-
1
-
-
0025183708
-
Basic local alignment search tool
-
Altschul, S., Gish, W., Miller, W., Myers, E., and Lipman, D. (1990). Basic local alignment search tool. JOURNAL OF MOLECULAR BIOLOGY, 215(3), 403-410.
-
(1990)
Journal of Molecular Biology
, vol.215
, Issue.3
, pp. 403-410
-
-
Altschul, S.1
Gish, W.2
Miller, W.3
Myers, E.4
Lipman, D.5
-
2
-
-
0000241874
-
Genmark - parallel gene recognition for both dna strands
-
Borodovsky, M. and Mcininch, J. (1993). Genmark - parallel gene recognition for both dna strands. COMPUTERS & CHEMISTRY, 17(2), 123-133.
-
(1993)
Computers & Chemistry
, vol.17
, Issue.2
, pp. 123-133
-
-
Borodovsky, M.1
Mcininch, J.2
-
3
-
-
80051895746
-
Genmark - parallel gene recognition for both dna strands
-
TELLURIDE, CO, JUL 19-AUG 02, 1992
-
Borodovsky, M. and Mcininch, J. (1993). Genmark - parallel gene recognition for both dna strands, 2ND INTERNATIONAL WORKSHOP ON OPEN PROBLEMS OF COMPUTATIONAL MOLECULAR BIOLOGY, TELLURIDE, CO, JUL 19-AUG 02, 1992.
-
(1993)
International Workshop on Open Problems of Computational Molecular Biology
-
-
Borodovsky, M.1
Mcininch, J.2
-
4
-
-
18744414524
-
GOAnno: GO annotation based on multiple alignment
-
DOI 10.1093/bioinformatics/bti252
-
Chalmel, F., Lardenois, A., Thompson, J., Muller, J., Sahel, J., Leveillard, T., and Poch, O. (2005). Goanno: Go annotation based on multiple alignment. BIOINFORMATICS, 21(9), 2095-2096. doi: 10.1093/bioinformatics/bti252. (Pubitemid 40668053)
-
(2005)
Bioinformatics
, vol.21
, Issue.9
, pp. 2095-2096
-
-
Chalmel, F.1
Lardenois, A.2
Thompson, J.D.3
Muller, J.4
Sahel, J.-A.5
Leveillard, T.6
Poch, O.7
-
5
-
-
25444512373
-
Integrating alternative splicing detection into gene prediction
-
DOI 10.1186/1471-2105-6-25
-
Foissac, S. and Schiex, T. (2005). Integrating alternative splicing detection into gene prediction. BMC Bioinformatics, 6. doi:10.1186/1471-2105-6- 25. (Pubitemid 41357989)
-
(2005)
BMC Bioinformatics
, vol.6
, pp. 25
-
-
Foissac, S.1
Schiex, T.2
-
6
-
-
27144533653
-
Reconstructing the metabolic network of a bacterium from its genome
-
DOI 10.1016/j.tim.2005.09.001, PII S0966842X05002490
-
Francke, C., Siezen, R., and Teusink, B. (2005). Reconstructing the metabolic network of a bacterium from its genome. TRENDS IN MICROBIOLOGY, 13(11), 550-558. doi:10.1016/j.tim.2005.09.001. (Pubitemid 41506897)
-
(2005)
Trends in Microbiology
, vol.13
, Issue.11
, pp. 550-558
-
-
Francke, C.1
Siezen, R.J.2
Teusink, B.3
-
7
-
-
51749088608
-
Biojava: An open-source framework for bioinformatics
-
doi:10.1093/bioinformatics/btn397
-
Holland, R.C.G., Down, T.A., Pocock, M., Prlic, A., Huen, D., James, K., Foisy, S., Draeger, A., Yates, A., Heuer, M., and Schreiber, M.J. (2008). Biojava: an open-source framework for bioinformatics. BIOINFORMATICS, 24(18), 2096-2097. doi:10.1093/bioinformatics/btn397.
-
(2008)
Bioinformatics
, vol.24
, Issue.18
, pp. 2096-2097
-
-
Holland, R.C.G.1
Down, T.A.2
Pocock, M.3
Prlic, A.4
Huen, D.5
James, K.6
Foisy, S.7
Draeger, A.8
Yates, A.9
Heuer, M.10
Schreiber, M.J.11
-
8
-
-
0037342537
-
The systems biology markup language (SBML): A medium for representation and exchange of biochemical network models
-
DOI 10.1093/bioinformatics/btg015
-
Hucka, M. and et al (2003). The systems biology markup language (sbml): a medium for representation and exchange of biochemical network models. BIOINFORMATICS, 19(4), 524-531. doi: 10.1093/bioinformatics/btg015. (Pubitemid 36336519)
-
(2003)
Bioinformatics
, vol.19
, Issue.4
, pp. 524-531
-
-
Hucka, M.1
Finney, A.2
Sauro, H.M.3
Bolouri, H.4
Doyle, J.C.5
Kitano, H.6
Arkin, A.P.7
Bornstein, B.J.8
Bray, D.9
Cornish-Bowden, A.10
Cuellar, A.A.11
Dronov, S.12
Gilles, E.D.13
Ginkel, M.14
Gor, V.15
Goryanin, I.I.16
Hedley, W.J.17
Hodgman, T.C.18
Hofmeyr, J.-H.19
Hunter, P.J.20
Juty, N.S.21
Kasberger, J.L.22
Kremling, A.23
Kummer, U.24
Le Novere, N.25
Loew, L.M.26
Lucio, D.27
Mendes, P.28
Minch, E.29
Mjolsness, E.D.30
Nakayama, Y.31
Nelson, M.R.32
Nielsen, P.F.33
Sakurada, T.34
Schaff, J.C.35
Shapiro, B.E.36
Shimizu, T.S.37
Spence, H.D.38
Stelling, J.39
Takahashi, K.40
Tomita, M.41
Wagner, J.42
Wang, J.43
more..
-
9
-
-
15844394036
-
Function prediction for hypothetical proteins in yeast saccharomyces cerevisiae using multiple sources of high-throughput data
-
8th World Multi-Conference on Systemics, Cybernetics and Informatics, Orlando, FL, JUL 18-21, 2004
-
Joshi, T., Chen, Y., Becker, J., Alexandrov, N., and Xu, D. (2004). Function prediction for hypothetical proteins in yeast saccharomyces cerevisiae using multiple sources of high-throughput data. OMICS: A Journal of Integrative Biology, 17-22. 8th World Multi-Conference on Systemics, Cybernetics and Informatics, Orlando, FL, JUL 18-21, 2004.
-
(2004)
OMICS: A Journal of Integrative Biology
, pp. 17-22
-
-
Joshi, T.1
Chen, Y.2
Becker, J.3
Alexandrov, N.4
Xu, D.5
-
10
-
-
0033982936
-
KEGG: Kyoto encyclopedia of genes and genomes
-
Kanehisa, M. and Goto, S. (2000). Kegg: Kyoto encyclopedia of genes and genomes. NUCLEIC ACIDS RESEARCH, 28(1), 27-30. (Pubitemid 30047706)
-
(2000)
Nucleic Acids Research
, vol.28
, Issue.1
, pp. 27-30
-
-
Kanehisa, M.1
Goto, S.2
-
11
-
-
33846904978
-
GISMO - Gene identification using a support vector machine for ORF classification
-
DOI 10.1093/nar/gkl1083
-
Krause, L., McHardy, A.C., Nattkemper, T.W., Puehler, A., Stoye, J., and Meyer, F. (2007). Gismo - gene identication using a support vector machine for orf classication. NUCLEIC ACIDS RESEARCH, 35(2), 540-549. doi:10.1093/nar/ gkl1083. (Pubitemid 46232070)
-
(2007)
Nucleic Acids Research
, vol.35
, Issue.2
, pp. 540-549
-
-
Krause, L.1
McHardy, A.C.2
Nattkemper, T.W.3
Puhler, A.4
Stoye, J.5
Meyer, F.6
-
12
-
-
0021919480
-
Rapid and sensitive protein similarity searches
-
Lipman, D. and Pearson, W. (1985). Rapid and sensitive protein similarity searches. SCIENCE, 227(4693), 1435-1441. (Pubitemid 15146986)
-
(1985)
Science
, vol.227
, Issue.4693
, pp. 1435-1441
-
-
Lipman, D.J.1
Pearson, W.R.2
-
13
-
-
33644873697
-
The integrated microbial genomes (img) system
-
doi: 10.1093/nar/gkj024
-
Markowitz, V.M., Korzeniewski, F., Palaniappan, K., Szeto, E., Werner, G., Padki, A., Zhao, X., Dubchak, I., Hugenholtz, P., Anderson, I., Lykidis, A., Mavromatis, K., Ivanova, N., and Kyrpides, N.C. (2006). The integrated microbial genomes (img) system. NUCLEIC ACIDS RESEARCH, 34(Sp. Iss. SI), D344-D348. doi: 10.1093/nar/gkj024.
-
(2006)
Nucleic Acids Research
, vol.34
, Issue.SPEC. ISSUE SI
-
-
Markowitz, V.M.1
Korzeniewski, F.2
Palaniappan, K.3
Szeto, E.4
Werner, G.5
Padki, A.6
Zhao, X.7
Dubchak, I.8
Hugenholtz, P.9
Anderson, I.10
Lykidis, A.11
Mavromatis, K.12
Ivanova, N.13
Kyrpides, N.C.14
-
14
-
-
36949032098
-
Annotation, comparison and databases for hundreds of bacterial genomes
-
DOI 10.1016/j.resmic.2007.09.009, PII S0923250807001829, Microbial Genomics
-
Medigue, C. and Moszer, I. (2007). Annotation, comparison and databases for hundreds of bacterial genomes. RESEARCH IN MICROBIOLOGY, 158(10), 724-736. doi:10.1016/j.resmic.2007.09.009. (Pubitemid 350245437)
-
(2007)
Research in Microbiology
, vol.158
, Issue.10
, pp. 724-736
-
-
Medigue, C.1
Moszer, I.2
-
15
-
-
0036175276
-
The past, present and future of genome-wide re-annotation
-
doi:10.1186/gb-2002-3-2-comment2001, URL
-
Ouzounis, C. and Karp, P. (2002). The past, present and future of genome-wide re-annotation. Genome Biology, 3(2). doi:10.1186/gb-2002-3-2- comment2001. URL http://genomebiology.com/2002/3/2/comment/2001.
-
(2002)
Genome Biology
, vol.3
, Issue.2
-
-
Ouzounis, C.1
Karp, P.2
-
16
-
-
40549127097
-
Design and application of genome-scale reconstructed metabolic models
-
(Clifton, NJ), 409
-
Rocha, I., Förster, J., and Nielsen, J. (2008). Design and application of genome-scale reconstructed metabolic models. Methods in molecular biology (Clifton, NJ), 416, 409.
-
(2008)
Methods in Molecular Biology
, vol.416
-
-
Rocha, I.1
Förster, J.2
Nielsen, J.3
-
17
-
-
77950960250
-
OptFlux: An open-source software platform for in silico metabolic engineering
-
Rocha, I., Maia, P., Evangelista, P., Vilaca, P., Soares, S., Pinto, J., Nielsen, J., Patil, K., Ferreira, E., and Rocha, M. (2010). OptFlux: an open-source software platform for in silico metabolic engineering. BMC Systems Biology, 4(1), 45.
-
(2010)
BMC Systems Biology
, vol.4
, Issue.1
, pp. 45
-
-
Rocha, I.1
Maia, P.2
Evangelista, P.3
Vilaca, P.4
Soares, S.5
Pinto, J.6
Nielsen, J.7
Patil, K.8
Ferreira, E.9
Rocha, M.10
-
18
-
-
0032518163
-
Microbial gene identification using interpolated Markov models
-
DOI 10.1093/nar/26.2.544
-
Salzberg, S., Delcher, A., Kasif, S., and White, O. (1998). Microbial gene identication using interpolated markov models. NUCLEIC ACIDS RESEARCH, 26(2), 544-548. (Pubitemid 28291582)
-
(1998)
Nucleic Acids Research
, vol.26
, Issue.2
, pp. 544-548
-
-
Salzberg, S.L.1
Deicher, A.L.2
Kasif, S.3
White, O.4
-
19
-
-
34147162107
-
Genome re-annotation: A wiki solution?
-
DOI 10.1186/gb-2007-8-1-102
-
Salzberg, S.L. (2007). Genome re-annotation: a wiki solution? GENOME BIOLOGY, 8(1). doi:10.1186/gb- 2007-8-1-102. (Pubitemid 351910987)
-
(2007)
Genome Biology
, vol.8
, Issue.1
, pp. 102
-
-
Salzberg, S.L.1
-
20
-
-
18644368714
-
The Bioperl toolkit: Perl modules for the life sciences
-
DOI 10.1101/gr.361602
-
Stajich, J. and et al (2002). The bioperl toolkit: Perl modules for the life sciences. GENOME RESEARCH, 12(10), 1611-1618. doi:10.1101/gr.361602. (Pubitemid 35175100)
-
(2002)
Genome Research
, vol.12
, Issue.10
, pp. 1611-1618
-
-
Stajich, J.E.1
Block, D.2
Boulez, K.3
Brenner, S.E.4
Chervitz, S.A.5
Dagdigian, C.6
Fuellen, G.7
Gilbert, J.G.R.8
Korf, I.9
Lapp, H.10
Lehvaslaiho, H.11
Matsalla, C.12
Mungall, C.J.13
Osborne, B.I.14
Pocock, M.R.15
Schattner, P.16
Senger, M.17
Stein, L.D.18
Stupka, E.19
Wilkinson, M.D.20
Birney, E.21
more..
-
21
-
-
34250180888
-
Restauro-G: A rapid genome re-annotation system for comparative genomics
-
DOI 10.1016/S1672-0229(07)60014-X, PII S167202290760014X
-
Tamaki, S., Arakawa, K., Kono, N., and Tomita, M. (2007). Restauro-G: a rapid genome re-annotation system for comparative genomics. Genomics, Proteomics & Bioinformatics, 5(1), 53-58. (Pubitemid 46899647)
-
(2007)
Genomics, Proteomics and Bioinformatics
, vol.5
, Issue.1
, pp. 53-58
-
-
Tamaki, S.1
Arakawa, K.2
Kono, N.3
Tomita, M.4
-
22
-
-
31844453162
-
Gene-function wiki would let biologists pool worldwide resources [1]
-
DOI 10.1038/439534a, PII 439534A
-
Wang, K. (2006). Gene-function wiki would let biologists pool worldwide resources. NATURE, 439(7076), 534. doi:10.1038/439534a. (Pubitemid 43185362)
-
(2006)
Nature
, vol.439
, Issue.7076
, pp. 534
-
-
Wang, K.1
|