-
1
-
-
1842843558
-
Progress in bioinformatics and the importance of being earnest
-
Attwood, T. K., and Miller, C. J. 2002. Progress in bioinformatics and the importance of being earnest. Biotechnol. Annu. Rev. 8:1–54.
-
(2002)
Biotechnol. Annu. Rev
, vol.8
, pp. 1-54
-
-
Attwood, T.K.1
Miller, C.J.2
-
2
-
-
1642457294
-
Dna and the revolution of molecular evolution, computational biology, and bioinformatics
-
Golding, G. B. 2003. DNA and the revolution of molecular evolution, computational biology, and bioinformatics. Genome 46: 930–5.
-
(2003)
Genome
, vol.46
, pp. 930-935
-
-
Golding, G.B.1
-
3
-
-
0036469893
-
Biological data becomes computer literature: New advances in bioinformatics
-
Goodman, N. 2002. Biological data becomes computer literature: New advances in bioinformatics. Curr. Opin. Biotechnol. 13: 68–71.
-
(2002)
Curr. Opin. Biotechnol
, vol.13
, pp. 68-71
-
-
Goodman, N.1
-
4
-
-
0034571467
-
The origin of bioinformatics
-
Hagen, J. B. 2000. The origin of bioinformatics. Nat. Rev. Genetics 1: 231–6.
-
(2000)
Nat. Rev. Genetics
, vol.1
, pp. 231-236
-
-
Hagen, J.B.1
-
5
-
-
0037370478
-
Bioinformatics in the post-sequence era
-
Kanehisa, M., and Bork, P. 2003. Bioinformatics in the post-sequence era. Nat. Genet. 33 Suppl: 305–10.
-
(2003)
Nat. Genet
, vol.33
, pp. 305-310
-
-
Kanehisa, M.1
Bork, P.2
-
6
-
-
0037676231
-
Bioinformatics and genomic medicine
-
Kim, J. H. 2002. Bioinformatics and genomic medicine. Genet. Med. 4 Suppl: 62S–5S.
-
(2002)
Genet. Med
, vol.4
-
-
Kim, J.H.1
-
7
-
-
0034868592
-
What is bioinformatics? A proposed definition and overview of the field
-
Luscombe, N. M., Greenbaum, D., and Gerstein, M. 2001. What is bioinformatics? A proposed definition and overview of the field. Methods Inf. Med. 40: 346–58.
-
(2001)
Methods Inf. Med
, vol.40
, pp. 346-358
-
-
Luscombe, N.M.1
Greenbaum, D.2
Gerstein, M.3
-
8
-
-
0344896614
-
Early bioinformatics: The birth of a discipline –apersonal view
-
Ouzounis, C. A., and Valencia, A. 2003. Early bioinformatics: The birth of a discipline –Apersonal view. Bioinformatics 19: 2176–90.
-
(2003)
Bioinformatics
, vol.19
, pp. 2176-2190
-
-
Ouzounis, C.A.1
Valencia, A.2
-
9
-
-
0033926482
-
Protein sequence databases
-
Apweiler, R. 2000. Protein sequence databases. Adv. Protein Chem. 54: 31–71.
-
(2000)
Adv. Protein Chem
, vol.54
, pp. 31-71
-
-
Apweiler, R.1
-
10
-
-
0036594916
-
Information extraction in molecular biology
-
Blaschke, C., Hirschman, L., and Valencia, A. 2002. Information extraction in molecular biology. Brief. Bioinform. 3: 154–65.
-
(2002)
Brief. Bioinform
, vol.3
, pp. 154-165
-
-
Blaschke, C.1
Hirschman, L.2
Valencia, A.3
-
11
-
-
0142087866
-
Entrez: Making use of its power
-
Geer, R. C., and Sayers, E.W. 2003. Entrez: Making use of its power. Brief. Bioinform. 4: 179–84.
-
(2003)
Brief. Bioinform
, vol.4
, pp. 179-184
-
-
Geer, R.C.1
Sayers, E.W.2
-
12
-
-
0035234465
-
Sequence databases and the internet
-
Hughes, A. E. 2001. Sequence databases and the Internet. Methods Mol. Biol. 167: 215–23.
-
(2001)
Methods Mol. Biol
, vol.167
, pp. 215-223
-
-
Hughes, A.E.1
-
13
-
-
0035253386
-
Use of on-line tools and databases for routine sequence analyses
-
Patnaik, S. K., and Blumenfeld, O. O. 2001. Use of on-line tools and databases for routine sequence analyses. Anal. Biochem. 289: 1–9.
-
(2001)
Anal. Biochem
, vol.289
, pp. 1-9
-
-
Patnaik, S.K.1
Blumenfeld, O.O.2
-
14
-
-
0038745614
-
Integrating biological databases
-
Stein, L. D. 2003. Integrating biological databases. Nat. Rev. Genet. 4: 337–45.
-
(2003)
Nat. Rev. Genet
, vol.4
, pp. 337-345
-
-
Stein, L.D.1
-
15
-
-
17244379179
-
The many faces of sequence alignment
-
Batzoglou, S. 2005. The many faces of sequence alignment. Brief. Bioinformatics 6: 6–22.
-
(2005)
Brief. Bioinformatics
, vol.6
, pp. 6-22
-
-
Batzoglou, S.1
-
16
-
-
0032568596
-
Assessing sequence comparison methods with reliable structurally identified distant evolutionary relationships
-
Brenner, S. E., Chothia, C., and Hubbard, T. J. 1998. Assessing sequence comparison methods with reliable structurally identified distant evolutionary relationships. Proc.Natl. Acad. Sci.USA 95: 6073–8.
-
(1998)
Proc.Natl. Acad. Sci.Usa
, vol.95
, pp. 6073-6078
-
-
Brenner, S.E.1
Chothia, C.2
Hubbard, T.J.3
-
17
-
-
0026693729
-
Aligning two sequences within a specified diagonal band
-
Chao, K.-M., Pearson, W. R., and Miller, W. 1992. Aligning two sequences within a specified diagonal band. Comput. Appl. Biosci. 8: 481–7.
-
(1992)
Comput. Appl. Biosci
, vol.8
, pp. 481-487
-
-
Chao, K.-M.1
Pearson, W.R.2
Miller, W.3
-
18
-
-
0026458378
-
Amino acid substitution matrices from protein blocks
-
Henikoff, S., and Henikoff, J. G. 1992. Amino acid substitution matrices from protein blocks. Proc. Natl. Acad. Sci. U S A 89: 10915–19.
-
(1992)
Proc. Natl. Acad. Sci. U S A
, vol.89
, pp. 10915-10919
-
-
Henikoff, S.1
Henikoff, J.G.2
-
19
-
-
0028304908
-
On global sequence alignment
-
Huang, X. 1994. On global sequence alignment. Comput. Appl. Biosci. 10: 227–35.
-
(1994)
Comput. Appl. Biosci
, vol.10
, pp. 227-235
-
-
Huang, X.1
-
20
-
-
0035292408
-
Making sense of score statistics for sequence alignments
-
Pagni, M., and Jongeneel, V. 2001. Making sense of score statistics for sequence alignments. Brief. Bioinformatics 2: 51–67.
-
(2001)
Brief. Bioinformatics
, vol.2
, pp. 51-67
-
-
Pagni, M.1
Jongeneel, V.2
-
21
-
-
0029933671
-
Effective protein sequence comparison
-
Pearson, W. R. 1996. Effective protein sequence comparison. Methods Enzymol. 266: 227–58.
-
(1996)
Methods Enzymol
, vol.266
, pp. 227-258
-
-
Pearson, W.R.1
-
22
-
-
0032962457
-
Twilight zone of protein sequence alignments
-
Rost, B. 1999. Twilight zone of protein sequence alignments. Protein Eng. 12: 85–94.
-
(1999)
Protein Eng
, vol.12
, pp. 85-94
-
-
Rost, B.1
-
23
-
-
0002164370
-
Improved sensitivity of nucleic acid database searches using application-specific scoring matrices
-
States, D. J., Gish, W., and Altschul, S. F. 1991. Improved sensitivity of nucleic acid database searches using application-specific scoring matrices. Methods 3: 66–70.
-
(1991)
Methods
, vol.3
, pp. 66-70
-
-
States, D.J.1
Gish, W.2
Altschul, S.F.3
-
24
-
-
0036681416
-
Scoring residue conservation
-
Valdar, W. S. 2002. Scoring residue conservation. Proteins. 48: 227–41.
-
(2002)
Proteins
, vol.48
, pp. 227-241
-
-
Valdar, W.S.1
-
25
-
-
0028047892
-
Sequence alignment and penalty scores
-
Vingron, M., and Waterman, M. S. 1994. Sequence alignment and penalty scores. J. Mol. Biol. 235: 1–12.
-
(1994)
J. Mol. Biol
, vol.235
, pp. 1-12
-
-
Vingron, M.1
Waterman, M.S.2
-
26
-
-
0028289467
-
Issues in searching molecular sequences databases
-
Altschul, S. F., Boguski, M. S., Gish, W., and Wootton, J. C. 1994. Issues in searching molecular sequences databases. Nat. Genet. 6: 119–29.
-
(1994)
Nat. Genet
, vol.6
, pp. 119-129
-
-
Altschul, S.F.1
Boguski, M.S.2
Gish, W.3
Wootton, J.C.4
-
27
-
-
0030801002
-
Gapped blast and psi-blast: A new generation of protein database search programs
-
Altschul, S. F., Madden, T. L., Schaffer, A. A., Zhang, J., Zhang, Z., Miller, W., and Lipman, D. J. 1997.Gapped BLAST and PSI-BLAST: A new generation of protein database search programs. Nucleic Acids Res. 25: 3389–402.
-
(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
-
28
-
-
0346252359
-
Assessing sequence comparison methods with the average precision criterion
-
Chen, Z. 2003. Assessing sequence comparison methods with the average precision criterion. Bioinformatics 19: 2456–60.
-
(2003)
Bioinformatics
, vol.19
, pp. 2456-2460
-
-
Chen, Z.1
-
29
-
-
0027175241
-
Applications and statistics for multiple high-scoring segments in molecular sequences
-
Karlin, S., and Altschul, S. F. 1993. Applications and statistics for multiple high-scoring segments in molecular sequences. Proc. Natl. Acad. Sci. USA 90: 5873–7.
-
(1993)
Proc. Natl. Acad. Sci. USA
, vol.90
, pp. 5873-5877
-
-
Karlin, S.1
Altschul, S.F.2
-
31
-
-
0034139835
-
Database searching with dna and protein sequences: An introduction
-
Sansom, C. 2000. Database searching with DNA and protein sequences: An introduction. Brief. Bioinform. 1: 22–32.
-
(2000)
Brief. Bioinform
, vol.1
, pp. 22-32
-
-
Sansom, C.1
-
32
-
-
0031829618
-
Statistics of large-scale sequence searching
-
Spang, R., and Vingron, M. 1998. Statistics of large-scale sequence searching. Bioinformatics 14: 279–84.
-
(1998)
Bioinformatics
, vol.14
, pp. 279-284
-
-
Spang, R.1
Vingron, M.2
-
33
-
-
0031903739
-
Sequence alignment in molecular biology
-
Apostolico, A., and Giancarlo, R. 1998. Sequence alignment in molecular biology. J. Comput. Biol. 5: 173–96.
-
(1998)
J. Comput. Biol
, vol.5
, pp. 173-196
-
-
Apostolico, A.1
Giancarlo, R.2
-
34
-
-
0034222034
-
Multiple sequence alignment tools on theweb
-
Gaskell, G. J. 2000.Multiple sequence alignment tools on theWeb. Biotechniques 29: 60–2.
-
(2000)
Biotechniques
, vol.29
, pp. 60-62
-
-
Gaskell, G.J.1
-
35
-
-
0032789448
-
Multiple sequence alignment: Algorithms and applications
-
Gotoh, O. 1999. Multiple sequence alignment: Algorithms and applications. Adv. Biophys. 36: 159–206.
-
(1999)
Adv. Biophys
, vol.36
, pp. 159-206
-
-
Gotoh, O.1
-
36
-
-
0035972742
-
Multiple alignment of complete sequences (macs) in the post-genomic era
-
Lecompte, O., Thompson, J. D., Plewniak, F., Thierry, J., and Poch, O. 2001. Multiple alignment of complete sequences (MACS) in the post-genomic era. Gene 270: 17–30.
-
(2001)
Gene
, vol.270
, pp. 17-30
-
-
Lecompte, O.1
Thompson, J.D.2
Plewniak, F.3
Thierry, J.4
Poch, O.5
-
37
-
-
0032945593
-
Dialign 2: Improvement of the segment-to-segment approach to multiple sequence alignment
-
Morgenstern, B. 1999. DIALIGN 2: improvement of the segment-to-segment approach to multiple sequence alignment. Bioinformatics 15: 211–8.
-
(1999)
Bioinformatics
, vol.15
, pp. 211-218
-
-
Morgenstern, B.1
-
38
-
-
0029861894
-
Multiple dna and protein sequence alignment based on segment-to-segment comparison
-
Morgenstern, B., Dress, A., andWerner T. 1996.Multiple DNA and protein sequence alignment based on segment-to-segment comparison. Proc. Natl. Acad. Sci. USA 93: 12098–103.
-
(1996)
Proc. Natl. Acad. Sci. USA
, vol.93
, pp. 12098-12103
-
-
Morgenstern, B.1
Dress, A.2
Andwerner, T.3
-
39
-
-
0038802447
-
Multiple sequence alignment – the gateway to further analysis
-
Mullan, L. J. 2002. Multiple sequence alignment – The gateway to further analysis. Brief. Bioinform. 3: 303–5.
-
(2002)
Brief. Bioinform
, vol.3
, pp. 303-305
-
-
Mullan, L.J.1
-
40
-
-
0036189312
-
Strategies for multiple sequence alignment
-
Nicholas, H.B., Ropelewski, A. J., and Deerfield, D.W. 2002. Strategies for multiple sequence alignment. Biotechniques 32: 572–91.
-
(2002)
Biotechniques
, vol.32
, pp. 572-591
-
-
Nicholas, H.B.1
Ropelewski, A.J.2
Deerfield, D.W.3
-
41
-
-
0036208872
-
Recent progress in multiple sequence alignment: A survey
-
Notredame, C. 2002. Recent progress in multiple sequence alignment: A survey. Pharmacogenomics 3: 131–44.
-
(2002)
Pharmacogenomics
, vol.3
, pp. 131-144
-
-
Notredame, C.1
-
42
-
-
0034623005
-
T-coffee: A novel method for fast and accurate multiple sequence alignment
-
Notredame, C., Higgins, D. G., and Heringa, J. 2000. T-Coffee: A novel method for fast and accurate multiple sequence alignment. J.Mol. Biol. 302: 205–17.
-
(2000)
J.Mol. Biol
, vol.302
, pp. 205-217
-
-
Notredame, C.1
Higgins, D.G.2
Heringa, J.3
-
43
-
-
0027968068
-
Clustal w: Improving the sensitivity of progressive multiple sequence alignment through sequence weighting, position-specific gap penalties and weight matrix choice
-
Thompson, J.D., Higgins, D. G., and Gibson, T. J. 1994. CLUSTAL W: Improving the sensitivity of progressive multiple sequence alignment through sequence weighting, position-specific gap penalties and weight matrix choice. Nucleic Acids Res. 22: 4673–80.
-
(1994)
Nucleic Acids Res
, vol.22
, pp. 4673-4680
-
-
Thompson, J.D.1
Higgins, D.G.2
Gibson, T.J.3
-
44
-
-
0033168097
-
A comprehensive comparison of multiple sequence alignment programs
-
Thompson, J. D., Plewniak, F., and Poch, O. 1999. A comprehensive comparison of multiple sequence alignment programs. Nucleic Acids Res. 27: 2682–90.
-
(1999)
Nucleic Acids Res
, vol.27
, pp. 2682-2690
-
-
Thompson, J.D.1
Plewniak, F.2
Poch, O.3
-
45
-
-
0031793928
-
Iterated profile searches with psi-blast – a tool for discovery in protein databases
-
Altschul, S. F., and Koonin, E. V. 1998. Iterated profile searches with PSI-BLAST – A tool for discovery in protein databases. Trends Biochem. Sci. 23: 444–7.
-
(1998)
Trends Biochem. Sci
, vol.23
, pp. 444-447
-
-
Altschul, S.F.1
Koonin, E.V.2
-
46
-
-
0028011075
-
Hidden markov models of biological primary sequence information
-
Baldi, P., Chauvin, Y., Hunkapiller, T., and McClure M. A. 1994. Hidden Markov models of biological primary sequence information. Proc. Natl. Acad. Sci. USA 91: 1059–63.
-
(1994)
Proc. Natl. Acad. Sci. USA
, vol.91
, pp. 1059-1063
-
-
Baldi, P.1
Chauvin, Y.2
Hunkapiller, T.3
McClure, M.A.4
-
48
-
-
0031743421
-
Profile hiddenmarkov models
-
Eddy, S. R. 1998. Profile hiddenMarkov models. Bioinformatics 14: 755–63.
-
(1998)
Bioinformatics
, vol.14
, pp. 755-763
-
-
Eddy, S.R.1
-
50
-
-
0036145804
-
Acomparison of position-specific score matrices based on sequence and structure alignments
-
Panchenko, A. R., and Bryant, S. H. 2002.Acomparison of position-specific score matrices based on sequence and structure alignments. Protein Sci. 11: 361–70.
-
(2002)
Protein Sci
, vol.11
, pp. 361-370
-
-
Panchenko, A.R.1
Bryant, S.H.2
-
51
-
-
0033986922
-
The quest to deduce protein function from sequence: The role of pattern databases
-
Attwood, T. K. 2000. The quest to deduce protein function from sequence: The role of pattern databases. Int. J. Biochem. Cell. Biol. 32: 139–55.
-
(2000)
Int. J. Biochem. Cell. Biol
, vol.32
, pp. 139-155
-
-
Attwood, T.K.1
-
52
-
-
0037787816
-
The prints database: A resource for identification of protein families
-
Attwood, T. K. 2002. The PRINTS database: A resource for identification of protein families. Brief. Bioinform. 3: 252–63.
-
(2002)
Brief. Bioinform
, vol.3
, pp. 252-263
-
-
Attwood, T.K.1
-
53
-
-
0000742582
-
Applications of interpro in protein annotation and genome analysis
-
Biswas, M., O’Rourke, J. F., Camon, E., Fraser, G., Kanapin, A., Karavidopoulou, Y., Kersey, P., et al. Applications of InterPro in protein annotation and genome analysis. Brief. Bioinform. 3: 285–95.
-
Brief. Bioinform
, vol.3
, pp. 285-295
-
-
Biswas, M.1
O’Rourke, J.F.2
Camon, E.3
Fraser, G.4
Kanapin, A.5
Karavidopoulou, Y.6
Kersey, P.7
-
54
-
-
0036421036
-
Sequence analysis of multidomain proteins: Past perspectives and future directions
-
Copley, R. R., Ponting, C. P., Schultz, J., and Bork, P. 2002. Sequence analysis of multidomain proteins: Past perspectives and future directions. Adv. Protein Chem. 61: 75–98.
-
(2002)
Adv. Protein Chem
, vol.61
, pp. 75-98
-
-
Copley, R.R.1
Ponting, C.P.2
Schultz, J.3
Bork, P.4
-
55
-
-
0037370478
-
Bioinformatics in the post-sequence era
-
Kanehisa, M., and Bork, P. 2003. Bioinformatics in the post-sequence era. Nat.Genet. 33 (Suppl): 305–10.
-
(2003)
Nat.Genet
, vol.33
, pp. 305-310
-
-
Kanehisa, M.1
Bork, P.2
-
56
-
-
16644363065
-
Delineation of modular proteins: Domain boundary prediction from sequence information
-
Kong, L., and Ranganathan, S. 2004. Delineation of modular proteins: Domain boundary prediction from sequence information. Brief. Bioinform. 5: 179–92.
-
(2004)
Brief. Bioinform
, vol.5
, pp. 179-192
-
-
Kong, L.1
Ranganathan, S.2
-
58
-
-
0037305939
-
Domains, motifs and clusters in the protein universe
-
Liu, J., and Rost, B. 2003. Domains, motifs and clusters in the protein universe. Curr.Opin. Chem. Biol. 7: 5–11.
-
(2003)
Curr.Opin. Chem. Biol
, vol.7
, pp. 5-11
-
-
Liu, J.1
Rost, B.2
-
59
-
-
0035453312
-
Common pitfalls in bioinformatics-based analyses: Look before you leap
-
Peri, S., Ibarrola, N., Blagoev, B., Mann, M., and Pandey, A. 2001. Common pitfalls in bioinformatics-based analyses: Look before you leap. Trends Genet. 17: 541–5.
-
(2001)
Trends Genet
, vol.17
, pp. 541-545
-
-
Peri, S.1
Ibarrola, N.2
Blagoev, B.3
Mann, M.4
Pandey, A.5
-
60
-
-
0000120520
-
Prodom: Automated clustering of homologous domains
-
Servant, F., Bru, C., Carrere, S., Courcelle, E., Gouzy, J., Peyruc, D., and Kahn, D. 2002. ProDom: Automated clustering of homologous domains. Brief. Bioinform. 3: 246–51.
-
(2002)
Brief. Bioinform
, vol.3
, pp. 246-251
-
-
Servant, F.1
Bru, C.2
Carrere, S.3
Courcelle, E.4
Gouzy, J.5
Peyruc, D.6
Kahn, D.7
-
61
-
-
0001290045
-
Prosite: A documented database using patterns and profiles as motif descriptors
-
Sigrist, C. J., Cerutti, L., Hulo, N., Gattiker, A., Falquet, L., Pagni, M., Bairoch, A., and Bucher, P. 2002. PROSITE: A documented database using patterns and profiles as motif descriptors. Brief. Bioinform. 3: 265–74.
-
(2002)
Brief. Bioinform
, vol.3
, pp. 265-274
-
-
Sigrist, C.J.1
Cerutti, L.2
Hulo, N.3
Gattiker, A.4
Falquet, L.5
Pagni, M.6
Bairoch, A.7
Bucher, P.8
-
62
-
-
0041922344
-
Protein family classificationandfunctional annotation
-
Wu, C. H., Huang, H., Yeh, L. S., and Barker, W.C. 2003.Protein family classificationandfunctional annotation. Comput. Biol. Chem. 27: 37–47.
-
(2003)
Comput. Biol. Chem
, vol.27
, pp. 37-47
-
-
Wu, C.H.1
Huang, H.2
Yeh, L.S.3
Barker, W.C.4
-
63
-
-
0036205874
-
Ab initio gene identification: Prokaryote genome annotation with genescan and glimmer
-
Aggarwal, G., and Ramaswamy, R. 2002. Ab initio gene identification: Prokaryote genome annotation with GeneScan and GLIMMER. J. Biosci. 27: 7–14.
-
(2002)
J. Biosci
, vol.27
, pp. 7-14
-
-
Aggarwal, G.1
Ramaswamy, R.2
-
65
-
-
16644401595
-
Probabilistic methods of identifying genes in prokaryotic genomes: Connections to the hmm theory
-
Azad, R. K., and Borodovsky, M. 2004. Probabilistic methods of identifying genes in prokaryotic genomes: Connections to the HMM theory. Brief. Bioinform. 5: 118–30.
-
(2004)
Brief. Bioinform
, vol.5
, pp. 118-130
-
-
Azad, R.K.1
Borodovsky, M.2
-
66
-
-
0038206894
-
Compositional features of eukaryotic genomes for checking predicted genes
-
Cruveiller, S., Jabbari, K., Clay, O., and Bemardi, G. 2003. Compositional features of eukaryotic genomes for checking predicted genes. Brief. Bioinform. 4: 43–52.
-
(2003)
Brief. Bioinform
, vol.4
, pp. 43-52
-
-
Cruveiller, S.1
Jabbari, K.2
Clay, O.3
Bemardi, G.4
-
67
-
-
1542758518
-
Computer software tofindgenes in plant genomicdna
-
E. Grotewold, Totowa, NJ: Human Press
-
Davuluri, R.V., and Zhang, M.Q. 2003. “Computer software tofindgenes in plant genomicDNA.” In Plant Functional Genomics, edited by E. Grotewold, 87–108. Totowa, NJ: Human Press.
-
(2003)
In Plant Functional Genomics
, pp. 87-108
-
-
Davuluri, R.V.1
Zhang, M.Q.2
-
68
-
-
2942519269
-
Gene prediction accuracy in large dna sequences
-
M. Y. Galperin and E. V. Koonin, Norfolk, UK: Caister Academic Press
-
Guigo, R., andWiehe, T. 2003. “Gene prediction accuracy in large DNA sequences.” In Frontiers in Computational Genomics, edited by M. Y. Galperin and E. V. Koonin, 1–33. Norfolk, UK: Caister Academic Press.
-
(2003)
In Frontiers in Computational Genomics
, pp. 1-33
-
-
Guigo, R.1
Andwiehe, T.2
-
69
-
-
0037417884
-
Comparison of mouse and human genomes followed by experimental verification yields an estimated 1,019 additional genes
-
Guigo, R., Dermitzakis, E. T., Agarwal, P., Ponting, C. P., Parra, G., Reymond, A., Abril, J. F., et al. 2003. Comparison of mouse and human genomes followed by experimental verification yields an estimated 1,019 additional genes. Proc. Natl. Acad. Sci. USA 100: 1140–5.
-
(2003)
Proc. Natl. Acad. Sci. USA
, vol.100
, pp. 1140-1145
-
-
Guigo, R.1
Dermitzakis, E.T.2
Agarwal, P.3
Ponting, C.P.4
Parra, G.5
Reymond, A.6
Abril, J.F.7
-
70
-
-
0036680505
-
Discovering new genes with advanced homology detection
-
Li, W., and Godzik, A. 2002. Discovering new genes with advanced homology detection. Trends Biotechnol. 20: 315–16.
-
(2002)
Trends Biotechnol
, vol.20
, pp. 315-316
-
-
Li, W.1
Godzik, A.2
-
71
-
-
0036596123
-
Computer programs for eukaryotic gene prediction
-
Makarov, V. 2002. Computer programs for eukaryotic gene prediction. Brief. Bioinform. 3: 195–9.
-
(2002)
Brief. Bioinform
, vol.3
, pp. 195-199
-
-
Makarov, V.1
-
72
-
-
0036796369
-
Current methods of gene prediction, their strengths and weaknesses
-
Mathe, C., Sagot, M. F., Schiex, T., and Rouze, P. 2002. Current methods of gene prediction, their strengths and weaknesses. Nucleic Acids Res. 30: 4103–17.
-
(2002)
Nucleic Acids Res
, vol.30
, pp. 4103-4117
-
-
Mathe, C.1
Sagot, M.F.2
Schiex, T.3
Rouze, P.4
-
73
-
-
0037268583
-
Comparative gene prediction in human and mouse
-
Parra, G., Agarwal, P., Abril, J. F., Wiehe, T., Fickett, J. W., and Guigo, R. 2003. Comparative gene prediction in human and mouse. Genome Res. 13: 108–17.
-
(2003)
Genome Res
, vol.13
, pp. 108-117
-
-
Parra, G.1
Agarwal, P.2
Abril, J.F.3
Wiehe, T.4
Fickett, J.W.5
Guigo, R.6
-
74
-
-
0042880980
-
Vertebrate gene predictions and the problem of large genes
-
Wang, J., Li, S., Zhang, Y., Zheng, H., Xu, Z., Ye, J., Yu, J., and Wong, G. K. 2003. Vertebrate gene predictions and the problem of large genes. Nat. Rev. Genet. 4: 741–9.
-
(2003)
Nat. Rev. Genet
, vol.4
, pp. 741-749
-
-
Wang, J.1
Li, S.2
Zhang, Y.3
Zheng, H.4
Xu, Z.5
Ye, J.6
Yu, J.7
Wong, G.K.8
-
75
-
-
24644516306
-
A brief review of computational gene prediction methods
-
Wang, Z., Chen, Y., and Li, Y. 2004. A brief review of computational gene prediction methods. Geno. Prot. Bioinfo. 4: 216–21.
-
(2004)
Geno. Prot. Bioinfo
, vol.4
, pp. 216-221
-
-
Wang, Z.1
Chen, Y.2
Li, Y.3
-
76
-
-
0036733640
-
Computational prediction of eukaryotic protein coding genes
-
Zhang, M. Q. 2002. Computational prediction of eukaryotic protein coding genes. Nat. Rev. Genetics. 3: 698–709.
-
(2002)
Nat. Rev. Genetics
, vol.3
, pp. 698-709
-
-
Zhang, M.Q.1
-
77
-
-
0036518814
-
The computational challenges of applying comparative-based computational methods to whole genomes
-
Dubchak, I., and Pachter, L. 2002. The computational challenges of applying comparative-based computational methods to whole genomes. Brief. Bioinform. 3: 18–22.
-
(2002)
Brief. Bioinform
, vol.3
, pp. 18-22
-
-
Dubchak, I.1
Pachter, L.2
-
78
-
-
0035236049
-
Promoter prediction in the human genome
-
Hannenhalli, S., and Levy, S. 2001. Promoter prediction in the human genome. Bioinformatics 17(Suppl): S90–6.
-
(2001)
Bioinformatics
, vol.17
-
-
Hannenhalli, S.1
Levy, S.2
-
79
-
-
0035206286
-
Database-assisted promoteranalysis
-
Hehl, R., and Wingender, E. 2001.Database-assisted promoteranalysis. TrendsPlant Sci. 6: 251–5.
-
(2001)
Trendsplant Sci
, vol.6
, pp. 251-255
-
-
Hehl, R.1
Wingender, E.2
-
80
-
-
0035252126
-
Identification and analysis of eukaryotic promoters: Recent computational approaches
-
Ohler, U., and Niemann, H. 2001. Identification and analysis of eukaryotic promoters: Recent computational approaches. Trends Genet. 17: 56–60.
-
(2001)
Trends Genet
, vol.17
, pp. 56-60
-
-
Ohler, U.1
Niemann, H.2
-
81
-
-
0141839748
-
Finding the needle in the haystack: Computational strategies for discovering regulatory sequences in genomes
-
Ovcharenko, I., and Loots, G.G. 2003. Finding the needle in the haystack: Computational strategies for discovering regulatory sequences in genomes. Curr. Genomics 4: 557–68.
-
(2003)
Curr. Genomics
, vol.4
, pp. 557-568
-
-
Ovcharenko, I.1
Loots, G.G.2
-
82
-
-
0041829442
-
Recent advances in computational promoter analysis in understanding the transcriptional regulatory network
-
Qiu, P. 2003. Recent advances in computational promoter analysis in understanding the transcriptional regulatory network. Biochem. Biophys. Res. Commun. 309: 495–501.
-
(2003)
Biochem. Biophys. Res. Commun
, vol.309
, pp. 495-501
-
-
Qiu, P.1
-
83
-
-
0038376923
-
Computational approaches to identify promoters and cis-regulatory elements in plant genomes
-
Rombauts S., Florquin K., Lescot M., Marchal K., Rouze P., and van de Peer Y. 2003. Computational approaches to identify promoters and cis-regulatory elements in plant genomes. Plant Physiol. 132: 1162–76.
-
(2003)
Plant Physiol
, vol.132
, pp. 1162-1176
-
-
Rombauts, S.1
Florquin, K.2
Lescot, M.3
Marchal, K.4
Rouze, P.5
Van De Peer, Y.6
-
84
-
-
0034612277
-
Operons in escherichia coli: Genomic analyses and predictions
-
Salgado, H., Moreno-Hagelsieb, G., Smith, T. F., and Collado-Vides, J. 2000. Operons in Escherichia coli: Genomic analyses and predictions. Proc. Natl. Acad. Sci. USA 97: 6652–7.
-
(2000)
Proc. Natl. Acad. Sci. USA
, vol.97
, pp. 6652-6657
-
-
Salgado, H.1
Moreno-Hagelsieb, G.2
Smith, T.F.3
Collado-Vides, J.4
-
85
-
-
3142674779
-
Genome-wide operon prediction in staphylococcus aureus
-
Wang, L., Trawick, J. D., Yamamoto, R., and Zamudio, C. 2004. Genome-wide operon prediction in Staphylococcus aureus. Nucleic Acids Res. 32: 3689–702.
-
(2004)
Nucleic Acids Res
, vol.32
, pp. 3689-3702
-
-
Wang, L.1
Trawick, J.D.2
Yamamoto, R.3
Zamudio, C.4
-
86
-
-
0037869270
-
The state of the art of mammalian promoter recognition
-
Werner, T. 2003. The state of the art of mammalian promoter recognition. Brief. Bioinform. 4: 22–30.
-
(2003)
Brief. Bioinform
, vol.4
, pp. 22-30
-
-
Werner, T.1
-
88
-
-
0033910362
-
Amino acid-based phylogeny and alignment
-
Higgins, D.G. 2000. Amino acid-based phylogeny and alignment. Adv. Protein Chem. 54: 99–135.
-
(2000)
Adv. Protein Chem
, vol.54
, pp. 99-135
-
-
Higgins, D.G.1
-
91
-
-
0034578465
-
Gene family evolution and homology: Genomics meets phylogenetics
-
Thornton, J. W., and DeSalle, R. 2000. Gene family evolution and homology: Genomics meets phylogenetics. Annu. Rev. Genomics Hum. Genet. 1: 41–73.
-
(2000)
Annu. Rev. Genomics Hum. Genet
, vol.1
, pp. 41-73
-
-
Thornton, J.W.1
Desalle, R.2
-
92
-
-
0035339920
-
Molecular phylogenetics: State of the art methods for looking into the past
-
Whelan, S., Lio, P., and Goldman, N. 2001.Molecular phylogenetics: State of the art methods for looking into the past. Trends Genet. 17: 262–72.
-
(2001)
Trends Genet
, vol.17
, pp. 262-272
-
-
Whelan, S.1
Lio, P.2
Goldman, N.3
-
95
-
-
0035861456
-
Bayesian inference of phylogeny and its impact on evolutionary biology
-
Huelsenbeck J. P., Ronquist, F., Nielsen R., and Bollback, J. P. 2001. Bayesian inference of phylogeny and its impact on evolutionary biology. Science. 294: 2310–14.
-
(2001)
Science
, vol.294
, pp. 2310-2314
-
-
Huelsenbeck, J.P.1
Ronquist, F.2
Nielsen, R.3
Bollback, J.P.4
-
98
-
-
0001336205
-
Phylogenetic inference
-
2nd ed., edited by D. M. Hillis, C.Moritz, and B. K.Mable Sunderland, MA: Sinauer Associates
-
Swofford, D. L., Olsen, G. J., Waddel, P. J., and Hillis, D. M. 1996. ”Phylogenetic inference.” In Molecular Systematics. 2nd ed., edited by D. M. Hillis, C.Moritz, and B. K.Mable Sunderland, MA: Sinauer Associates.
-
(1996)
In Molecular Systematics
-
-
Swofford, D.L.1
Olsen, G.J.2
Waddel, P.J.3
Hillis, D.M.4
-
100
-
-
0037270931
-
Fundamentals of protein structure
-
P. E. Bourne and H.Weissig, Hoboken, NJ: Wiley-Liss
-
Scheeff, E. D., and Fink, J. L. 2003. “Fundamentals of protein structure.” In Structural Bioinformatics, edited by P. E. Bourne and H.Weissig, 15–39. Hoboken, NJ: Wiley-Liss.
-
(2003)
In Structural Bioinformatics
, pp. 15-39
-
-
Scheeff, E.D.1
Fink, J.L.2
-
101
-
-
0037264585
-
The pdb format, mmcif and other data formats
-
edited by P. E. Bourne and H. Weissig, Hoboken, NJ: Wiley-Liss
-
Westbrook, J. D., and Fitzgerald, P. M. D. 2003. “The PDB format, mmCIF and other data formats.” In Structural Bioinformatics, edited by P. E. Bourne and H. Weissig, 161–79. Hoboken, NJ: Wiley-Liss.
-
(2003)
Structural Bioinformatics
, pp. 161-179
-
-
Westbrook, J.D.1
Fitzgerald, P.M.D.2
-
102
-
-
0037267407
-
Structure comparison and alignment
-
P. E. Bourne and H.Weissig, Hoboken, NJ: Wiley-Liss
-
Bourne, P. E., and Shindyalov, I. N. 2003. “Structure comparison and alignment.” In Structural Bioinformatics, edited by P. E. Bourne and H.Weissig, 321–37. Hoboken, NJ: Wiley-Liss.
-
(2003)
In Structural Bioinformatics
, pp. 321-337
-
-
Bourne, P.E.1
Shindyalov, I.N.2
-
103
-
-
0035996767
-
Recent progress in protein 3d structure comparison
-
Carugo, O., and Pongor, S. 2002. Recent progress in protein 3D structure comparison. Curr. Protein Pept. Sci. 3: 441–9.
-
(2002)
Curr. Protein Pept. Sci
, vol.3
, pp. 441-449
-
-
Carugo, O.1
Pongor, S.2
-
104
-
-
0033200307
-
A systematic comparison of protein structure classifications: Scop, cath, and fssp
-
Hadley, C., and Jones, D. T. 1999. A systematic comparison of protein structure classifications: SCOP, CATH, and FSSP. Structure 7: 1099–112.
-
(1999)
Structure
, vol.7
, pp. 1099-1112
-
-
Hadley, C.1
Jones, D.T.2
-
105
-
-
0036226347
-
Novel sequences propel familiar folds
-
Jawad, Z., and Paoli, M. 2002. Novel sequences propel familiar folds. Structure 10: 447–54.
-
(2002)
Structure
, vol.10
, pp. 447-454
-
-
Jawad, Z.1
Paoli, M.2
-
106
-
-
0036600834
-
Evolution of protein structures and functions
-
Kinch, L. N., and Grishin, N. V. 2002. Evolution of protein structures and functions. Curr. Opin. Struct. Biol. 12: 400–8.
-
(2002)
Curr. Opin. Struct. Biol
, vol.12
, pp. 400-408
-
-
Kinch, L.N.1
Grishin, N.V.2
-
107
-
-
0035367071
-
Protein structure similarities
-
Koehl, P. 2001. Protein structure similarities. Curr. Opin. Struct. Biol. 11: 348–53.
-
(2001)
Curr. Opin. Struct. Biol
, vol.11
, pp. 348-353
-
-
Koehl, P.1
-
108
-
-
0037265212
-
The cath domain structure database
-
P. E. Bourne and H. Weissig, Hoboken, NJ: Wiley-Liss
-
Orengo, C. A., Pearl, F. M. G., and Thornton, J. M. 2003. “The CATH domain structure database.” In Structural Bioinformatics, edited by P. E. Bourne and H. Weissig, 249–71. Hoboken, NJ: Wiley-Liss.
-
(2003)
In Structural Bioinformatics
, pp. 249-271
-
-
Orengo, C.A.1
Pearl, F.M.G.2
Thornton, J.M.3
-
109
-
-
0038141205
-
Classification schemes for protein structure and function
-
Ouzounis, C. A., Coulson, R. M., Enright, A. J., Kunin, V., and Pereira-Leal, J. B. 2003. Classification schemes for protein structure and function. Nat. Rev. Genet. 4: 508–19.
-
(2003)
Nat. Rev. Genet
, vol.4
, pp. 508-519
-
-
Ouzounis, C.A.1
Coulson, R.M.2
Enright, A.J.3
Kunin, V.4
Pereira-Leal, J.B.5
-
110
-
-
0037263830
-
Protein structure evolution and the scop database
-
P. E. Bourne and H.Weissig, Hoboken, NJ: Wiley-Liss
-
Reddy, B. J. 2003. “Protein structure evolution and the scop database.” In Structural Bioinformatics, edited by P. E. Bourne and H.Weissig, 239–48. Hoboken, NJ: Wiley-Liss.
-
(2003)
In Structural Bioinformatics
, pp. 239-248
-
-
Reddy, B.J.1
-
111
-
-
0036154946
-
Classification of protein folds
-
Russell, R. B. 2002. Classification of protein folds. Mol. Biotechnol. 20: 17–28.
-
(2002)
Mol. Biotechnol
, vol.20
, pp. 17-28
-
-
Russell, R.B.1
-
112
-
-
0037265210
-
Molecular visualization
-
P. E. Bourne and H.Weissig, Hoboken, NJ: Wiley-Liss
-
Tate, J. 2003. “Molecular visualization.” In Structural Bioinformatics, edited by P. E. Bourne and H.Weissig, 135–58. Hoboken, NJ: Wiley-Liss.
-
(2003)
In Structural Bioinformatics
, pp. 135-158
-
-
Tate, J.1
-
113
-
-
0037323213
-
Bioinformatics methods to predict protein structure and function. A practical approach
-
Edwards, Y. J., and Cottage, A. 2003. Bioinformatics methods to predict protein structure and function. A practical approach. Mol. Biotechnol. 23: 139-66.
-
(2003)
Mol. Biotechnol
, vol.23
, pp. 139-166
-
-
Edwards, Y.J.1
Cottage, A.2
-
114
-
-
0034334542
-
Computational methods for protein secondary structure prediction using multiple sequence alignments
-
Heringa J. 2002. Computational methods for protein secondary structure prediction using multiple sequence alignments. Curr. Protein Pept. Sci. 1: 273-301.
-
(2002)
Curr. Protein Pept. Sci
, vol.1
, pp. 273-301
-
-
Heringa, J.1
-
115
-
-
20944444557
-
Computational analysis of membrane proteins: Genomic occurrence, structure prediction and helix interactions
-
Lehnert, U., Xia, Y., Royce, T. E., Goh, C. S., Liu, Y., Senes, A., Yu, H., Zhang, Z. L., Engelman, D. M, and Gerstein M. 2004. Computational analysis of membrane proteins: Genomic occurrence, structure prediction and helix interactions. Q. Rev. Biophys. 37: 121-46.
-
(2004)
Q. Rev. Biophys
, vol.37
, pp. 121-146
-
-
Lehnert, U.1
Xia, Y.2
Royce, T.E.3
Goh, C.S.4
Liu, Y.5
Senes, A.6
Yu, H.7
Zhang, Z.L.8
Engelman, D.M.9
Gerstein, M.10
-
116
-
-
0034899781
-
Evaluation of methods for the prediction of membrane spanning regions
-
Möller, S., Croning, M. D. R., and Apweiler, R. 2001. Evaluation of methods for the prediction of membrane spanning regions. Bioinformatics 17: 646-53.
-
(2001)
Bioinformatics
, vol.17
, pp. 646-653
-
-
Möller, S.1
Croning, M.D.R.2
Apweiler, R.3
-
117
-
-
0036467068
-
Alignments grow, secondary structure prediction improves
-
Przybylski, D., and Rost, B. 2002. Alignments grow, secondary structure prediction improves. Proteins 46: 197–205.
-
(2002)
Proteins
, vol.46
, pp. 197-205
-
-
Przybylski, D.1
Rost, B.2
-
118
-
-
0035782925
-
Review: Protein secondary structure prediction continues to rise
-
Rost B. 2001. Review: Protein secondary structure prediction continues to rise. J. Struct. Biol. 134: 204–18.
-
(2001)
J. Struct. Biol
, vol.134
, pp. 204-218
-
-
Rost, B.1
-
119
-
-
0037264353
-
Prediction in 1d: Secondary structure, membrane helices, and accessibility
-
P. E. Bourne and H. Weissig, Hoboken, NJ: Wiley–Liss
-
Rost B. 2003. Prediction in 1D: Secondary structure, membrane helices, and accessibility. In Structural Bioinformatics, edited by P. E. Bourne and H. Weissig, 559–87. Hoboken, NJ: Wiley–Liss.
-
(2003)
In Structural Bioinformatics
, pp. 559-587
-
-
Rost, B.1
-
120
-
-
0035252674
-
Protein structure prediction
-
Al-Lazikani, B., Jung, J., Xiang, Z., and Honig, B. 2001. Protein structure prediction. Curr. Opin. Chem. Biol. 5: 51–6.
-
(2001)
Curr. Opin. Chem. Biol
, vol.5
, pp. 51-56
-
-
Al-Lazikani, B.1
Jung, J.2
Xiang, Z.3
Honig, B.4
-
121
-
-
0035812694
-
Protein structure prediction and structural genomics
-
Baker, D., and Sali, A. 2001. Protein structure prediction and structural genomics. Science. 294: 93–6.
-
(2001)
Science
, vol.294
, pp. 93-96
-
-
Baker, D.1
Sali, A.2
-
122
-
-
0034985005
-
Ab initio protein structure prediction: Progress and prospects
-
Bonneau, R., and Baker, D. 2001. Ab initio protein structure prediction: Progress and prospects. Annu. Rev. Biophys. Biomol. Struct. 30: 173–89.
-
(2001)
Annu. Rev. Biophys. Biomol. Struct
, vol.30
, pp. 173-189
-
-
Bonneau, R.1
Baker, D.2
-
123
-
-
0037263887
-
Csap and cafasp experiments and their findings
-
P. E. Bourne and H.Weissig, Hoboken, NJ: Wiley-Liss
-
Bourne, P. E. 2003. “CSAP and CAFASP experiments and their findings.” In Structural Bioinformatics, edited by P. E. Bourne and H.Weissig, 501–7. Hoboken, NJ: Wiley-Liss.
-
(2003)
In Structural Bioinformatics
, pp. 501-507
-
-
Bourne, P.E.1
-
124
-
-
0037267910
-
Ab initio methods
-
P. E. Bourne and H.Weissig, Hoboken, NJ: Wiley-Liss
-
Chivian, D., Robertson, T., Bonneau, R., and Baker, D. 2003. “Ab initio methods.” In Structural Bioinformatics, edited by P. E. Bourne and H.Weissig, 547–56. Hoboken, NJ: Wiley-Liss.
-
(2003)
In Structural Bioinformatics
, pp. 547-556
-
-
Chivian, D.1
Robertson, T.2
Bonneau, R.3
Baker, D.4
-
125
-
-
0037323213
-
Bioinformatics methods to predict protein structure and function. A practical approach
-
Edwards, Y. J., and Cottage, A. 2003. Bioinformatics methods to predict protein structure and function. A practical approach. Mol Biotechnol. 23: 139–66.
-
(2003)
Mol Biotechnol
, vol.23
, pp. 139-166
-
-
Edwards, Y.J.1
Cottage, A.2
-
126
-
-
0036890697
-
The protein folding problem: A biophysical enigma
-
Fetrow, J. S., Giammona, A., Kolinski, A., and Skolnick, J. 2002. The protein folding problem: A biophysical enigma. Curr. Pharm. Biotechnol. 3: 329–47.
-
(2002)
Curr. Pharm. Biotechnol
, vol.3
, pp. 329-347
-
-
Fetrow, J.S.1
Giammona, A.2
Kolinski, A.3
Skolnick, J.4
-
127
-
-
0036005957
-
Molecular modelling in structural biology
-
Forster, M. J. 2000. Molecular modelling in structural biology. Micron 33: 365–84.
-
(2000)
Micron
, vol.33
, pp. 365-384
-
-
Forster, M.J.1
-
128
-
-
17144425763
-
Practical lessons from protein structure prediction
-
Ginalski, K., Grishin, N. V., Godzik, A., and Rychlewski, L. 2005. Practical lessons from protein structure prediction. Nucleic Acids Res. 33: 1874–91.
-
(2005)
Nucleic Acids Res
, vol.33
, pp. 1874-1891
-
-
Ginalski, K.1
Grishin, N.V.2
Godzik, A.3
Rychlewski, L.4
-
129
-
-
0037271276
-
Fold recognition methods
-
P. E. Bourne and H.Weissig, Hoboken, NJ: Wiley-Liss
-
Godzik, A. 2003. “Fold recognition methods.” In Structural Bioinformatics, edited by P. E. Bourne and H.Weissig, 525–46. Hoboken, NJ: Wiley-Liss.
-
(2003)
In Structural Bioinformatics
, pp. 525-546
-
-
Godzik, A.1
-
130
-
-
0036535974
-
Abinitio protein structure prediction
-
Hardin, C., Pogorelov, T. V., and Luthey-Schulten, Z. 2002. Abinitio protein structure prediction. Curr. Opin. Struct. Biol. 12: 176–81.
-
(2002)
Curr. Opin. Struct. Biol
, vol.12
, pp. 176-181
-
-
Hardin, C.1
Pogorelov, T.V.2
Luthey-Schulten, Z.3
-
131
-
-
0037264352
-
Homology modeling
-
P. E. Bourne and H.Weissig, Hoboken, NJ: Wiley-Liss
-
Krieger, E., Nabuurs, S. B., and Vriend, G. 2003. “Homology modeling.” In Structural Bioinformatics, edited by P. E. Bourne and H.Weissig, 509–23. Hoboken, NJ: Wiley-Liss.
-
(2003)
In Structural Bioinformatics
, pp. 509-523
-
-
Krieger, E.1
Nabuurs, S.B.2
Vriend, G.3
-
132
-
-
0033873929
-
Comparative protein structure modeling of genes and genomes
-
Marti-Renom, M. A., Stuart, A. C., Fiser, A., Sanchez, R., Melo, F., and Sali, A. 2000. Comparative protein structure modeling of genes and genomes. Annu. Rev. Biophys. Biomol. Struct. 29: 291–325.
-
(2000)
Annu. Rev. Biophys. Biomol. Struct
, vol.29
, pp. 291-325
-
-
Marti-Renom, M.A.1
Stuart, A.C.2
Fiser, A.3
Sanchez, R.4
Melo, F.5
Sali, A.6
-
133
-
-
0034236449
-
Computational tools for protein modeling
-
Xu, D., Xu, Y., and Uberbacher, E. C. 2000. Computational tools for protein modeling. Curr. Protein Pept. Sci. 1: 1–21.
-
(2000)
Curr. Protein Pept. Sci
, vol.1
, pp. 1-21
-
-
Xu, D.1
Xu, Y.2
Uberbacher, E.C.3
-
134
-
-
13344279384
-
Evaluation of the suitability of free-energy minimization using nearest-neighbor energy parameters for rna secondary structure prediction
-
Doshi, K. J., Cannone, J. J., Cobaugh, C. W., and Gutell, R. R. 2004. Evaluation of the suitability of free-energy minimization using nearest-neighbor energy parameters for RNA secondary structure prediction. BMC Bioinformatics 5: 105.
-
(2004)
BMC Bioinformatics
, vol.5
-
-
Doshi, K.J.1
Cannone, J.J.2
Cobaugh, C.W.3
Gutell, R.R.4
-
136
-
-
13344262673
-
A comprehensive comparison of comparative rna structure prediction approaches
-
Gardner, P. P., and Giegerich, R. 2004. A comprehensive comparison of comparative RNA structure prediction approaches. BMC Bioinformatics 5: 140.
-
(2004)
BMC Bioinformatics
, vol.5
-
-
Gardner, P.P.1
Giegerich, R.2
-
137
-
-
0035873307
-
Discovering common stem-loop motifs in unaligned rna sequences
-
Gorodkin, J., Stricklin, S. L., and Stormo, G. D. 2001. Discovering common stem-loop motifs in unaligned RNA sequences. Nucleic Acids. Res. 10: 2135–44.
-
(2001)
Nucleic Acids. Res
, vol.10
, pp. 2135-2144
-
-
Gorodkin, J.1
Stricklin, S.L.2
Stormo, G.D.3
-
138
-
-
0036760665
-
Motif prediction in ribosomal rnas lessons and prospects for automated motif prediction in homologous rna molecules
-
Leontis, N. B., Stombaugh, J., andWesthof, E. 2002.Motif prediction in ribosomal RNAs lessons and prospects for automated motif prediction in homologous RNA molecules. Biochimie 84: 961–73.
-
(2002)
Biochimie
, vol.84
, pp. 961-973
-
-
Leontis, N.B.1
Stombaugh, J.2
Andwesthof, E.3
-
139
-
-
0035367877
-
Computational methods for rna structure determination
-
Major, F., and Griffey, R. 2001. Computational methods for RNA structure determination. Curr. Opin. Struct. Biol. 11: 282–6.
-
(2001)
Curr. Opin. Struct. Biol
, vol.11
, pp. 282-286
-
-
Major, F.1
Griffey, R.2
-
140
-
-
0342962976
-
Dna and rna structure prediction
-
M. J. Bishop and C. J. Rawlings, Oxford, UK: IRL Press
-
Westhof, E., Auffinger, P., and Gaspin, C. 1997. “DNA and RNA structure prediction.: In: DNA and Protein Sequence Analysis, edited by M. J. Bishop and C. J. Rawlings, 255–78. Oxford, UK: IRL Press.
-
(1997)
In: DNA and Protein Sequence Analysis
, pp. 255-278
-
-
Westhof, E.1
Auffinger, P.2
Gaspin, C.3
-
141
-
-
0037023308
-
Opening the door to comparative plant biology
-
Bennetzen, J. 2002. Opening the door to comparative plant biology. Science 296: 60–3.
-
(2002)
Science
, vol.296
, pp. 60-63
-
-
Bennetzen, J.1
-
142
-
-
0142056169
-
An applications-focused review of comparative genomics tools: Capabilities, limitations and future challenges
-
Chain, P., Kurtz, S., Ohlebusch, E., and Slezak, T. 2003. An applications-focused review of comparative genomics tools: Capabilities, limitations and future challenges. Brief. Bioinform. 4: 105–23.
-
(2003)
Brief. Bioinform
, vol.4
, pp. 105-123
-
-
Chain, P.1
Kurtz, S.2
Ohlebusch, E.3
Slezak, T.4
-
143
-
-
0032169271
-
Conservation of gene order: A fingerprint of proteins that physically interact
-
Dandekar, T, Snel, B., Huynen, M., and Bork, P. 1998. Conservation of gene order: A fingerprint of proteins that physically interact. Trends Biochem. Sci. 23: 324–8.
-
(1998)
Trends Biochem. Sci
, vol.23
, pp. 324-328
-
-
Dandekar, T.1
Snel, B.2
Huynen, M.3
Bork, P.4
-
144
-
-
0037271322
-
Cross-species sequence comparisons: A review of methods and available resources
-
Frazer, K. A., Elnitski, L., Church, D. M., Dubchak, I., and Hardison, R. C. 2003. Cross-species sequence comparisons: A review of methods and available resources. Genome Res. 13: 1–12.
-
(2003)
Genome Res
, vol.13
, pp. 1-12
-
-
Frazer, K.A.1
Elnitski, L.2
Church, D.M.3
Dubchak, I.4
Hardison, R.C.5
-
146
-
-
0037494681
-
Genome comparisons and analysis
-
Karlin, S., Mrazek, J., and Gentles, A. J. 2003. Genome comparisons and analysis. Curr. Opin. Struct. Biol. 13: 344–52.
-
(2003)
Curr. Opin. Struct. Biol
, vol.13
, pp. 344-352
-
-
Karlin, S.1
Mrazek, J.2
Gentles, A.J.3
-
148
-
-
0037338287
-
Statistical bioinformatic methods in microbial genome analysis
-
Lio, P. 2003. Statistical bioinformatic methods in microbial genome analysis. BioEssays 25: 266–73.
-
(2003)
Bioessays
, vol.25
, pp. 266-273
-
-
Lio, P.1
-
149
-
-
0036792550
-
Protein sequence analysis in silico: Application of structure-based bioinformatics to genomic initiatives
-
Michalovich, D., Overington, J., and Fagan, R. 2002. Protein sequence analysis in silico: Application of structure-based bioinformatics to genomic initiatives. Curr. Opin. Pharmacol. 2: 574–80.
-
(2002)
Curr. Opin. Pharmacol
, vol.2
, pp. 574-580
-
-
Michalovich, D.1
Overington, J.2
Fagan, R.3
-
150
-
-
0037398488
-
Comparative genomic tools and databases: Providing insights into the human genome
-
Pennacchio, L. A., and Rubin, E. M. 2003. Comparative genomic tools and databases: Providing insights into the human genome. J. Clin. Invest. 111: 1099–106.
-
(2003)
J. Clin. Invest
, vol.111
, pp. 1099-1106
-
-
Pennacchio, L.A.1
Rubin, E.M.2
-
152
-
-
0035408587
-
Genome annotation: From sequence to biology
-
Stein, L. 2001. Genome annotation: From sequence to biology. Nat. Rev. Genetics 2: 493–503.
-
(2001)
Nat. Rev. Genetics
, vol.2
, pp. 493-503
-
-
Stein, L.1
-
153
-
-
0033991416
-
Sequence analysis of gene and genomes
-
Sterky, F., and Lundeberg, J. 2000. Sequence analysis of gene and genomes. J.Biotechnol. 76: 1–31.
-
(2000)
J.Biotechnol
, vol.76
, pp. 1-31
-
-
Sterky, F.1
Lundeberg, J.2
-
154
-
-
0037380723
-
Comparative genomics: Genome-wide analysis of metazoan eukaryotes
-
Ureta-Vidal, A., Ettwiller, L., and Birney, E. 2003. Comparative genomics: Genome-wide analysis of metazoan eukaryotes. Nature Rev. Genetics 4: 251–62.
-
(2003)
Nature Rev. Genetics
, vol.4
, pp. 251-262
-
-
Ureta-Vidal, A.1
Ettwiller, L.2
Birney, E.3
-
155
-
-
1542563409
-
Initial sequencing and comparative analysis of the mouse genome
-
Waterston, R. H., Lindblad-Toh, K., Birney, E., Rogers, J., Abril, J. F., Agarwal, P., Agarwala, R., et al. 2002. Initial sequencing and comparative analysis of the mouse genome. Nature 420: 520–62.
-
(2002)
Nature
, vol.420
, pp. 520-562
-
-
Waterston, R.H.1
Lindblad-Toh, K.2
Birney, E.3
Rogers, J.4
Abril, J.F.5
Agarwal, P.6
Agarwala, R.7
-
156
-
-
0036435802
-
Comparative genomics approaches to study organism similarities and differences
-
Wei, L., Liu, Y., Dubchak, I., Shon, J., and Park, J. 2002. Comparative genomics approaches to study organism similarities and differences. J. Biomed. Inform. 35: 142–50.
-
(2002)
J. Biomed. Inform
, vol.35
, pp. 142-150
-
-
Wei, L.1
Liu, Y.2
Dubchak, I.3
Shon, J.4
Park, J.5
-
157
-
-
0034622999
-
Molecular evidence for the early evolution of photosynthesi
-
Xiong, J., Fischer, W. M., Inoue, K., Nakahara, M., and Bauer, C. E. 2000.Molecular evidence for the early evolution of photosynthesis. Science 289: 1724–30.
-
(2000)
Science
, vol.289
, pp. 1724-1730
-
-
Xiong, J.1
Fischer, W.M.2
Inoue, K.3
Nakahara, M.4
Bauer, C.E.5
-
158
-
-
1842564359
-
-
Malden, MA: Blackwell
-
Causton, H.C., Quackenbush, J., and Brazma, A. 2003. MicroarrayGeneExpressionDataAnalysis: A Beginner’s Guide. Malden, MA: Blackwell.
-
(2003)
Microarraygeneexpressiondataanalysis: A Beginner’S Guide
-
-
Causton, H.C.1
Quackenbush, J.2
Brazma, A.3
-
159
-
-
0042353903
-
Experiments using microarray technology: Limitations and standard operating procedure
-
Forster, T., Roy, D., and Ghazal, P. 2003. Experiments using microarray technology: Limitations and standard operating procedure. J. Endocrinol. 178: 195–204.
-
(2003)
J. Endocrinol
, vol.178
, pp. 195-204
-
-
Forster, T.1
Roy, D.2
Ghazal, P.3
-
160
-
-
0033648987
-
Rapid in silico cloning of genes using expressed sequence tags (ests)
-
Gill, R.W., and Sanseau, P. 2000. Rapid in silico cloning of genes using expressed sequence tags (ESTs). Biotechnol. Annu. Rev. 5: 25–44.
-
(2000)
Biotechnol. Annu. Rev
, vol.5
, pp. 25-44
-
-
Gill, R.W.1
Sanseau, P.2
-
161
-
-
0036898577
-
Microarray data normalizationandtransformation
-
Quackenbush, J. 2002.Microarray data normalizationandtransformation. Nat Genet. 32(Suppl): 496–501.
-
(2002)
Nat Genet
, vol.32
, pp. 496-501
-
-
Quackenbush, J.1
-
162
-
-
0035233085
-
Global transcript expression profiling by serial analysis of gene expression (sage)
-
Scott, H. S., and Chrast, R. 2001.Global transcript expression profiling by Serial Analysis of Gene Expression (SAGE). Genet. Eng. 23: 201–19.
-
(2001)
Genet. Eng
, vol.23
, pp. 201-219
-
-
Scott, H.S.1
Chrast, R.2
-
163
-
-
0036899286
-
From patterns to pathways: Gene expression data analysis comes of age
-
Slonim, D. K. 2002. From patterns to pathways: Gene expression data analysis comes of age. Nat. Genet. 32(Suppl): 502–8.
-
(2002)
Nat. Genet
, vol.32
, pp. 502-508
-
-
Slonim, D.K.1
-
164
-
-
0034880790
-
Methods to profile gene expression
-
Stanton, L.W. 2001.Methods to profile gene expression. Trends Cardiovasc. Med. 11: 49–54.
-
(2001)
Trends Cardiovasc. Med
, vol.11
, pp. 49-54
-
-
Stanton, L.W.1
-
165
-
-
1242300778
-
-
Cambridge, UK: Cambridge University Press
-
Stekel, D. 2003. Microarray Bioinformatics. Cambridge, UK: Cambridge University Press.
-
(2003)
Microarray Bioinformatics
-
-
Stekel, D.1
-
166
-
-
0036728931
-
Gene expression profiling of human diseases by serial analysis of gene expression
-
Ye, S. Q., Usher, D. C., and Zhang, L. Q. 2002. Gene expression profiling of human diseases by serial analysis of gene expression. J. Biomed. Sci. 9: 384–94.
-
(2002)
J. Biomed. Sci
, vol.9
, pp. 384-394
-
-
Ye, S.Q.1
Usher, D.C.2
Zhang, L.Q.3
-
167
-
-
0037435030
-
Mass spectrometry-based proteomics
-
Aebersold, R., andMann, M. 2003.Mass spectrometry-based proteomics. Nature 422: 198–207.
-
(2003)
Nature
, vol.422
, pp. 198-207
-
-
Aebersold, R.1
Andmann, M.2
-
168
-
-
0037253089
-
Protein arrays: The current state-of-the-art
-
Cutler, P. 2003. Protein arrays: The current state-of-the-art. Proteomics 3: 3–18.
-
(2003)
Proteomics
, vol.3
, pp. 3-18
-
-
Cutler, P.1
-
169
-
-
24644450611
-
Predicting protein subcellular localization: Past, present, and future
-
Donnes, P., andHoglund, A. 2004. Predicting protein subcellular localization: past, present, and future. Genomics Proteomics Bioinformatics 2: 209–15.
-
(2004)
Genomics Proteomics Bioinformatics
, vol.2
, pp. 209-215
-
-
Donnes, P.1
Andhoglund, A.2
-
170
-
-
17844389616
-
Experimental and bioinformatic approaches for interrogating protein-protein interactions to determine protein function
-
Droit, A., Poirier, G. G., and Hunter, J.M. 2005. Experimental and bioinformatic approaches for interrogating protein-protein interactions to determine protein function. J.Mol. Endocrinol. 34: 263–80.
-
(2005)
J.Mol. Endocrinol
, vol.34
, pp. 263-280
-
-
Droit, A.1
Poirier, G.G.2
Hunter, J.M.3
-
171
-
-
0344376550
-
Prediction of post-translational modifications from amino acid sequence: Problems, pitfalls, and methodological hints
-
M. A. Andrade, Wymondham, UK: Horizon Scientific Press
-
Eisenhaber, F., Eisenhaber, B., and Maurer-Stroh, S. 2003. “Prediction of post-translational modifications from amino acid sequence: Problems, pitfalls, and methodological hints.” In Bioinformatics and Genomes: Current Perspectives, edited by M. A. Andrade, 81–105.Wymondham, UK: Horizon Scientific Press.
-
(2003)
In Bioinformatics and Genomes: Current Perspectives
, pp. 81-105
-
-
Eisenhaber, F.1
Eisenhaber, B.2
Maurer-Stroh, S.3
-
172
-
-
0141872898
-
Predicting protein subcellular localisation from amino acid sequence information
-
Emanuelsson, O. 2002. Predicting protein subcellular localisation from amino acid sequence information. Brief. Bioinform. 3: 361–76.
-
(2002)
Brief. Bioinform
, vol.3
, pp. 361-376
-
-
Emanuelsson, O.1
-
173
-
-
0037377181
-
Function prediction and protein networks
-
Huynen, M. A., Snel, B., Mering, C., and Bork, P. 2003. Function prediction and protein networks. Curr. Opin. Cell Biol. 15: 191–8.
-
(2003)
Curr. Opin. Cell Biol
, vol.15
, pp. 191-198
-
-
Huynen, M.A.1
Snel, B.2
Mering, C.3
Bork, P.4
-
174
-
-
0037338365
-
Proteomic analysis of post-translational modifications
-
Mann, M., and Jensen, O. N. 2003. Proteomic analysis of post-translational modifications. Nature Biotechnol. 21: 255–61.
-
(2003)
Nature Biotechnol
, vol.21
, pp. 255-261
-
-
Mann, M.1
Jensen, O.N.2
-
175
-
-
0033909566
-
Protein sorting signals and prediction of subcellular localization
-
Nakai, K. 2000. Protein sorting signals and prediction of subcellular localization. Adv. Protein Chem. 54: 277–344.
-
(2000)
Adv. Protein Chem
, vol.54
, pp. 277-344
-
-
Nakai, K.1
-
176
-
-
0035782686
-
Review: Prediction of in vivo fates of proteins in the era of genomics and proteomics
-
Nakai, K. 2001. Review: Prediction of in vivo fates of proteins in the era of genomics and proteomics. J. Struct. Biol. 134: 103–16.
-
(2001)
J. Struct. Biol
, vol.134
, pp. 103-116
-
-
Nakai, K.1
-
177
-
-
0037435022
-
Protein analysis on a proteomic scale
-
Phizicky, E., Bastiaens, P. I. H., Zhu, H., Snyder, M., and Fields, S. 2003. Protein analysis on a proteomic scale. Nature 422: 208–15.
-
(2003)
Nature
, vol.422
, pp. 208-215
-
-
Phizicky, E.1
Bastiaens, P.I.H.2
Zhu, H.3
Snyder, M.4
Fields, S.5
-
178
-
-
18744398125
-
Large-scale database searching using tandem mass spectra: Looking up the answer in the back of the book
-
Sadygov, R. G., Cociorva, D., and Yates, J. R. III. 2004. Large-scale database searching using tandem mass spectra: Looking up the answer in the back of the book. Nat. Methods 1: 195–202.
-
(2004)
Nat. Methods
, vol.1
, pp. 195-202
-
-
Sadygov, R.G.1
Cociorva, D.2
Yates, J.R.3
-
179
-
-
0037434980
-
From genomics to proteomics
-
Tyers, M., andMann, M. 2003. From genomics to proteomics. Nature 422: 193–7.
-
(2003)
Nature
, vol.422
, pp. 193-197
-
-
Tyers, M.1
Andmann, M.2
-
180
-
-
0036601150
-
Computational methods for the prediction of protein interactions
-
Valencia, A., and Pazos, F. 2002. Computational methods for the prediction of protein interactions. Curr. Opin. Struct. Biol. 12: 368–73.
-
(2002)
Curr. Opin. Struct. Biol
, vol.12
, pp. 368-373
-
-
Valencia, A.1
Pazos, F.2
-
181
-
-
0037265213
-
Prediction of protein-protein interactions from evolutionary information
-
Valencia, A., and Pazos, F. 2003. Prediction of protein-protein interactions from evolutionary information. Methods Biochem. Anal. 44: 411–26.
-
(2003)
Methods Biochem. Anal
, vol.44
, pp. 411-426
-
-
Valencia, A.1
Pazos, F.2
|