-
1
-
-
10244239321
-
Life with 6000 genes
-
Goffeau A., Barrell B.G., Bussey H., Davis R.W., Dujon B., Feldmann H., Galibert F., Hoheisel J.D., Jacq C., Johnston M., et al. Life with 6000 genes. Science 274 (1996) 563-567
-
(1996)
Science
, vol.274
, pp. 563-567
-
-
Goffeau, A.1
Barrell, B.G.2
Bussey, H.3
Davis, R.W.4
Dujon, B.5
Feldmann, H.6
Galibert, F.7
Hoheisel, J.D.8
Jacq, C.9
Johnston, M.10
-
2
-
-
0032509302
-
Genome sequence of the nematode C. elegans: a platform for investigating biology
-
C. elegans Sequencing Consortium
-
C. elegans Sequencing Consortium. Genome sequence of the nematode C. elegans: a platform for investigating biology. Science 282 (1998) 2012-2018
-
(1998)
Science
, vol.282
, pp. 2012-2018
-
-
-
3
-
-
0034708480
-
The genome sequence of Drosophila melanogaster
-
Adams M.D., Celniker S.E., Holt R.A., Evans C.A., Gocayne J.D., Amanatides P.G., Scherer S.E., Li P.W., Hoskins R.A., Galle R.F., et al. The genome sequence of Drosophila melanogaster. Science 287 (2000) 2185-2195
-
(2000)
Science
, vol.287
, 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
-
4
-
-
0034649566
-
Analysis of the genome sequence of the flowering plant Arabidopsis thaliana
-
The Arabidopsis Genome Initiative. Analysis of the genome sequence of the flowering plant Arabidopsis thaliana. Nature 408 (2000) 768-815
-
(2000)
Nature
, vol.408
, pp. 768-815
-
-
The Arabidopsis Genome Initiative1
-
5
-
-
2042437650
-
Initial sequencing and analysis of the human genome
-
International Human Genome Sequencing Consortium. Initial sequencing and analysis of the human genome. Nature 409 (2001) 860-921
-
(2001)
Nature
, vol.409
, pp. 860-921
-
-
International Human Genome Sequencing Consortium1
-
6
-
-
1542563409
-
Initial sequencing and comparative analysis of the mouse genome
-
Mouse Genome Sequencing Consortium. Initial sequencing and comparative analysis of the mouse genome. Nature 420 (2002) 520-562
-
(2002)
Nature
, vol.420
, pp. 520-562
-
-
Mouse Genome Sequencing Consortium1
-
7
-
-
0031586003
-
Prediction of complete gene structures in human genomic DNA
-
Burge C., and Karlin S. Prediction of complete gene structures in human genomic DNA. J Mol Biol 268 (1997) 78-94
-
(1997)
J Mol Biol
, vol.268
, pp. 78-94
-
-
Burge, C.1
Karlin, S.2
-
9
-
-
8844252293
-
TigrScan and GlimmerHMM: two open source ab initio eukaryotic gene-finders
-
Majoros W.H., Pertea M., and Salzberg S.L. TigrScan and GlimmerHMM: two open source ab initio eukaryotic gene-finders. Bioinformatics 20 (2004) 2878-2879
-
(2004)
Bioinformatics
, vol.20
, pp. 2878-2879
-
-
Majoros, W.H.1
Pertea, M.2
Salzberg, S.L.3
-
10
-
-
2942544417
-
Gene finding in novel genomes
-
Korf I. Gene finding in novel genomes. BMC Bioinformatics 5 (2004) 59-68
-
(2004)
BMC Bioinformatics
, vol.5
, pp. 59-68
-
-
Korf, I.1
-
11
-
-
17844368081
-
Closing in on the C. elegans ORFeome by cloning TWINSCAN predictions
-
This paper demonstrates the advantage of comparative analysis over ab initio gene model prediction. The study shows that the new genes identified by TwinScan are more divergent than previously annotated models, suggesting that population genetic parameters such as Ka/Ks may be informative in gene prediction frameworks.
-
Wei C., Lamesch P., Arumugam M., Rosenberg J., Hu P., Vidal M., and Brent M.R. Closing in on the C. elegans ORFeome by cloning TWINSCAN predictions. Genome Res 15 (2005) 577-582. This paper demonstrates the advantage of comparative analysis over ab initio gene model prediction. The study shows that the new genes identified by TwinScan are more divergent than previously annotated models, suggesting that population genetic parameters such as Ka/Ks may be informative in gene prediction frameworks.
-
(2005)
Genome Res
, vol.15
, pp. 577-582
-
-
Wei, C.1
Lamesch, P.2
Arumugam, M.3
Rosenberg, J.4
Hu, P.5
Vidal, M.6
Brent, M.R.7
-
12
-
-
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., Keibler E., Lyle R., Ucla C., et al. Comparison of mouse and human genomes followed by experimental verification yields an estimated 1,019 additional genes. Proc Natl Acad Sci USA 100 (2003) 1140-1145
-
(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
Keibler, E.8
Lyle, R.9
Ucla, C.10
-
13
-
-
24644516306
-
A brief review of computational gene prediction methods
-
Wang Z., Chen Y., and Li Y. A brief review of computational gene prediction methods. Genomics Proteomics Bioinformatics 2 (2004) 216-221
-
(2004)
Genomics Proteomics Bioinformatics
, vol.2
, pp. 216-221
-
-
Wang, Z.1
Chen, Y.2
Li, Y.3
-
14
-
-
0033381623
-
Evaluation of gene prediction software using a genomic data set: application to Arabidopsis thaliana sequences
-
Pavy N., Rombauts S., Dehais P., Mathe C., Ramana D.V.V., Leroy P., and Rouze P. Evaluation of gene prediction software using a genomic data set: application to Arabidopsis thaliana sequences. Bioinformatics 15 (1999) 887-899
-
(1999)
Bioinformatics
, vol.15
, pp. 887-899
-
-
Pavy, N.1
Rombauts, S.2
Dehais, P.3
Mathe, C.4
Ramana, D.V.V.5
Leroy, P.6
Rouze, P.7
-
15
-
-
20244383989
-
Evaluation of five ab initio gene prediction programs for the discovery of maize genes
-
Yao H., Guo L., Fu Y., Borsuk L.A., Wen T.-J., Skibbe D.S., Cui X., Scheffler B.E., Cao J., Emrich S.J., et al. Evaluation of five ab initio gene prediction programs for the discovery of maize genes. Plant Mol Biol 57 (2005) 445-460
-
(2005)
Plant Mol Biol
, vol.57
, pp. 445-460
-
-
Yao, H.1
Guo, L.2
Fu, Y.3
Borsuk, L.A.4
Wen, T.-J.5
Skibbe, D.S.6
Cui, X.7
Scheffler, B.E.8
Cao, J.9
Emrich, S.J.10
-
16
-
-
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. The Ensembl genome database project. Nucleic Acids Res 30 (2002) 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
-
18
-
-
3042764025
-
ESTMAP: a system for expressed sequence tags mapping on genomic sequences
-
Milanesi L., and Rogozin I.B. ESTMAP: a system for expressed sequence tags mapping on genomic sequences. IEEE Trans Nanobioscience 2 (2003) 75-78
-
(2003)
IEEE Trans Nanobioscience
, vol.2
, pp. 75-78
-
-
Milanesi, L.1
Rogozin, I.B.2
-
19
-
-
10944247962
-
EAnnot: a genome annotation tool using experimental evidence
-
Ding L., Sabo A., Berkowicz N., Meyer R.R., Shotland Y., Johnson M.R., Pepin K.H., Wilson R.K., and Spieth J. EAnnot: a genome annotation tool using experimental evidence. Genome Res 14 (2004) 2503-2509
-
(2004)
Genome Res
, vol.14
, pp. 2503-2509
-
-
Ding, L.1
Sabo, A.2
Berkowicz, N.3
Meyer, R.R.4
Shotland, Y.5
Johnson, M.R.6
Pepin, K.H.7
Wilson, R.K.8
Spieth, J.9
-
20
-
-
2442690356
-
Gene structure prediction from consensus spliced alignment of multiple ESTs matching the same genomic locus
-
Brendel V., Xing L., and Zhu W. Gene structure prediction from consensus spliced alignment of multiple ESTs matching the same genomic locus. Bioinformatics 20 (2004) 1157-1169
-
(2004)
Bioinformatics
, vol.20
, pp. 1157-1169
-
-
Brendel, V.1
Xing, L.2
Zhu, W.3
-
21
-
-
17444437765
-
Integrating genomic homology into gene structure prediction
-
Korf I., Flicek P., Duan D., and Brent M.R. Integrating genomic homology into gene structure prediction. Bioinformatics 17 (2001) S140-S148
-
(2001)
Bioinformatics
, vol.17
-
-
Korf, I.1
Flicek, P.2
Duan, D.3
Brent, M.R.4
-
22
-
-
0037350957
-
SLAM: cross-species gene finding and alignment with a generalized pair hidden Markov model
-
Alexandersson M., Cawley S., and Pachter L. SLAM: cross-species gene finding and alignment with a generalized pair hidden Markov model. Genome Res 13 (2003) 496-502
-
(2003)
Genome Res
, vol.13
, pp. 496-502
-
-
Alexandersson, M.1
Cawley, S.2
Pachter, L.3
-
23
-
-
0037268583
-
Comparative gene prediction in human and mouse
-
Parra G., Agarwal P., Abril J.F., Wiehe T., Fickett J.W., and Guigo R. Comparative gene prediction in human and mouse. Genome Res 13 (2003) 108-117
-
(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
-
24
-
-
0346888663
-
Gene structure prediction in syntenic DNA segments
-
Moore J.E., and Lake J.A. Gene structure prediction in syntenic DNA segments. Nucleic Acids Res 31 (2003) 7271-7279
-
(2003)
Nucleic Acids Res
, vol.31
, pp. 7271-7279
-
-
Moore, J.E.1
Lake, J.A.2
-
25
-
-
26844488764
-
EVOPRINTER, a multigenomic comparative tool for rapid identification of functionally important DNA
-
This study demonstrates that multiple species comparison can achieve near single nucleotide resolution in the identification of conserved features, both coding and noncoding.
-
Odenwald W.F., Rasband W., Kuzin A., and Brody T. EVOPRINTER, a multigenomic comparative tool for rapid identification of functionally important DNA. Proc Natl Acad Sci USA 102 (2005) 14700-14705. This study demonstrates that multiple species comparison can achieve near single nucleotide resolution in the identification of conserved features, both coding and noncoding.
-
(2005)
Proc Natl Acad Sci USA
, vol.102
, pp. 14700-14705
-
-
Odenwald, W.F.1
Rasband, W.2
Kuzin, A.3
Brody, T.4
-
26
-
-
18744378026
-
Exploring the plant transcriptome through phylogenetic profiling
-
A comparative approach using transcriptome data from within Plantae. The paper effectively highlights the technical challenges associated with plant comparative genomics that arise from segmental and tandem duplications. Approximately 19 000 gene functions are identified; total numbers are comparable for both monocots and eudicots. The paper provides evidence of genome reduction in both A. thaliana and O. sativa.
-
Vandepoele K., and Van de Peer Y. Exploring the plant transcriptome through phylogenetic profiling. Plant Physiol 137 (2005) 31-42. A comparative approach using transcriptome data from within Plantae. The paper effectively highlights the technical challenges associated with plant comparative genomics that arise from segmental and tandem duplications. Approximately 19 000 gene functions are identified; total numbers are comparable for both monocots and eudicots. The paper provides evidence of genome reduction in both A. thaliana and O. sativa.
-
(2005)
Plant Physiol
, vol.137
, pp. 31-42
-
-
Vandepoele, K.1
Van de Peer, Y.2
-
27
-
-
0942287072
-
Proteogenomic mapping as a complementary method to perform genome annotation
-
Jaffe J.D., Berg H.C., and Church G.M. Proteogenomic mapping as a complementary method to perform genome annotation. Proteomics 4 (2004) 59-77
-
(2004)
Proteomics
, vol.4
, pp. 59-77
-
-
Jaffe, J.D.1
Berg, H.C.2
Church, G.M.3
-
28
-
-
0242300620
-
Empirical analysis of transcriptional activity in the Arabidopsis genome
-
Yamada K., Lim J., Dale J.M., Chen H., Shinn P., Palm C.J., Southwick A.M., Wu H.C., Kim C., Nguyen M., et al. Empirical analysis of transcriptional activity in the Arabidopsis genome. Science 302 (2003) 842-846
-
(2003)
Science
, vol.302
, pp. 842-846
-
-
Yamada, K.1
Lim, J.2
Dale, J.M.3
Chen, H.4
Shinn, P.5
Palm, C.J.6
Southwick, A.M.7
Wu, H.C.8
Kim, C.9
Nguyen, M.10
-
29
-
-
0038781885
-
Quantitative estimates of sequence divergence for comparative analyses of Mamm genomes
-
Cooper G.M., Brudno M., Nisc C.S.P., Green E.D., Batzoglou S., and Sidow A. Quantitative estimates of sequence divergence for comparative analyses of Mamm genomes. Genome Res 13 (2003) 813-820
-
(2003)
Genome Res
, vol.13
, pp. 813-820
-
-
Cooper, G.M.1
Brudno, M.2
Nisc, C.S.P.3
Green, E.D.4
Batzoglou, S.5
Sidow, A.6
-
30
-
-
14644390333
-
A model of the statistical power of comparative genome sequence analysis
-
An excellent statistical treatment of the efficacy of multiple species comparisons as applied to gene or sequence feature discovery. The article is well written and clear, even for the non-statistically minded.
-
Eddy S.R. A model of the statistical power of comparative genome sequence analysis. PLoS Biol 3 (2005) e10. An excellent statistical treatment of the efficacy of multiple species comparisons as applied to gene or sequence feature discovery. The article is well written and clear, even for the non-statistically minded.
-
(2005)
PLoS Biol
, vol.3
-
-
Eddy, S.R.1
-
31
-
-
26444578198
-
Transcription factors in rice: a genome-wide comparative analysis between monocots and eudicots
-
Xiong Y., Liu T., Tian C., Sun S., Li J., and Chen M. Transcription factors in rice: a genome-wide comparative analysis between monocots and eudicots. Plant Mol Biol 59 (2005) 191-203
-
(2005)
Plant Mol Biol
, vol.59
, pp. 191-203
-
-
Xiong, Y.1
Liu, T.2
Tian, C.3
Sun, S.4
Li, J.5
Chen, M.6
-
32
-
-
0038349948
-
Sequencing and comparison of yeast species to identify genes and regulatory elements
-
Kellis M., Patterson N., Endrizzi M., Birren B., and Lander E.S. Sequencing and comparison of yeast species to identify genes and regulatory elements. Nature 423 (2003) 241-254
-
(2003)
Nature
, vol.423
, pp. 241-254
-
-
Kellis, M.1
Patterson, N.2
Endrizzi, M.3
Birren, B.4
Lander, E.S.5
-
33
-
-
0030801002
-
Gapped BLAST and PSI-BLAST: a new generation of protein database search programs
-
Altschul S.F., Madden T.L., Schaeffer A.A., Zhang J., Zhang Z., Miller W., and Lipman D.J. Gapped BLAST and PSI-BLAST: a new generation of protein database search programs. Nucleic Acids Res 25 (1997) 3389-3402
-
(1997)
Nucleic Acids Res
, vol.25
, pp. 3389-3402
-
-
Altschul, S.F.1
Madden, T.L.2
Schaeffer, A.A.3
Zhang, J.4
Zhang, Z.5
Miller, W.6
Lipman, D.J.7
-
34
-
-
8744251285
-
Gene prediction and verification in a compact genome with numerous small introns
-
This study uses the fungal pathogen C. neoformans to demonstrate the accuracy that TwinScan can achieve in the prediction of atypical introns. Further, this work shows that TwinScan performance improves when empirical models of intron length are substituted for the geometric probability of intron lengths used in the standard TwinScan/GenScan implementations.
-
Tenney A.E., Brown R.H., Vaske C., Lodge J.K., Doering T.L., and Brent M.R. Gene prediction and verification in a compact genome with numerous small introns. Genome Res 14 (2004) 2330-2335. This study uses the fungal pathogen C. neoformans to demonstrate the accuracy that TwinScan can achieve in the prediction of atypical introns. Further, this work shows that TwinScan performance improves when empirical models of intron length are substituted for the geometric probability of intron lengths used in the standard TwinScan/GenScan implementations.
-
(2004)
Genome Res
, vol.14
, pp. 2330-2335
-
-
Tenney, A.E.1
Brown, R.H.2
Vaske, C.3
Lodge, J.K.4
Doering, T.L.5
Brent, M.R.6
-
35
-
-
0037315819
-
Systematic discovery of new genes in the Saccharomyces cerevisiae genome
-
Kessler M.M., Zeng Q., Hogan S., Cook R., Morales A.J., and Cottarel G. Systematic discovery of new genes in the Saccharomyces cerevisiae genome. Genome Res 13 (2003) 264-271
-
(2003)
Genome Res
, vol.13
, pp. 264-271
-
-
Kessler, M.M.1
Zeng, Q.2
Hogan, S.3
Cook, R.4
Morales, A.J.5
Cottarel, G.6
-
36
-
-
1842818736
-
Accurate identification of novel human genes through simultaneous gene prediction in human, mouse, and rat
-
This study uses SLAM to identify nearly 3700 orthologous triples in the mammalian species. Novel human gene models identified in this study display restricted transcription and tissue specificity, demonstrating an advantage of similarity-based gene prediction over evidence-based prediction.
-
Dewey C., Wu J.Q., Cawley S., Alexandersson M., Gibbs R., and Pachter L. Accurate identification of novel human genes through simultaneous gene prediction in human, mouse, and rat. Genome Res 14 (2004) 661-664. This study uses SLAM to identify nearly 3700 orthologous triples in the mammalian species. Novel human gene models identified in this study display restricted transcription and tissue specificity, demonstrating an advantage of similarity-based gene prediction over evidence-based prediction.
-
(2004)
Genome Res
, vol.14
, pp. 661-664
-
-
Dewey, C.1
Wu, J.Q.2
Cawley, S.3
Alexandersson, M.4
Gibbs, R.5
Pachter, L.6
-
37
-
-
17844378690
-
Whole genome shotgun sequencing of Brassica oleracea and its application to gene discovery and annotation in Arabidopsis
-
This study, and the following reference, use the partial genome sequence of B. oleracea to identify unannotated, transcribed coding sequences in A. thaliana, thereby demonstrating that a substantial proportion of coding sequences remain unidentified in this model system.
-
Ayele M., Haas B.J., Kumar N., Wu H., Xiao Y., Van Aken S., Utterback T.R., Wortman J.R., White O.R., and Town C.D. Whole genome shotgun sequencing of Brassica oleracea and its application to gene discovery and annotation in Arabidopsis. Genome Res 15 (2005) 487-495. This study, and the following reference, use the partial genome sequence of B. oleracea to identify unannotated, transcribed coding sequences in A. thaliana, thereby demonstrating that a substantial proportion of coding sequences remain unidentified in this model system.
-
(2005)
Genome Res
, vol.15
, pp. 487-495
-
-
Ayele, M.1
Haas, B.J.2
Kumar, N.3
Wu, H.4
Xiao, Y.5
Van Aken, S.6
Utterback, T.R.7
Wortman, J.R.8
White, O.R.9
Town, C.D.10
-
39
-
-
12144288780
-
Whole genome sequence comparisons and 'full-length' cDNA sequences: a combined approach to evaluate and improve Arabidopsis genome annotation
-
Castelli V., Aury J.-M., Jaillon O., Wincker P., Clepet C., Menard M., Cruaud C., Quetier F., Scarpelli C., Schachter V., et al. Whole genome sequence comparisons and 'full-length' cDNA sequences: a combined approach to evaluate and improve Arabidopsis genome annotation. Genome Res 14 (2004) 406-413
-
(2004)
Genome Res
, vol.14
, pp. 406-413
-
-
Castelli, V.1
Aury, J.-M.2
Jaillon, O.3
Wincker, P.4
Clepet, C.5
Menard, M.6
Cruaud, C.7
Quetier, F.8
Scarpelli, C.9
Schachter, V.10
-
40
-
-
0035955361
-
An abundant class of tiny RNAs with probable regulatory roles in Caenorhabditis elegans
-
Lau N.C., Lim L.P., Weinstein E.G., and Bartel D.P. An abundant class of tiny RNAs with probable regulatory roles in Caenorhabditis elegans. Science 294 (2001) 858-862
-
(2001)
Science
, vol.294
, pp. 858-862
-
-
Lau, N.C.1
Lim, L.P.2
Weinstein, E.G.3
Bartel, D.P.4
-
41
-
-
3843089328
-
Detection of 91 potential conserved plant microRNAs in Arabidopsis thaliana and Oryza sativa identifies important target genes
-
Bonnet E., Wuyts J., Rouze P., and Van de Peer Y. Detection of 91 potential conserved plant microRNAs in Arabidopsis thaliana and Oryza sativa identifies important target genes. Proc Natl Acad Sci USA 101 (2004) 11511-11516
-
(2004)
Proc Natl Acad Sci USA
, vol.101
, pp. 11511-11516
-
-
Bonnet, E.1
Wuyts, J.2
Rouze, P.3
Van de Peer, Y.4
-
42
-
-
2942672580
-
Computational identification of plant microRNAs and their targets, including a stress-induced miRNA
-
Jones-Rhoades M.W., and Bartel D.P. Computational identification of plant microRNAs and their targets, including a stress-induced miRNA. Mol Cell 14 (2004) 787-799
-
(2004)
Mol Cell
, vol.14
, pp. 787-799
-
-
Jones-Rhoades, M.W.1
Bartel, D.P.2
-
43
-
-
11844262661
-
Phylogenetic shadowing and computational identification of human microRNA genes
-
In this study, phylogenetic shadowing of 10 primate species was applied to identify key structural features of genomic miRNA regions. The analysis was extended to human-mouse and human-rat comparisons for the identification of ∼1000 candidate miRNAs, nearly 700 of which are conserved among vertebrates.
-
Berezikov E., Guryev V., van de Belt J., Wienholds E., Plasterk R.H.A., and Cuppen E. Phylogenetic shadowing and computational identification of human microRNA genes. Cell 120 (2005) 21-24. In this study, phylogenetic shadowing of 10 primate species was applied to identify key structural features of genomic miRNA regions. The analysis was extended to human-mouse and human-rat comparisons for the identification of ∼1000 candidate miRNAs, nearly 700 of which are conserved among vertebrates.
-
(2005)
Cell
, vol.120
, pp. 21-24
-
-
Berezikov, E.1
Guryev, V.2
van de Belt, J.3
Wienholds, E.4
Plasterk, R.H.A.5
Cuppen, E.6
-
44
-
-
27144491328
-
Adaptive evolution of non-coding DNA in Drosophila
-
This study not only identifies conserved non-coding sequences in Drosophila, but provides evidence that a substantial proportion of non-coding DNA is more diverged than predicted under neutrality. Thus, sequence signatures of adaptive evolution also provide a signal for the identification of biologically meaningful non-coding sequences.
-
Andolfatto P. Adaptive evolution of non-coding DNA in Drosophila. Nature 437 (2005) 1149-1152. This study not only identifies conserved non-coding sequences in Drosophila, but provides evidence that a substantial proportion of non-coding DNA is more diverged than predicted under neutrality. Thus, sequence signatures of adaptive evolution also provide a signal for the identification of biologically meaningful non-coding sequences.
-
(2005)
Nature
, vol.437
, pp. 1149-1152
-
-
Andolfatto, P.1
-
45
-
-
1842768392
-
Identification of rat genes by TWINSCAN gene prediction, RT-PCP, and direct sequencing
-
Wu J.Q., Shteynberg D., Arumugam M., Gibbs R.A., and Brent M.R. Identification of rat genes by TWINSCAN gene prediction, RT-PCP, and direct sequencing. Genome Res 14 (2004) 665-671
-
(2004)
Genome Res
, vol.14
, pp. 665-671
-
-
Wu, J.Q.1
Shteynberg, D.2
Arumugam, M.3
Gibbs, R.A.4
Brent, M.R.5
-
46
-
-
3042569597
-
Annotation transfer between genomes: protein-protein interologs and protein-DNA regulogs
-
Yu H., Luscombe N.M., Lu H.X., Zhu X., Xia Y., Han J-DJ, Bertin N., Chung S., Vidal M., and Gerstein M. Annotation transfer between genomes: protein-protein interologs and protein-DNA regulogs. Genome Res 14 (2004) 1107-1118
-
(2004)
Genome Res
, vol.14
, pp. 1107-1118
-
-
Yu, H.1
Luscombe, N.M.2
Lu, H.X.3
Zhu, X.4
Xia, Y.5
Han J-DJ6
Bertin, N.7
Chung, S.8
Vidal, M.9
Gerstein, M.10
-
47
-
-
0036226603
-
BLAT: The BLAST-like alignment tool
-
Kent W.J. BLAT: The BLAST-like alignment tool. Genome Res 12 (2002) 656-664
-
(2002)
Genome Res
, vol.12
, pp. 656-664
-
-
Kent, W.J.1
-
48
-
-
0000508290
-
Estimate of human gene number provided by genome-wide analysis using Tetraodon nigroviridis DNA sequence
-
Roest Crollius H., Jaillon O., Bernot A., Dasilva C., Bouneau L., Fischer C., Fizames C., Wincker P., Brottier P., Quetier F., et al. Estimate of human gene number provided by genome-wide analysis using Tetraodon nigroviridis DNA sequence. Nat Genet 25 (2000) 235-238
-
(2000)
Nat Genet
, vol.25
, pp. 235-238
-
-
Roest Crollius, H.1
Jaillon, O.2
Bernot, A.3
Dasilva, C.4
Bouneau, L.5
Fischer, C.6
Fizames, C.7
Wincker, P.8
Brottier, P.9
Quetier, F.10
-
49
-
-
0036772510
-
Comparative ab initio prediction of gene structures using pair HMMs
-
Meyer I.M., and Durbin R. Comparative ab initio prediction of gene structures using pair HMMs. Bioinformatics 18 (2002) 1309-1318
-
(2002)
Bioinformatics
, vol.18
, pp. 1309-1318
-
-
Meyer, I.M.1
Durbin, R.2
-
50
-
-
1342263801
-
Gene structure conservation aids similarity based gene prediction
-
Meyer I.M., and Durbin R. Gene structure conservation aids similarity based gene prediction. Nucleic Acids Res 32 (2004) 776-783
-
(2004)
Nucleic Acids Res
, vol.32
, pp. 776-783
-
-
Meyer, I.M.1
Durbin, R.2
-
52
-
-
18744364746
-
Efficient implementation of a generalized pair hidden Markov model for comparative gene finding
-
Majoros W.H., Pertea M., and Salzberg S.L. Efficient implementation of a generalized pair hidden Markov model for comparative gene finding. Bioinformatics 21 (2005) 1782-1788
-
(2005)
Bioinformatics
, vol.21
, pp. 1782-1788
-
-
Majoros, W.H.1
Pertea, M.2
Salzberg, S.L.3
|