-
1
-
-
43849100950
-
Predictive methods using DNA sequences
-
(Baxevanis, A.D. and Ouellette, B.F.F. Eds). Wiley-Interscience: Hoboken, NJ, p. xviii
-
Blanco, E., and R. Guigó (2005) Predictive methods using DNA sequences, in Bioinfor-matics: A Practical Guide to the Analysis of Genes and Proteins (Baxevanis, A.D. and Ouellette, B.F.F. Eds). Wiley-Interscience: Hoboken, NJ, p. xviii, 540 p.
-
(2005)
Bioinfor-matics: A Practical Guide to the Analysis of Genes and Proteins
, pp. 540
-
-
Blanco, E.1
Guigó, R.2
-
2
-
-
34250305146
-
Identification and analysis of functional elements in 1% of the human genome by the ENCODE pilot project
-
ENCODE Project Consortium
-
ENCODE Project Consortium (2007) Identification and analysis of functional elements in 1% of the human genome by the ENCODE pilot project. Nature 447(7146), 799-816.
-
(2007)
Nature
, vol.447
, Issue.7146
, pp. 799-816
-
-
-
3
-
-
0036733640
-
Computational prediction of eukaryotic protein-coding genes
-
DOI 10.1038/nrg890
-
Zhang, M. Q. (2002) Computational prediction of eukaryotic protein-coding genes. Nat Rev Genet 3(9), 698-709. (Pubitemid 34984258)
-
(2002)
Nature Reviews Genetics
, vol.3
, Issue.9
, pp. 698-709
-
-
Zhang, M.Q.1
-
4
-
-
0035895505
-
The sequence of the human genome
-
Venter, J. C., et al. (2001) The sequence of the human genome. Science 291(5507), 1304-51.
-
(2001)
Science
, vol.291
, Issue.5507
, pp. 1304-1351
-
-
Venter, J.C.1
-
5
-
-
33846474760
-
A hitchhiker's guide to expressed sequence tag (EST) analysis
-
DOI 10.1093/bib/bbl015
-
Nagaraj, S. H., Gasser, R. B., and Ranganathan, S. (2007) A hitchhiker's guide to expressed sequence tag (EST) analysis. Brief Bioinform 8(1), 6-21. (Pubitemid 46157926)
-
(2007)
Briefings in Bioinformatics
, vol.8
, Issue.1
, pp. 6-21
-
-
Nagaraj, S.H.1
Gasser, R.B.2
Ranganathan, S.3
-
6
-
-
33748674197
-
AUGUSTUS at EGASP: Using EST, protein and genomic alignments for improved gene prediction in the human genome
-
Stanke, M., Tzvetkova, A., and Morgenstern, B. (2006) AUGUSTUS at EGASP: using EST, protein and genomic alignments for improved gene prediction in the human genome. Genome Biol 7 Suppl 1, S11 1-8.
-
(2006)
Genome Biol
, vol.7
, Issue.SUPPL. 1
-
-
Stanke, M.1
Tzvetkova, A.2
Morgenstern, B.3
-
7
-
-
24644485994
-
JIGSAW: Integration of multiple sources of evidence for gene prediction
-
DOI 10.1093/bioinformatics/bti609
-
Allen, J. E., and Salzberg, S. L. (2005) JIGSAW: integration of multiple sources of evidence for gene prediction. Bioinformatics 21(18), 3596-603. (Pubitemid 41264093)
-
(2005)
Bioinformatics
, vol.21
, Issue.18
, pp. 3596-3603
-
-
Allen, J.E.1
Salzberg, S.L.2
-
8
-
-
33846078622
-
The UCSC genome browser database: Update 2007
-
DOI 10.1093/nar/gkl928
-
Kuhn, R. M., et al. (2007) The UCSC genome browser database: update 2007. Nucleic Acids Res 35(Database issue), D668-73. (Pubitemid 46056289)
-
(2007)
Nucleic Acids Research
, vol.35
, Issue.SUPPL. 1
-
-
Kuhn, R.M.1
Karolchik, D.2
Zweig, A.S.3
Trumbower, H.4
Thomas, D.J.5
Thakkapallayil, A.6
Sugnet, C.W.7
Stanke, M.8
Smith, K.E.9
Siepel, A.10
Rosenbloom, K.R.11
Rhead, B.12
Raney, B.J.13
Pohl, A.14
Pedersen, J.S.15
Hsu, F.16
Hinrichs, A.S.17
Harte, R.A.18
Diekhans, M.19
Clawson, H.20
Bejerano, G.21
Barber, G.P.22
Baertsch, R.23
Haussler, D.24
Kent, W.J.25
more..
-
9
-
-
33846039019
-
Ensembl 2007
-
DOI 10.1093/nar/gkl996
-
Hubbard, T. J., et al. (2007) Ensembl 2007. Nucleic Acids Res 35(Database issue), D610-7. (Pubitemid 46056279)
-
(2007)
Nucleic Acids Research
, vol.35
, Issue.SUPPL. 1
-
-
Hubbard, T.J.P.1
Aken, B.L.2
Beal, K.3
Ballester, B.4
Caccamo, M.5
Chen, Y.6
Clarke, L.7
Coates, G.8
Cunningham, F.9
Cutts, T.10
Down, T.11
Dyer, S.C.12
Fitzgerald, S.13
Fernandez-Banet, J.14
Graf, S.15
Haider, S.16
Hammond, M.17
Herrero, J.18
Holland, R.19
Howe, K.20
Howe, K.21
Johnson, N.22
Kahari, A.23
Keefe, D.24
Kokocinski, F.25
Kulesha, E.26
Lawson, D.27
Longden, I.28
Melsopp, C.29
Megy, K.30
Meidl, P.31
Ouverdin, B.32
Parker, A.33
Prlic, A.34
Rice, S.35
Rios, D.36
Schuster, M.37
Sealy, I.38
Severin, J.39
Slater, G.40
Smedley, D.41
Spudich, G.42
Trevanion, S.43
Vilella, A.44
Vogel, J.45
White, S.46
Wood, M.47
Cox, T.48
Curwen, V.49
Durbin, R.50
Fernandez-Suarez, X.M.51
Flicek, P.52
Kasprzyk, A.53
Proctor, G.54
Searle, S.55
Smith, J.56
Ureta-Vidal, A.57
Birney, E.58
more..
-
10
-
-
33846062023
-
Database resources of the National Center for Biotechnology Information
-
DOI 10.1093/nar/gkl1031
-
Wheeler, D. L., et al. (2007) Database resources of the National Center for Biotechnology Information. Nucleic Acids Res 35(Database issue), D5-12. (Pubitemid 46056160)
-
(2007)
Nucleic Acids Research
, vol.35
, Issue.SUPPL. 1
-
-
Wheeler, D.L.1
Barrett, T.2
Benson, D.A.3
Bryant, S.H.4
Canese, K.5
Chetvernin, V.6
Church, D.M.7
DiCuccio, M.8
Edgar, R.9
Federhen, S.10
Geer, L.Y.11
Kapustin, Y.12
Khovayko, O.13
Landsman, D.14
Lipman, D.J.15
Madden, T.L.16
Maglott, D.R.17
Ostell, J.18
Miller, V.19
Pruitt, K.D.20
Schuler, G.D.21
Sequeira, E.22
Sherry, S.T.23
Sirotkin, K.24
Souvorov, A.25
Starchenko, G.26
Tatusov, R.L.27
Tatusova, T.A.28
Wagner, L.29
Yaschenko, E.30
more..
-
11
-
-
0026647310
-
Prediction of gene structure
-
Guigo, R., et al. (1992) Prediction of gene structure. J Mol Biol 226(1), 141-57.
-
(1992)
J Mol Biol
, vol.226
, Issue.1
, pp. 141-157
-
-
Guigo, R.1
-
12
-
-
0034061137
-
GeneId in Drosophila
-
DOI 10.1101/gr.10.4.511
-
Parra, G., Blanco, E., and Guigo, R. (2000) GeneID in Drosophila. Genome Res 10(4), 511-5. (Pubitemid 30259080)
-
(2000)
Genome Research
, vol.10
, Issue.4
, pp. 511-515
-
-
Parra, G.1
Blanco, E.2
Guigo, R.3
-
13
-
-
77951238625
-
Using geneid to identify genes in Current Protocols
-
(Baxevanis, A. D. et al., Eds). John Wiley & Sons: New York Unit 4.3
-
Blanco, E., Parra, G., and Guigó, R. (2007) Using geneid to identify genes in Current Protocols in Bioinformatics (Baxevanis, A. D. et al., Eds). John Wiley & Sons: New York, p. 1-28 (Unit 4.3).
-
(2007)
Bioinformatics
, pp. 1-28
-
-
Blanco, E.1
Parra, G.2
Guigó, R.3
-
14
-
-
0031586003
-
Prediction of complete gene structures in human genomic DNA
-
DOI 10.1006/jmbi.1997.0951
-
Burge, C., and Karlin, S. (1997) Prediction of complete gene structures in human geno-mic DNA. J Mol Biol 268(1), 78-94. (Pubitemid 27192680)
-
(1997)
Journal of Molecular Biology
, vol.268
, Issue.1
, pp. 78-94
-
-
Burge, C.1
Karlin, S.2
-
15
-
-
23144452801
-
GeneMark: Web software for gene finding in prokaryotes, eukaryotes and viruses
-
Web Server issue
-
Besemer, J., and Borodovsky, M. (2005) GeneMark: web software for gene finding in prokaryotes, eukaryotes and viruses. Nucleic Acids Res 33(Web Server issue), W451-4.
-
(2005)
Nucleic Acids Res
, vol.33
-
-
Besemer, J.1
Borodovsky, M.2
-
17
-
-
0034065724
-
Ab initio gene finding in Drosophila genomic DNA
-
DOI 10.1101/gr.10.4.516
-
Salamov, A. A., and Solovyev, V. V. (2000) Ab initio gene finding in Drosophila geno-mic DNA. Genome Res 10(4), 516-22. (Pubitemid 30259081)
-
(2000)
Genome Research
, vol.10
, Issue.4
, pp. 516-522
-
-
Salamov, A.A.1
Solovyev, V.V.2
-
18
-
-
0034098729
-
Genome annotation assessment in Drosophila melanogaster
-
DOI 10.1101/gr.10.4.483
-
Reese, M. G., et al. (2000) Genome annotation assessment in Drosophila melanoga-ster. Genome Res 10(4), 483-501. (Pubitemid 30259078)
-
(2000)
Genome Research
, vol.10
, Issue.4
, pp. 483-501
-
-
Reese, M.G.1
Hartzell, G.2
Harris, N.L.3
Ohler, U.4
Abril, J.F.5
Lewis, S.E.6
-
19
-
-
0037019308
-
Sequence and analysis of chromosome 2 of Dictyostelium discoideum
-
DOI 10.1038/nature00847
-
Glockner, G., et al. (2002) Sequence and analysis of chromosome 2 of Dictyostelium discoideum. Nature 418(6893), 79-85. (Pubitemid 34742574)
-
(2002)
Nature
, vol.418
, Issue.6893
, pp. 79-85
-
-
Glockner, G.1
Eichinger, L.2
Szafranski, K.3
Pachebat, J.A.4
Bankier, A.T.5
Dear, P.H.6
Lehmann, R.7
Baumgart, C.8
Parra, G.9
Abril, J.F.10
Guigo, R.11
Kumpf, K.12
Tunggal, B.13
Cox, E.14
Quail, M.A.15
Platzer, M.16
Rosenthal, A.17
Noegel, A.A.18
-
20
-
-
7244259101
-
Genome duplication in the teleost fish Tetraodon nigrovir-idis reveals the early vertebrate proto-karyotype
-
Jaillon, O., et al. (2004) Genome duplication in the teleost fish Tetraodon nigrovir-idis reveals the early vertebrate proto-karyotype. Nature 431(7011), 946-57.
-
(2004)
Nature
, vol.431
, Issue.7011
, pp. 946-957
-
-
Jaillon, O.1
-
21
-
-
33750858684
-
Global trends of whole-genome duplications revealed by the ciliate Paramecium tetraurelia
-
Aury, J. M., et al. (2006) Global trends of whole-genome duplications revealed by the ciliate Paramecium tetraurelia. Nature 444(7116), 171-8.
-
(2006)
Nature
, vol.444
, Issue.7116
, pp. 171-178
-
-
Aury, J.M.1
-
22
-
-
33748641351
-
EGASP: The human ENCODE Genome Annotation Assessment Project
-
Guigo, R., et al. (2006) EGASP: the human ENCODE Genome Annotation Assessment Project. Genome Biol 7 Suppl 1, S2 1-31.
-
(2006)
Genome Biol
, vol.7
, Issue.SUPPL. 1
-
-
Guigo, R.1
-
23
-
-
34250308428
-
Origin of pheno-types: Genes and transcripts
-
Gingeras, T. R. (2007) Origin of pheno-types: genes and transcripts. Genome Res 17(6), 682-90.
-
(2007)
Genome Res
, vol.17
, Issue.6
, pp. 682-690
-
-
Gingeras, T.R.1
-
24
-
-
0036429269
-
Finding signals that regulate alternative splicing in the post-genomic era
-
Ladd, A. N., and Cooper, T. A. (2002) Finding signals that regulate alternative splicing in the post-genomic era. Genome Biol 3(11), reviews0008.
-
(2002)
Genome Biol
, vol.3
, Issue.11
-
-
Ladd, A.N.1
Cooper, T.A.2
-
25
-
-
0029894345
-
Knowing when not to stop: Selenocysteine incorporation in eukaryotes
-
DOI 10.1016/0968-0004(96)10025-6
-
Low, S. C., and Berry, M. J. (1996) Knowing when not to stop: selenocysteine incorporation in eukaryotes. Trends Biochem Sci 21(6), 203-8. (Pubitemid 26191223)
-
(1996)
Trends in Biochemical Sciences
, vol.21
, Issue.6
, pp. 203-208
-
-
Low, S.C.1
Berry, M.J.2
-
26
-
-
1242321034
-
Reconsidering the evolution of eukaryotic selenoproteins: A novel nonmammalian family with scattered phylogenetic distribution
-
DOI 10.1038/sj.embor.7400036
-
Castellano, S., et al. (2004) Reconsidering the evolution of eukaryotic selenoproteins: a novel nonmammalian family with scattered phylogenetic distribution. EMBO Rep 5(1), 71-7. (Pubitemid 38228531)
-
(2004)
EMBO Reports
, vol.5
, Issue.1
, pp. 71-77
-
-
Castellano, S.1
Novoselov, S.V.2
Kryukov, G.V.3
Lescure, A.4
Blanco, E.5
Krol, A.6
Gladyshev, V.N.7
Guigo, R.8
-
27
-
-
33846057724
-
NCBI reference sequences (RefSeq): A curated non-redundant sequence database of genomes, transcripts and proteins
-
DOI 10.1093/nar/gkl842
-
Pruitt, K. D., Tatusova, T., and Maglott, D. R. (2007) NCBI reference sequences (RefSeq): a curated non-redundant sequence database of genomes, transcripts and proteins. Nucleic Acids Res 35(Data-base issue), D61-5. (Pubitemid 46056171)
-
(2007)
Nucleic Acids Research
, vol.35
, Issue.SUPPL. 1
-
-
Pruitt, K.D.1
Tatusova, T.2
Maglott, D.R.3
-
28
-
-
33846040145
-
FlyBase: Genomes by the dozen
-
DOI 10.1093/nar/gkl827
-
Crosby, M. A., et al. (2007) FlyBase: genomes by the dozen. Nucleic Acids Res 35(Database issue), D486-91. (Pubitemid 46056256)
-
(2007)
Nucleic Acids Research
, vol.35
, Issue.SUPPL. 1
-
-
Crosby, M.A.1
Goodman, J.L.2
Strelets, V.B.3
Zhang, P.4
Gelbart, W.M.5
-
29
-
-
0032456609
-
Assembling genes from predicted exons in linear time with dynamic programming
-
Guigo, R. (1998) Assembling genes from predicted exons in linear time with dynamic programming.J Comput Biol 5(4), 681-702. (Pubitemid 29095271)
-
(1998)
Journal of Computational Biology
, vol.5
, Issue.4
, pp. 681-702
-
-
Guigo, R.1
-
30
-
-
0036226603
-
BLAT - The BLAST-like alignment tool
-
DOI 10.1101/gr.229202. Article published online before March 2002
-
Kent, W. J. (2002) BLAT - the BLAST-like alignment tool. Genome Res 12(4), 656-64. (Pubitemid 34308645)
-
(2002)
Genome Research
, vol.12
, Issue.4
, pp. 656-664
-
-
Kent, W.J.1
-
31
-
-
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(22), 4673-80. (Pubitemid 24354800)
-
(1994)
Nucleic Acids Research
, vol.22
, Issue.22
, pp. 4673-4680
-
-
Thompson, J.D.1
Higgins, D.G.2
Gibson, T.J.3
-
32
-
-
2442713832
-
GeneWise and Genomewise
-
DOI 10.1101/gr.1865504
-
Birney, E., Clamp, M., and Durbin, R. (2004) GeneWise and Genomewise. Genome Res 14(5), 988-95. (Pubitemid 38660520)
-
(2004)
Genome Research
, vol.14
, Issue.5
, pp. 988-995
-
-
Birney, E.1
Clamp, M.2
Durbin, R.3
-
33
-
-
0033745748
-
Gff2ps: Visualizing genomic annotations
-
Abril, J. F., and Guigo, R. (2000) gff2ps: visualizing genomic annotations. Bioinfor-matics 16(8), 743-4.
-
(2000)
Bioinfor-matics
, vol.16
, Issue.8
, pp. 743-744
-
-
Abril, J.F.1
Guigo, R.2
-
35
-
-
0343986271
-
Relief of gene repression by Torso RTK signaling: Role of capicua in Drosophila terminal and dorsoventral patterning
-
Jimenez, G., et al. (2000) Relief of gene repression by torso RTK signaling: role of capicua in Drosophila terminal and dorso-ventral patterning. Genes Dev 14(2), 224-31. (Pubitemid 30070987)
-
(2000)
Genes and Development
, vol.14
, Issue.2
, pp. 224-231
-
-
Jimenez, G.1
Guichet, A.2
Ephrussi, A.3
Casanova, J.4
-
36
-
-
0034708480
-
The genome sequence of Drosophila melanogaster
-
DOI 10.1126/science.287.5461.2185
-
Adams, M. D., et al. (2000) The genome sequence of Drosophila melanogaster. Science 287(5461), 2185-95. (Pubitemid 30177013)
-
(2000)
Science
, vol.287
, Issue.5461
, pp. 2185-2195
-
-
Adams, M.D.1
Celniker, S.E.2
Holt, R.A.3
Evans, C.A.4
Gocayne, J.D.5
Amanatides, P.G.6
Scherer, S.E.7
Li, P.W.8
Hoskins, R.A.9
Galle, R.F.10
George, R.A.11
Lewis, S.E.12
Richards, S.13
Ashburner, M.14
Henderson, S.N.15
Sutton, G.G.16
Wortman, J.R.17
Yandell, M.D.18
Zhang, Q.19
Chen, L.X.20
Brandon, R.C.21
Rogers, Y.C.22
Blazej, R.G.23
Champe, M.24
Pfeiffer, B.D.25
Wan, K.H.26
Doyle, C.27
Baxter, E.G.28
Helt, G.29
Nelson, C.R.30
Gabor Miklos, G.L.31
Abril, J.F.32
Agbayani, A.33
An, H.-J.34
Andrews-Pfannkoch, C.35
Baldwin, D.36
Ballew, R.M.37
Basu, A.38
Baxendale, J.39
Bayraktaroglu, L.40
Beasley, E.M.41
Beeson, K.Y.42
Benos, P.V.43
Berman, B.P.44
Bhandari, D.45
Bolshakov, S.46
Borkova, D.47
Botchan, M.R.48
Bouck, J.49
Brokstein, P.50
Brottier, P.51
Burtis, K.C.52
Busam, D.A.53
Butler, H.54
Cadieu, E.55
Center, A.56
Chandra, I.57
Cherry, J.M.58
Cawley, S.59
Dahlke, C.60
Davenport, L.B.61
Davies, P.62
De Pablos, B.63
Delcher, A.64
Deng, Z.65
Mays, A.D.66
Dew, I.67
Dietz, S.M.68
Dodson, K.69
Doup, L.E.70
Downes, M.71
Dugan-Rocha, S.72
Dunkov, B.C.73
Dunn, P.74
Durbin, K.J.75
Evangelista, C.C.76
Ferraz, C.77
Ferriera, S.78
Fleischmann, W.79
Fosler, C.80
Gabrielian, A.E.81
Garg, N.S.82
Gelbart, W.M.83
Glasser, K.84
Glodek, A.85
Gong, F.86
Gorrell, J.H.87
Gu, Z.88
Guan, P.89
Harris, M.90
Harris, N.L.91
Harvey, D.92
Heiman, T.J.93
Hernandez, J.R.94
Houck, J.95
Hostin, D.96
Houston, K.A.97
Howland, T.J.98
Wei, M.-H.99
more..
-
37
-
-
0037268583
-
Comparative gene prediction in human and mouse
-
Parra, G., et al. (2003) Comparative gene prediction in human and mouse. Genome Res 13(1), 108-17.
-
(2003)
Genome Res
, vol.13
, Issue.1
, pp. 108-117
-
-
Parra, G.1
-
38
-
-
3242701258
-
The effects of evolutionary distance on TWINSCAN, an algorithm for pair-wise comparative gene prediction
-
Wang, M., Buhler, J., and Brent, M. R. (2003) The effects of evolutionary distance on TWINSCAN, an algorithm for pair-wise comparative gene prediction. Cold Spring Harb Symp Quant Biol 68, 125-30. (Pubitemid 38955559)
-
(2003)
Cold Spring Harbor Symposia on Quantitative Biology
, vol.68
, pp. 125-130
-
-
Wang, M.1
Buhler, J.2
Brent, M.R.3
-
39
-
-
17244379179
-
The many faces of sequence alignment
-
DOI 10.1093/bib/6.1.6
-
Batzoglou, S. (2005) The many faces of sequence alignment. Brief Bioinform 6(1), 6-22. (Pubitemid 40528576)
-
(2005)
Briefings in Bioinformatics
, vol.6
, Issue.1
, pp. 6-22
-
-
Batzoglou, S.1
|