-
1
-
-
61449116914
-
Orthoproteogenomics: Multiple proteomes investigation through orthology and a new MS-based protocol
-
Gallien, S., Perrodou, E., Carapito, C., Deshayes, C., Reyrat, J. M., Van Dorsselaer, A., Poch, O., Schaeffer, C., and Lecompte, O. (2009) Orthoproteogenomics: multiple proteomes investigation through orthology and a new MS-based protocol. Genome Res. 19, 128-135.
-
(2009)
Genome Res.
, vol.19
, pp. 128-135
-
-
Gallien, S.1
Perrodou, E.2
Carapito, C.3
Deshayes, C.4
Reyrat, J.M.5
Van Dorsselaer, A.6
Poch, O.7
Schaeffer, C.8
Lecompte, O.9
-
2
-
-
34250886391
-
Large-scale identification of N-terminal peptides in the halophilic Archaea Halobacterium salinarum and Natronomonas pharaonis
-
DOI 10.1021/pr0700347
-
Aivaliotis, M., Gevaert, K., Falb, M., Tebbe, A., Konstantinidis, K., Bisle, B., Klein, C., Martens, L., Staes, A., Timmerman, E., Van Damme, J., Siedler, F., Pfeiffer, F., Van de kerckhove, J., and Oesterhelt, D. (2007) Large-scale identification of N-terminal peptides in the halophilic archaea Halobacterium salinarum and Natronomonas pharaonis. J. Proteome Res. 6, 2195-2204. (Pubitemid 46985106)
-
(2007)
Journal of Proteome Research
, vol.6
, Issue.6
, pp. 2195-2204
-
-
Aivaliotis, M.1
Gevaert, K.2
Falb, M.3
Tebbe, A.4
Konstantinidis, K.5
Bisle, B.6
Klein, C.7
Martens, L.8
Staes, A.9
Timmerman, E.10
Van Damme, J.11
Siedler, F.12
Pfeiffer, F.13
Vandekerckhove, J.14
Oesterhelt, D.15
-
3
-
-
77951987273
-
Proteomicsbased confirmation of protein expression and correction of annotation errors in the Brucella abortus genome
-
Lamontagne, J., Bé land, M., Forest, A., Cô té -Martin, A., Nassif, N., Tomaki, F., Moriyon, I., Moreno, E., and Paramithiotis, E. (2010) Proteomicsbased confirmation of protein expression and correction of annotation errors in the Brucella abortus genome. BMC. Genomics 11, 300.
-
(2010)
BMC. Genomics
, vol.11
, pp. 300
-
-
Lamontagne, J.1
Bé Land, M.2
Forest, A.3
Côté-Martin, A.4
Nassif, N.5
Tomaki, F.6
Moriyon, I.7
Moreno, E.8
Paramithiotis, E.9
-
4
-
-
43749090090
-
Comparative proteogenomics: Combining mass spectrometry and comparative genomics to analyze multiple genomes
-
DOI 10.1101/gr.074344.107
-
Gupta, N., Benhamida, J., Bhargava, V., Goodman, D., Kain, E., Kerman, I., Nguyen, N., Ollikainen, N., Rodriguez, J., Wang, J., Lipton, M. S., Romine, M., Bafna, V., Smith, R. D., and Pevzner, P. A. (2008) Comparative proteogenomics: combining mass spectrometry and comparative genomics to analyze multiple genomes. Genome Res. 18, 1133-1142. (Pubitemid 351931164)
-
(2008)
Genome Research
, vol.18
, Issue.7
, pp. 1133-1142
-
-
Gupta, N.1
Benhamida, J.2
Bhargava, V.3
Goodman, D.4
Kain, E.5
Kerman, I.6
Nguyen, N.7
Ollikainen, N.8
Rodriguez, J.9
Wang, J.10
Lipton, M.S.11
Romine, M.12
Bafna, V.13
Smith, R.D.14
Pevzner, P.A.15
-
5
-
-
83055173265
-
Proteogenomic analysis of Mycobacterium tuberculosis by high resolution mass spectrometry
-
Kelkar, D. S., Kumar, D., Kumar, P., Balakrishnan, L., Muthusamy, B., Yadav, A. K., Shrivastava, P., Marimuthu, A., Anand, S., Sundaram, H., Kingsbury, R., Harsha, H. C., Nair, B., Prasad, T. S., Chauhan, D. S., Katoch, K., Katoch, V. M., Kumar, P., Chaerkady, R., Ramachandran, S., Dash, D., and Pandey, A. (2011) Proteogenomic analysis of Mycobacterium tuberculosis by high resolution mass spectrometry. Mol. Cell Proteomics 10, M111.
-
(2011)
Mol. Cell Proteomics
, vol.10
-
-
Kelkar, D.S.1
Kumar, D.2
Kumar, P.3
Balakrishnan, L.4
Muthusamy, B.5
Yadav, A.K.6
Shrivastava, P.7
Marimuthu, A.8
Anand, S.9
Sundaram, H.10
Kingsbury, R.11
Harsha, H.C.12
Nair, B.13
Prasad, T.S.14
Chauhan, D.S.15
Katoch, K.16
Katoch, V.M.17
Kumar, P.18
Chaerkady, R.19
Ramachandran, S.20
Dash, D.21
Pandey, A.22
more..
-
6
-
-
84860575662
-
Proteogenomic analysis of bacteria and archaea: A 46 organism case study
-
Venter, E., Smith, R. D., and Payne, S. H. (2011) Proteogenomic analysis of bacteria and archaea: A 46 organism case study. PLoS. One. 6, e27587.
-
(2011)
PLoS. One
, vol.6
-
-
Venter, E.1
Smith, R.D.2
Payne, S.H.3
-
7
-
-
0029645432
-
Mining genomes: Correlating tandem mass spectra of modified and unmodified peptides to sequences in nucleotide databases
-
Yates, J. R. 3rd, Eng, J. K., and McCormack, A. L. (1995) Mining genomes: correlating tandem mass spectra of modified and unmodified peptides to sequences in nucleotide databases. Anal. Chem. 67, 3202-3210.
-
(1995)
Anal. Chem.
, vol.67
, pp. 3202-3210
-
-
Yates III, J.R.1
Eng, J.K.2
McCormack, A.L.3
-
8
-
-
0942287072
-
Proteogenomic mapping as a complementary method to perform genome annotation
-
DOI 10.1002/pmic.200300511
-
Jaffe, J. D., Berg, H. C., and Church, G. M. (2004) Proteogenomic mapping as a complementary method to perform genome annotation. Proteomics 4, 59-77. (Pubitemid 38140875)
-
(2004)
Proteomics
, vol.4
, Issue.1
, pp. 59-77
-
-
Jaffe, J.D.1
Berg, H.C.2
Church, G.M.3
-
9
-
-
76649085822
-
Proteomics-based refinement of Deinococcus deserti genome annotation reveals an unwonted use of non-canonical translation initiation codons
-
Baudet, M., Ortet, P., Gaillard, J. C., Fernandez, B., Gué rin, P., Enjalbal, C., Subra, G., de, G. A., Barakat, M., Dedieu, A., and Armengaud, J. (2010) Proteomics-based refinement of Deinococcus deserti genome annotation reveals an unwonted use of non-canonical translation initiation codons. Mol. Cell Proteomics 9, 415-426.
-
(2010)
Mol. Cell Proteomics
, vol.9
, pp. 415-426
-
-
Baudet, M.1
Ortet, P.2
Gaillard, J.C.3
Fernandez, B.4
Gué Rin, P.5
Enjalbal, C.6
Subra, G.7
De, G.A.8
Barakat, M.9
Dedieu, A.10
Armengaud, J.11
-
10
-
-
84857006793
-
High-throughput proteogenomics of Ruegeria pomeroyi: Seeding a better genomic annotation for the whole marine Roseobacter clade
-
Christie-Oleza, J. A., Miotello, G., and Armengaud, J. (2012) High-throughput proteogenomics of Ruegeria pomeroyi: seeding a better genomic annotation for the whole marine Roseobacter clade. BMC. Genomics 13, 73.
-
(2012)
BMC. Genomics
, vol.13
, pp. 73
-
-
Christie-Oleza, J.A.1
Miotello, G.2
Armengaud, J.3
-
11
-
-
58549101102
-
Discovery and revision of Arabidopsis genes by proteo genomics
-
Castellana, N. E., Payne, S. H., Shen, Z., Stanke, M., Bafna, V., and Briggs, S. P. (2008) Discovery and revision of Arabidopsis genes by proteo genomics. Proc. Natl. Acad. Sci. U.S.A. 105, 21034-21038.
-
(2008)
Proc. Natl. Acad. Sci. U.S.A
, vol.105
, pp. 21034-21038
-
-
Castellana, N.E.1
Payne, S.H.2
Shen, Z.3
Stanke, M.4
Bafna, V.5
Briggs, S.P.6
-
12
-
-
80555142954
-
A proteogenomic analysis of anopheles gambiae using high resolution Fourier transform mass spectrometry
-
Chaerkady, R., Kelkar, D. S., Muthusamy, B., Kandasamy, K., Dwivedi, S. B., Sahasrabuddhe, N. A., Kim, M. S., Renuse, S., Pinto, S. M., Sharma, R., Pawar, H., Sekhar, N. R., Mohanty, A. K., Getnet, D., Yang, Y., Zhong, J., Dash, A. P., MacCallum, R. M., Delanghe, B., Mlambo, G., Kumar, A., Keshava Prasad, T. S., Okulate, M., Kumar, N., and Pandey, A. (2011) A proteogenomic analysis of Anopheles gambiae using high resolution Fourier transform mass spectrometry. Genome Res. 21, 1872-1881.
-
(2011)
Genome Res.
, vol.21
, pp. 1872-1881
-
-
Chaerkady, R.1
Kelkar, D.S.2
Muthusamy, B.3
Kandasamy, K.4
Dwivedi, S.B.5
Sahasrabuddhe, N.A.6
Kim, M.S.7
Renuse, S.8
Pinto, S.M.9
Sharma, R.10
Pawar, H.11
Sekhar, N.R.12
Mohanty, A.K.13
Getnet, D.14
Yang, Y.15
Zhong, J.16
Dash, A.P.17
MacCallum, R.M.18
Delanghe, B.19
Mlambo, G.20
Kumar, A.21
Keshava Prasad, T.S.22
Okulate, M.23
Kumar, N.24
Pandey, A.25
more..
-
13
-
-
79961209179
-
Comparative proteogenomic analysis of the Leptospira interrogans virulence-attenuated strain IPAV against the pathogenic strain 56601
-
Zhong, Y., Chang, X., Cao, X. J., Zhang, Y., Zheng, H., Zhu, Y., Cai, C., Cui, Z., Zhang, Y., Li, Y. Y., Jiang, X. G., Zhao, G. P., Wang, S., Li, Y., Zeng, R., Li, X., and Guo, X. K. (2011) Comparative proteogenomic analysis of the Leptospira interrogans virulence-attenuated strain IPAV against the pathogenic strain 56601. Cell Res. 21, 1210-1229.
-
(2011)
Cell Res.
, vol.21
, pp. 1210-1229
-
-
Zhong, Y.1
Chang, X.2
Cao, X.J.3
Zhang, Y.4
Zheng, H.5
Zhu, Y.6
Cai, C.7
Cui, Z.8
Zhang, Y.9
Li, Y.Y.10
Jiang, X.G.11
Zhao, G.P.12
Wang, S.13
Li, Y.14
Zeng, R.15
Li, X.16
Guo, X.K.17
-
14
-
-
77957237701
-
Proteogenomics to discover the full coding content of genomes: A computational perspective
-
Castellana, N., and Bafna, V. (2010) Proteogenomics to discover the full coding content of genomes: A computational perspective. J. Proteomics 73, 2124-2135.
-
(2010)
J. Proteomics
, vol.73
, pp. 2124-2135
-
-
Castellana, N.1
Bafna, V.2
-
15
-
-
77949768663
-
Maximizing the sensitivity and reliability of peptide identification in large-scale proteomic experiments by harnessing multiple search engines
-
Yu, W., Taylor, J. A., Davis, M. T., Bonilla, L. E., Lee, K. A., Auger, P. L., Farnsworth, C. C., Welcher, A. A., and Patterson, S. D. (2010) Maximizing the sensitivity and reliability of peptide identification in large-scale proteomic experiments by harnessing multiple search engines. Proteomics 10, 1172-1189.
-
(2010)
Proteomics
, vol.10
, pp. 1172-1189
-
-
Yu, W.1
Taylor, J.A.2
Davis, M.T.3
Bonilla, L.E.4
Lee, K.A.5
Auger, P.L.6
Farnsworth, C.C.7
Welcher, A.A.8
Patterson, S.D.9
-
16
-
-
80052552293
-
A systematic analysis of eluted fraction of plasma post immunoaffinity depletion: Implications in biomarker discovery
-
Yadav, A. K., Bhardwaj, G., Basak, T., Kumar, D., Ahmad, S., Priyadarshini, R., Singh, A. K., Dash, D., and Sengupta, S. (2011) A systematic analysis of eluted fraction of plasma post immunoaffinity depletion: implications in biomarker discovery. PLoS. One 6, e24442.
-
(2011)
PLoS. One
, vol.6
-
-
Yadav, A.K.1
Bhardwaj, G.2
Basak, T.3
Kumar, D.4
Ahmad, S.5
Priyadarshini, R.6
Singh, A.K.7
Dash, D.8
Sengupta, S.9
-
17
-
-
0036928484
-
Complete genomic sequence of nitrogen-fixing symbiotic bacterium Bradyrhizobium japonicum USDA110
-
DOI 10.1093/dnares/9.6.189
-
Kaneko, T., Nakamura, Y., Sato, S., Minamisawa, K., Uchiumi, T., Sasamoto, S., Watanabe, A., Idesawa, K., Iriguchi, M., Kawashima, K., Kohara, M., Matsumoto, M., Shimpo, S., Tsuruoka, H., Wada, T., Yamada, M., and Tabata, S. (2002) Complete genomic sequence of nitrogen-fixing symbiotic bacterium Bradyrhizobium japonicum USDA110. DNA Res. 9, 189-197. (Pubitemid 36307023)
-
(2002)
DNA Research
, vol.9
, Issue.6
, pp. 189-197
-
-
Kaneko, T.1
Nakamura, Y.2
Sato, S.3
Minamisawa, K.4
Uchiumi, T.5
Sasamoto, S.6
Watanabe, A.7
Idesawa, K.8
Iriguchi, M.9
Kawashima, K.10
Kohara, M.11
Matsumoto, M.12
Shimpo, S.13
Tsuruoka, H.14
Wada, T.15
Yamada, M.16
Tabata, S.17
-
18
-
-
34147132825
-
Identifying bacterial genes and endosymbiont DNA with Glimmer
-
DOI 10.1093/bioinformatics/btm009
-
Delcher, A. L., Bratke, K. A., Powers, E. C., and Salzberg, S. L. (2007) Identifying bacterial genes and endosymbiont DNA with Glimmer. Bioinformatics 23, 673-679. (Pubitemid 46554717)
-
(2007)
Bioinformatics
, vol.23
, Issue.6
, pp. 673-679
-
-
Delcher, A.L.1
Bratke, K.A.2
Powers, E.C.3
Salzberg, S.L.4
-
19
-
-
77952691277
-
Rhizobial adaptation to hosts, a new facet in the legume root-nodule symbiosis
-
Koch, M., Delmotte, N., Rehrauer, H., Vorholt, J. A., Pessi, G., and Hennecke, H. (2010) Rhizobial adaptation to hosts, a new facet in the legume root-nodule symbiosis. Mol. Plant Microbe Interact. 23, 784-790.
-
(2010)
Mol. Plant Microbe Interact
, vol.23
, pp. 784-790
-
-
Koch, M.1
Delmotte, N.2
Rehrauer, H.3
Vorholt, J.A.4
Pessi, G.5
Hennecke, H.6
-
20
-
-
77950679651
-
An integrated proteomics and transcriptomics reference data set provides new insights into the Bradyrhizobium japonicum bacteroid metabolism in soybean root nodules
-
Delmotte, N., Ahrens, C. H., Knief, C., Qeli, E., Koch, M., Fischer, H. M., Vorholt, J. A., Hennecke, H., and Pessi, G. (2010) An integrated proteomics and transcriptomics reference data set provides new insights into the Bradyrhizobium japonicum bacteroid metabolism in soybean root nodules. Proteomics 10, 1391-1400.
-
(2010)
Proteomics
, vol.10
, pp. 1391-1400
-
-
Delmotte, N.1
Ahrens, C.H.2
Knief, C.3
Qeli, E.4
Koch, M.5
Fischer, H.M.6
Vorholt, J.A.7
Hennecke, H.8
Pessi, G.9
-
21
-
-
75549089545
-
The Proteomics Identifications database: 2010 update
-
Vizcaino, J. A., Cô té, R., Reisinger, F., Barsnes, H., Foster, J. M., Rameseder, J., Hermjakob, H., and Martens, L. (2010) The Proteomics Identifications database: 2010 update. Nucleic Acids Res. 38, D736- D742.
-
(2010)
Nucleic Acids Res.
, vol.38
-
-
Vizcaino, J.A.1
Côté, R.2
Reisinger, F.3
Barsnes, H.4
Foster, J.M.5
Rameseder, J.6
Hermjakob, H.7
Martens, L.8
-
22
-
-
79955864497
-
Mass wiz: A novel scoring algorithm with target-decoy based analysis pipeline for tandem mass spectrometry
-
Yadav, A. K., Kumar, D., and Dash, D. (2011) Mass Wiz: A novel scoring algorithm with target-decoy based analysis pipeline for tandem mass spectrometry. J. Proteome. Res. 10, 2154-2160.
-
(2011)
J. Proteome. Res.
, vol.10
, pp. 2154-2160
-
-
Yadav, A.K.1
Kumar, D.2
Dash, D.3
-
23
-
-
7044246160
-
Open mass spectrometry search algorithm
-
DOI 10.1021/pr0499491
-
Geer, L. Y., Markey, S. P., Kowalak, J. A., Wagner, L., Xu, M., Maynard, D. M., Yang, X., Shi, W., and Bryant, S. H. (2004) Open mass spectrometry search algorithm. J. Proteome. Res. 3, 958-964. (Pubitemid 39425651)
-
(2004)
Journal of Proteome Research
, vol.3
, Issue.5
, pp. 958-964
-
-
Geer, L.Y.1
Markey, S.P.2
Kowalak, J.A.3
Wagner, L.4
Xu, M.5
Maynard, D.M.6
Yang, X.7
Shi, W.8
Bryant, S.H.9
-
24
-
-
3142702204
-
TANDEM: Matching proteins with tandem mass spectra
-
DOI 10.1093/bioinformatics/bth092
-
Craig, R., and Beavis, R. C. (2004) TANDEM: matching proteins with tandem mass spectra. Bioinformatics 20, 1466-1467. (Pubitemid 38931421)
-
(2004)
Bioinformatics
, vol.20
, Issue.9
, pp. 1466-1467
-
-
Craig, R.1
Beavis, R.C.2
-
25
-
-
27544511899
-
InsPecT: Identification of posttranslationally modified peptides from tandem mass spectra
-
DOI 10.1021/ac050102d
-
Tanner, S., Shu, H., Frank, A., Wang, L. C., Zandi, E., Mumby, M., Pevzner, P. A., and Bafna, V. (2005) Ins PecT: identification of post translation ally modified peptides from tandem mass spectra. Anal. Chem. 77, 4626-4639. (Pubitemid 41542287)
-
(2005)
Analytical Chemistry
, vol.77
, Issue.14
, pp. 4626-4639
-
-
Tanner, S.1
Shu, H.2
Frank, A.3
Wang, L.-C.4
Zandi, E.5
Mumby, M.6
Pevzner, P.A.7
Bafna, V.8
-
26
-
-
63049120021
-
Improving sensitivity in proteome studies by analysis of false discovery rates for multiple search engines
-
Jones, A. R., Siepen, J. A., Hubbard, S. J., and Paton, N. W. (2009) Improving sensitivity in proteome studies by analysis of false discovery rates for multiple search engines. Proteomics 9, 1220-1229.
-
(2009)
Proteomics
, vol.9
, pp. 1220-1229
-
-
Jones, A.R.1
Siepen, J.A.2
Hubbard, S.J.3
Paton, N.W.4
-
27
-
-
38649083118
-
Assigning significance to peptides identified by tandem mass spectrometry using decoy databases
-
DOI 10.1021/pr700600n
-
Kä ll, L., Storey, J. D., MacCoss, M. J., and Noble, W. S. (2008) Assigning significance to peptides identified by tandem mass spectrometry using decoy databases. J. Proteome. Res. 7, 29-34. (Pubitemid 351171110)
-
(2008)
Journal of Proteome Research
, vol.7
, Issue.1
, pp. 29-34
-
-
Kall, L.1
Storey, J.D.2
MacCoss, M.J.3
Noble, W.S.4
-
28
-
-
0032519353
-
GeneMark.Hmm: New solutions for gene finding
-
DOI 10.1093/nar/26.4.1107
-
Lukashin, A. V., and Borodovsky, M. (1998) GeneMark.hmm: new solutions for gene finding. Nucleic Acids Res. 26, 1107-1115. (Pubitemid 28291669)
-
(1998)
Nucleic Acids Research
, vol.26
, Issue.4
, pp. 1107-1115
-
-
Lukashin, A.V.1
Borodovsky, M.2
-
29
-
-
77952299957
-
Prodigal: Prokaryotic gene recognition and translation initiation site identification
-
Hyatt, D., Chen, G. L., Locascio, P. F., Land, M. L., Larimer, F. W., and Hauser, L. J. (2010) Prodigal: prokaryotic gene recognition and translation initiation site identification. BMC. Bioinformatics 11, 119.
-
(2010)
BMC. Bioinformatics
, vol.11
, pp. 119
-
-
Hyatt, D.1
Chen, G.L.2
Locascio, P.F.3
Land, M.L.4
Larimer, F.W.5
Hauser, L.J.6
-
31
-
-
84858077472
-
The Pfam protein families database
-
Punta, M., Coggill, P. C., Eberhardt, R. Y., Mistry, J., Tate, J., Boursnell, C., Pang, N., Forslund, K., Ceric, G., Clements, J., Heger, A., Holm, L., Sonnhammer, E. L., Eddy, S. R., Bateman, A., and Finn, R. D. (2012) The Pfam protein families database. Nucleic Acids Res. 40, D290-D301.
-
(2012)
Nucleic Acids Res.
, vol.40
-
-
Punta, M.1
Coggill, P.C.2
Eberhardt, R.Y.3
Mistry, J.4
Tate, J.5
Boursnell, C.6
Pang, N.7
Forslund, K.8
Ceric, G.9
Clements, J.10
Heger, A.11
Holm, L.12
Sonnhammer, E.L.13
Eddy, S.R.14
Bateman, A.15
Finn, R.D.16
-
32
-
-
33750483615
-
Ag Base: A functional genomics resource for agriculture
-
McCarthy, F. M., Wang, N., Magee, G. B., Nanduri, B., Lawrence, M. L., Camon, E. B., Barrell, D. G., Hill, D. P., Dolan, M. E., Williams, W. P., Luthe, D. S., Bridges, S. M., and Burgess, S. C. (2006) Ag Base: A functional genomics resource for agriculture. BMC. Genomics 7, 229.
-
(2006)
BMC, Genomics
, vol.7
, pp. 229
-
-
McCarthy, F.M.1
Wang, N.2
Magee, G.B.3
Nanduri, B.4
Lawrence, M.L.5
Camon, E.B.6
Barrell, D.G.7
Hill, D.P.8
Dolan, M.E.9
Williams, W.P.10
Luthe, D.S.11
Bridges, S.M.12
Burgess, S.C.13
-
33
-
-
40549120596
-
The RAST server: Rapid annotations using subsystems technology
-
Aziz, R. K., Bartels, D., Best, A. A., DeJongh, M., Disz, T., Edwards, R. A., Formsma, K., Gerdes, S., Glass, E. M., Kubal, M., Meyer, F., Olsen, G. J., Olson, R., Osterman, A. L., Overbeek, R. A., McNeil, L. K., Paarmann, D., Paczian, T., Parrello, B., Pusch, G. D., Reich, C., Stevens, R., Vassieva, O., Vonstein, V., Wilke, A., and Zagnitko, O. (2008) The RAST Server: rapid annotations using subsystems technology. BMC. Genomics 9, 75.
-
(2008)
BMC. Genomics
, vol.9
, pp. 75
-
-
Aziz, R.K.1
Bartels, D.2
Best, A.A.3
DeJongh, M.4
Disz, T.5
Edwards, R.A.6
Formsma, K.7
Gerdes, S.8
Glass, E.M.9
Kubal, M.10
Meyer, F.11
Olsen, G.J.12
Olson, R.13
Osterman, A.L.14
Overbeek, R.A.15
McNeil, L.K.16
Paarmann, D.17
Paczian, T.18
Parrello, B.19
Pusch, G.D.20
Reich, C.21
Stevens, R.22
Vassieva, O.23
Vonstein, V.24
Wilke, A.25
Zagnitko, O.26
more..
-
34
-
-
35748972060
-
Semi-supervised learning for peptide identification from shotgun proteomics datasets
-
DOI 10.1038/nmeth1113, PII NMETH1113
-
Kä ll, L., Canterbury, J. D., Weston, J., Noble, W. S., and MacCoss, M. J. (2007) Semi-supervised learning for peptide identification from shotgun proteomics datasets. Nat. Methods 4, 923-925. (Pubitemid 350042380)
-
(2007)
Nature Methods
, vol.4
, Issue.11
, pp. 923-925
-
-
Kall, L.1
Canterbury, J.D.2
Weston, J.3
Noble, W.S.4
MacCoss, M.J.5
-
35
-
-
67049118923
-
Accurate and sensitive peptide identification with mascot percolator
-
Brosch, M., Yu, L., Hubbard, T., and Choudhary, J. (2009) Accurate and sensitive peptide identification with Mascot Percolator. J. Proteome. Res. 8, 3176-3181.
-
(2009)
J. Proteome. Res.
, vol.8
, pp. 3176-3181
-
-
Brosch, M.1
Yu, L.2
Hubbard, T.3
Choudhary, J.4
-
36
-
-
84870040445
-
Learning from decoys to improve the sensitivity and specificity of proteomics database search results
-
Yadav, A. K., Kumar, D., and Dash, D. (2012) Learning from decoys to improve the sensitivity and specificity of proteomics database search results. PLoS. One 7, e50651.
-
(2012)
PLoS. One
, vol.7
-
-
Yadav, A.K.1
Kumar, D.2
Dash, D.3
-
37
-
-
79953725441
-
FDR analysis: A tool for the integrated analysis of tandem mass spectrometry identification results from multiple search engines
-
Wedge, D. C., Krishna, R., Blackhurst, P., Siepen, J. A., Jones, A. R., and Hubbard, S. J. (2011) FDR Analysis: A tool for the integrated analysis of tandem mass spectrometry identification results from multiple search engines. J. Proteome. Res. 10, 2088-2094.
-
(2011)
J. Proteome. Res.
, vol.10
, pp. 2088-2094
-
-
Wedge, D.C.1
Krishna, R.2
Blackhurst, P.3
Siepen, J.A.4
Jones, A.R.5
Hubbard, S.J.6
-
38
-
-
34547838618
-
54 regulon, and identification of a ferredoxin gene (fdxN) for symbiotic nitrogen fixation
-
DOI 10.1007/s00438-007-0246-9
-
Hauser, F., Pessi, G., Friberg, M., Weber, C., Rusca, N., Lindemann, A., Fischer, H. M., and Hennecke, H. (2007) Dissection of the Bradyrhizobium japonicum NifA-sigma54 regulon, and identification of a ferredoxin gene (fdxN) for symbiotic nitrogen fixation. Mol. Genet. Genomics 278, 255-271. (Pubitemid 47247268)
-
(2007)
Molecular Genetics and Genomics
, vol.278
, Issue.3
, pp. 255-271
-
-
Hauser, F.1
Pessi, G.2
Friberg, M.3
Weber, C.4
Rusca, N.5
Lindemann, A.6
Fischer, H.-M.7
Hennecke, H.8
-
39
-
-
35348929944
-
Genome-wide transcript analysis of Bradyrhizobium japonicum bacteroids in soybean root nodules
-
DOI 10.1094/MPMI-20-11-1353
-
Pessi, G., Ahrens, C. H., Rehrauer, H., Lindemann, A., Hauser, F., Fischer, H. M., and Hennecke, H. (2007) Genome-wide transcript analysis of Brad yrhizobium japonicum bacteroids in soybean root nodules. Mol. Plant Microbe Interact. 20, 1353-1363. (Pubitemid 47612498)
-
(2007)
Molecular Plant-Microbe Interactions
, vol.20
, Issue.11
, pp. 1353-1363
-
-
Pessi, G.1
Ahrens, C.H.2
Rehrauer, H.3
Lindemann, A.4
Hauser, F.5
Fischer, H.-M.6
Hennecke, H.7
-
40
-
-
84055199940
-
Complete genome sequence of the soybean symbiont bradyrhizobium japonicum strain usda6t
-
Kaneko, T. (2011) Complete Genome Sequence of the Soybean Symbiont Bradyrhizobium japonicum Strain USDA6T. Genes 2, 763-787.
-
(2011)
Genes
, vol.2
, pp. 763-787
-
-
Kaneko, T.1
-
41
-
-
84867894008
-
Complete genome sequence of brad yrhizobium sp, s23321: Insights into symbiosis evolution in soil oligotrophs
-
Okubo, T., Tsukui, T., Maita, H., Okamoto, S., Oshima, K., Fujisawa, T., Saito, A., Futamata, H., Hattori, R., Shimomura, Y., Haruta, S., Morimoto, S., Wang, Y., Sakai, Y., Hattori, M., Aizawa, S., Nagashima, K. V., Masuda, S., Hattori, T., Yamashita, A., Bao, Z., Hayatsu, M., Kajiya- Kanegae, H., Yoshinaga, I., Sakamoto, K., Toyota, K., Nakao, M., Kohara, M., Anda, M., Niwa, R., Jung-Hwan, P., Sameshima-Saito, R., Tokuda, S., Yamamoto, S., Yamamoto, S., Yokoyama, T., Akutsu, T., Nakamura, Y., Nakahira-Yanaka, Y., Takada, H. Y., Hirakawa, H., Mitsui, H., Terasawa, K., Itakura, M., Sato, S., Ikeda-Ohtsubo, W., Sakakura, N., Kaminuma, E., and Minamisawa, K. (2012) Complete Genome Sequence of Brad yrhizobium sp. S23321: Insights into Symbiosis Evolution in Soil Oligotrophs. Microbes. Environ. 27, 306-315.
-
(2012)
Microbes. Environ
, vol.27
, pp. 306-315
-
-
Okubo, T.1
Tsukui, T.2
Maita, H.3
Okamoto, S.4
Oshima, K.5
Fujisawa, T.6
Saito, A.7
Futamata, H.8
Hattori, R.9
Shimomura, Y.10
Haruta, S.11
Morimoto, S.12
Wang, Y.13
Sakai, Y.14
Hattori, M.15
Aizawa, S.16
Nagashima, K.V.17
Masuda, S.18
Hattori, T.19
Yamashita, A.20
Bao, Z.21
Hayatsu, M.22
Kajiya- Kanegae, H.23
Yoshinaga, I.24
Sakamoto, K.25
Toyota, K.26
Nakao, M.27
Kohara, M.28
Anda, M.29
Niwa, R.30
Jung-Hwan, P.31
Sameshima-Saito, R.32
Tokuda, S.33
Yamamoto, S.34
Yamamoto, S.35
Yokoyama, T.36
Akutsu, T.37
Nakamura, Y.38
Nakahira-Yanaka, Y.39
Takada, H.Y.40
Hirakawa, H.41
Mitsui, H.42
Terasawa, K.43
Itakura, M.44
Sato, S.45
Ikeda-Ohtsubo, W.46
Sakakura, N.47
Kaminuma, E.48
Minamisawa, K.49
more..
-
42
-
-
0035143664
-
Potential symbiosis-specific genes uncovered by sequencing a 410-kilobase DNA region of the Bradyrhizobium japonicum chromosome
-
DOI 10.1128/JB.183.4.1405-1412.2001
-
Gö ttfert, M., Rö thlisberger, S., Kü ndig, C., Beck, C., Marty, R., and Hennecke, H. (2001) Potential symbiosis-specific genes uncovered by sequencing a 410-kilobase DNA region of the Bradyrhizobium japonicum chromosome. J. Bacteriol. 183, 1405-1412. (Pubitemid 32107737)
-
(2001)
Journal of Bacteriology
, vol.183
, Issue.4
, pp. 1405-1412
-
-
Gottfert, M.1
Rothlisberger, S.2
Kundig, C.3
Beck, C.4
Marty, R.5
Hennecke, H.6
-
43
-
-
0026026963
-
The Bradyrhizobium japonicum nolA gene and its involvement in the renotype-specific nodulation of soybeans
-
Sadowsky, M. J., Cregan, P. B., Gottfert, M., Sharma, A., Gerhold, D., Rodriguez-Quinones, F., Keyser, H. H., Hennecke, H., and Stacey, G. (1991) The Bradyrhizobium japonicum nolA gene and its involvement in the genotype-specific nodulation of soybeans. Proc. Natl. Acad. Sci. U.S.A. 88, 637-641. (Pubitemid 21915521)
-
(1991)
Proceedings of the National Academy of Sciences of the United States of America
, vol.88
, Issue.2
, pp. 637-641
-
-
Sadowsky, M.J.1
Cregan, P.B.2
Gottfert, M.3
Sharma, A.4
Gerhold, D.5
Rodriguez-Quinones, F.6
Keyser, H.H.7
Hennecke, H.8
Stacey, G.9
-
44
-
-
0032985668
-
The Bradyrhizobium japonicum nolA gene encodes three functionally distinct proteins
-
Loh, J., Stacey, M. G., Sadowsky, M. J., and Stacey, G. (1999) The Bradyrhizobium japonicum nolA gene encodes three functionally distinct proteins. J. Bacteriol. 181, 1544-1554. (Pubitemid 29110815)
-
(1999)
Journal of Bacteriology
, vol.181
, Issue.5
, pp. 1544-1554
-
-
Loh, J.1
Stacey, M.G.2
Sadowsky, M.J.3
Stacey, G.4
-
45
-
-
33750127867
-
GAPP: A fully automated software for the confident identification of human peptides from tandem mass spectra
-
DOI 10.1021/pr060205s
-
Shadforth, I., Xu, W., Crowther, D., and Bessant, C. (2006) GAPP: A fully automated software for the confident identification of human peptides from tandem mass spectra. J. Proteome. Res. 5, 2849-2852. (Pubitemid 44595185)
-
(2006)
Journal of Proteome Research
, vol.5
, Issue.10
, pp. 2849-2852
-
-
Shadforth, I.1
Xu, W.2
Crowther, D.3
Bessant, C.4
-
46
-
-
52049102297
-
PepLine: A software pipeline for high-throughput direct mapping of tandem mass spectrometry data on genomic sequences
-
Ferro, M., Tardif, M., Reguer, E., Cahuzac, R., Bruley, C., Vermat, T., Nugues, E., Vigouroux, M., Vandenbrouck, Y., Garin, J., and Viari, A. (2008) PepLine: A software pipeline for high-throughput direct mapping of tandem mass spectrometry data on genomic sequences. J. Proteome. Res. 7, 1873-1883.
-
(2008)
J. Proteome. Res.
, vol.7
, pp. 1873-1883
-
-
Ferro, M.1
Tardif, M.2
Reguer, E.3
Cahuzac, R.4
Bruley, C.5
Vermat, T.6
Nugues, E.7
Vigouroux, M.8
Vandenbrouck, Y.9
Garin, J.10
Viari, A.11
-
47
-
-
11144310562
-
Estimation of the number of authentic orphan genes in bacterial genomes
-
Fukuchi, S., and Nishikawa, K. (2004) Estimation of the number of authentic orphan genes in bacterial genomes. DNA Res. 11, 219-231, 311-313.
-
(2004)
DNA Res.
, vol.11
, Issue.219-231
, pp. 311-313
-
-
Fukuchi, S.1
Nishikawa, K.2
-
48
-
-
77957836421
-
Protein acetylation in archaea, bacteria, and eukaryotes
-
Soppa, J. (2010) Protein acetylation in archaea, bacteria, and eukaryotes. Archaea. 2010, 1-9.
-
(2010)
Archaea, 2010
, pp. 1-9
-
-
Soppa, J.1
-
49
-
-
77954013335
-
Bacterial protein acetylation: The dawning of a new age
-
Hu, L. I., Lima, B. P., and Wolfe, A. J. (2010) Bacterial protein acetylation: The dawning of a new age. Mol. Microbiol. 77, 15-21.
-
(2010)
Mol. Microbiol
, vol.77
, pp. 15-21
-
-
Hu, L.I.1
Lima, B.P.2
Wolfe, A.J.3
-
50
-
-
84887098433
-
N-terminal protein processing: A comparative proteogenomic analysis
-
Bonissone, S., Gupta, N., Romine, M., Bradshaw, R. A., and Pevzner, P. A. (2012) N-terminal protein processing: A comparative proteogenomic analysis. Mol. Cell Proteomics.
-
(2012)
Mol. Cell Proteomics
-
-
Bonissone, S.1
Gupta, N.2
Romine, M.3
Bradshaw, R.A.4
Pevzner, P.A.5
|