-
1
-
-
19144367138
-
Prediction of functional modules based on comparative genome analysis and Gene Ontology application
-
Wu,H., Su,Z., Mao,F., Olman,V. and Xu,Y. (2005) Prediction of functional modules based on comparative genome analysis and Gene Ontology application. Nucleic Acids Res., 33, 2822-2837.
-
(2005)
Nucleic Acids Res.
, vol.33
, pp. 2822-2837
-
-
Wu, H.1
Su, Z.2
Mao, F.3
Olman, V.4
Xu, Y.5
-
2
-
-
2342512807
-
Operon prediction by comparative genomics: An application to the Synechococcus sp. WH8102 genome
-
Chen,X., Su,Z., Dam,P., Palenik,B., Xu,Y. and Jiang,T. (2004) Operon prediction by comparative genomics: An application to the Synechococcus sp. WH8102 genome. Nucleic Acids Res., 32, 2147-2157.
-
(2004)
Nucleic Acids Res.
, vol.32
, pp. 2147-2157
-
-
Chen, X.1
Su, Z.2
Dam, P.3
Palenik, B.4
Xu, Y.5
Jiang, T.6
-
3
-
-
25144464549
-
Comparative genomics analysis of NtcA regulations in cyanobacteria: Regulation of nitrogen assimilation and its coupling to photosynthesis
-
Su,Z., Olman,V., Mao,F. and Xu,Y. (2005) Comparative genomics analysis of NtcA regulations in cyanobacteria: Regulation of nitrogen assimilation and its coupling to photosynthesis. Nucleic Acids Res., 33, 5156-5171.
-
(2005)
Nucleic Acids Res.
, vol.33
, pp. 5156-5171
-
-
Su, Z.1
Olman, V.2
Mao, F.3
Xu, Y.4
-
4
-
-
14044249642
-
Computational inference of regulatory pathways in microbes: An application to the construction of phosphorus assimilation pathways in Synechococcus WH8102
-
Su,Z., Dam,A., Chen,X., Olman,V., Jiang,T., Palenik,B. and Xu,Y. (2003) Computational inference of regulatory pathways in microbes: An application to the construction of phosphorus assimilation pathways in Synechococcus WH8102. Genome Inform Ser Workshop Genome Inform., 14, 3-13.
-
(2003)
Genome Inform Ser Workshop Genome Inform.
, vol.14
, pp. 3-13
-
-
Su, Z.1
Dam, A.2
Chen, X.3
Olman, V.4
Jiang, T.5
Palenik, B.6
Xu, Y.7
-
5
-
-
30444456098
-
In silico construction of the carbon fixation pathway in Synechococcus sp. WH8102
-
Dam,P., Su,Z., Olman,V. and Xu,Y. (2004) In silico construction of the carbon fixation pathway in Synechococcus sp. WH8102. J. Biol. Syst., 12, 97-125.
-
(2004)
J. Biol. Syst.
, vol.12
, pp. 97-125
-
-
Dam, P.1
Su, Z.2
Olman, V.3
Xu, Y.4
-
6
-
-
30444439922
-
Computational prediction of operons in Synechococcus sp. WH8102
-
Chen,X., Su,Z., Xu,Y. and Jiang,T. (2004) Computational prediction of operons in Synechococcus sp. WH8102. Genome Inform Ser Workshop Genome Inform., 15, 211-222.
-
(2004)
Genome Inform Ser Workshop Genome Inform.
, vol.15
, pp. 211-222
-
-
Chen, X.1
Su, Z.2
Xu, Y.3
Jiang, T.4
-
7
-
-
13944268797
-
A novel method for accurate operon predictions in all sequenced prokaryotes
-
Price,M.N., Huang,K.H., Alm,E.J. and Arkin,A.P. (2005) A novel method for accurate operon predictions in all sequenced prokaryotes. Nucleic Acids Res., 33, 880-892.
-
(2005)
Nucleic Acids Res.
, vol.33
, pp. 880-892
-
-
Price, M.N.1
Huang, K.H.2
Alm, E.J.3
Arkin, A.P.4
-
8
-
-
16344390358
-
Operon prediction without a training set
-
Westover,B.P., Buhler,J.D., Sonnenburg,J.L. and Gordon,J.I. (2005) Operon prediction without a training set. Bioinformatics, 21, 880-888.
-
(2005)
Bioinformatics
, vol.21
, pp. 880-888
-
-
Westover, B.P.1
Buhler, J.D.2
Sonnenburg, J.L.3
Gordon, J.I.4
-
9
-
-
1842559849
-
Using functional and organizational information to improve genome-wide computational prediction of transcription units on pathway-genome databases
-
Romero,P.R. and Karp,P.D. (2004) Using functional and organizational information to improve genome-wide computational prediction of transcription units on pathway-genome databases. Bioinformatics, 20, 709-717.
-
(2004)
Bioinformatics
, vol.20
, pp. 709-717
-
-
Romero, P.R.1
Karp, P.D.2
-
10
-
-
0033662287
-
The organization of metabolic reaction networks: A signal-oriented approach to cellular models
-
Kremling,A., Jahreis,K., Lengeler,J.W. and Gilles,E.D. (2000) The organization of metabolic reaction networks: A signal-oriented approach to cellular models. Metab. Eng., 2, 190-200.
-
(2000)
Metab. Eng.
, vol.2
, pp. 190-200
-
-
Kremling, A.1
Jahreis, K.2
Lengeler, J.W.3
Gilles, E.D.4
-
12
-
-
30444435179
-
Mapping of orthologous genes in the context of biological pathways: An application of integer programming
-
Mao,F., Su,Z., Olman,V., Dam,P., Liu,Z. and Xu,Y. (2006) Mapping of orthologous genes in the context of biological pathways: An application of integer programming. Proc. Natl Acad. Sci. USA, 103, 129-134.
-
(2006)
Proc. Natl Acad. Sci. USA
, vol.103
, pp. 129-134
-
-
Mao, F.1
Su, Z.2
Olman, V.3
Dam, P.4
Liu, Z.5
Xu, Y.6
-
13
-
-
14044273667
-
Mapping of microbial pathways through constrained mapping of orthologous genes
-
Olman,V., Peng,H., Su,Z. and Xu,Y. (2004) Mapping of microbial pathways through constrained mapping of orthologous genes. Proc IEEE Comput Syst Bioinform Conf., pp. 363-370.
-
(2004)
Proc IEEE Comput Syst Bioinform Conf.
, pp. 363-370
-
-
Olman, V.1
Peng, H.2
Su, Z.3
Xu, Y.4
-
14
-
-
0034306448
-
Gene context conservation of a higher order than operons
-
Lathe,W.C.,IIIrd, Snel B. and Bork,P. (2000) Gene context conservation of a higher order than operons. Trends. Biochem. Sci., 25, 474-479.
-
(2000)
Trends. Biochem. Sci.
, vol.25
, pp. 474-479
-
-
Lathe III, W.C.1
Snel, B.2
Bork, P.3
-
15
-
-
13444262374
-
EcoCyc: A comprehensive database resource for Escherichia coli
-
Keseler,I.M., Collado-Vides,J., Gama-Castro,S., Ingraham,J., Paley,S., Paulsen,I.T., Peralta-Gil,M. and Karp,P.D. (2005) EcoCyc: A comprehensive database resource for Escherichia coli. Nucleic Acids Res., 33, D334-D337.
-
(2005)
Nucleic Acids Res.
, vol.33
-
-
Keseler, I.M.1
Collado-Vides, J.2
Gama-Castro, S.3
Ingraham, J.4
Paley, S.5
Paulsen, I.T.6
Peralta-Gil, M.7
Karp, P.D.8
-
16
-
-
0034069495
-
Gene Ontology: Tool for the unification of biology
-
The Gene Ontology Consortium
-
Ashburner,M., Ball,C.A., Blake,J.A., Botstein,D., Butler,H., Cherry,J.M., Davis,A.P., Dolinski,K., Dwight,S.S., Eppig,J.T. et al. (2000) Gene Ontology: Tool for the unification of biology. The Gene Ontology Consortium. Nature Genet., 25, 25-29.
-
(2000)
Nature Genet.
, vol.25
, pp. 25-29
-
-
Ashburner, M.1
Ball, C.A.2
Blake, J.A.3
Botstein, D.4
Butler, H.5
Cherry, J.M.6
Davis, A.P.7
Dolinski, K.8
Dwight, S.S.9
Eppig, J.T.10
-
17
-
-
0034893812
-
Orthologs and paralogs - We need to get it right
-
INTERACTIONS1002
-
Jensen,R.A. (2001) Orthologs and paralogs - we need to get it right. Genome Biol., 2(4): INTERACTIONS1002.
-
(2001)
Genome Biol.
, vol.2
, Issue.4
-
-
Jensen, R.A.1
-
18
-
-
0035027535
-
An apology for orthologs - Or brave new memes
-
COMMENT1005
-
Koonin,E.V. (2001) An apology for orthologs - or brave new memes. Genome Biol., 2(4): COMMENT1005.
-
(2001)
Genome Biol.
, vol.2
, Issue.4
-
-
Koonin, E.V.1
-
19
-
-
0035110578
-
Homologuephobia
-
COMMENT1002
-
Petsko,G.A. (2001) Homologuephobia. Genome Biol., 2(2): COMMENT1002.
-
(2001)
Genome Biol.
, vol.2
, Issue.2
-
-
Petsko, G.A.1
-
20
-
-
0029789824
-
A minimal gene set for cellular life derived by comparison of complete bacterial genomes
-
Mushegian,A.R. and Koonin,E.V. (1996) A minimal gene set for cellular life derived by comparison of complete bacterial genomes. Proc. Natl Acad. Sci. USA, 93, 10268-10273.
-
(1996)
Proc. Natl Acad. Sci. USA
, vol.93
, pp. 10268-10273
-
-
Mushegian, A.R.1
Koonin, E.V.2
-
21
-
-
0141626909
-
Detecting putative orthologs
-
Wall,D.P., Fraser,H.B. and Hirsh,A.E. (2003) Detecting putative orthologs. Bioinformatics, 19, 1710-1711.
-
(2003)
Bioinformatics
, vol.19
, pp. 1710-1711
-
-
Wall, D.P.1
Fraser, H.B.2
Hirsh, A.E.3
-
22
-
-
0030660581
-
A genomic perspective on protein families
-
Tatusov,R.L., Koonin,E.V. and Lipman,D.J. (1997) A genomic perspective on protein families. Science, 278, 631-637.
-
(1997)
Science
, vol.278
, pp. 631-637
-
-
Tatusov, R.L.1
Koonin, E.V.2
Lipman, D.J.3
-
23
-
-
33745506838
-
Accurate prediction of orthologous gene groups in microbes
-
Wu,H., Mao,F., Olman,V. and Xu,Y. (2005) Accurate prediction of orthologous gene groups in microbes. Proc. IEEE Comput. Syst. Bioinform. Conf., pp. 73-79.
-
(2005)
Proc. IEEE Comput. Syst. Bioinform. Conf.
, pp. 73-79
-
-
Wu, H.1
Mao, F.2
Olman, V.3
Xu, Y.4
-
24
-
-
0003524084
-
-
Macmilliam Press Ltd., London, UK & Elsevier Science Publishing Co., Inc., NY, US
-
Bondy,J.A. and Murty,U.S.R. (1976) Graph Theory with Applications. Macmilliam Press Ltd., London, UK & Elsevier Science Publishing Co., Inc., NY, US.
-
(1976)
Graph Theory With Applications
-
-
Bondy, J.A.1
Murty, U.S.R.2
-
25
-
-
23744454242
-
A cluster algorithm for graphs
-
Technical Report INS-R0010, National Research Institute for Mathematics and Computer Science in the Netherlands. Amsterdam, Netherlands
-
Dongen,S.v. (2000) A cluster algorithm for graphs. Technical Report INS-R0010, National Research Institute for Mathematics and Computer Science in the Netherlands. Amsterdam, Netherlands.
-
(2000)
-
-
Dongen, S.V.1
-
26
-
-
0043163718
-
Protein families and TRIBES in genome sequence space
-
Enright,A.J., Kunin,V. and Ouzounis,C.A. (2003) Protein families and TRIBES in genome sequence space. Nucleic Acids Res., 31, 4632-4638.
-
(2003)
Nucleic Acids Res.
, vol.31
, pp. 4632-4638
-
-
Enright, A.J.1
Kunin, V.2
Ouzounis, C.A.3
-
27
-
-
0141519279
-
OrthoMCL: Identification of ortholog groups for eukaryotic genomes
-
Li,L., Stoeckert,C.J.,Jr and Roos,D.S. (2003) OrthoMCL: Identification of ortholog groups for eukaryotic genomes. Genome Res., 13, 2178-2189.
-
(2003)
Genome Res.
, vol.13
, pp. 2178-2189
-
-
Li, L.1
Stoeckert Jr., C.J.2
Roos, D.S.3
-
28
-
-
0346156102
-
Detection of functional modules from protein interaction networks
-
Pereira-Leal,J.B., Enright,A.J. and Ouzounis,C.A. (2004) Detection of functional modules from protein interaction networks. Proteins, 54, 49-57.
-
(2004)
Proteins
, vol.54
, pp. 49-57
-
-
Pereira-Leal, J.B.1
Enright, A.J.2
Ouzounis, C.A.3
-
29
-
-
0345863935
-
The KEGG resource for deciphering the genome
-
Kanehisa,M., Goto,S., Kawashima,S., Okuno,Y. and Hattori,M. (2004) The KEGG resource for deciphering the genome. Nucleic Acids Res., 32, D277-D280.
-
(2004)
Nucleic Acids Res.
, vol.32
-
-
Kanehisa, M.1
Goto, S.2
Kawashima, S.3
Okuno, Y.4
Hattori, M.5
-
30
-
-
0034444676
-
Coupling of flagellar gene expression to flagellar assembly in Salmonella enterica serovar typhimurium and Escherichia coli
-
Chilcott,G.S. and Hughes,K.T. (2000) Coupling of flagellar gene expression to flagellar assembly in Salmonella enterica serovar typhimurium and Escherichia coli. Microbiol. Mol. Biol. Rev., 64, 694-708.
-
(2000)
Microbiol. Mol. Biol. Rev.
, vol.64
, pp. 694-708
-
-
Chilcott, G.S.1
Hughes, K.T.2
-
31
-
-
18244386245
-
Nebulon: A system for the inference of functional relationships of gene products from the rearrangement of predicted operons
-
Janga,S.C., Collado-Vides,J. and Moreno-Hagelsieb,G. (2005) Nebulon: A system for the inference of functional relationships of gene products from the rearrangement of predicted operons. Nucleic Acids Res., 33, 2521-2530.
-
(2005)
Nucleic Acids Res.
, vol.33
, pp. 2521-2530
-
-
Janga, S.C.1
Collado-Vides, J.2
Moreno-Hagelsieb, G.3
-
32
-
-
0033995794
-
Sulfur metabolism in Escherichia coli and related bacteria: Facts and fiction
-
Sekowska,A., Kung,H.F. and Danchin,A. (2000) Sulfur metabolism in Escherichia coli and related bacteria: Facts and fiction. J. Mol. Microbiol. Biotechnol., 2, 145-177.
-
(2000)
J. Mol. Microbiol. Biotechnol.
, vol.2
, pp. 145-177
-
-
Sekowska, A.1
Kung, H.F.2
Danchin, A.3
-
33
-
-
0032793852
-
Selfish operons: The evolutionary impact of gene clustering in prokaryotes and eukaryotes
-
Lawrence,J. (1999) Selfish operons: The evolutionary impact of gene clustering in prokaryotes and eukaryotes. Curr. Opin. Genet. Dev., 9, 642-648.
-
(1999)
Curr. Opin. Genet. Dev.
, vol.9
, pp. 642-648
-
-
Lawrence, J.1
-
34
-
-
0028206349
-
Rhs elements of Escherichia coli: A family of genetic composites each encoding a large mosaic protein
-
Hill,C.W., Sandt,C.H. and Vlazny,D.A. (1994) Rhs elements of Escherichia coli: A family of genetic composites each encoding a large mosaic protein. Mol. Microbiol., 12, 865-871.
-
(1994)
Mol. Microbiol.
, vol.12
, pp. 865-871
-
-
Hill, C.W.1
Sandt, C.H.2
Vlazny, D.A.3
|