-
1
-
-
2042437650
-
The International Human Genome Sequencing Consortium Initial sequencing and analysis of the human genome
-
The International Human Genome Sequencing Consortium (2001) Initial sequencing and analysis of the human genome. Nature, 409, 860-921.
-
(2001)
Nature
, vol.409
, pp. 860-921
-
-
-
2
-
-
0034649566
-
The Arabidopsis Genome Initiative Analysis of the genome sequence of the flowering plant Arabidopsis thaliana
-
The Arabidopsis Genome Initiative (2000) Analysis of the genome sequence of the flowering plant Arabidopsis thaliana. Nature, 408, 796-815.
-
(2000)
Nature
, vol.408
, pp. 796-815
-
-
-
3
-
-
0037023349
-
A draft sequence of the rice genome (Oryza sativa L. ssp. japonica)
-
Goff,S.A., Ricke,D., Lan,T.H, Presting,G., Wang,R., Dunn,M., Glazebrook,J., Sessions,A., Oeller,P., Varma,H. et al. (2002). A draft sequence of the rice genome (Oryza sativa L. ssp. japonica). Science, 296, 92-100.
-
(2002)
Science
, vol.296
, pp. 92-100
-
-
Goff, S.A.1
Ricke, D.2
Lan, T.H.3
Presting, G.4
Wang, R.5
Dunn, M.6
Glazebrook, J.7
Sessions, A.8
Oeller, P.9
Varma, H.10
-
4
-
-
0034708758
-
A whole-genome assembly of Drosophila
-
Myers,E., Sutton,G., Delcher,A., Dew,I., Fasulo,D., Flanigan,M., Kravitz,S,. Mobarry,C., Reinert,K., Remington,K., et al. (2000) A whole-genome assembly of Drosophila. Science, 287, 2196-2204.
-
(2000)
Science
, vol.287
, pp. 2196-2204
-
-
Myers, E.1
Sutton, G.2
Delcher, A.3
Dew, I.4
Fasulo, D.5
Flanigan, M.6
Kravitz, S.7
Mobarry, C.8
Reinert, K.9
Remington, K.10
-
5
-
-
0031298796
-
The difficulty of identifying genes in anonymous vertebrate sequences
-
Claverie,J.M., Poirot,O. and Lopez,F. (1997) The difficulty of identifying genes in anonymous vertebrate sequences. Comput. Chem., 21, 203-214.
-
(1997)
Comput. Chem
, vol.21
, pp. 203-214
-
-
Claverie, J.M.1
Poirot, O.2
Lopez, F.3
-
6
-
-
0035313211
-
Computational methods for gene annotation: The Arabidopsis genome
-
Cho,Y. and Walbot,V. (2001) Computational methods for gene annotation: the Arabidopsis genome. Curr. Opin. Biotechnol., 12, 126-130.
-
(2001)
Curr. Opin. Biotechnol
, vol.12
, pp. 126-130
-
-
Cho, Y.1
Walbot, V.2
-
7
-
-
0028004414
-
Intrinsic and and extrinsic approached for detecting genes in a bacterial genome
-
Borodovsky,M., Rudd,K.E. and Koonin,E.V. (1994) Intrinsic and and extrinsic approached for detecting genes in a bacterial genome. Nucleic Acids Res., 22, 4756-4767.
-
(1994)
Nucleic Acids Res
, vol.22
, pp. 4756-4767
-
-
Borodovsky, M.1
Rudd, K.E.2
Koonin, E.V.3
-
8
-
-
0000377189
-
The gene identification problem: An overview for developer
-
Fickett,J.W. (1996) The gene identification problem: an overview for developer. Comput. Chem., 20, 103-118.
-
(1996)
Comput. Chem
, vol.20
, pp. 103-118
-
-
Fickett, J.W.1
-
9
-
-
0033118642
-
Genome annotation: Which tools do we have for it?
-
Rouzé,P., Pavy,N. and Rombauts,S. (1999) Genome annotation: which tools do we have for it? Curr. Opin. Plant Biol., 2, 90-95.
-
(1999)
Curr. Opin. Plant Biol
, vol.2
, pp. 90-95
-
-
Rouzé, P.1
Pavy, N.2
Rombauts, S.3
-
10
-
-
0030218799
-
Finding genes by computer: The state of the art
-
Fickett,J.W. (1996) Finding genes by computer: the state of the art. Trends Genet., 12, 316-320.
-
(1996)
Trends Genet
, vol.12
, pp. 316-320
-
-
Fickett, J.W.1
-
11
-
-
0030768930
-
Computational methods for the identification of genes in vertebrate genomic sequences
-
Claverie,J.M. (1997) Computational methods for the identification of genes in vertebrate genomic sequences. Hum. Mol. Genet., 6, 1735-1744.
-
(1997)
Hum. Mol. Genet
, vol.6
, pp. 1735-1744
-
-
Claverie, J.M.1
-
12
-
-
0031298797
-
Computational gene identification: An open problem
-
Guigó,R. (1997) Computational gene identification: an open problem. Comput. Chem., 21, 215-222.
-
(1997)
Comput. Chem
, vol.21
, pp. 215-222
-
-
Guigó, R.1
-
13
-
-
11544300316
-
Computational genefinding
-
Haussler,D. (1998) Computational genefinding. Trends Biochem. Sci., 12-15.
-
(1998)
Trends Biochem. Sci
, pp. 12-15
-
-
Haussler, D.1
-
15
-
-
0030585734
-
Evaluation of gene structure prediction programs
-
Burset,M. and Guigó,R. (1996) Evaluation of gene structure prediction programs. Genomics, 34, 353-367.
-
(1996)
Genomics
, vol.34
, pp. 353-367
-
-
Burset, M.1
Guigó, R.2
-
16
-
-
0035002807
-
Evaluation of gene-finding programs on mammalian sequences
-
Rogic,S., Mackworth,A. and Ouellette,F. (2001) Evaluation of gene-finding programs on mammalian sequences. Genome Res., 11, 817-832.
-
(2001)
Genome Res
, vol.11
, pp. 817-832
-
-
Rogic, S.1
Mackworth, A.2
Ouellette, F.3
-
17
-
-
0033381623
-
Evaluation of gene prediction software using a genomic data set: Application to Arabidopsis thaliana sequences
-
Pavy,N., Rombauts,S., Déhais,P., Mathé,C., Ramana,D.V.V., Leroy,P. and Rouzé,P. (1999) Evaluation of gene prediction software using a genomic data set: application to Arabidopsis thaliana sequences. Bioinformatics, 15, 887-899.
-
(1999)
Bioinformatics
, vol.15
, pp. 887-899
-
-
Pavy, N.1
Rombauts, S.2
Déhais, P.3
Mathé, C.4
Ramana, D.V.V.5
Leroy, P.6
Rouzé, P.7
-
18
-
-
0036207282
-
Untranslated regions of mRNAs
-
reviews0004.1-0004.10
-
Mignone,F., Gissi,C., Liuni,S. and Pesole,G. (2002) Untranslated regions of mRNAs. Genome Biol., 3, reviews0004.1-0004.10.
-
(2002)
Genome Biol
, vol.3
-
-
Mignone, F.1
Gissi, C.2
Liuni, S.3
Pesole, G.4
-
19
-
-
0023989064
-
Improved tools for biological sequence comparison
-
Pearson,W.R. and Lipman,D.J. (1988) Improved tools for biological sequence comparison. Proc. Natl Acad. Sci. USA, 85, 2444-2448.
-
(1988)
Proc. Natl Acad. Sci. USA
, vol.85
, pp. 2444-2448
-
-
Pearson, W.R.1
Lipman, D.J.2
-
20
-
-
0025183708
-
Basic local alignment search tool
-
Altschul,S.F., Gish,W., Miller,W., Myers,E.W. and Lipman,D.J. (1990) 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
-
21
-
-
2642630755
-
Analysis of EST-driven gene annotation in human genomic sequence
-
Bailey,L.C., Searls,D.B. and Overton,G.C. (1998) Analysis of EST-driven gene annotation in human genomic sequence. Genome Res., 8, 362-376.
-
(1998)
Genome Res
, vol.8
, pp. 362-376
-
-
Bailey, L.C.1
Searls, D.B.2
Overton, G.C.3
-
22
-
-
0029259041
-
ORFs and genes: How strong a connection?
-
Fickett,J.W. (1995) ORFs and genes: how strong a connection? J. Comput. Biol., 2, 117-123.
-
(1995)
J. Comput. Biol
, vol.2
, pp. 117-123
-
-
Fickett, J.W.1
-
23
-
-
0027059264
-
Assessment of protein coding measures
-
Fickett J.W. and Tung,C.S. (1992) Assessment of protein coding measures. Nucleic Acids Res., 20, 6441-6450.
-
(1992)
Nucleic Acids Res
, vol.20
, pp. 6441-6450
-
-
Fickett, J.W.1
Tung, C.S.2
-
24
-
-
0026623434
-
The prediction of exons through an analysis of spliceable open reading frames
-
Hutchinson,G.B. and Hayden,M.R. (1992) The prediction of exons through an analysis of spliceable open reading frames. Nucleic Acids Res., 20, 3453-3462.
-
(1992)
Nucleic Acids Res
, vol.20
, pp. 3453-3462
-
-
Hutchinson, G.B.1
Hayden, M.R.2
-
25
-
-
0001785052
-
GenView: A computing tool for protein-coding regions prediction in nucleotide sequences
-
Lim,H.A., Fickett,J.W., Cantor,C.R. and Robbins,R.J. (eds), Proceedings of the Second International Conference on Bioinformatics, Supercomputing and Complex Genome Analysis. World Scientific Publishing, Singapore
-
Milanesi,L., Kolchanov,N.A., Rogozin,I.B., Ischenko,I.V., Kel,A.E., Orlov,Y.L., Ponomarenko,M.P. and Vezzoni,P. (1993) GenView: a computing tool for protein-coding regions prediction in nucleotide sequences. In Lim,H.A., Fickett,J.W., Cantor,C.R. and Robbins,R.J. (eds), Proceedings of the Second International Conference on Bioinformatics, Supercomputing and Complex Genome Analysis. World Scientific Publishing, Singapore, pp. 573-588.
-
(1993)
, pp. 573-588
-
-
Milanesi, L.1
Kolchanov, N.A.2
Rogozin, I.B.3
Ischenko, I.V.4
Kel, A.E.5
Orlov, Y.L.6
Ponomarenko, M.P.7
Vezzoni, P.8
-
26
-
-
0031027525
-
Identification of protein coding regions in the human genome by quadratic discriminant analysis
-
[Erratum (1997) Proc. Natl Acad. Sci. USA, 94, 5495]
-
Zhang,M.Q. (1997) Identification of protein coding regions in the human genome by quadratic discriminant analysis. Proc. Natl Acad. Sci. USA, 94, 565-568. [Erratum (1997) Proc. Natl Acad. Sci. USA, 94, 5495]
-
(1997)
Proc. Natl Acad. Sci. USA
, vol.94
, pp. 565-568
-
-
Zhang, M.Q.1
-
27
-
-
0028965444
-
Identification of protein coding regions in genomic DNA
-
Snyder,E.E. and Stormo,G.D. (1995) Identification of protein coding regions in genomic DNA. J. Mol. Biol., 248, 1-18.
-
(1995)
J. Mol. Biol
, vol.248
, pp. 1-18
-
-
Snyder, E.E.1
Stormo, G.D.2
-
28
-
-
0030627562
-
The Gene-Finder computer tools for analysis of human and model organisms genome sequences
-
Gaasterland,T., Karp,P., Karplus,K. Ouzounis,C., Sander,C. and Valencia,A. (eds), The Fifth International Conference on Intelligent Systems for Molecular Biology. AAAI Press, Menlo Park, CA
-
Solovyev,V. and Salamov,A. (1997) The Gene-Finder computer tools for analysis of human and model organisms genome sequences. In Gaasterland,T., Karp,P., Karplus,K. Ouzounis,C., Sander,C. and Valencia,A. (eds), The Fifth International Conference on Intelligent Systems for Molecular Biology. AAAI Press, Menlo Park, CA, pp. 294-302.
-
(1997)
, pp. 294-302
-
-
Solovyev, V.1
Salamov, A.2
-
29
-
-
0000241874
-
GENMARK: Parallel gene recognition for both DNA strands
-
Borodovsky,M. and McIninch,J. (1993) GENMARK: parallel gene recognition for both DNA strands. Comput. Chem., 17, 123-133.
-
(1993)
Comput. Chem
, vol.17
, pp. 123-133
-
-
Borodovsky, M.1
McIninch, J.2
-
30
-
-
0031586003
-
Prediction of complete gene structures in human genomic DNA
-
Burge,C. and Karlin,S. (1997) Prediction of complete gene structures in human genomic DNA. J. Mol. Biol., 268, 78-94.
-
(1997)
J. Mol. Biol
, vol.268
, pp. 78-94
-
-
Burge, C.1
Karlin, S.2
-
31
-
-
84959057192
-
EuGène: An eukaryotic gene finder that combines several sources of evidence
-
Gascuel,O. and Sagot,M.-F. (eds), First International Conference on Biology, Informatics, and Mathematics, JOBIM 2000. Springer-Verlag, Germany
-
Schiex,T., Moisan,A. and Rouzé,P. (2001) EuGène: an eukaryotic gene finder that combines several sources of evidence. In Gascuel,O. and Sagot,M.-F. (eds), Lecture Notes in Computer Science, Vol. 2006, First International Conference on Biology, Informatics, and Mathematics, JOBIM 2000. Springer-Verlag, Germany, pp. 111-125.
-
(2001)
Lecture Notes in Computer Science
, vol.2006
, pp. 111-125
-
-
Schiex, T.1
Moisan, A.2
Rouzé, P.3
-
32
-
-
0032518163
-
Microbial gene identification using interpolated Markov models
-
Salzberg,S. Delcher,A. Kasif,S. and White,O. (1998) Microbial gene identification using interpolated Markov models. Nucleic Acids Res., 26, 544-548.
-
(1998)
Nucleic Acids Res
, vol.26
, pp. 544-548
-
-
Salzberg, S.1
Delcher, A.2
Kasif, S.3
White, O.4
-
33
-
-
0033166634
-
Interpolated Markov models for eukaryotic gene finding
-
Salzberg,S.L., Pertea,M., Delcher,A.L., Gardner,M.J and Tettelin,H. (1999) Interpolated Markov models for eukaryotic gene finding. Genomics, 59, 24-31.
-
(1999)
Genomics
, vol.59
, pp. 24-31
-
-
Salzberg, S.L.1
Pertea, M.2
Delcher, A.L.3
Gardner, M.J.4
Tettelin, H.5
-
34
-
-
0033485517
-
Improve microbial gene identification with GLIMMER
-
Delcher,A.L., Harmon,D., Kasif,S. White,O. and Salzberg S.L. (1999) Improve microbial gene identification with GLIMMER. Nucleic Acids Res., 27, 4636-4641.
-
(1999)
Nucleic Acids Res
, vol.27
, pp. 4636-4641
-
-
Delcher, A.L.1
Harmon, D.2
Kasif, S.3
White, O.4
Salzberg, S.L.5
-
35
-
-
0032519353
-
GeneMark.hmm: New solutions for gene findings
-
Lukashin,A.V. and Borodovsky,M. (1998) GeneMark.hmm: new solutions for gene findings. Nucleic Acids Res., 26, 1107-1115.
-
(1998)
Nucleic Acids Res
, vol.26
, pp. 1107-1115
-
-
Lukashin, A.V.1
Borodovsky, M.2
-
36
-
-
0024805395
-
The isochore organization of the human genome
-
Bernardi,G. (1989) The isochore organization of the human genome. Annu. Rev. Genet., 23, 637-661.
-
(1989)
Annu. Rev. Genet
, vol.23
, pp. 637-661
-
-
Bernardi, G.1
-
37
-
-
0025361547
-
Gene distribution and isochore organization in the nuclear genome of plants
-
Montero,L.M., Salinas,J., Malassi,G. and Bernardi,G. (1990) Gene distribution and isochore organization in the nuclear genome of plants. Nucleic Acids Res., 18, 1859-1867.
-
(1990)
Nucleic Acids Res
, vol.18
, pp. 1859-1867
-
-
Montero, L.M.1
Salinas, J.2
Malassi, G.3
Bernardi, G.4
-
38
-
-
0028963020
-
Statistical analysis of vertebrate sequences reveals that long genes are scarce in GC-rich isochores
-
Duret,L., Mouchiroud,D. and Gautier,C. (1995) Statistical analysis of vertebrate sequences reveals that long genes are scarce in GC-rich isochores. J. Mol. Evol., 40, 308-317.
-
(1995)
J. Mol. Evol
, vol.40
, pp. 308-317
-
-
Duret, L.1
Mouchiroud, D.2
Gautier, C.3
-
39
-
-
0030787856
-
Analysis of donor splice signals in different organisms
-
Rogozin,I.B., and Milanesi,L. (1997) Analysis of donor splice signals in different organisms. J. Mol. Evol., 45, 50-59.
-
(1997)
J. Mol. Evol
, vol.45
, pp. 50-59
-
-
Rogozin, I.B.1
Milanesi, L.2
-
40
-
-
0029822410
-
Logitlinear models for the prediction of splice sites in plant pre-mRNA sequences
-
Kleffe,J., Hermann,K., Vahrson,W., Wittig,B. and Brendel,V. (1996) Logitlinear models for the prediction of splice sites in plant pre-mRNA sequences. Nucleic Acids Res., 24, 4709-4718.
-
(1996)
Nucleic Acids Res
, vol.24
, pp. 4709-4718
-
-
Kleffe, J.1
Hermann, K.2
Vahrson, W.3
Wittig, B.4
Brendel, V.5
-
41
-
-
0025744474
-
Prediction of human mRNA donor and acceptor sites from the DNA sequence
-
Brunak,S., Engelbrecht,J. and Knudsen,S. (1991) Prediction of human mRNA donor and acceptor sites from the DNA sequence. J. Mol. Biol., 220, 49-65.
-
(1991)
J. Mol. Biol
, vol.220
, pp. 49-65
-
-
Brunak, S.1
Engelbrecht, J.2
Knudsen, S.3
-
42
-
-
0029791403
-
Splice site prediction in Arabidopsis thaliana pre mRNA by combining local and global sequence information
-
Hebsgaard,S.M., Korning,P.G., Tolstrup,N., Engelbrecht,J., Rouzé,P. and Brunak,S. (1996) Splice site prediction in Arabidopsis thaliana pre mRNA by combining local and global sequence information. Nucleic Acids Res., 24, 3439-3452.
-
(1996)
Nucleic Acids Res
, vol.24
, pp. 3439-3452
-
-
Hebsgaard, S.M.1
Korning, P.G.2
Tolstrup, N.3
Engelbrecht, J.4
Rouzé, P.5
Brunak, S.6
-
43
-
-
0030878280
-
A branch point consensus from Arabidopsis found by non-circular analysis allows for better prediction of acceptor sites
-
Tolstrup,N., Rouzé,P. and Brunak,S. (1997) A branch point consensus from Arabidopsis found by non-circular analysis allows for better prediction of acceptor sites. Nucleic Acids Res., 25, 3159-3163.
-
(1997)
Nucleic Acids Res
, vol.25
, pp. 3159-3163
-
-
Tolstrup, N.1
Rouzé, P.2
Brunak, S.3
-
44
-
-
0030713573
-
Improved splice site detection in Genie
-
Istrail,S., Pevzner,P. and Waterman,M. (eds), (RECOMB). ACM Press, New York, NY
-
Reese,M.G., Eeckman,F.H., Kulp,D. and Haussler,D. (1997) Improved splice site detection in Genie. In Istrail,S., Pevzner,P. and Waterman,M. (eds), First Annual International Conference on Computational Molecular Biology (RECOMB). ACM Press, New York, NY, pp. 232-240.
-
(1997)
First Annual International Conference on Computational Molecular Biology
, pp. 232-240
-
-
Reese, G.1
Eeckman, F.H.2
Kulp, D.3
Haussler, D.4
-
45
-
-
0027377256
-
A weight array method for splicing signal analysis
-
Zhang,M.Q. and Marr,T.G. (1993) A weight array method for splicing signal analysis. Comput. Appl. Biosci., 9, 499-509.
-
(1993)
Comput. Appl. Biosci
, vol.9
, pp. 499-509
-
-
Zhang, M.Q.1
Marr, T.G.2
-
46
-
-
0030869663
-
A method for identifying splice sites and translational start sites in eukaryotic mRNA
-
Salzberg,S.L. (1997) A method for identifying splice sites and translational start sites in eukaryotic mRNA. Comput. Appl. Biosci., 13, 365-376.
-
(1997)
Comput. Appl. Biosci
, vol.13
, pp. 365-376
-
-
Salzberg, S.L.1
-
47
-
-
0030810993
-
Finding genes in human DNA with a hidden Markov model
-
Henderson,J., Salzberg,S. and Fasman,K. (1997) Finding genes in human DNA with a hidden Markov model. J. Comput. Biol., 4, 127-141.
-
(1997)
J. Comput. Biol
, vol.4
, pp. 127-141
-
-
Henderson, J.1
Salzberg, S.2
Fasman, K.3
-
48
-
-
0032449018
-
A decision tree system for finding genes in DNA
-
Salzberg,S., Delcher,A., Fasman,K. and Henderson,J. (1998) A decision tree system for finding genes in DNA. J. Comput. Biol., 5, 667-680.
-
(1998)
J. Comput. Biol
, vol.5
, pp. 667-680
-
-
Salzberg, S.1
Delcher, A.2
Fasman, K.3
Henderson, J.4
-
49
-
-
0024610919
-
A tutorial on hidden Markov models and selected applications for speech recognition
-
Rabiner,L.R. (1989) A tutorial on hidden Markov models and selected applications for speech recognition. Proc. IEEE, 77, 257-285.
-
(1989)
Proc. IEEE
, vol.77
, pp. 257-285
-
-
Rabiner, L.R.1
-
50
-
-
0002430987
-
An introduction to hidden Markov models for biological sequences
-
Salzberg,S.L., Searls,D.B. and Kasif,S. (eds), Elsevier, Amsterdam, The Netherlands
-
Krogh,A. (1998) An introduction to hidden Markov models for biological sequences. In Salzberg,S.L., Searls,D.B. and Kasif,S. (eds), Computational Methods in Molecular Biology. Elsevier, Amsterdam, The Netherlands, pp. 46-63.
-
(1998)
Computational Methods in Molecular Biology
, pp. 46-63
-
-
Krogh, A.1
-
51
-
-
0036371458
-
Pre-mRNA secondary structure prediction aids splice site prediction
-
Altman,R.B., Dunker,A.K., Hunter,L., Lauderdale,K. and Klein,T.E. (eds), World Scientific, Singapore
-
Patterson,D.J., Yasuhara,K. and Ruzzo,W.L. (2002) Pre-mRNA secondary structure prediction aids splice site prediction. In Altman,R.B., Dunker,A.K., Hunter,L., Lauderdale,K. and Klein,T.E. (eds), Pacific Symposium on Biocomputing, Vol. 7, World Scientific, Singapore, pp. 223-234.
-
(2002)
Pacific Symposium on Biocomputing
, vol.7
, pp. 223-234
-
-
Patterson, D.J.1
Yasuhara, K.2
Ruzzo, W.L.3
-
52
-
-
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
-
53
-
-
0033563512
-
The biology of eukaryotic promoter prediction - A review
-
Pedersen,A.G., Baldi,P., Chauvin,Y. and Brunak,S. (1999) The biology of eukaryotic promoter prediction - a review. Comput. Chem., 23, 191-207.
-
(1999)
Comput. Chem
, vol.23
, pp. 191-207
-
-
Pedersen, A.G.1
Baldi, P.2
Chauvin, Y.3
Brunak, S.4
-
54
-
-
0030627982
-
Neural network prediction of translation initiation sites in eukaryotes: Perspectives for EST and genome analysis
-
Gaasterland,T., Karp,P., Karplus,K., Ouzounis,C., Sander,C. and Valencia,A. (eds), AAAI Press, Menlo Park, CA
-
Pedersen,A.G. and Nielsen,H. (1997) Neural network prediction of translation initiation sites in eukaryotes: perspectives for EST and genome analysis. In Gaasterland,T., Karp,P., Karplus,K., Ouzounis,C., Sander,C. and Valencia,A. (eds), The Fifth International Conference on Intelligent Systems for Molecular Biology. AAAI Press, Menlo Park, CA, pp. 226-233.
-
(1997)
The Fifth International Conference on Intelligent Systems for Molecular Biology
, pp. 226-233
-
-
Pedersen, A.G.1
Nielsen, H.2
-
55
-
-
0033670134
-
Engineering support vector machine kernels that recognize translation initiation sites
-
Zien,A., Ratsch,G., Mika,S., Scholkopf,B., Lengauer,T. and Muller,K. (2000) Engineering support vector machine kernels that recognize translation initiation sites. Bioinformatics, 16, 799-807.
-
(2000)
Bioinformatics
, vol.16
, pp. 799-807
-
-
Zien, A.1
Ratsch, G.2
Mika, S.3
Scholkopf, B.4
Lengauer, T.5
Muller, K.6
-
56
-
-
0034521884
-
Prediction whether a human cDNA sequence contains initiation codon by combining statistical information and similarity with protein sequences
-
Nishikawa,T., Ota,T. and Isogai,T. (2000) Prediction whether a human cDNA sequence contains initiation codon by combining statistical information and similarity with protein sequences. Bioinformatics, 16, 960-967.
-
(2000)
Bioinformatics
, vol.16
, pp. 960-967
-
-
Nishikawa, T.1
Ota, T.2
Isogai, T.3
-
57
-
-
0025040574
-
gm: A practical tool for automating DNA sequence analysis
-
Fields,C.A. and Soderlund,C.A. (1990) gm: a practical tool for automating DNA sequence analysis. Comput. Appl. Biosci., 6, 263-270.
-
(1990)
Comput. Appl. Biosci
, vol.6
, pp. 263-270
-
-
Fields, C.A.1
Soderlund, C.A.2
-
58
-
-
0025000924
-
Computer prediction of the exon-intron structure of mammalian pre-mRNAs
-
Gelfand,M.S. (1990) Computer prediction of the exon-intron structure of mammalian pre-mRNAs. Nucleic Acids Res., 18, 5865-5869.
-
(1990)
Nucleic Acids Res
, vol.18
, pp. 5865-5869
-
-
Gelfand, M.S.1
-
59
-
-
0029830044
-
Gene recognition via spliced sequence alignment
-
Gelfand,M.S., Mironov,A.A. and Pevzner,P.A. (1996) Gene recognition via spliced sequence alignment. Proc. Natl Acad. Sci. USA, 93, 9061-9066.
-
(1996)
Proc. Natl Acad. Sci. USA
, vol.93
, pp. 9061-9066
-
-
Gelfand, M.S.1
Mironov, A.A.2
Pevzner, P.A.3
-
60
-
-
0030628597
-
Dynamite; a flexible code generating language for dynamic programming methods need in sequence comparison
-
Birney,E. and Durbin,R. (1997) Dynamite; a flexible code generating language for dynamic programming methods need in sequence comparison. Proc. Int. Conf. Intell. Syst. Mol. Biol., 5, 56-64.
-
(1997)
Proc. Int. Conf. Intell. Syst. Mol. Biol
, vol.5
, pp. 56-64
-
-
Birney, E.1
Durbin, R.2
-
61
-
-
0029955046
-
Gene structure prediction using information on homologous protein sequence
-
Rogozin,I.B. Milanesi,L. and Kolchanov,N.A. (1996) Gene structure prediction using information on homologous protein sequence. Comput. Appl. Biosci., 12, 161-170.
-
(1996)
Comput. Appl. Biosci
, vol.12
, pp. 161-170
-
-
Rogozin, I.B.1
Milanesi, L.2
Kolchanov, N.A.3
-
62
-
-
0034129662
-
Homology-based gene structure prediction: Simplified matching algorithm using a translated codon (tron) and improved accuracy by allowing for long gaps
-
Gotoh,O. (2000) Homology-based gene structure prediction: simplified matching algorithm using a translated codon (tron) and improved accuracy by allowing for long gaps. Bioinformatics, 16, 190-202.
-
(2000)
Bioinformatics
, vol.16
, pp. 190-202
-
-
Gotoh, O.1
-
63
-
-
0031878236
-
Finding intron/exon splice junctions using INFO. INterruption Finder and Organizer
-
Laub,M.T. and Smith,D.W. (1998) Finding intron/exon splice junctions using INFO. INterruption Finder and Organizer. J. Comput. Biol., 5, 307-321.
-
(1998)
J. Comput. Biol
, vol.5
, pp. 307-321
-
-
Laub, M.T.1
Smith, D.W.2
-
64
-
-
0032743426
-
A dictionary-based approach for gene annotation
-
Pachter,L. Batzoglou,S., Spitkovsky,V.I., Banks,E., Lander,E.S., Kleitman,D.J. and Berger,A. (1999) A dictionary-based approach for gene annotation. J. Comput. Biol., 6, 419-430.
-
(1999)
J. Comput. Biol
, vol.6
, pp. 419-430
-
-
Pachter, L.1
Batzoglou, S.2
Spitkovsky, V.I.3
Banks, E.4
Lander, E.S.5
Kleitman, D.J.6
Berger, A.7
-
65
-
-
0034047754
-
Detection of protein coding sequences using a mixture model for local protein amino acid sequence
-
Thayer,E., Bystroff,C. and Baker,D. (2000) Detection of protein coding sequences using a mixture model for local protein amino acid sequence. J. Comput. Biol., 7, 317-327.
-
(2000)
J. Comput. Biol
, vol.7
, pp. 317-327
-
-
Thayer, E.1
Bystroff, C.2
Baker, D.3
-
66
-
-
0031573382
-
A tool for analyzing and annotating genomic sequences
-
Huang,X., Adams,M.D., Zhou,H. and Kerlavage,A.R. (1997) A tool for analyzing and annotating genomic sequences. Genomics, 46, 37-45.
-
(1997)
Genomics
, vol.46
, pp. 37-45
-
-
Huang, X.1
Adams, M.D.2
Zhou, H.3
Kerlavage, A.R.4
-
67
-
-
0034646570
-
Gene structure prediction by spliced alignment of genomic DNA with protein sequences: Increased accuracy by differential splice site scoring
-
Usuka,J. and Brendel,V. (2000) Gene structure prediction by spliced alignment of genomic DNA with protein sequences: increased accuracy by differential splice site scoring. J. Mol. Biol., 297, 1075-1085.
-
(2000)
J. Mol. Biol
, vol.297
, pp. 1075-1085
-
-
Usuka, J.1
Brendel, V.2
-
68
-
-
0034129194
-
Optimal spliced alignment of homologous cDNA to a genomic DNA template
-
Usuka,J., Zhu,W. and Brendel,V. (2000) Optimal spliced alignment of homologous cDNA to a genomic DNA template. Bioinformatics, 16, 203-211.
-
(2000)
Bioinformatics
, vol.16
, pp. 203-211
-
-
Usuka, J.1
Zhu, W.2
Brendel, V.3
-
69
-
-
0031732094
-
A computer program for aligning a cDNA sequence with a genomic DNA sequence
-
Florea,L., Hartzell,G., Zhang,Z., Rubin,G.M. and Miller,W. (1998) A computer program for aligning a cDNA sequence with a genomic DNA sequence. Genome Res., 8, 967-974.
-
(1998)
Genome Res
, vol.8
, pp. 967-974
-
-
Florea, L.1
Hartzell, G.2
Zhang, Z.3
Rubin, G.M.4
Miller, W.5
-
70
-
-
0035189310
-
Spidey: A tool for mRNA-to-genomic alignments
-
Wheelan,S.J., Church,D.M. and Ostell,J.M. (2001) Spidey: a tool for mRNA-to-genomic alignments. Genome Res., 11, 1952-1957.
-
(2001)
Genome Res
, vol.11
, pp. 1952-1957
-
-
Wheelan, S.J.1
Church, D.M.2
Ostell, J.M.3
-
71
-
-
0033373273
-
Prediction of human cDNA from its homologous mouse full-length cDNA and human shotgun database
-
Fukunishi,Y., Suzuki,H., Yoshino,M., Konno,H. and Hayashizaki,Y. (1999) Prediction of human cDNA from its homologous mouse full-length cDNA and human shotgun database. FEBS Lett., 464, 129-132.
-
(1999)
FEBS Lett
, vol.464
, pp. 129-132
-
-
Fukunishi, Y.1
Suzuki, H.2
Yoshino, M.3
Konno, H.4
Hayashizaki, Y.5
-
72
-
-
0033534799
-
Protein-coding regions prediction combining similarity searches and conservative evolutionary properties of protein-coding sequences
-
Rogozin,I.B., D'Angelo,D. and Milanesi,L. (1999) Protein-coding regions prediction combining similarity searches and conservative evolutionary properties of protein-coding sequences. Gene, 226, 129-137.
-
(1999)
Gene
, vol.226
, pp. 129-137
-
-
Rogozin, I.B.1
D'Angelo, D.2
Milanesi, L.3
-
73
-
-
0031954877
-
EbEST: An automated tool using expressed sequence tags to delineate gene structure
-
Jiang,J. and Jacob,H.J. (1998) EbEST: an automated tool using expressed sequence tags to delineate gene structure. Genome Res., 8, 268-275.
-
(1998)
Genome Res
, vol.8
, pp. 268-275
-
-
Jiang, J.1
Jacob, H.J.2
-
74
-
-
0030870076
-
ESTNOME: A program to align spliced DNA sequences to unspliced genomic DNA
-
Mott,R. (1997) ESTNOME: a program to align spliced DNA sequences to unspliced genomic DNA. Comput. Appl. Biosci., 13, 477-478.
-
(1997)
Comput. Appl. Biosci
, vol.13
, pp. 477-478
-
-
Mott, R.1
-
75
-
-
0035036534
-
Gene structure prediction and alternative splicing analysis using genomically aligned ESTs
-
Kan,Z., Rouchka,E.C., Gish,W.R. and States,D.J. (2001) Gene structure prediction and alternative splicing analysis using genomically aligned ESTs. Genome Res., 11, 889-900.
-
(2001)
Genome Res
, vol.11
, pp. 889-900
-
-
Kan, Z.1
Rouchka, E.C.2
Gish, W.R.3
States, D.J.4
-
76
-
-
0033153375
-
Alignment of whole genomes
-
Delcher,A.L., Kasif,S., Fleischmann,R.D., Peterson,J., White,O. and Salzberg,S.L. (1999) Alignment of whole genomes. Nucleic Acids Res., 27, 2369-2376.
-
(1999)
Nucleic Acids Res
, vol.27
, pp. 2369-2376
-
-
Delcher, A.L.1
Kasif, S.2
Fleischmann, R.D.3
Peterson, J.4
White, O.5
Salzberg, S.L.6
-
77
-
-
0033832676
-
Conservation, regulation, synteny, and introns in a large-scale C. briggsae-C. elegans genomic alignment
-
Kent,W.J. and Zahler,A.M. (2000) Conservation, regulation, synteny, and introns in a large-scale C. briggsae-C. elegans genomic alignment. Genome Res., 10, 1115-1125.
-
(2000)
Genome Res
, vol.10
, pp. 1115-1125
-
-
Kent, W.J.1
Zahler, A.M.2
-
78
-
-
0034020416
-
PipMaker - A web server for aligning two genomic DNA sequences
-
Schwartz,S., Zhang,Z., Frazer,K., Smit,A., Riemer,C,, Bouck,J., Gibbs,R., Hardison,R. and Miller,W. (2000) PipMaker - a web server for aligning two genomic DNA sequences. Genome Res., 10, 577-586.
-
(2000)
Genome Res
, vol.10
, pp. 577-586
-
-
Schwartz, S.1
Zhang, Z.2
Frazer, K.3
Smit, A.4
Riemer, C.5
Bouck, J.6
Gibbs, R.7
Hardison, R.8
Miller, W.9
-
79
-
-
0033636013
-
A space-efficient algorithm for aligning large genomic sequences
-
Morgenstern,B. (2000) A space-efficient algorithm for aligning large genomic sequences. Bioinformatics, 16, 948-949.
-
(2000)
Bioinformatics
, vol.16
, pp. 948-949
-
-
Morgenstern, B.1
-
80
-
-
0033861549
-
Human and mouse gene structure: Comparative analysis and application to exon prediction
-
Batzoglou,S., Pachter,L., Mesirov,J., Berger,B. and Lander,E.S. (2000) Human and mouse gene structure: comparative analysis and application to exon prediction. Genome Res., 10, 950-958.
-
(2000)
Genome Res
, vol.10
, pp. 950-958
-
-
Batzoglou, S.1
Pachter, L.2
Mesirov, J.3
Berger, B.4
Lander, E.S.5
-
81
-
-
0034565167
-
The conserved exon method for gene finding
-
Bourne,P., Gribskov,M., Altman,R., Jensen,N., Hope,D., Lengauer,T., Mitchell,J., Scheeff,E., Smith,C., Strande,S. and Weissig,H. (eds), AAAI Press, Menlo Park, CA
-
Bafna,V. and Huson,D. (2000) The conserved exon method for gene finding. In Bourne,P., Gribskov,M., Altman,R., Jensen,N., Hope,D., Lengauer,T., Mitchell,J., Scheeff,E., Smith,C., Strande,S. and Weissig,H. (eds), Eighth International Conference on Intelligent Systems for Molecular Biology. AAAI Press, Menlo Park, CA, pp. 3-12.
-
(2000)
Eighth International Conference on Intelligent Systems for Molecular Biology
, pp. 3-12
-
-
Bafna, V.1
Huson, D.2
-
82
-
-
0034832202
-
SGP-1: Prediction and validation of homologous genes based on sequence alignments
-
Wiehe,T., Gebauer-Jung,S., Mitchell-Olds,T. and Guigo,R. (2001) SGP-1: prediction and validation of homologous genes based on sequence alignments. Genome Res., 11, 1574-1583.
-
(2001)
Genome Res
, vol.11
, pp. 1574-1583
-
-
Wiehe, T.1
Gebauer-Jung, S.2
Mitchell-Olds, T.3
Guigo, R.4
-
83
-
-
0035177648
-
Gene recognition in eukaryotic DNA by comparison of genomic sequences
-
Novichkov,P.S., Gelfand,M.S. and Mironov,A.A. (2001) Gene recognition in eukaryotic DNA by comparison of genomic sequences. Bioinformatics, 17, 1011-1018.
-
(2001)
Bioinformatics
, vol.17
, pp. 1011-1018
-
-
Novichkov, P.S.1
Gelfand, M.S.2
Mironov, A.A.3
-
85
-
-
0036112213
-
Applications of generalized pair hidden Markov models to alignment and gene finding problems
-
Pachter,L., Alexandersson,M. and Cawley,S. (2002) Applications of generalized pair hidden Markov models to alignment and gene finding problems. J. Comput. Biol., 9, 389-399.
-
(2002)
J. Comput. Biol
, vol.9
, pp. 389-399
-
-
Pachter, L.1
Alexandersson, M.2
Cawley, S.3
-
86
-
-
0030094146
-
CENSOR - A program for identification and elimination of repetitive elements from DNA sequences
-
Jurka,J., Klonowski,P., Dagman,V. and Pelton,P. (1996) CENSOR - a program for identification and elimination of repetitive elements from DNA sequences. Comput. Chem., 20, 119-112.
-
(1996)
Comput. Chem
, vol.20
, pp. 112-119
-
-
Jurka, J.1
Klonowski, P.2
Dagman, V.3
Pelton, P.4
-
87
-
-
0031299666
-
Combinatorial approaches to gene recognition
-
Roytberg,M.A., Astakhova,T.V. and Gelfand,M.S. (1997) Combinatorial approaches to gene recognition. Comput. Chem., 21, 229-235.
-
(1997)
Comput. Chem
, vol.21
, pp. 229-235
-
-
Roytberg, M.A.1
Astakhova, T.V.2
Gelfand, M.S.3
-
88
-
-
0032456609
-
Assembling genes from predicted exons in linear time with dynamic programming
-
Guigó,R. (1998) Assembling genes from predicted exons in linear time with dynamic programming. J. Comput. Biol., 5, 681-702.
-
(1998)
J. Comput. Biol
, vol.5
, pp. 681-702
-
-
Guigó, R.1
-
89
-
-
0026647310
-
Prediction of gene structure
-
Guigó,R., Knudsen,S., Drake,N. and Smith,T. (1992) Prediction of gene structure. J. Mol. Biol., 226, 141-157.
-
(1992)
J. Mol. Biol
, vol.226
, pp. 141-157
-
-
Guigó, R.1
Knudsen, S.2
Drake, N.3
Smith, T.4
-
90
-
-
0028605559
-
Constructing gene models from accurately predicted exons: An application of dynamic programming
-
Xu,Y., Mural,R.J. and Uberbaker,E.C. (1994) Constructing gene models from accurately predicted exons: an application of dynamic programming. Comput. Appl. Biosci., 10, 613-623.
-
(1994)
Comput. Appl. Biosci
, vol.10
, pp. 613-623
-
-
Xu, Y.1
Mural, R.J.2
Uberbaker, E.C.3
-
91
-
-
17344390287
-
Gene recognition based on DAG shortest paths
-
Chuang,J.S. and Roth,D. (2001) Gene recognition based on DAG shortest paths. Bioinformatics, 1, 1-9.
-
(2001)
Bioinformatics
, vol.1
, pp. 1-9
-
-
Chuang, J.S.1
Roth, D.2
-
92
-
-
0031825707
-
GeneGenerator-a flexible algorithm for gene prediction and its application to maize sequences
-
Kleffe,J., Hermann,K., Vahrson,W., Wittig,B. and Brendel,V. (1998) GeneGenerator-a flexible algorithm for gene prediction and its application to maize sequences. Bioinformatics, 14, 232-243.
-
(1998)
Bioinformatics
, vol.14
, pp. 232-243
-
-
Kleffe, J.1
Hermann, K.2
Vahrson, W.3
Wittig, B.4
Brendel, V.5
-
93
-
-
84935113569
-
Error bounds for convolutional codes and an asymptotically optimal decoding algorithm
-
Viterbi,A. (1967) Error bounds for convolutional codes and an asymptotically optimal decoding algorithm. IEEE Trans. Informat. Theor., IT-13, 260-269.
-
(1967)
IEEE Trans. Informat. Theor
, vol.13 IT
, pp. 260-269
-
-
Viterbi, A.1
-
94
-
-
0003787146
-
-
Princeton University Press, Princeton, NJ
-
Bellman,R.E. (1957) Dynamic Programming. Princeton University Press, Princeton, NJ.
-
(1957)
Dynamic Programming
-
-
Bellman, R.E.1
-
95
-
-
0027944605
-
A hidden Markov model that finds genes in E. coli DNA
-
Krogh,A., Mian,I.S. and Haussler,D. (1994) A hidden Markov model that finds genes in E. coli DNA. Nucleic Acids Res., 22, 4768-4778.
-
(1994)
Nucleic Acids Res
, vol.22
, pp. 4768-4778
-
-
Krogh, A.1
Mian, I.S.2
Haussler, D.3
-
96
-
-
0030333286
-
A generalized Hidden Markov Model for the recognition of human genes in DNA
-
States,D.J., Agarwal,P., Gaasterland,T., Hunter,L. and Smith,R.F. (eds), Proceedings of the Fourth International Conference on Intelligent Systems for Molecular Biology. AAAI Press, Menlo Park, CA
-
Kulp,D., Haussler,D., Reese,M.G. and Eeckman,F.H. (1996) A generalized Hidden Markov Model for the recognition of human genes in DNA. In States,D.J., Agarwal,P., Gaasterland,T., Hunter,L. and Smith,R.F. (eds), Proceedings of the Fourth International Conference on Intelligent Systems for Molecular Biology. AAAI Press, Menlo Park, CA, pp. 134-142.
-
(1996)
, pp. 134-142
-
-
Kulp, D.1
Haussler, D.2
Reese, M.G.3
Eeckman, F.H.4
-
97
-
-
0033931903
-
Prediction of genetic structure in eukaryotic DNA using reference point logistic regression and sequence alignment
-
Hooper,P., Zhang,H. and Wishart,D. (2000) Prediction of genetic structure in eukaryotic DNA using reference point logistic regression and sequence alignment. Bioinformatics, 16, 425-438.
-
(2000)
Bioinformatics
, vol.16
, pp. 425-438
-
-
Hooper, P.1
Zhang, H.2
Wishart, D.3
-
98
-
-
0030623944
-
Two methods for improving performace of a HMM and their application for gene finding
-
Gaasterland,T., Karp,P., Karplus,K., Ouzounis,C., Sander,C. and Valencia,A. (eds), AAAI Press, Menlo Park, CA
-
Krogh,A. (1997) Two methods for improving performace of a HMM and their application for gene finding. In Gaasterland,T., Karp,P., Karplus,K., Ouzounis,C., Sander,C. and Valencia,A. (eds), The Fifth International Conference on Intelligent Systems for Molecular Biology. AAAI Press, Menlo Park, CA, pp. 179-186.
-
(1997)
The Fifth International Conference on Intelligent Systems for Molecular Biology
, pp. 179-186
-
-
Krogh, A.1
-
99
-
-
0035002015
-
Computational inference of homologous gene structures in the human genome
-
Yeh,R.-F., Lim,L.P. and Burge,C.B. (2001) Computational inference of homologous gene structures in the human genome. Genome Res., 11, 803-816.
-
(2001)
Genome Res
, vol.11
, pp. 803-816
-
-
Yeh, R.-F.1
Lim, L.P.2
Burge, C.B.3
-
100
-
-
17444437765
-
Integrating genomic homology into gene structure prediction
-
Korf,I., Flicek,P., Duan,D. and Brent,M.R. (2001) Integrating genomic homology into gene structure prediction. Bioinformatics, 17, S140-S148.
-
(2001)
Bioinformatics
, vol.17
-
-
Korf, I.1
Flicek, P.2
Duan, D.3
Brent, M.R.4
-
101
-
-
0031761144
-
Gene recognition by combination of several gene-finding programs
-
Murakami,K. and Tagaki,T. (1998) Gene recognition by combination of several gene-finding programs. Bioinformatics, 14, 665-675.
-
(1998)
Bioinformatics
, vol.14
, pp. 665-675
-
-
Murakami, K.1
Tagaki, T.2
-
102
-
-
0032944241
-
INFOGENE: A database of known gene structures and predicted genes and proteins in sequences of genome sequencing projects
-
Solovyev,V.V. and Salamov,A.A. (1999) INFOGENE: a database of known gene structures and predicted genes and proteins in sequences of genome sequencing projects. Nucleic Acids Res., 27, 248-250.
-
(1999)
Nucleic Acids Res
, vol.27
, pp. 248-250
-
-
Solovyev, V.V.1
Salamov, A.A.2
-
103
-
-
0036173326
-
A Bayesian framework for combining gene predictions
-
Pavlovic,V., Garg,A. and Kasif,S. (2002) A Bayesian framework for combining gene predictions. Bioinformatics, 18, 19-27.
-
(2002)
Bioinformatics
, vol.18
, pp. 19-27
-
-
Pavlovic, V.1
Garg, A.2
Kasif, S.3
-
104
-
-
0030881249
-
Genotator: A workbench for sequence annotation
-
Harris,N.L. (1997) Genotator: a workbench for sequence annotation. Genome Res., 7, 754-762.
-
(1997)
Genome Res
, vol.7
, pp. 754-762
-
-
Harris, N.L.1
-
105
-
-
0029828166
-
Fully automated genome analysis that reflects user needs and preferences. A detailed introduction to the MAGPIE system architecture
-
Gaasterland,T. and Sensen,C.W. (1996) Fully automated genome analysis that reflects user needs and preferences. A detailed introduction to the MAGPIE system architecture. Biochimie, 78, 302-310.
-
(1996)
Biochimie
, vol.78
, pp. 302-310
-
-
Gaasterland, T.1
Sensen, C.W.2
-
106
-
-
18444402182
-
The Ensembl genome database project
-
Hubbard,T., Barker,D., Birney,E., Cameron,G. Chen,Y., Clark,L., Cox,T., Cuff,J., Curwen,V., Down,T. et al. (2002) The Ensembl genome database project. Nucleic Acids Res. 30, 38-41.
-
(2002)
Nucleic Acids Res
, vol.30
, pp. 38-41
-
-
Hubbard, T.1
Barker, D.2
Birney, E.3
Cameron, G.4
Chen, Y.5
Clark, L.6
Cox, T.7
Cuff, J.8
Curwen, V.9
Down, T.10
-
107
-
-
0034742461
-
Identifying the 3′-terminal exon in human DNA
-
Tabaska,J. Davuluri,R. and Zhang,M. (2001) Identifying the 3′-terminal exon in human DNA. Bioinformatics, 17, 602-607.
-
(2001)
Bioinformatics
, vol.17
, pp. 602-607
-
-
Tabaska, J.1
Davuluri, R.2
Zhang, M.3
-
108
-
-
0035735265
-
Computational identification of promoters and first exons in the human genome
-
Davuluri,R.V. Groose,I. and Zhang,M.Q. (2001) Computational identification of promoters and first exons in the human genome. Nature Genet., 29, 412-417.
-
(2001)
Nature Genet
, vol.29
, pp. 412-417
-
-
Davuluri, R.V.1
Groose, I.2
Zhang, M.Q.3
-
109
-
-
0036123111
-
Computational detection and location of transcription start sites in mammalian genomic DNA
-
Down,T.A. and Hubbard,T.J. (2002) Computational detection and location of transcription start sites in mammalian genomic DNA. Genome Res., 12, 458-461.
-
(2002)
Genome Res
, vol.12
, pp. 458-461
-
-
Down, T.A.1
Hubbard, T.J.2
-
110
-
-
0033598805
-
In silico detection of control signals: mRNA 3′-end-processing sequences in diverse species
-
Graber,J.H., Canter,C.R., Molar,S.C. and Smith,T.F. (1999) In silico detection of control signals: mRNA 3′-end-processing sequences in diverse species. Proc. Natl Acad. USA, 96, 14055-14060.
-
(1999)
Proc. Natl Acad. USA
, vol.96
, pp. 14055-14060
-
-
Graber, J.H.1
Canter, C.R.2
Molar, S.C.3
Smith, T.F.4
-
111
-
-
0033782834
-
An assessment of gene prediction accuracy in large DNA sequences
-
Guigó,R. Agarwal,P., Abril,J., Burset,M. and Fickett,J. (2000) An assessment of gene prediction accuracy in large DNA sequences. Genome Res, 10, 1631-1642.
-
(2000)
Genome Res
, vol.10
, pp. 1631-1642
-
-
Guigó, R.1
Agarwal, P.2
Abril, J.3
Burset, M.4
Fickett, J.5
-
112
-
-
0030700474
-
Exon-intron organization of the human dystrophin gene
-
Nobile,C., Marchi,J., Nigro,V., Roberts,R.G. and Danieli,G.A. (1997) Exon-intron organization of the human dystrophin gene. Genomics, 45, 421-424.
-
(1997)
Genomics
, vol.45
, pp. 421-424
-
-
Nobile, C.1
Marchi, J.2
Nigro, V.3
Roberts, R.G.4
Danieli, G.A.5
-
113
-
-
0027280998
-
Strong conservation of vertebrate non-coding sequences during vertebrate evolution: Potential involvement in post-transcriptional regulation of gene expression
-
Duret,L., Dorkeld,F. and Gautier,C. (1993) Strong conservation of vertebrate non-coding sequences during vertebrate evolution: potential involvement in post-transcriptional regulation of gene expression. Nucleic Acids Res., 21, 2315-2322.
-
(1993)
Nucleic Acids Res
, vol.21
, pp. 2315-2322
-
-
Duret, L.1
Dorkeld, F.2
Gautier, C.3
-
114
-
-
0032884653
-
Comparative analysis of noncoding regions of 77 orthologous mouse and human gene pairs
-
Jareborg,N., Birney,E. and Durbin,R. (1999) Comparative analysis of noncoding regions of 77 orthologous mouse and human gene pairs. Genome Res., 9, 815-824.
-
(1999)
Genome Res
, vol.9
, pp. 815-824
-
-
Jareborg, N.1
Birney, E.2
Durbin, R.3
-
115
-
-
0032722057
-
OTC and AUL1, two convergent and overlapping genes in the nuclear genome of Arabidopsis thaliana
-
Quesada,V., Ponce,M.R. and Micol,J.L. (1999) OTC and AUL1, two convergent and overlapping genes in the nuclear genome of Arabidopsis thaliana. FEBS Lett., 461, 101-106.
-
(1999)
FEBS Lett
, vol.461
, pp. 101-106
-
-
Quesada, V.1
Ponce, M.R.2
Micol, J.L.3
-
116
-
-
0022475084
-
Gene within a gene: Nested Drosophila genes encode unrelated proteins on opposite DNA strands
-
Henikoff,S., Keene,M.A., Fechtel,K. and Fristrom,J.W. (1986) Gene within a gene: nested Drosophila genes encode unrelated proteins on opposite DNA strands. Cell, 44, 33-42.
-
(1986)
Cell
, vol.44
, pp. 33-42
-
-
Henikoff, S.1
Keene, M.A.2
Fechtel, K.3
Fristrom, J.W.4
-
117
-
-
0030749116
-
Clusters of multiple different small nucleolar RNA genes in plants are expressed as and processed from polycistronic presnoRNAs
-
Leader,D.J., Clark,G.P., Watters,J., Beven,A.F., Shaw,P.J. and Brown,J.W. (1997) Clusters of multiple different small nucleolar RNA genes in plants are expressed as and processed from polycistronic presnoRNAs. EMBO J., 16, 5742-5751.
-
(1997)
EMBO J
, vol.16
, pp. 5742-5751
-
-
Leader, D.J.1
Clark, G.P.2
Watters, J.3
Beven, A.F.4
Shaw, P.J.5
Brown, J.W.6
-
118
-
-
0032103829
-
Gene clusters and polycistronic transcription in eukaryotes
-
Blumenthal,T. (1998) Gene clusters and polycistronic transcription in eukaryotes. Bioessays, 20, 480-487.
-
(1998)
Bioessays
, vol.20
, pp. 480-487
-
-
Blumenthal, T.1
-
119
-
-
0035113035
-
Pro-Frame: Similarity-based gene recognition in eukaryotic DNA sequences with errors
-
Mironov,A.A., Novichkov,P.S. and Gelfand,M.S. (2001) Pro-Frame: similarity-based gene recognition in eukaryotic DNA sequences with errors. Bioinformatics, 17, 13-15.
-
(2001)
Bioinformatics
, vol.17
, pp. 13-15
-
-
Mironov, A.A.1
Novichkov, P.S.2
Gelfand, M.S.3
-
120
-
-
0029134925
-
A frameshift error detection algorithm for DNA sequencing projects
-
Fichant,G.A. and Quentin,Y. (1995) A frameshift error detection algorithm for DNA sequencing projects. Nucleic Acids Res., 23, 2900-2908.
-
(1995)
Nucleic Acids Res
, vol.23
, pp. 2900-2908
-
-
Fichant, G.A.1
Quentin, Y.2
-
121
-
-
0037203829
-
Genome sequence of the plant pathogen Ralstonia solanacearum
-
Salanoubat,M., Genin,S., Artiguenave,F., Gouzy,J., Mangenot,S., Arlat,M., Billault,A., Brottier,P., Camus,J.C., Cattolico,L. et al. (2002) Genome sequence of the plant pathogen Ralstonia solanacearum. Nature, 415, 497-502.
-
(2002)
Nature
, vol.415
, pp. 497-502
-
-
Salanoubat, M.1
Genin, S.2
Artiguenave, F.3
Gouzy, J.4
Mangenot, S.5
Arlat, M.6
Billault, A.7
Brottier, P.8
Camus, J.C.9
Cattolico, L.10
-
122
-
-
0033290515
-
ESTScan: A program for detecting, evaluating, and reconstructing potential coding regions in EST sequences
-
Iseli,C., Jongeneel,C.V. and Bucher,P. (1999) ESTScan: a program for detecting, evaluating, and reconstructing potential coding regions in EST sequences. Proc. Int. Conf. Intell. Syst. Mol. Biol., 138-148.
-
(1999)
Proc. Int. Conf. Intell. Syst. Mol. Biol
, pp. 138-148
-
-
Iseli, C.1
Jongeneel, C.V.2
Bucher, P.3
-
123
-
-
0032570603
-
Cloning and characterization of promoter and 5′-UTR of the NMDA receptor subunit epsilon 2: Evidence for alternative splicing of 5′-noncoding exon
-
Klein,M., Pieri,I., Uhlmann,F., Pfizenmaier,K. and Eisel,U. (1998) Cloning and characterization of promoter and 5′-UTR of the NMDA receptor subunit epsilon 2: evidence for alternative splicing of 5′-noncoding exon, Gene, 208, 259-269.
-
(1998)
Gene
, vol.208
, pp. 259-269
-
-
Klein, M.1
Pieri, I.2
Uhlmann, F.3
Pfizenmaier, K.4
Eisel, U.5
-
124
-
-
0031456850
-
Classification of introns: U2-type or U12-type
-
Sharp,P.A. and Burge,C.B. (1997) Classification of introns: U2-type or U12-type. Cell, 91, 875-879.
-
(1997)
Cell
, vol.91
, pp. 875-879
-
-
Sharp, P.A.1
Burge, C.B.2
-
125
-
-
0034326362
-
Analysis of canonical and non-canonical splice sites in mammalian genomes
-
Burset,M., Seledtsov,I. and Solovyev,V. (2000) Analysis of canonical and non-canonical splice sites in mammalian genomes. Nucleic Acids Res., 28, 4364-4375.
-
(2000)
Nucleic Acids Res
, vol.28
, pp. 4364-4375
-
-
Burset, M.1
Seledtsov, I.2
Solovyev, V.3
-
126
-
-
0034029236
-
ISIS, the intron information system, reveals the high frequency of alternative splicing in the human genome
-
Croft,L., Schandorff,S., Clark.F., Burrage,K., Arctander,P. and Mattick,J. (2000) ISIS, the intron information system, reveals the high frequency of alternative splicing in the human genome. Nature Genet., 24, 340-341.
-
(2000)
Nature Genet
, vol.24
, pp. 340-341
-
-
Croft, L.1
Schandorff, S.2
Clark, F.3
Burrage, K.4
Arctander, P.5
Mattick, J.6
-
127
-
-
0035393343
-
Genome-wide detection of alternative splicing in expressed sequences of human genes
-
Modrek,B., Resch,A., Grasso,C. and Lee,C. (2001) Genome-wide detection of alternative splicing in expressed sequences of human genes. Nucleic Acids Res., 29, 2850-2859.
-
(2001)
Nucleic Acids Res
, vol.29
, pp. 2850-2859
-
-
Modrek, B.1
Resch, A.2
Grasso, C.3
Lee, C.4
-
128
-
-
0036337915
-
A genomic view of alternative splicing
-
Modrek,B. and Lee,C. (2002) A genomic view of alternative splicing. Nature Genet., 30, 13-19.
-
(2002)
Nature Genet
, vol.30
, pp. 13-19
-
-
Modrek, B.1
Lee, C.2
-
130
-
-
0031859991
-
Alternate polyadenylation in human mRNAs: A large-scale analysis by EST clustering
-
Gautheret,D., Poirot,O., Lopez,F., Audic,S. and Claverie Jean,M. (1998) Alternate polyadenylation in human mRNAs: a large-scale analysis by EST clustering. Genome Res., 8, 524-530.
-
(1998)
Genome Res
, vol.8
, pp. 524-530
-
-
Gautheret, D.1
Poirot, O.2
Lopez, F.3
Audic, S.4
Claverie Jean, M.5
-
131
-
-
0033061571
-
Initiation of translation in prokaryotes and eukaryotes
-
Kozak,M. (1999) Initiation of translation in prokaryotes and eukaryotes. Gene, 234, 187-208.
-
(1999)
Gene
, vol.234
, pp. 187-208
-
-
Kozak, M.1
-
132
-
-
0033513099
-
Non-AUG initiation of AGAMOUS mRNA translation in Arabidpsis thaliana
-
Riechmann,J.L., Ito,T. and Meyerowitz,E. (1999) Non-AUG initiation of AGAMOUS mRNA translation in Arabidpsis thaliana. Mol. Cell. Biol., 19, 8505-8512.
-
(1999)
Mol. Cell. Biol
, vol.19
, pp. 8505-8512
-
-
Riechmann, J.L.1
Ito, T.2
Meyerowitz, E.3
-
133
-
-
0030474826
-
Translation of CUG but not AUG-initiated forms of human fibroblast growth factor 2 is activated in transformed and stressed cells
-
Vagner,S., Touriol,C., Galy,B., Audigier,S., Gensac,M. Amalric,F., Bayard,F., Prats,H. and Prats,A. (1996) Translation of CUG but not AUG-initiated forms of human fibroblast growth factor 2 is activated in transformed and stressed cells. J. Cell Biol., 135, 1391-1402.
-
(1996)
J. Cell Biol
, vol.135
, pp. 1391-1402
-
-
Vagner, S.1
Touriol, C.2
Galy, B.3
Audigier, S.4
Gensac, M.5
Amalric, F.6
Bayard, F.7
Prats, H.8
Prats, A.9
-
134
-
-
0032544103
-
Self-identification of protein-coding regions in microbial genomes
-
Audic,S. and Claverie,J.-M. (1998) Self-identification of protein-coding regions in microbial genomes. Proc. Natl Acad. Sci. USA, 95, 10026-10031.
-
(1998)
Proc. Natl Acad. Sci. USA
, vol.95
, pp. 10026-10031
-
-
Audic, S.1
Claverie, J.-M.2
-
135
-
-
0033214628
-
Heuristic approach to deriving models for gene finding
-
Besemer,J. and Borodovsky,M. (1999) Heuristic approach to deriving models for gene finding. Nucleic Acids Res., 27, 3911-3920.
-
(1999)
Nucleic Acids Res
, vol.27
, pp. 3911-3920
-
-
Besemer, J.1
Borodovsky, M.2
-
136
-
-
0026332291
-
Evidence for horizontal gene transfer in Escherichia coli speciation
-
Médigue,C., Rouxel,T., Vigier,P., Hénaut,A. and Danchin,A. (1991) Evidence for horizontal gene transfer in Escherichia coli speciation. J. Mol. Biol., 222, 851-856.
-
(1991)
J. Mol. Biol
, vol.222
, pp. 851-856
-
-
Médigue, C.1
Rouxel, T.2
Vigier, P.3
Hénaut, A.4
Danchin, A.5
-
137
-
-
0033524964
-
Classification of Arabidopsis thaliana gene sequences: Clustering of coding sequences into two groups according to codon usage improves gene prediction
-
Mathé,C., Peresetsky,A., Déhais,P., Van Montagu,M. and Rouzé,P. (1999) Classification of Arabidopsis thaliana gene sequences: clustering of coding sequences into two groups according to codon usage improves gene prediction. J. Mol. Biol., 285, 1977-1991.
-
(1999)
J. Mol. Biol
, vol.285
, pp. 1977-1991
-
-
Mathé, C.1
Peresetsky, A.2
Déhais, P.3
Van Montagu, M.4
Rouzé, P.5
-
138
-
-
0029056051
-
Detection of new genes in a bacterial genome using Markov models for three gene classes
-
Borodovsky,M., McIninch,J.D., Koonin,E.V., Rudd,K.E., Médigue,C. and Danchin,A. (1995) Detection of new genes in a bacterial genome using Markov models for three gene classes. Nucleic Acids Res., 23, 3554-3562.
-
(1995)
Nucleic Acids Res
, vol.23
, pp. 3554-3562
-
-
Borodovsky, M.1
McIninch, J.D.2
Koonin, E.V.3
Rudd, K.E.4
Médigue, C.5
Danchin, A.6
-
139
-
-
0032415865
-
How to interpret an anonymous bacterial genome: Machine learning approach to gene identification
-
Hayes,W.S. and Borodovsky,M. (1998) How to interpret an anonymous bacterial genome: machine learning approach to gene identification. Genome Res., 8, 1154-1171.
-
(1998)
Genome Res
, vol.8
, pp. 1154-1171
-
-
Hayes, W.S.1
Borodovsky, M.2
-
140
-
-
0035875343
-
GeneMarkS: A self-training method for prediction of gene starts in microbial genomes. Implications for finding sequence motifs in regulatory regions
-
Besemer,J., Lomsadze,A. and Borodovsky,M. (2001) GeneMarkS: a self-training method for prediction of gene starts in microbial genomes. Implications for finding sequence motifs in regulatory regions. Nucleic Acids Res., 29, 2607-2618.
-
(2001)
Nucleic Acids Res
, vol.29
, pp. 2607-2618
-
-
Besemer, J.1
Lomsadze A. Borodovsky, M.2
-
141
-
-
0343527384
-
Gene prediction and gene classes in Arabidopsis thaliana
-
Mathé,C., Déhais,P., Pavy,N., Rombauts,S., Van Montagu,M. and Rouzé,P. (2000) Gene prediction and gene classes in Arabidopsis thaliana. J. Biotechnol., 78, 293-299.
-
(2000)
J. Biotechnol
, vol.78
, pp. 293-299
-
-
Mathé, C.1
Déhais, P.2
Pavy, N.3
Rombauts, S.4
Van Montagu, M.5
Rouzé, P.6
-
142
-
-
0033569629
-
Keeping genome databases clean and up to date
-
Pennisi,E. (1999) Keeping genome databases clean and up to date. Science, 286, 447-450.
-
(1999)
Science
, vol.286
, pp. 447-450
-
-
Pennisi, E.1
-
143
-
-
0032127026
-
Functional genomics-bioinformatics is ready for the challenge
-
Smith,T.F. (1998) Functional genomics-bioinformatics is ready for the challenge. Trends Genet., 14, 291-293.
-
(1998)
Trends Genet
, vol.14
, pp. 291-293
-
-
Smith, T.F.1
-
144
-
-
0034887203
-
The Gene Ontology Consortium Creating the gene ontology resource: Design and implementation
-
The Gene Ontology Consortium (2001) Creating the gene ontology resource: design and implementation. Genome Res., 11, 1425-1433.
-
(2001)
Genome Res
, vol.11
, pp. 1425-1433
-
-
-
145
-
-
0035098865
-
On the importance of standardisation in life sciences
-
Brazma,A. (2001) On the importance of standardisation in life sciences. Bioinformatics, 17, 113-114.
-
(2001)
Bioinformatics
, vol.17
, pp. 113-114
-
-
Brazma, A.1
-
146
-
-
0035011227
-
Comparison of genomic DNA sequences: Solved and unsolved problems
-
Miller,W. (2001) Comparison of genomic DNA sequences: solved and unsolved problems. Bioinformatics, 17, 391-397.
-
(2001)
Bioinformatics
, vol.17
, pp. 391-397
-
-
Miller, W.1
-
147
-
-
0034707216
-
Genomic scrap yard: How genomes utilize all that junk
-
Makalowski,W. (2000) Genomic scrap yard: how genomes utilize all that junk. Gene, 259, 61-67.
-
(2000)
Gene
, vol.259
, pp. 61-67
-
-
Makalowski, W.1
-
148
-
-
0034883255
-
Analysis of concerved noncoding DNA in Drosophila reveals similar constraints in intergenic and intronic sequences
-
Bergman,C. and Kreitman,M. (2001) Analysis of concerved noncoding DNA in Drosophila reveals similar constraints in intergenic and intronic sequences. Genome, Res., 11, 1335-1345.
-
(2001)
Genome, Res
, vol.11
, pp. 1335-1345
-
-
Bergman, C.1
Kreitman, M.2
-
149
-
-
0032785505
-
Noncoding RNA genes
-
Eddy,S.R. (1999) Noncoding RNA genes. Curr. Opin. Genet. Dev., 9, 695-699.
-
(1999)
Curr. Opin. Genet. Dev
, vol.9
, pp. 695-699
-
-
Eddy, S.R.1
-
150
-
-
0033954323
-
Non-coding, mRNA-like RNAs database Y2K
-
Erdmann,V., Szymanski,M. Hochberg,A., Groot,N. and Barciszewski,J. (2000) Non-coding, mRNA-like RNAs database Y2K. Nucleic Acids Res., 28, 197-200.
-
(2000)
Nucleic Acids Res
, vol.28
, pp. 197-200
-
-
Erdmann, V.1
Szymanski, M.2
Hochberg, A.3
Groot, N.4
Barciszewski, J.5
-
151
-
-
0033765362
-
Secondary structure alone is generally not statistically significant for the detection of noncoding RNAs
-
Rivas,E. and Eddy,S. (2000) Secondary structure alone is generally not statistically significant for the detection of noncoding RNAs. Bioinformatics, 16, 583-605.
-
(2000)
Bioinformatics
, vol.16
, pp. 583-605
-
-
Rivas, E.1
Eddy, S.2
-
152
-
-
0035282695
-
GeneSplicer: A new computational method for splice site prediction
-
Pertea,M., Lin,X. and Salzberg,S. (2001) GeneSplicer: a new computational method for splice site prediction. Nucleic Acids Res., 29, 1185-1190.
-
(2001)
Nucleic Acids Res
, vol.29
, pp. 1185-1190
-
-
Pertea, M.1
Lin, X.2
Salzberg, S.3
-
153
-
-
0032512716
-
Prediction of splice sites in plant pre-mRNA from sequence properties
-
Brendel,V., Kleffe.J., Carle Urioste,J.C. and Walbot, V. (1998) Prediction of splice sites in plant pre-mRNA from sequence properties. J. Mol. Biol., 276, 85-104.
-
(1998)
J. Mol. Biol
, vol.276
, pp. 85-104
-
-
Brendel, V.1
Kleffe, J.2
Carle Urioste, J.C.3
Walbot, V.4
-
154
-
-
0027944162
-
Gene structure prediction by linguistic methods
-
Dong,S and Searls,D.B. (1994) Gene structure prediction by linguistic methods, Genomics, 23, 540-551.
-
(1994)
Genomics
, vol.23
, pp. 540-551
-
-
Dong, S.1
Searls, D.B.2
-
155
-
-
0030786488
-
Automated gene identification in large-scale genomic sequences
-
Xu,Y.X. and Uberbacher,E.C. (1997) Automated gene identification in large-scale genomic sequences. J. Comput. Biol., 4, 325-338.
-
(1997)
J. Comput. Biol
, vol.4
, pp. 325-338
-
-
Xu, Y.X.1
Uberbacher, E.C.2
-
156
-
-
77957187566
-
A probabilistic model for detecting coding regions in DNA sequences
-
Thomas,A. and Skolnick,M.H. (1994) A probabilistic model for detecting coding regions in DNA sequences. IMA J. Math. Appl. Med. Biol., 11, 149-160.
-
(1994)
IMA J. Math. Appl. Med. Biol
, vol.11
, pp. 149-160
-
-
Thomas, A.1
Skolnick, M.H.2
|