-
1
-
-
33846460774
-
Enrichment of functional redox reactive proteins and identification by mass spectrometry results in several terminal Fe(III)-reducing candidate proteins in Shewanella oneidensis MR-1
-
Elias, D.A., Yang, F., Mottaz, H.M., Belieav, A.S. and Lipton, M.S. (2007) Enrichment of functional redox reactive proteins and identification by mass spectrometry results in several terminal Fe(III)-reducing candidate proteins in Shewanella oneidensis MR-1. J. Microbiol. Methods, 68, 367-375.
-
(2007)
J. Microbiol. Methods
, vol.68
, pp. 367-375
-
-
Elias, D.A.1
Yang, F.2
Mottaz, H.M.3
Belieav, A.S.4
Lipton, M.S.5
-
2
-
-
33747337245
-
Temporal transcriptomic analysis as Desulfovibrio vulgaris Hildenborough transitions into stationary phase during electron donor depletion
-
Clark, M.E., He, Q., He, Z., Huang, K.H., Alm, E.J., Wan, X.F., Hazen, T.C., Arkin, A.P., Wall, J.D., Zhou, J.Z. et al. (2006) Temporal transcriptomic analysis as Desulfovibrio vulgaris Hildenborough transitions into stationary phase during electron donor depletion. Appl. Environ. Microbiol., 72, 5578-5588.
-
(2006)
Appl. Environ. Microbiol
, vol.72
, pp. 5578-5588
-
-
Clark, M.E.1
He, Q.2
He, Z.3
Huang, K.H.4
Alm, E.J.5
Wan, X.F.6
Hazen, T.C.7
Arkin, A.P.8
Wall, J.D.9
Zhou, J.Z.10
-
3
-
-
33745605747
-
A proteomic view of Desulfovibrio vulgaris metabolism as determined by liquid chromatography coupled with tandem mass spectrometry
-
Zhang, W., Gritsenko, M.A., Moore, R.J., Culley, D.E., Nie, L., Petritis, K., Strittmatter, E.F., Smith, R.D. and Brockman, F.J. (2006) A proteomic view of Desulfovibrio vulgaris metabolism as determined by liquid chromatography coupled with tandem mass spectrometry. Proteomics, 6, 4286-4299.
-
(2006)
Proteomics
, vol.6
, pp. 4286-4299
-
-
Zhang, W.1
Gritsenko, M.A.2
Moore, R.J.3
Culley, D.E.4
Nie, L.5
Petritis, K.6
Strittmatter, E.F.7
Smith, R.D.8
Brockman, F.J.9
-
4
-
-
0036331039
-
Microarray transcription profiling of a Shewanella oneidensis etrA mutant
-
Beliaev, A.S., Thompson, D.K., Fields, M.W., Wu, L., Lies, D.P., Nealson, K.H. and Zhou, J. (2002) Microarray transcription profiling of a Shewanella oneidensis etrA mutant. J. Bacteriol., 184 4612-4616.
-
(2002)
J. Bacteriol
, vol.184
, pp. 4612-4616
-
-
Beliaev, A.S.1
Thompson, D.K.2
Fields, M.W.3
Wu, L.4
Lies, D.P.5
Nealson, K.H.6
Zhou, J.7
-
5
-
-
0036408363
-
Gene and protein expression profiles of Shewanella oneidensis during anaerobic growth with different electron acceptors
-
Beliaev, A.S., Thompson, D.K., Khare, T., Lim, H., Brandt, C.C., Li, G., Murray, A.E., Heidelberg, J.F., Giometti, C.S., Yates, J. III et al. (2002) Gene and protein expression profiles of Shewanella oneidensis during anaerobic growth with different electron acceptors. Omics, 6, 39-60.
-
(2002)
Omics
, vol.6
, pp. 39-60
-
-
Beliaev, A.S.1
Thompson, D.K.2
Khare, T.3
Lim, H.4
Brandt, C.C.5
Li, G.6
Murray, A.E.7
Heidelberg, J.F.8
Giometti, C.S.9
Yates III, J.10
-
6
-
-
34147157826
-
Reporter proteins for in vivo fluorescence without oxygen
-
Drepper, T., Eggert, T., Circolone, F., Heck, A., Kraub, U., Guterl, J., Wendorff, M., Losi, A., Gartner, W. and Jaeger, K. (2007) Reporter proteins for in vivo fluorescence without oxygen. Nat. Biotechnol., 25, 443-445.
-
(2007)
Nat. Biotechnol
, vol.25
, pp. 443-445
-
-
Drepper, T.1
Eggert, T.2
Circolone, F.3
Heck, A.4
Kraub, U.5
Guterl, J.6
Wendorff, M.7
Losi, A.8
Gartner, W.9
Jaeger, K.10
-
7
-
-
33644808569
-
SNAP-tag™ mediated live cell labeling as an alternative to GFP in anaerobic organisms
-
Regoes, A. and Hehl, A.B. (2005) SNAP-tag™ mediated live cell labeling as an alternative to GFP in anaerobic organisms. Biotechnology, 39, 809-812.
-
(2005)
Biotechnology
, vol.39
, pp. 809-812
-
-
Regoes, A.1
Hehl, A.B.2
-
8
-
-
13444283630
-
Interaction network containing conserved and essential protein complexes in Escherichia coli
-
Butland, G., Peregrín-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
Peregrín-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
-
9
-
-
66249106756
-
-
Dahl, C. and Friedrich, C.G, eds, Springer-Verlag, Berlin, pp
-
Wall, J.D., Arkin, P., Balci, N.C. and Rapp-Giles, B.J. (2007) In Dahl, C. and Friedrich, C.G. (eds), Microbial Sulfur Metabolism. Springer-Verlag, Berlin, pp. 1-11.
-
(2007)
Microbial Sulfur Metabolism
, pp. 1-11
-
-
Wall, J.D.1
Arkin, P.2
Balci, N.C.3
Rapp-Giles, B.J.4
-
10
-
-
34548505486
-
Analysis of a ferric uptake regulator (Fur) mutant of Desulfovibrio vulgaris Hildenborough
-
Bender, K.S., Yen, H.B., Hemme, C.L., Yang, Z., He, Z., He, Q., Zhou, J., Huang, K.H., Alm, E.J., Hazen, T.C. et al. (2007) Analysis of a ferric uptake regulator (Fur) mutant of Desulfovibrio vulgaris Hildenborough. Appl. Environ. Microbiol., 73, 5389-5400.
-
(2007)
Appl. Environ. Microbiol
, vol.73
, pp. 5389-5400
-
-
Bender, K.S.1
Yen, H.B.2
Hemme, C.L.3
Yang, Z.4
He, Z.5
He, Q.6
Zhou, J.7
Huang, K.H.8
Alm, E.J.9
Hazen, T.C.10
-
11
-
-
0031754775
-
Shewanella putrefaciens mtrB encodes an outer membrane protein required for Fe(III) and Mn(IV) reduction
-
Beliaev, A.S. and Saffarini, D.A. (1998) Shewanella putrefaciens mtrB encodes an outer membrane protein required for Fe(III) and Mn(IV) reduction. J. Bacteriol., 180, 6292-6297.
-
(1998)
J. Bacteriol
, vol.180
, pp. 6292-6297
-
-
Beliaev, A.S.1
Saffarini, D.A.2
-
12
-
-
0035131413
-
MtrC, an outer membrane decahaem c cytochrome required for metal reduction in Shewanella putrefaciens MR-1
-
Beliaev, A.S., Saffarini, D.A., McLaughlin, J.L. and Hunnicutt, D. (2001) MtrC, an outer membrane decahaem c cytochrome required for metal reduction in Shewanella putrefaciens MR-1. Mol. Microbiol., 39, 722-730.
-
(2001)
Mol. Microbiol
, vol.39
, pp. 722-730
-
-
Beliaev, A.S.1
Saffarini, D.A.2
McLaughlin, J.L.3
Hunnicutt, D.4
-
13
-
-
2342526611
-
Identification and functional analysis of hypothetical genes expressed in Haemophilus influenzae
-
Kolker, E., Makarova, K.S., Shabalina, S., Picone, A.F., Purvine, S., Holzman, T., Cherny, T., Armbruster, D., Munson, R.S., Kolesov, G. et al. (2004) Identification and functional analysis of hypothetical genes expressed in Haemophilus influenzae. Nucleic Acids Res., 32, 2353-2361.
-
(2004)
Nucleic Acids Res
, vol.32
, pp. 2353-2361
-
-
Kolker, E.1
Makarova, K.S.2
Shabalina, S.3
Picone, A.F.4
Purvine, S.5
Holzman, T.6
Cherny, T.7
Armbruster, D.8
Munson, R.S.9
Kolesov, G.10
-
14
-
-
0033485517
-
Improved microbial gene identification with GLIMMER
-
Delcher, A.L., Harmon, D., Kasif, S., White, O. and Salzberg, S.L. (1999) Improved microbial gene identification with GLIMMER. Nucleic Acids Res., 27, 4636-4641.
-
(1999)
Nucleic Acids Res
, vol.27
, pp. 4636-4641
-
-
Delcher, A.L.1
Harmon, D.2
Kasif, S.3
White, O.4
Salzberg, S.L.5
-
15
-
-
0032518163
-
Microbial gene identification using interpolated Markov models
-
Salzberg, S.L., Delcher, A.L., Kasif, S. and White, O. (1998) Microbial gene identification using interpolated Markov models. Nucleic Acids Res., 26, 544-548.
-
(1998)
Nucleic Acids Res
, vol.26
, pp. 544-548
-
-
Salzberg, S.L.1
Delcher, A.L.2
Kasif, S.3
White, O.4
-
16
-
-
13444309602
-
Functional clues for hypothetical proteins based on genomic context analysis in prokaryotes
-
Doerks, T., vonMering, C. and Bork, P. (2004) Functional clues for hypothetical proteins based on genomic context analysis in prokaryotes. Nucleic Acids Res., 32, 6321-6326.
-
(2004)
Nucleic Acids Res
, vol.32
, pp. 6321-6326
-
-
Doerks, T.1
vonMering, C.2
Bork, P.3
-
17
-
-
0033832615
-
Predicting protein function by genomic context: Quantitative evaluation and qualitative inferences
-
Huynen, M., Snel, B.W.L. III and Bork, P. (2000) Predicting protein function by genomic context: Quantitative evaluation and qualitative inferences. Gen. Res., 10, 1204-1210.
-
(2000)
Gen. Res
, vol.10
, pp. 1204-1210
-
-
Huynen, M.1
Snel III, B.W.L.2
Bork, P.3
-
18
-
-
13444261288
-
PA-GOSUB: A searchable database of model organism protein sequences with their predicted gene ontology molecular function and subcellular localization
-
Lu, P., Szafron, D., Greiner, R., Wishart, D.S., Fyshe, A., Pearcy, B., Poulin, B., Eisner, R., Ngo, D. and Lamb, N. (2005) PA-GOSUB: A searchable database of model organism protein sequences with their predicted gene ontology molecular function and subcellular localization. Nucleic Acids Res., 33, D147-D153.
-
(2005)
Nucleic Acids Res
, vol.33
-
-
Lu, P.1
Szafron, D.2
Greiner, R.3
Wishart, D.S.4
Fyshe, A.5
Pearcy, B.6
Poulin, B.7
Eisner, R.8
Ngo, D.9
Lamb, N.10
-
19
-
-
13444249988
-
STRING: Known and predicted protein-protein associations, integrated and transferred across organisms
-
vonMering, C., Jensen, L.J., Snel, B., Hooper, S.D., Krupp, M., Foglierini, M., Jouffre, N., Huynen, M.A. and Bork, P. (2005) STRING: known and predicted protein-protein associations, integrated and transferred across organisms. Nucleic Acids Res., 33, D433-D437.
-
(2005)
Nucleic Acids Res
, vol.33
-
-
vonMering, C.1
Jensen, L.J.2
Snel, B.3
Hooper, S.D.4
Krupp, M.5
Foglierini, M.6
Jouffre, N.7
Huynen, M.A.8
Bork, P.9
-
20
-
-
0042622203
-
Phydbac (phylogenomic display of bacterial genes): An interactive resource for the annotation of bacterial genomes
-
Enault, F., Suhre, K., Poirot, O., Abergel, C. and Claverie, J. (2003) Phydbac (phylogenomic display of bacterial genes): An interactive resource for the annotation of bacterial genomes. Nucleic Acids Res. 31, 3720-3722.
-
(2003)
Nucleic Acids Res
, vol.31
, pp. 3720-3722
-
-
Enault, F.1
Suhre, K.2
Poirot, O.3
Abergel, C.4
Claverie, J.5
-
21
-
-
1042280957
-
Phylogenomic inference of protein molecular function: Advances and challenges
-
Sjölander, K. (2004) Phylogenomic inference of protein molecular function: Advances and challenges. Bioinformatics, 20, 170-179.
-
(2004)
Bioinformatics
, vol.20
, pp. 170-179
-
-
Sjölander, K.1
-
22
-
-
23844468451
-
Global detection and characterization of hypothetical proteins in Shewanella oneidensis MR-1 using LC-MS based proteomics
-
Elias, D.A., Monroe, M.E., Marshall, M.J., Romine, M.F., Beliaev, A.S., Fredrickson, J.K., Anderson, G.A., Smith, R.D. and Lipton, M.S. (2005) Global detection and characterization of hypothetical proteins in Shewanella oneidensis MR-1 using LC-MS based proteomics. Proteomics, 5, 3120-3130.
-
(2005)
Proteomics
, vol.5
, pp. 3120-3130
-
-
Elias, D.A.1
Monroe, M.E.2
Marshall, M.J.3
Romine, M.F.4
Beliaev, A.S.5
Fredrickson, J.K.6
Anderson, G.A.7
Smith, R.D.8
Lipton, M.S.9
-
23
-
-
33746923052
-
Confirmation of the expression of a large set of conserved hypothetical proteins in Shewanella oneidensis MR-1
-
Elias, D.A., Monroe, M.E., Smith, R.D., Fredrickson, J.K. and Lipton, M.S. (2006) Confirmation of the expression of a large set of conserved hypothetical proteins in Shewanella oneidensis MR-1. J. Microbiol. Methods, 66, 223-233.
-
(2006)
J. Microbiol. Methods
, vol.66
, pp. 223-233
-
-
Elias, D.A.1
Monroe, M.E.2
Smith, R.D.3
Fredrickson, J.K.4
Lipton, M.S.5
-
24
-
-
13844316454
-
Global profiling of Shewanella oneidensis MR-1: Expression of hypothetical genes and improved functional annotations
-
Kolker, E., Picone, A.F., Galperin, M.Y., Romine, M.F., Higdon, R., Makarova, K.S., Kolker, N., Anderson, G.A., Qiu, X., Auberry, K.J. et al. (2005) Global profiling of Shewanella oneidensis MR-1: expression of hypothetical genes and improved functional annotations. Proc. Natl Acad. Sci. USA, 102, 2099-2104.
-
(2005)
Proc. Natl Acad. Sci. USA
, vol.102
, pp. 2099-2104
-
-
Kolker, E.1
Picone, A.F.2
Galperin, M.Y.3
Romine, M.F.4
Higdon, R.5
Makarova, K.S.6
Kolker, N.7
Anderson, G.A.8
Qiu, X.9
Auberry, K.J.10
-
25
-
-
2342475768
-
The genome sequence of the anaerobic, sulfate-reducing bacterium Desulfovibrio vulgaris Hildenborough
-
Heidelberg, J.F., Seshadri, R., Haveman, S.A., Hemme, C.L., Paulsen, I.T., Kolonay, J.F., Eisen, J.A., Ward, N., Methe, B., Brinkac, L.M. et al. (2004) The genome sequence of the anaerobic, sulfate-reducing bacterium Desulfovibrio vulgaris Hildenborough. Nat. Biotechnol., 22, 554-559.
-
(2004)
Nat. Biotechnol
, vol.22
, pp. 554-559
-
-
Heidelberg, J.F.1
Seshadri, R.2
Haveman, S.A.3
Hemme, C.L.4
Paulsen, I.T.5
Kolonay, J.F.6
Eisen, J.A.7
Ward, N.8
Methe, B.9
Brinkac, L.M.10
-
26
-
-
33644748620
-
Global analysis of heat shock response in Desulfovibrio vulgaris Hildenborough
-
Chhabra, S.R., He, Q., Huang, K.H., Gaucher, S.P., Alm, E.J., He, Z., Hadi, M.Z., Hazen, T.C., Wall, J.D., Zhou, J. et al. (2006) Global analysis of heat shock response in Desulfovibrio vulgaris Hildenborough. J. Bacteriol., 188, 1817-1828.
-
(2006)
J. Bacteriol
, vol.188
, pp. 1817-1828
-
-
Chhabra, S.R.1
He, Q.2
Huang, K.H.3
Gaucher, S.P.4
Alm, E.J.5
He, Z.6
Hadi, M.Z.7
Hazen, T.C.8
Wall, J.D.9
Zhou, J.10
-
27
-
-
27944473728
-
Response of the anaerobe Desulfovibrio vulgaris Hildenborough to oxidative conditions: Proteome and transcript analysis
-
Fournier, M., Aubert, C., Dermoun, Z., Durand, M., Moinier, D. and Dolla, A. (2006) Response of the anaerobe Desulfovibrio vulgaris Hildenborough to oxidative conditions: Proteome and transcript analysis. Biochimica, 88, 85-94.
-
(2006)
Biochimica
, vol.88
, pp. 85-94
-
-
Fournier, M.1
Aubert, C.2
Dermoun, Z.3
Durand, M.4
Moinier, D.5
Dolla, A.6
-
28
-
-
33744776637
-
Salt stress in Desulfovibrio vulgaris Hildenborough: An integrated genomics approach
-
Mukhopadhyay, A., He, Z., Alm, E.J., Arkin, A.P., Baidoo, E.E., Borglin, S.C., Chen, W., Hazen, T.C., He, Q., Holman, H. et al. (2006) Salt stress in Desulfovibrio vulgaris Hildenborough: An integrated genomics approach. J. Bacteriol., 188, 4068-4078.
-
(2006)
J. Bacteriol
, vol.188
, pp. 4068-4078
-
-
Mukhopadhyay, A.1
He, Z.2
Alm, E.J.3
Arkin, A.P.4
Baidoo, E.E.5
Borglin, S.C.6
Chen, W.7
Hazen, T.C.8
He, Q.9
Holman, H.10
-
29
-
-
33646743746
-
Global transcriptomic analysis of Desulfovibrio vulgaris on different electron donors
-
Zhang, W., Culley, D.E., Scholten, J.C.M., Hogan, M., Vitiritti, L. and Brockman, F.J. (2006) Global transcriptomic analysis of Desulfovibrio vulgaris on different electron donors. Anton. van Leeuwen., 89, 221-237.
-
(2006)
Anton. van Leeuwen
, vol.89
, pp. 221-237
-
-
Zhang, W.1
Culley, D.E.2
Scholten, J.C.M.3
Hogan, M.4
Vitiritti, L.5
Brockman, F.J.6
-
30
-
-
0004233143
-
-
2nd edn. Cambridge University Press, Cambridge, MA, USA
-
Postgate, J.R. (1984) The Sulphate-Reducing Bacteria, 2nd edn. Cambridge University Press, Cambridge, MA, USA.
-
(1984)
The Sulphate-Reducing Bacteria
-
-
Postgate, J.R.1
-
31
-
-
0043287832
-
Characterization of microbial activities and U reduction in a shallow aquifer contaminated by uranium mill tailings
-
Elias, D.A., Krumholz, L.R., Wong, D., Long, P.E. and Suflita, J.M. (2003) Characterization of microbial activities and U reduction in a shallow aquifer contaminated by uranium mill tailings. Microb. Ecol. 46, 83-91.
-
(2003)
Microb. Ecol
, vol.46
, pp. 83-91
-
-
Elias, D.A.1
Krumholz, L.R.2
Wong, D.3
Long, P.E.4
Suflita, J.M.5
-
34
-
-
33748801202
-
LC-MS/MS based proteomic analysis and functional inference of hypothetical proteins in Desulfovibrio vulgaris
-
Zhang, W., Culley, D.E., Gritsenko, M.A., Moore, R.J., Nie, L., Scholten, J.C.M., Petritis, K., Strittmatter, E.F., Smith, R.D. et al. (2006) LC-MS/MS based proteomic analysis and functional inference of hypothetical proteins in Desulfovibrio vulgaris. Biochem. Biophys. Res. Commun., 349, 1412-1419.
-
(2006)
Biochem. Biophys. Res. Commun
, vol.349
, pp. 1412-1419
-
-
Zhang, W.1
Culley, D.E.2
Gritsenko, M.A.3
Moore, R.J.4
Nie, L.5
Scholten, J.C.M.6
Petritis, K.7
Strittmatter, E.F.8
Smith, R.D.9
-
35
-
-
33748533479
-
Study of nitrate stress in Desulfovibrio vulgaris Hildenborough using iTRAQ proteomics
-
Redding, A.M., Mukhopadhyay, A., Joyner, D.C., Hazen, T.C. and Keasling, J.D. (2006) Study of nitrate stress in Desulfovibrio vulgaris Hildenborough using iTRAQ proteomics. Brief. Funct. Gen. Prot., 1-11.
-
(2006)
Brief. Funct. Gen. Prot
, pp. 1-11
-
-
Redding, A.M.1
Mukhopadhyay, A.2
Joyner, D.C.3
Hazen, T.C.4
Keasling, J.D.5
-
36
-
-
33745152320
-
Energetic consequences of nitrite stress in Desulfovibrio vulgaris Hildenborough inferred from global transcriptional analysis
-
He, Q., Huang, K.H., He, Z., Alm, E.J., Fields, M.W., Hazen, T.C., Arkin, A.P., Wall, J.D. and Zhou, J. (2006) Energetic consequences of nitrite stress in Desulfovibrio vulgaris Hildenborough inferred from global transcriptional analysis. Appl. Environ. Microbiol., 72, 4370-4381.
-
(2006)
Appl. Environ. Microbiol
, vol.72
, pp. 4370-4381
-
-
He, Q.1
Huang, K.H.2
He, Z.3
Alm, E.J.4
Fields, M.W.5
Hazen, T.C.6
Arkin, A.P.7
Wall, J.D.8
Zhou, J.9
-
37
-
-
37449020577
-
Response of Desulfovibrio vulgaris to alkaline stress
-
Stolyar, S., He, Q., Joachimiak, M.P., He, Z., Yang, Z.K., Borglin, S.E., Joyner, D.C., Huang, K., Alm, E., Hazen, T.C. et al. (2007) Response of Desulfovibrio vulgaris to alkaline stress. J. Bacteriol., 189, 8944-8952.
-
(2007)
J. Bacteriol
, vol.189
, pp. 8944-8952
-
-
Stolyar, S.1
He, Q.2
Joachimiak, M.P.3
He, Z.4
Yang, Z.K.5
Borglin, S.E.6
Joyner, D.C.7
Huang, K.8
Alm, E.9
Hazen, T.C.10
-
38
-
-
34547757942
-
Cell-wide responses to low-oxygen exposure in Desulfovibrio vulgaris Hildenborough
-
Mukhopadhyay, A., Redding, A.M., Joachimiak, M.P., Arkin, A.P., Borglin, S.E., Dehal, P.S., Chakraborty, R., Geller, J.T., Hazen, T.C., He, Q. et al. (2007) Cell-wide responses to low-oxygen exposure in Desulfovibrio vulgaris Hildenborough. J. Bacteriol., 189, 5996-6010.
-
(2007)
J. Bacteriol
, vol.189
, pp. 5996-6010
-
-
Mukhopadhyay, A.1
Redding, A.M.2
Joachimiak, M.P.3
Arkin, A.P.4
Borglin, S.E.5
Dehal, P.S.6
Chakraborty, R.7
Geller, J.T.8
Hazen, T.C.9
He, Q.10
-
39
-
-
25144487554
-
Use of microarrays with different probe sizes for monitoring gene expression
-
He, Z., Wu, L., Fields, M.W. and Zhou, J. (2005) Use of microarrays with different probe sizes for monitoring gene expression. Appl. Environ. Microbiol., 71, 5154-5162.
-
(2005)
Appl. Environ. Microbiol
, vol.71
, pp. 5154-5162
-
-
He, Z.1
Wu, L.2
Fields, M.W.3
Zhou, J.4
-
40
-
-
22244489084
-
The MicrobesOnline web site for comparative genomics
-
Alm, E.J., Huang, K.H., Price, M.N., Koche, R.P., Keller, K., Dubchak, I.L. and Arkin, A.P. (2005) The MicrobesOnline web site for comparative genomics. Gen. Res., 15, 1015-1022.
-
(2005)
Gen. Res
, vol.15
, pp. 1015-1022
-
-
Alm, E.J.1
Huang, K.H.2
Price, M.N.3
Koche, R.P.4
Keller, K.5
Dubchak, I.L.6
Arkin, A.P.7
-
41
-
-
0037143692
-
Global analysis of the Deinococcus radiodurans proteome by using accurate mass tags
-
Lipton, M.S., Pasa-Tolic, L., Anderson, G.A., Anderson, D.J., Auberry, D.L., Battista, J.R., Daly, M.J., Fredrickson, J., Hixson, K.K., Kostandarithes, H. et al. (2002) Global analysis of the Deinococcus radiodurans proteome by using accurate mass tags. Proc Natl Acad Sci USA, 99, 11049-11054.
-
(2002)
Proc Natl Acad Sci USA
, vol.99
, pp. 11049-11054
-
-
Lipton, M.S.1
Pasa-Tolic, L.2
Anderson, G.A.3
Anderson, D.J.4
Auberry, D.L.5
Battista, J.R.6
Daly, M.J.7
Fredrickson, J.8
Hixson, K.K.9
Kostandarithes, H.10
-
42
-
-
0000857494
-
An approach to correlate tandem mass spectral data of peptides with amino acid sequences in a protein database
-
Eng, J.K., McCormack, A.L. and Ill, J.R.Y. (1994) An approach to correlate tandem mass spectral data of peptides with amino acid sequences in a protein database. J. Am. Soc. Mass. Spectrosc., 5, 976-989.
-
(1994)
J. Am. Soc. Mass. Spectrosc
, vol.5
, pp. 976-989
-
-
Eng, J.K.1
McCormack, A.L.2
Ill, J.R.Y.3
-
43
-
-
0036099050
-
ESI-FTICR mass spectrometry employing data-dependent external ion selection and accumulation
-
Harkewicz, R., Belov, M.E., Anderson, G.A., Pasa-Tolic, L., Masselon, C.D., Prior, D.C., Udseth, H.R. and Smith, R.D. (2002) ESI-FTICR mass spectrometry employing data-dependent external ion selection and accumulation. J. Am. Soc. Mass Spectrosc., 13, 144-154.
-
(2002)
J. Am. Soc. Mass Spectrosc
, vol.13
, pp. 144-154
-
-
Harkewicz, R.1
Belov, M.E.2
Anderson, G.A.3
Pasa-Tolic, L.4
Masselon, C.D.5
Prior, D.C.6
Udseth, H.R.7
Smith, R.D.8
-
44
-
-
0037108887
-
Empirical statistical model to estimate the accuracy of peptide identifications made by MS/MS and database search
-
Keller, A., Nesvizhskii, A.I., Kolker, E. and Aebersold, R. (2002) Empirical statistical model to estimate the accuracy of peptide identifications made by MS/MS and database search. Anal. Chem., 74, 5383-5392.
-
(2002)
Anal. Chem
, vol.74
, pp. 5383-5392
-
-
Keller, A.1
Nesvizhskii, A.I.2
Kolker, E.3
Aebersold, R.4
-
45
-
-
4444350538
-
Application of peptide LC retention time information in a discriminant function for peptide identification by tandem mass spectrometry
-
Strittmatter, E.F., Kangas, L.J., Petritis, K., Mottaz, H.M., Anderson, G.A., Shen, Y., Jacobs, J.M.D.G.C. II and Smith, R.D. (2004) Application of peptide LC retention time information in a discriminant function for peptide identification by tandem mass spectrometry. J. Prot. Res., 3, 760-769.
-
(2004)
J. Prot. Res
, vol.3
, pp. 760-769
-
-
Strittmatter, E.F.1
Kangas, L.J.2
Petritis, K.3
Mottaz, H.M.4
Anderson, G.A.5
Shen, Y.6
Jacobs II, J.M.D.G.C.7
Smith, R.D.8
-
46
-
-
0037173615
-
Functional profiling of the Saccharomyces cerevisiae genome
-
Giaever, G., Chu, A.M., Ni, L., Connelly, C., Riles, L., Veronneau, S., Dow, S., Lucau-Danila, A., Anderson, K., Andre, B. et al. (2002) Functional profiling of the Saccharomyces cerevisiae genome. Nature, 418, 387-391.
-
(2002)
Nature
, vol.418
, pp. 387-391
-
-
Giaever, G.1
Chu, A.M.2
Ni, L.3
Connelly, C.4
Riles, L.5
Veronneau, S.6
Dow, S.7
Lucau-Danila, A.8
Anderson, K.9
Andre, B.10
-
47
-
-
0029804246
-
Quantitative phenotypic analysis of yeast deletion mutants using a highly parallel molecular bar-coding strategy
-
Shoemaker, D., Lashkari, D.A., Morris, D., Mittmann, M. and Davis., R.W. (1996) Quantitative phenotypic analysis of yeast deletion mutants using a highly parallel molecular bar-coding strategy. Nat. Gen., 14 450-456.
-
(1996)
Nat. Gen
, vol.14
, pp. 450-456
-
-
Shoemaker, D.1
Lashkari, D.A.2
Morris, D.3
Mittmann, M.4
Davis, R.W.5
-
48
-
-
56349166788
-
FastBLAST: Homology relationships for millions of proteins
-
Price, M.N., Dehal, P.S. and Arkin, A.P. (2008) FastBLAST: Homology relationships for millions of proteins. PLoS One, 3, e3589.
-
(2008)
PLoS One
, vol.3
-
-
Price, M.N.1
Dehal, P.S.2
Arkin, A.P.3
-
49
-
-
0035162594
-
RefSeq and Locus Link: NCBI gene-centered resources
-
Pruitt, K.D. and Maglott, D.R. (2001) RefSeq and Locus Link: NCBI gene-centered resources. Nucleic Acids Res., 29, 137-140.
-
(2001)
Nucleic Acids Res
, vol.29
, pp. 137-140
-
-
Pruitt, K.D.1
Maglott, D.R.2
-
50
-
-
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
-
51
-
-
0042902833
-
The COG database: An updated version includes eukaryotes
-
Tatusov, R.L., Fedorova, N.D., Jackson, J.D., Jacobs, A.R., Kiryutin, B., Koonin, E.V., Krylov, D.M., Mazumder, R., Mekhedov, S.L., Nikolskaya, A.N. et al. (2003) The COG database: An updated version includes eukaryotes. BMC Bioinformatics, 4, 41-55.
-
(2003)
BMC Bioinformatics
, vol.4
, pp. 41-55
-
-
Tatusov, R.L.1
Fedorova, N.D.2
Jackson, J.D.3
Jacobs, A.R.4
Kiryutin, B.5
Koonin, E.V.6
Krylov, D.M.7
Mazumder, R.8
Mekhedov, S.L.9
Nikolskaya, A.N.10
-
52
-
-
0036087630
-
CDD: A database of conserved domain alignments with links to domain three-dimensional structure
-
Marchler-Bauer, A., Panchenko, A.R., Shoemaker, B.A., Thiessen, P.A., Geer, L.Y. and Bryant, S.H. (2002) CDD: A database of conserved domain alignments with links to domain three-dimensional structure. Nucleic Acids Res., 30, 281-283.
-
(2002)
Nucleic Acids Res
, vol.30
, pp. 281-283
-
-
Marchler-Bauer, A.1
Panchenko, A.R.2
Shoemaker, B.A.3
Thiessen, P.A.4
Geer, L.Y.5
Bryant, S.H.6
-
53
-
-
15844431346
-
PSORTb v.2.0: Expanded prediction of bacterial protein subcellular localization and insights gained from comparative proteome analysis
-
Gardy, J.L., Laird, M.R., Chen, F., Rey, S., Walsh, C.J., Ester, M. and Brinkman, F.S.L. (2005) PSORTb v.2.0: Expanded prediction of bacterial protein subcellular localization and insights gained from comparative proteome analysis. Bioinformatics, 21, 617-623.
-
(2005)
Bioinformatics
, vol.21
, pp. 617-623
-
-
Gardy, J.L.1
Laird, M.R.2
Chen, F.3
Rey, S.4
Walsh, C.J.5
Ester, M.6
Brinkman, F.S.L.7
-
54
-
-
0042622254
-
PSORT-B: Improving protein subcellular localization prediction for Gram-negative bacteria
-
Gardy, J.L., Spencer, C., Wang, K., Ester, M., Tusnady, G.E., Simon, I., Hua, S., deFays, K., Lambert, C., Nakai, K. et al. (2003) PSORT-B: improving protein subcellular localization prediction for Gram-negative bacteria. Nucleic Acids Res., 31, 3613-3617.
-
(2003)
Nucleic Acids Res
, vol.31
, pp. 3613-3617
-
-
Gardy, J.L.1
Spencer, C.2
Wang, K.3
Ester, M.4
Tusnady, G.E.5
Simon, I.6
Hua, S.7
deFays, K.8
Lambert, C.9
Nakai, K.10
-
55
-
-
0035910270
-
Predicting transmembrane protein topology with a hidden markov model: Application to complete genomes
-
Krogh, A., Larsson, B., Heijne, G.v. and Sonnhammer, E.L.L. (2001) Predicting transmembrane protein topology with a hidden markov model: application to complete genomes. J. Mol. Biol., 305, 567-580.
-
(2001)
J. Mol. Biol
, vol.305
, pp. 567-580
-
-
Krogh, A.1
Larsson, B.2
Heijne, G.V.3
Sonnhammer, E.L.L.4
-
56
-
-
22544432327
-
Reconstruction of regulatory and metabolic pathways in metal-reducing δ-proteobacteria
-
Rodionov, D.A., Dubchak, I., Arkin, A.P., Alm, E. and Gelfand, M.S. (2004) Reconstruction of regulatory and metabolic pathways in metal-reducing δ-proteobacteria. Gen. Biol., 5, R90.1-R90.27.
-
(2004)
Gen. Biol
, vol.5
-
-
Rodionov, D.A.1
Dubchak, I.2
Arkin, A.P.3
Alm, E.4
Gelfand, M.S.5
-
57
-
-
0344172832
-
Opening the iron box: Transcriptional metalloregulation by the Fur protein
-
Escolar, L.A., Perez-Martin, J. and Lorenzo, V.D. (1999) Opening the iron box: Transcriptional metalloregulation by the Fur protein. J. Bacteriol., 181, 6223-6229.
-
(1999)
J. Bacteriol
, vol.181
, pp. 6223-6229
-
-
Escolar, L.A.1
Perez-Martin, J.2
Lorenzo, V.D.3
-
58
-
-
0035069457
-
Iron and metal regulation in bacteria
-
Hantke, K. (2001) Iron and metal regulation in bacteria. Curr. Opin. Microbiol., 4, 172-177.
-
(2001)
Curr. Opin. Microbiol
, vol.4
, pp. 172-177
-
-
Hantke, K.1
-
59
-
-
0030024164
-
Duplicate isochorismate synthase genes of Bacillus subtilis: Regulation and involvement in the biosyntheses of menaquinone and 2, 3-dihydroxybenzoate
-
Rowland, B.M. and Taber, H.W. (1996) Duplicate isochorismate synthase genes of Bacillus subtilis: Regulation and involvement in the biosyntheses of menaquinone and 2, 3-dihydroxybenzoate. Mol. Microbiol., 178, 854-861.
-
(1996)
Mol. Microbiol
, vol.178
, pp. 854-861
-
-
Rowland, B.M.1
Taber, H.W.2
-
60
-
-
0027468111
-
Iron-hydroxamate uptake systems in Bacillus subtilis: Identification of a lipoprotein as part of a binding proteindependent transport system
-
Schneider, R. and Hantke, K. (1993) Iron-hydroxamate uptake systems in Bacillus subtilis: Identification of a lipoprotein as part of a binding proteindependent transport system. Mol. Microbiol., 8 111-121.
-
(1993)
Mol. Microbiol
, vol.8
, pp. 111-121
-
-
Schneider, R.1
Hantke, K.2
-
61
-
-
0031850630
-
Bacillus subtilis contains multiple Fur homologues; identification of the iron uptake (Fur) and peroxide regulon (PerR) repressors
-
Bsat, N., Herbig, A., Casillas-Martínez, L., Setlow, P. and Helmann, J.D. (1998) Bacillus subtilis contains multiple Fur homologues; identification of the iron uptake (Fur) and peroxide regulon (PerR) repressors. Mol. Microbiol., 29, 189-198.
-
(1998)
Mol. Microbiol
, vol.29
, pp. 189-198
-
-
Bsat, N.1
Herbig, A.2
Casillas-Martínez, L.3
Setlow, P.4
Helmann, J.D.5
-
62
-
-
33645037891
-
2 by metal-catalysed histidine oxidation
-
2 by metal-catalysed histidine oxidation. Nature, 440, 363-367.
-
(2006)
Nature
, vol.440
, pp. 363-367
-
-
Lee, J.W.1
Helmann, J.D.2
-
63
-
-
0036842611
-
Genome sequence of the dissimilatory metal ion-reducing bacterium Shewanella oneidensis
-
Heidelberg, J.F., Paulsen, I.T., Nelson, K.E., Gaidos, E.J., Nelson, W.C., Read, T.D., Eisen, J.A., Seshadri, R., Ward, N., Methe, B. et al. (2002) Genome sequence of the dissimilatory metal ion-reducing bacterium Shewanella oneidensis. Nat. Biotechnol., 20, 1118-1123.
-
(2002)
Nat. Biotechnol
, vol.20
, pp. 1118-1123
-
-
Heidelberg, J.F.1
Paulsen, I.T.2
Nelson, K.E.3
Gaidos, E.J.4
Nelson, W.C.5
Read, T.D.6
Eisen, J.A.7
Seshadri, R.8
Ward, N.9
Methe, B.10
-
64
-
-
34548170304
-
Proteome analysis of Desulfovibrio desulfuricans G20 mutants using the accurate mass and time (AMT) tag approach
-
Luo, Q., Hixson, K.K., Callister, S.J., Lipton, M.S., Morris, B.E.L. and Krumholz, L.R. (2007) Proteome analysis of Desulfovibrio desulfuricans G20 mutants using the accurate mass and time (AMT) tag approach. J. Prot. Res., 6, 3042-3053.
-
(2007)
J. Prot. Res
, vol.6
, pp. 3042-3053
-
-
Luo, Q.1
Hixson, K.K.2
Callister, S.J.3
Lipton, M.S.4
Morris, B.E.L.5
Krumholz, L.R.6
-
65
-
-
7044241336
-
Validation of Shewanella oneidensis MR-1 small proteins by AMT tag-based proteome analysis
-
Romine, M.F., Elias, D.A., Monroe, M.E., Auberry, K., Fang, R., Fredrickson, J.K., Anderson, G.A., Smith, R.D. and Lipton, M.S. (2004) Validation of Shewanella oneidensis MR-1 small proteins by AMT tag-based proteome analysis. OMICS, 8, 239-254.
-
(2004)
OMICS
, vol.8
, pp. 239-254
-
-
Romine, M.F.1
Elias, D.A.2
Monroe, M.E.3
Auberry, K.4
Fang, R.5
Fredrickson, J.K.6
Anderson, G.A.7
Smith, R.D.8
Lipton, M.S.9
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