-
1
-
-
10744232769
-
Genome-scale analysis of the uses of the Escherichia coli genome: Model-driven analysis of heterogeneous data sets
-
Allen, T.E., Herrgard, M.J., Liu, M., Qiu, Y., Glasner, J.D., Blattner, F.R., and Palsson, B.Ø. 2003. Genome-scale analysis of the uses of the Escherichia coli genome: Model-driven analysis of heterogeneous data sets. J. Bacteriol. 185: 6392-6399.
-
(2003)
J. Bacteriol.
, vol.185
, pp. 6392-6399
-
-
Allen, T.E.1
Herrgard, M.J.2
Liu, M.3
Qiu, Y.4
Glasner, J.D.5
Blattner, F.R.6
Palsson, B.Ø.7
-
2
-
-
0742333984
-
A motif co-occurrence approach for genome-wide prediction of transcription-factor-binding sites in Escherichia coli
-
Bulyk, M.L., McGuire, A.M., Masuda, N. and Church, G.M. 2004. A motif co-occurrence approach for genome-wide prediction of transcription-factor- binding sites in Escherichia coli. Genome Res. 14: 201-208.
-
(2004)
Genome Res.
, vol.14
, pp. 201-208
-
-
Bulyk, M.L.1
McGuire, A.M.2
Masuda, N.3
Church, G.M.4
-
3
-
-
13444283630
-
Interaction network containing conserved and essential protein complexes in Escherichia coli
-
Butland, G., Peregrin-Alvarez, J.M., Li, J., Yang, W., Yang, X., Canadien, V., Starostine, A., Richards, D., Beattie, B., Krogan, N., et al. 2005. Interaction network containing conserved and essential protein complexes in Escherichia coli. Nature 433: 531-537.
-
(2005)
Nature
, vol.433
, pp. 531-537
-
-
Butland, G.1
Peregrin-Alvarez, J.M.2
Li, J.3
Yang, W.4
Yang, X.5
Canadien, V.6
Starostine, A.7
Richards, D.8
Beattie, B.9
Krogan, N.10
-
4
-
-
0037424667
-
Genome size and operon content
-
Cherry, J.L. 2003. Genome size and operon content. J. Theor. Biol. 221: 401-410.
-
(2003)
J. Theor. Biol.
, vol.221
, pp. 401-410
-
-
Cherry, J.L.1
-
5
-
-
0032169271
-
Conservation of gene order: A fingerprint of proteins that physically interact
-
Dandekar, T., Snel, B., Huynen, M., and Bork, P. 1998. Conservation of gene order: A fingerprint of proteins that physically interact. Trends Biochem. Sci. 23: 324-328.
-
(1998)
Trends Biochem. Sci.
, vol.23
, pp. 324-328
-
-
Dandekar, T.1
Snel, B.2
Huynen, M.3
Bork, P.4
-
6
-
-
3042569657
-
Bacterial genomes as new gene homes: The genealogy of ORFans in E. coli
-
Daubin, V. and Ochman, H. 2004. Bacterial genomes as new gene homes: The genealogy of ORFans in E. coli. Genome Res. 14: 1036-1042.
-
(2004)
Genome Res.
, vol.14
, pp. 1036-1042
-
-
Daubin, V.1
Ochman, H.2
-
7
-
-
0036306989
-
Analysis of the cellular functions of Escherichia coli operons and their conservation in Bacillus subtilis
-
de Daruvar, A., Collado-Vides, J., and Valencia, A. 2002. Analysis of the cellular functions of Escherichia coli operons and their conservation in Bacillus subtilis. J. Mol. Evol. 55: 211-221.
-
(2002)
J. Mol. Evol.
, vol.55
, pp. 211-221
-
-
De Daruvar, A.1
Collado-Vides, J.2
Valencia, A.3
-
8
-
-
0035282698
-
Prediction of operons in microbial genomes
-
Ermolaeva, M.D., White, O., and Salzberg, S.L. 2001. Prediction of operons in microbial genomes. Nucleic Acids Res. 29: 1216-1221.
-
(2001)
Nucleic Acids Res.
, vol.29
, pp. 1216-1221
-
-
Ermolaeva, M.D.1
White, O.2
Salzberg, S.L.3
-
9
-
-
0141504252
-
Experimental determination and system level analysis of essential genes in Escherichia coli MG1655
-
Gerdes, S.Y., Scholle, M.D., Campbell, J.W., Balazsi, G., Ravasz, E., Daugherty, M.D., Somera, A.L., Kyrpides, N.C., Anderson, I., Gelfand, M.S., et al. 2003. Experimental determination and system level analysis of essential genes in Escherichia coli MG1655. J. Bacteriol. 185: 5673-5684.
-
(2003)
J. Bacteriol.
, vol.185
, pp. 5673-5684
-
-
Gerdes, S.Y.1
Scholle, M.D.2
Campbell, J.W.3
Balazsi, G.4
Ravasz, E.5
Daugherty, M.D.6
Somera, A.L.7
Kyrpides, N.C.8
Anderson, I.9
Gelfand, M.S.10
-
10
-
-
0034351387
-
Likelihood-based tests of topologies in phylogenetics
-
Goldman, N., Anderson, J.P., and Rodrigo, A.G. 2000. Likelihood-based tests of topologies in phylogenetics. Syst. Biol. 49: 652-670.
-
(2000)
Syst. Biol.
, vol.49
, pp. 652-670
-
-
Goldman, N.1
Anderson, J.P.2
Rodrigo, A.G.3
-
11
-
-
0037249405
-
The Stanford Microarray Database: Data access and quality assessment tools
-
Gollub, J., Ball, C.A., Binkley, G., Demeter, J., Finkelstein, D.B., Hebert, J.M., Hernandez-Boussard, T., Jin, H., Kaloper, M., Matese, J.C., et al. 2003. The Stanford Microarray Database: Data access and quality assessment tools. Nucleic Acids Res. 31: 94-96.
-
(2003)
Nucleic Acids Res.
, vol.31
, pp. 94-96
-
-
Gollub, J.1
Ball, C.A.2
Binkley, G.3
Demeter, J.4
Finkelstein, D.B.5
Hebert, J.M.6
Hernandez-Boussard, T.7
Jin, H.8
Kaloper, M.9
Matese, J.C.10
-
12
-
-
0023850806
-
Valyl-tRNA synthetase gene of Escherichia coli K12. Molecular genetic characterization
-
Heck, J.D. and Hatfield, G.W. 1988. Valyl-tRNA synthetase gene of Escherichia coli K12. Molecular genetic characterization. J. Biol. Chem. 263: 857-867.
-
(1988)
J. Biol. Chem.
, vol.263
, pp. 857-867
-
-
Heck, J.D.1
Hatfield, G.W.2
-
13
-
-
13944254077
-
Chromosome organization is shaped by the transcription regulatory network
-
Hershberg, R., Yeger-Lotem, E., and Margalit, H. 2005. Chromosome organization is shaped by the transcription regulatory network. Trends Genet. 21: 138-142.
-
(2005)
Trends Genet.
, vol.21
, pp. 138-142
-
-
Hershberg, R.1
Yeger-Lotem, E.2
Margalit, H.3
-
14
-
-
0033832615
-
Predicting protein function by genomic context: Quantitative evaluation and qualitative inferences
-
Huynen, M., Snel, B., Lathe III, W., and Bork, P. 2000. Predicting protein function by genomic context: Quantitative evaluation and qualitative inferences. Genome Res. 10: 1204-1210.
-
(2000)
Genome Res.
, vol.10
, pp. 1204-1210
-
-
Huynen, M.1
Snel, B.2
Lathe III, W.A.3
Bork, P.4
-
15
-
-
0033058895
-
Evolutionary instability of operon structures disclosed by sequence comparisons of complete microbial genomes
-
Itoh, T., Takemoto, K., Mori, H., and Gojobori, T. 1999. Evolutionary instability of operon structures disclosed by sequence comparisons of complete microbial genomes. Mol. Biol. Evol. 16: 332-346.
-
(1999)
Mol. Biol. Evol.
, vol.16
, pp. 332-346
-
-
Itoh, T.1
Takemoto, K.2
Mori, H.3
Gojobori, T.4
-
17
-
-
0036084127
-
The EcoCyc database
-
Karp, P.D., Riley, M., Saier, M., Paulsen, I.T., Collado-Vides, J., Paley, S.M., Pellegrini-Toole, A., Bonavides, C., and Gama-Castro, S. 2002. The EcoCyc database. Nucleic Acids Res. 30: 56-58.
-
(2002)
Nucleic Acids Res.
, vol.30
, pp. 56-58
-
-
Karp, P.D.1
Riley, M.2
Saier, M.3
Paulsen, I.T.4
Collado-Vides, J.5
Paley, S.M.6
Pellegrini-Toole, A.7
Bonavides, C.8
Gama-Castro, S.9
-
19
-
-
3042703044
-
Analysis of genomic context: Prediction of functional associations from conserved bidirectionally transcribed gene pairs
-
Korbel, J.O., Jensen, L.J., von Mering, C., and Bork, P. 2004. Analysis of genomic context: Prediction of functional associations from conserved bidirectionally transcribed gene pairs. Nat. Biotechnol. 22: 911-917.
-
(2004)
Nat. Biotechnol.
, vol.22
, pp. 911-917
-
-
Korbel, J.O.1
Jensen, L.J.2
Von Mering, C.3
Bork, P.4
-
20
-
-
0032793852
-
Selfish operons: The evolutionary impact of gene clustering in prokaryotes and eukaryotes
-
Lawrence, J.G. 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.G.1
-
21
-
-
0032482924
-
Molecular archaeology of the Escherichia coli genome
-
Lawrence, J.G., and Ochman, H. 1998. Molecular archaeology of the Escherichia coli genome. Proc. Natl. Acad. Sci. 95: 9413-9417.
-
(1998)
Proc. Natl. Acad. Sci.
, vol.95
, pp. 9413-9417
-
-
Lawrence, J.G.1
Ochman, H.2
-
22
-
-
0029847554
-
Selfish operons: Horizontal transfer may drive the evolution of gene clusters
-
Lawrence, J.G. and Roth, J.R. 1996. Selfish operons: Horizontal transfer may drive the evolution of gene clusters. Genetics 143: 1843-1860.
-
(1996)
Genetics
, vol.143
, pp. 1843-1860
-
-
Lawrence, J.G.1
Roth, J.R.2
-
23
-
-
1342271382
-
From gene trees to organismal phylogeny in prokaryotes: The case of the γ-Proteobacteria
-
Lerat, E., Daubin, V., and Moran, N.A. 2003. From gene trees to organismal phylogeny in prokaryotes: The case of the γ-Proteobacteria. PLoS Biol. 1: E19.
-
(2003)
PLoS Biol.
, vol.1
-
-
Lerat, E.1
Daubin, V.2
Moran, N.A.3
-
24
-
-
0022413030
-
Characterization and properties of very large inversions of the E. coli chromosome along the origin-to-terminus axis
-
Louarn, J., Bouche, J., Legendre, F., Louarn, J., and Patte, J. 1985. Characterization and properties of very large inversions of the E. coli chromosome along the origin-to-terminus axis. Mol. Gen. Genet. 201: 467-476.
-
(1985)
Mol. Gen. Genet.
, vol.201
, pp. 467-476
-
-
Louarn, J.1
Bouche, J.2
Legendre, F.3
Louarn, J.4
Patte, J.5
-
25
-
-
0347126296
-
DBTBS: Database of transcriptional regulation in Bacillus subtilis and its contribution to comparative genomics
-
Makita, Y., Nakao, M., Ogasawara, N., and Nakai, K. 2004. DBTBS: Database of transcriptional regulation in Bacillus subtilis and its contribution to comparative genomics. Nucleic Acids Res. 32: D75-D77.
-
(2004)
Nucleic Acids Res.
, vol.32
-
-
Makita, Y.1
Nakao, M.2
Ogasawara, N.3
Nakai, K.4
-
26
-
-
0037252683
-
CDD: A curated Entrez database of conserved domain alignments
-
Marchler-Bauer, A., Anderson, J.B., DeWeese-Scott, C., Fedorova, N.D., Geer, L.Y., He, S., Hurwitz, D.I., Jackson, J.D., Jacobs, A.R., Lanczycki, C.J., et al. 2003. CDD: A curated Entrez database of conserved domain alignments. Nucleic Acids Res. 31: 383-387.
-
(2003)
Nucleic Acids Res.
, vol.31
, pp. 383-387
-
-
Marchler-Bauer, A.1
Anderson, J.B.2
DeWeese-Scott, C.3
Fedorova, N.D.4
Geer, L.Y.5
He, S.6
Hurwitz, D.I.7
Jackson, J.D.8
Jacobs, A.R.9
Lanczycki, C.J.10
-
27
-
-
0036798220
-
Factors influencing the identification of transcription factor binding sites by cross-species comparison
-
McCue, L.A., Thompson, W., Carmack, C.S., and Lawrence, C.E. 2002. Factors influencing the identification of transcription factor binding sites by cross-species comparison. Genome Res. 12: 1523-1532.
-
(2002)
Genome Res.
, vol.12
, pp. 1523-1532
-
-
McCue, L.A.1
Thompson, W.2
Carmack, C.S.3
Lawrence, C.E.4
-
28
-
-
0642312313
-
Evolution of mosaic operons by horizontal gene transfer and gene displacement in situ
-
Omelchenko, M.V., Makarova, K.S., Wolf, Y.I., Rogozin, I.B., and Koonin, E.V. 2003. Evolution of mosaic operons by horizontal gene transfer and gene displacement in situ. Genome Biol. 4: R55.
-
(2003)
Genome Biol.
, vol.4
-
-
Omelchenko, M.V.1
Makarova, K.S.2
Wolf, Y.I.3
Rogozin, I.B.4
Koonin, E.V.5
-
29
-
-
0033055062
-
The use of gene clusters to infer functional coupling
-
Overbeek, R., Fonstein, M., D'Souza, M., Pusch, G., and Maltsev, N. 1999. The use of gene clusters to infer functional coupling. Proc. Natl. Acad. Sci. 96: 2896-2901.
-
(1999)
Proc. Natl. Acad. Sci.
, vol.96
, pp. 2896-2901
-
-
Overbeek, R.1
Fonstein, M.2
D'Souza, M.3
Pusch, G.4
Maltsev, N.5
-
30
-
-
17144459133
-
Evidence against the selfish operon theory
-
Pal, C. and Hurst, L.D. 2004. Evidence against the selfish operon theory. Trends Genet. 20: 232-234.
-
(2004)
Trends Genet.
, vol.20
, pp. 232-234
-
-
Pal, C.1
Hurst, L.D.2
-
31
-
-
0033616661
-
Genomic evolution during a 10,000-generation experiment with bacteria
-
Papadopoulos, D., Schneider, D., Meier-Eiss, J., Arber, W., Lenski, R.E., and Blot, M. 1999. Genomic evolution during a 10,000-generation experiment with bacteria. Proc. Natl. Acad. Sci. 96: 3807-3812.
-
(1999)
Proc. Natl. Acad. Sci.
, vol.96
, pp. 3807-3812
-
-
Papadopoulos, D.1
Schneider, D.2
Meier-Eiss, J.3
Arber, W.4
Lenski, R.E.5
Blot, M.6
-
32
-
-
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
-
33
-
-
0035989433
-
Distributional profiles of homologous open reading frames among bacterial phyla: Implications for vertical and lateral transmission
-
Ragan, M.A. and Charlebois, R.L. 2002. Distributional profiles of homologous open reading frames among bacterial phyla: Implications for vertical and lateral transmission. Int. J. Syst. Evol. Microbiol. 52: 777-787.
-
(2002)
Int. J. Syst. Evol. Microbiol.
, vol.52
, pp. 777-787
-
-
Ragan, M.A.1
Charlebois, R.L.2
-
34
-
-
0032573426
-
A comprehensive library of DNA-binding site matrices for 55 proteins applied to the complete Escherichia coli K-12 genome
-
Robison, K., McGuire, A.M., and Church, G.M. 1998. A comprehensive library of DNA-binding site matrices for 55 proteins applied to the complete Escherichia coli K-12 genome. J. Mol. Biol. 284: 241-254.
-
(1998)
J. Mol. Biol.
, vol.284
, pp. 241-254
-
-
Robison, K.1
McGuire, A.M.2
Church, G.M.3
-
35
-
-
0037052935
-
Connected gene neighborhoods in prokaryotic genomes
-
Rogozin, I.B., Makarova, K.S., Murvai, J., Czabarka, E., Wolf, Y.I., Tatusov, R.L., Szekely, L.A., and Koonin, E.V. 2002. Connected gene neighborhoods in prokaryotic genomes. Nucleic Acids Res. 30: 2212-2223.
-
(2002)
Nucleic Acids Res.
, vol.30
, pp. 2212-2223
-
-
Rogozin, I.B.1
Makarova, K.S.2
Murvai, J.3
Czabarka, E.4
Wolf, Y.I.5
Tatusov, R.L.6
Szekely, L.A.7
Koonin, E.V.8
-
36
-
-
0036640105
-
Co-expression pattern from DNA microarray experiments as a tool for operon prediction
-
Sabatti, C., Rohlin, L., Oh, M.K., and Liao, J.C. 2002. Co-expression pattern from DNA microarray experiments as a tool for operon prediction. Nucleic Acids Res. 30: 2886-2893.
-
(2002)
Nucleic Acids Res.
, vol.30
, pp. 2886-2893
-
-
Sabatti, C.1
Rohlin, L.2
Oh, M.K.3
Liao, J.C.4
-
37
-
-
0034612277
-
Operons in Escherichia coli: Genomic analyses and predictions
-
Salgado, H., Moreno-Hagelsieb, G., Smith, T.F., and Collado-Vides, J. 2000. Operons in Escherichia coli: Genomic analyses and predictions. Proc. Natl. Acad. Sci. 97: 6652-6657.
-
(2000)
Proc. Natl. Acad. Sci.
, vol.97
, pp. 6652-6657
-
-
Salgado, H.1
Moreno-Hagelsieb, G.2
Smith, T.F.3
Collado-Vides, J.4
-
38
-
-
0035878724
-
Improving the accuracy of PSI-BLAST protein database searches with composition-based statistics and other refinements
-
Schaffer, A.A., Aravind, L., Madden, T.L., Shavirin, S., Spouge, J.L., Wolf, Y.I., Koonin, E.V., and Altschul, S.F. 2001. Improving the accuracy of PSI-BLAST protein database searches with composition-based statistics and other refinements. Nucleic Acids Res. 29: 2994-3005.
-
(2001)
Nucleic Acids Res.
, vol.29
, pp. 2994-3005
-
-
Schaffer, A.A.1
Aravind, L.2
Madden, T.L.3
Shavirin, S.4
Spouge, J.L.5
Wolf, Y.I.6
Koonin, E.V.7
Altschul, S.F.8
-
39
-
-
0021038161
-
Selection and endpoint distribution of bacterial inversion mutations
-
Schmid, M.B. and Roth, J.R. 1983. Selection and endpoint distribution of bacterial inversion mutations. Genetics 105: 539-557.
-
(1983)
Genetics
, vol.105
, pp. 539-557
-
-
Schmid, M.B.1
Roth, J.R.2
-
40
-
-
0036205377
-
TREE-PUZZLE: Maximum likelihood phylogenetic analysis using quartets and parallel computing
-
Schmidt, H.A., Strimmer, K., Vingron, M., and von Haeseler, A. 2002. TREE-PUZZLE: Maximum likelihood phylogenetic analysis using quartets and parallel computing. Bioinformatics 18: 502-504.
-
(2002)
Bioinformatics
, vol.18
, pp. 502-504
-
-
Schmidt, H.A.1
Strimmer, K.2
Vingron, M.3
Von Haeseler, A.4
-
41
-
-
8544264562
-
Efficient attenuation of stochasticity in gene expression through post-transcriptional control
-
Swain, P.S. 2004. Efficient attenuation of stochasticity in gene expression through post-transcriptional control. J. Mol. Biol. 344: 965-976.
-
(2004)
J. Mol. Biol.
, vol.344
, pp. 965-976
-
-
Swain, P.S.1
-
42
-
-
0035162592
-
The COG database: New developments in phylogenetic classification of proteins from complete genomes
-
Tatusov, R.L., Natale, D.A., Garkavtsev, I.V., Tatusova, T.A., Shankavaram, U.T., Rao, B.S., Kiryutin, B., Galperin, M.Y., Fedorova, N.D., and Koonin, E.V. 2001. The COG database: New developments in phylogenetic classification of proteins from complete genomes. Nucleic Acids Res. 29: 22-28.
-
(2001)
Nucleic Acids Res.
, vol.29
, pp. 22-28
-
-
Tatusov, R.L.1
Natale, D.A.2
Garkavtsev, I.V.3
Tatusova, T.A.4
Shankavaram, U.T.5
Rao, B.S.6
Kiryutin, B.7
Galperin, M.Y.8
Fedorova, N.D.9
Koonin, E.V.10
-
43
-
-
0035226487
-
Prediction of co-regulated genes in Bacillus subtilis on the basis of upstream elements conserved across three closely related species
-
research0048
-
Terai, G., Takagi, T., and Nakai, K. 2001. Prediction of co-regulated genes in Bacillus subtilis on the basis of upstream elements conserved across three closely related species. Genome Biol. 2: research0048.
-
(2001)
Genome Biol.
, vol.2
-
-
Terai, G.1
Takagi, T.2
Nakai, K.3
-
44
-
-
0027968068
-
CLUSTAL W: Improving the sensitivity of progressive multiple sequence alignment through sequence weighting, positions-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, positions-specific gap penalties and weight matrix choice. Nucleic Acids Res. 22: 4673-4680.
-
(1994)
Nucleic Acids Res.
, vol.22
, pp. 4673-4680
-
-
Thompson, J.D.1
Higgins, D.G.2
Gibson, T.J.3
|