannan, S. and Warnow; T.,
SIAM J. Computing, Vol. 24, 1995, pp. 511-519.
[KWY98] Computing the Local Consensus of Trees, Kannan, S., Warnow, T. and
Yooseph, S., SIAM Journal on Computing, Vol. 27, No. 6, Dec. 1998,
pp.1695-1724.
[LBC96] An Evolutionary Trace Method Defines Binding Surfaces Common to
Protein Families, Lichtarge, O., Bourne, H. R. and Cohen, F. E., Journal Comput.
Biol., Vol. 257, 1996, pp. 342-358.
[LCJDLG98]
Molecular Analysis of GB Virus C Isolates in Belgian
Hemodialysis Patients, Liu, H. F., Cornu, C., Jadoul, M., Dahan, K., Loute, G. and
Goubau, P., Journal of Medical Virology, Vol. 55, 1998, pp. 118-122.
[LMTDDG2000] High Prevalence of GB Virus C/Hepatities G Virus in
Kinshasa, Democratic Republic of Congo: A Phylogenetic Analysis, Liu, H. F.,
Muyembe-Tamfum, J. J., Dahan K., Desmyter, J. and Goubau, P., Journal of Medical
Virology, Vol. 60, 2000, pp. 159-165.
[S75] Minimum Mutation Tree of Sequences, Sankoff, D., SIAM J. Appl. Math.,
Vol. 28, 1975, pp. 35-42.
[S89] Origin of Early Modern Humans, Stringer, C. B., ibid, 1989, pp. 232-244.
12
[S92] The Complexity of Reconstructing Trees from Qualitative Characters
and Subtrees, Steel, M., Journal of Classification, Vol. 9, 1992 , pp. 91-116.
[SA83]
Phylogeny and Classification of Birds Based on the Data of
DNA-DNA-Hybridization, Sibley, C. G. and Ahlquist, J. E., Curr. Ornithol., Vol. 1,
1983, pp. 245-292.
[SA88] Genetic and Fossil Evidence for the Origin of Modern Humans, Stringer,
C. B. and Andrews, P., Science, Vol. 239, 1988, pp. 1263-1268.
[SH96] Quartet Puzzling : A Quartet Maximum-Likelihood Method for
Reconstructing Tree Topologies, Strimmer, K. and Haeseler, A. V., Molecular
Biology and Evolution, Vol. 13, 1996, pp. 964-969.
[SJBW90] Geographic Variation in Human Mitochondrial DNA from Papua
New Guinea, Stoneking, M., Jorde, L. B., Bhatia, K. and Wilson, A. C., Genetics, Vol.
124, 1990, pp.717-733.
[SN87] The Neighbor-Joining Method : A New Method for Reconstructing
Phylogenetic Trees, Staitou, N. and Nei, M., Molecular Biology and Evolution, Vol.
4, 1987, pp. 406-425.
[SV88] On Finding Lowest Common Ancestors: Simplification and
Parallelization, B. Schieber and U. Vishkin., SIAM J. Comput., Vol. 17, 1988,
pp.1253-1262.
[T91]
Human Origins and Analysis of Mitochondrial DNA Sequences,
Templeton, A., Science, Vol. 255, 1991, pp. 737.
[VPHKW89] Mitochondrial DNA Sequences in Single Hairs from a Southern
African Population, Vigilant, R., Pennington, Harpending, H., Kocher, T. D. and
Wilson, A. C., Proc. Natl. Acad. U.S.A., Vol. 86, 1989, pp. 9350-9354.
[VSHHW91] African Populations and the Evolution of Human Mitochondrial
DNA, Vigilant, L., Stoneking, M., Harpending, H., Hawkes, K. and Wilson, A. C.,
Science, Sept. Vol. 253, No. 27, 1991, pp. 1503-1507.
[WJ94] On the Complexity of Multiple Sequence Alignment, Wang, L. and Jiang,
T., Journal of Computational Biology, Vol. 1, No. 4, 1994, pp. 337-348.
13
[WLBCR2000] A Polynomial-Time Approximation Scheme for Minimum
Routing Cost Spanning Trees, Wu, B. Y., Lancia, G., Bafna, V., Chao, K. M., Ravi,
R. and Tang, C. Y., SIAM J. on Computing, Vol. 29, No. 3, Jan. 12, 2000, pp.
761-778.
[WSSB77] Additive Evolutionary Trees, Waterman, M. S., Smith, T. F., Singh, M.
and Beyer, W. A., Journal Theoretical Biology, Vol. 64, 1977, pp. 199-213.
[WZJS94] A System for Approximate Tree Matching, Wang, J. T. L., Zhang, K.,
Jeong, K. and Shasha, D., IEEE Transactions on Knowledge and Data
Engineering, Vol. 6, No. 4, Aug. 1994, pp. 559-571 1041-4347.
[VSHHW91] African Populations and the Evolution of Human Mitochondrial
DNA, Vigilant L., Stoneking M., Harpending H., Hawkers K. and Wilson A. C., Science,
New Series, Vol. 253, Issue 5027, 1991, pp.1503-1507.
14
On Superstrings
[AS95] Improved Length Bounds for the Shortest Superstring Problem, Armen,
C. and Stein, C., in Proceedings 5th International Workshop on Algorithms and
Data Structures, Lecture Notes in Comput. Sci., Vol. 955, 1995, pp. 494-505
[AS96] A 2 2/3 Approximation Algorithm for the Shortest Superstring Problem,
Armen, C. and Stein C., in Proceedings Combinational Pattern Matching, Lecture
Notes in Comput. Sci., Vol. 1075, 1996, pp. 87-101.
[AS98] 2 2/3 Superstring Approximation Algorithm, Armen, C. and Stein, C.,
Discrete Applied Mathematics, Vol. 88, No. 1-3, Nov. 9, 1998, pp. 29-57.
[BJJ97] Rotations of Periodic Strings and Short Superstrings, Breslauer, D.,
Jiang, T. and Jiang, Z., J. Algorithms, Vol. 24, No. 2, August, 1997, pp. 340-353.
[BJLTY91] Linear Approximation of Shrotest Superstrings, Blum, A., Jiang, T.,
Li, M.,Tromp, J. and Yannakakis, M., in Proceedings 23th Annual ACM
Symposium on Theory of Computing, ACM, 1991, pp. 328-336.
[E90] A linear time algorithm for finding approximate shortest common
superstrings, Esko, U., Algorithmica, Vol. 5, 1990, pp. 313-323.
[FS98] Greedy Algorithms for the Shortest Common Superstring that are
Asymptotically Optimal, Frieze, A. and Szpankowski, W., Algorithmica, Vol. 21,
No. 1, May, 1998, pp. 921-36.
[GMS80] On finding minimal length superstring, Gallant, J., Maier, D., and
Storer, J., Journal of Computer and System Sciences, Vol. 20, 1980, pp.50-58.
[J89] Approximation algorithms for the shortest common superstring problem,
Jonathan, T., Information and Computation, Vol. 83, 1989, pp. 1-20.
[JL95] On the Approximation of Shortest Common Supersequences and
Longest Common Subsequences, Jiang, T. and Li, M., SIAM Journal on
Computing, Vol. 24, No. 5, 1995, pp.1122-1139.
[JU88] A greedy approximation algorithm for constructing shortest common
15
superstrings, Jorma, T. and Ukkonen, E., Theoretical Computer Science, Vol. 57,
1988, pp. 131-145.
[KPS94] Long Tours and Short Superstrings, Kosaraju, S. R., Park, J. K. and
Stein, C., Proc. 35th Annual IEEE Symposium on Foundations of Computer
Science, 1994, pp. 166-177.
[S99] A 2 1/2 Approximation Algorithm for Shortest Superstring, Sweedyk, Z.,
SIAM J. on Computing, Vol. 29, No. 3, 1999, pp. 954-986.
[TY93] Approximating Shortest Superstrings, Teng, S. and Yao, F., Proc. 34th
Annual IEEE Symposium on Foundations of Computer Science, IEEE Computer
Society Press, Los Alamitos, CA, 1993, pp.158-165.
16
On Protein Structure
[A96] Protein Structure Alignment Using Dynamic Programming and Iterative
Improvement, Akutsu, T., IEICE Trans. Inf. & Syst., Vol. E78-D, No. 0, 1996,
pp.1-8.
[AGMML90] Basic Local Alignment Search Tool, Altschul, S. F., Gish, W.,
Miller, W., Myers, E. W., Lipman, D., J. Mol. Biol., Vol. 215, 1990, pp.403-410.
[AH94] On the approximation of largest common subtrees and largest common
point sets, Akutsu, T. and Halldorsson, M. M., Lecture Notes in Computer Science,
1994, pp. 405-413.
[AM97] On the Approximation of Protein Threading, Akutsu, T. and Miyano, S.,
RECOMB, 1997, pp. 3-8.
[AS99] Protein Threading Based on Multiple Protein Structure Alignment,
Akutsu, T. and Sim, K. L., Genome Informatics, Vol. 10, 1999, pp. 23-29.
[AT98] Linear programming based approach to the derivation of a contact
potential for protein threading, Akutsu, T. and Tashimo, H., Proc. Pacific
Symposium on Biocomputing 1998, 1998, pp. 413-424.
[AMSZZML97] Gapped BLAST and PSI BLAST: A new generation of protein
database search, Altschul, S. F., Madden, T. L., Schaffer, A. A., Zhang, J., Zhang, Z.,
Miller, W., and Lipman, D. J., Nucleic Acids Research, Vol. 25, No. 17, 1997,
pp.3389-3402.
[B76]
The Protein Data Bank: A computer-based archival file for
macromolecular structure, Bernstein, F. C. et. al., J. Molecular Biology, 1976, pp.
535-542.
[BKWMBRKST76] The Protein Data Bank: A Computer-Based Archival File
for Macromolecular Structures, Bernstein, F. C., Koetzle, T. F., Williams, G. J. B.,
Meyer jr., E. F., Brice, M. D., Rodgers, J. R., Kennard, O., Shimanouchi, T., and
Tasumi, M., J. Molecular Biology, Vol.112, 1976, pp.535-542.
17
[BL98]
Protein Folding in the Hydrophobic-Hydrophilic(HP) Model is
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