-
1
-
-
2342475726
-
Protein ranking: From local to global structure in the protein similarity network
-
Weston J, Elisseef A, Zhou D, Leslie C & Noble WS (2004) Protein ranking: from local to global structure in the protein similarity network. Proc Natl Acad Sci USA 101, 6559-6563.
-
(2004)
Proc Natl Acad Sci USA
, vol.101
, pp. 6559-6563
-
-
Weston, J.1
Elisseef, A.2
Zhou, D.3
Leslie, C.4
Noble, W.S.5
-
2
-
-
0019887799
-
Identification of common molecular subsequences
-
Smith T & Waterman M (1981) Identification of common molecular subsequences. J Mol Biol 147, 195-197.
-
(1981)
J Mol Biol
, vol.147
, pp. 195-197
-
-
Smith, T.1
Waterman, M.2
-
3
-
-
0025183708
-
A basic local alignment search tool
-
Altschul SF, Gish W, Miller W, Myers EW & Lipman DJ (1990) A basic local alignment search tool. J Mol Biol 215, 403-410.
-
(1990)
J Mol Biol
, vol.215
, pp. 403-410
-
-
Altschul, S.F.1
Gish, W.2
Miller, W.3
Myers, E.W.4
Lipman, D.J.5
-
4
-
-
0025272240
-
Rapid and sensitive sequence comparisons with FASTP and FASTA
-
Pearson WR (1985) Rapid and sensitive sequence comparisons with FASTP and FASTA. Methods Enzymol 183, 63-98.
-
(1985)
Methods Enzymol
, vol.183
, pp. 63-98
-
-
Pearson, W.R.1
-
5
-
-
0030801002
-
Gapped BLAST and PSI-BLAST: A new generation of protein database search programs
-
Altschul SF, Madden TL, Schaffer AA, Zhang J, Zhang Z, Miller W & Lipman DJ (1997) Gapped BLAST and PSI-BLAST: a new generation of protein database search programs. Nucleic Acids Res 25, 3389-3402.
-
(1997)
Nucleic Acids Res
, vol.25
, pp. 3389-3402
-
-
Altschul, S.F.1
Madden, T.L.2
Schaffer, A.A.3
Zhang, J.4
Zhang, Z.5
Miller, W.6
Lipman, D.J.7
-
6
-
-
0014757386
-
A general method applicable to the search for similarities in the amino acid sequences of two proteins
-
Needleman S & Wunsch C (1970) A general method applicable to the search for similarities in the amino acid sequences of two proteins. J Mol Biol 48, 443-453.
-
(1970)
J Mol Biol
, vol.48
, pp. 443-453
-
-
Needleman, S.1
Wunsch, C.2
-
7
-
-
0031576361
-
Intermediate sequences increase the detection of homology between sequences
-
Park J, Teichmann SA, Hubbard T & Chothia C (1997) Intermediate sequences increase the detection of homology between sequences. J Mol Biol 273, 1-6.
-
(1997)
J Mol Biol
, vol.273
, pp. 1-6
-
-
Park, J.1
Teichmann, S.A.2
Hubbard, T.3
Chothia, C.4
-
8
-
-
0031706891
-
Family-based homology detection via pairwise sequence comparison
-
(Istrail S, Pevzner P & Waterman M, eds). ACM Press, New York, NY, USA
-
Grundy WN (1998) Family-based homology detection via pairwise sequence comparison. In Proceedings of the Second Annual International Conference on Computational Molecular Biology (Istrail S, Pevzner P & Waterman M, eds), pp. 94-100. ACM Press, New York, NY, USA.
-
(1998)
Proceedings of the Second Annual International Conference on Computational Molecular Biology
, pp. 94-100
-
-
Grundy, W.N.1
-
9
-
-
0032726692
-
Protomap: Automatic classification of protein sequences, a hierarchy of protein families, and local maps of the protein space
-
Yona G, Linial N & Linial M (1999) Protomap: Automatic classification of protein sequences, a hierarchy of protein families, and local maps of the protein space. Proteins: Struct Funct Genet 37, 360-678.
-
(1999)
Proteins: Struct Funct Genet
, vol.37
, pp. 360-678
-
-
Yona, G.1
Linial, N.2
Linial, M.3
-
13
-
-
0032509105
-
Sequence comparisons using multiple sequences detect three times as many remote homologues as pairwise methods
-
Park J, Karplus K, Barrett C, Hughey R, Haussler D, Hubbard T & Chothia C (1998) Sequence comparisons using multiple sequences detect three times as many remote homologues as pairwise methods. J Mol Biol 284, 1201-1210.
-
(1998)
J Mol Biol
, vol.284
, pp. 1201-1210
-
-
Park, J.1
Karplus, K.2
Barrett, C.3
Hughey, R.4
Haussler, D.5
Hubbard, T.6
Chothia, C.7
-
14
-
-
0028091659
-
Detection of conserved segments in proteins: Iterative scanning of sequence databases with alignment blocks
-
Tatusov RL, Altschul SF & Koonin EV (1994) Detection of conserved segments in proteins: iterative scanning of sequence databases with alignment blocks. Proc Natl Acad Sci USA 91, 12091-12095.
-
(1994)
Proc Natl Acad Sci USA
, vol.91
, pp. 12091-12095
-
-
Tatusov, R.L.1
Altschul, S.F.2
Koonin, E.V.3
-
15
-
-
0032438987
-
Hidden Markov models for detecting remote protein homologies
-
Karplus K, Barrett C & Hughey R (1998) Hidden Markov models for detecting remote protein homologies. Bioinformatics 14 (10), 846-856.
-
(1998)
Bioinformatics
, vol.14
, Issue.10
, pp. 846-856
-
-
Karplus, K.1
Barrett, C.2
Hughey, R.3
-
16
-
-
0028961335
-
SCOP: A structural classification of proteins database for the investigation of sequences and structures
-
Murzin AG, Brenner SE, Hubbard T & Chothia C (1995) SCOP: a structural classification of proteins database for the investigation of sequences and structures. J Mol Biol 247, 536-540.
-
(1995)
J Mol Biol
, vol.247
, pp. 536-540
-
-
Murzin, A.G.1
Brenner, S.E.2
Hubbard, T.3
Chothia, C.4
-
17
-
-
23744454242
-
-
(INS-R0011). National Research Institute for Mathematics and Computer Science in the Netherlands, Amsterdam
-
Van Dongen S (2000) A new cluster algorithm for graphs. (INS-R0011). National Research Institute for Mathematics and Computer Science in the Netherlands, Amsterdam.
-
(2000)
A New Cluster Algorithm for Graphs.
-
-
Van Dongen, S.1
-
18
-
-
0036529479
-
An efficient algorithm for large-scale detection of protein families
-
Enright AJ, Van Dongen S & Ouzounis CA (2002) An efficient algorithm for large-scale detection of protein families. Nucleic Acids Res 30 (7), 1575-1584.
-
(2002)
Nucleic Acids Res
, vol.30
, Issue.7
, pp. 1575-1584
-
-
Enright, A.J.1
Van Dongen, S.2
Ouzounis, C.A.3
-
19
-
-
0141519279
-
OrthoMCL: Identification of ortholog groups for eukaryotic genomes
-
Li L, Stoeckert CJ & Roos DS (2003) OrthoMCL: Identification of ortholog groups for eukaryotic genomes. Genome Res 13, 2178-2189.
-
(2003)
Genome Res
, vol.13
, pp. 2178-2189
-
-
Li, L.1
Stoeckert, C.J.2
Roos, D.S.3
-
21
-
-
0038152786
-
Target selection and determination of function in structural genomics
-
Watson JD (2003) Target selection and determination of function in structural genomics. Int Union Biochem Mol Biol Life 55, 249-255.
-
(2003)
Int Union Biochem Mol Biol Life
, vol.55
, pp. 249-255
-
-
Watson, J.D.1
-
22
-
-
27144465224
-
Motif-based protein ranking by network propagation
-
doi: 10.1093/bioinformatics/bti608
-
Kuang R, Weston J, Noble WS & Leslie C (2005) Motif-based protein ranking by network propagation. Bioinformatics doi: 10.1093/bioinformatics/ bti608.
-
(2005)
Bioinformatics
-
-
Kuang, R.1
Weston, J.2
Noble, W.S.3
Leslie, C.4
-
23
-
-
0033944826
-
Generage: A robust algorithm for sequence clustering and domain detection
-
Enright AJ & Ouzounis CA (2000) Generage: a robust algorithm for sequence clustering and domain detection. Bioinformatics 16, 451-457.
-
(2000)
Bioinformatics
, vol.16
, pp. 451-457
-
-
Enright, A.J.1
Ouzounis, C.A.2
-
25
-
-
0023179570
-
Observation of phase transitions in spreading activation networks
-
Shrager J, Hogg T & Huberman BA (1987) Observation of phase transitions in spreading activation networks. Science 236, 1092-1094.
-
(1987)
Science
, vol.236
, pp. 1092-1094
-
-
Shrager, J.1
Hogg, T.2
Huberman, B.A.3
-
27
-
-
0002638429
-
-
(Minsky M, ed.). MIT Press, Cambridge, MA, USA
-
Quillian MR (1968) Semantic Information Processing (Minsky M, ed.), pp 216-270. MIT Press, Cambridge, MA, USA.
-
(1968)
Semantic Information Processing
, pp. 216-270
-
-
Quillian, M.R.1
-
30
-
-
58149409019
-
Using spreading activation to identify relevant help
-
Collins AM & Loftus EF (1975) Using spreading activation to identify relevant help. Psychol Rev 82, 407.
-
(1975)
Psychol Rev
, vol.82
, pp. 407
-
-
Collins, A.M.1
Loftus, E.F.2
-
31
-
-
11244293445
-
Ranking on data manifolds
-
Zhou D, Weston J, Gretton A, Bousquet O & Schoelkopf B (2003) Ranking on data manifolds. Adv Neural Info Processing Systems 16, 169-176.
-
(2003)
Adv Neural Info Processing Systems
, vol.16
, pp. 169-176
-
-
Zhou, D.1
Weston, J.2
Gretton, A.3
Bousquet, O.4
Schoelkopf, B.5
-
32
-
-
13444263430
-
Manifold-ranking based image retrieval
-
ACM Press, New York, NY, USA
-
He J, Li M, Zhang H, Tong H & Zhang C (2004) Manifold-ranking based image retrieval. In Proceedings of 12th ACM International Conference on Multimedia. ACM Press, New York, NY, USA.
-
(2004)
Proceedings of 12th ACM International Conference on Multimedia
-
-
He, J.1
Li, M.2
Zhang, H.3
Tong, H.4
Zhang, C.5
-
33
-
-
0033289037
-
Using the Fisher kernel method to detect remote protein homologies
-
AAAI Press, Menlo Park, CA
-
Jaakkola T, Diekhans M & Haussler D (1999) Using the Fisher kernel method to detect remote protein homologies. In Proceedings of the Seventh International Conference on Intelligent Systems for Molecular Biology, pp. 149-158. AAAI Press, Menlo Park, CA.
-
(1999)
Proceedings of the Seventh International Conference on Intelligent Systems for Molecular Biology
, pp. 149-158
-
-
Jaakkola, T.1
Diekhans, M.2
Haussler, D.3
-
34
-
-
0020083498
-
The meaning and use of the area under a receiver operating characteristic (ROC) curve
-
Hanley JA & McNeil BJ (1982) The meaning and use of the area under a receiver operating characteristic (ROC) curve. Radiology 143, 29-36.
-
(1982)
Radiology
, vol.143
, pp. 29-36
-
-
Hanley, J.A.1
McNeil, B.J.2
-
35
-
-
0001969211
-
Use of receiver operating characteristic (ROC) analysis to evaluate sequence matching
-
Gribskov M & Robinson NL (1996) Use of receiver operating characteristic (ROC) analysis to evaluate sequence matching. Computers Chem 20, 25-33.
-
(1996)
Computers Chem
, vol.20
, pp. 25-33
-
-
Gribskov, M.1
Robinson, N.L.2
-
36
-
-
0036079158
-
Human genome browser at UCSC
-
Kent WJ, Sugnet CW, Furey TS, Roskin KM, Pringle TH, Zahler AM & Haussler D (2002) Human genome browser at UCSC. Genome Res 12, 996-1006.
-
(2002)
Genome Res
, vol.12
, pp. 996-1006
-
-
Kent, W.J.1
Sugnet, C.W.2
Furey, T.S.3
Roskin, K.M.4
Pringle, T.H.5
Zahler, A.M.6
Haussler, D.7
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