-
1
-
-
44249084514
-
Proteogenomics: Needs and roles to be filled by proteomics in genome annotation
-
DOI 10.1093/bfgp/eln010
-
C. Ansong, S.O. Purvine, J.N. Adkins, M.S. Lipton, and R.D. Smith Proteogenomics: needs and roles to be filled by proteomics in genome annotation Brief. Funct. Genomics Proteomics 7 2008 50 62 (Pubitemid 351721150)
-
(2008)
Briefings in Functional Genomics and Proteomics
, vol.7
, Issue.1
, pp. 50-62
-
-
Ansong, C.1
Purvine, S.O.2
Adkins, J.N.3
Lipton, M.S.4
Smith, R.D.5
-
2
-
-
35848965006
-
Activity-based protein profiling for the functional annotation of enzymes
-
DOI 10.1038/nmeth1092, PII NMETH1092
-
K.T. Barglow, and B.F. Cravatt Activity-based protein profiling for the functional annotation of enzymes Nat. Methods 4 2007 822 827 (Pubitemid 350055579)
-
(2007)
Nature Methods
, vol.4
, Issue.10
, pp. 822-827
-
-
Barglow, K.T.1
Cravatt, B.F.2
-
3
-
-
0034060929
-
Powers and pitfalls in sequence analysis: The 70% hurdle
-
DOI 10.1101/gr.10.4.398
-
P. Bork Powers and pitfalls in sequence analysis: the 70% hurdle Genome Res. 10 2000 398 400 (Pubitemid 30259070)
-
(2000)
Genome Research
, vol.10
, Issue.4
, pp. 398-400
-
-
Bork, P.1
-
4
-
-
0031897589
-
Predicting functions from protein sequences - Where are the bottlenecks?
-
DOI 10.1038/ng0498-313
-
P. Bork, and E.V. Koonin Predicting functions from protein sequences - where are the bottlenecks? Nat. Genet. 18 1998 313 318 (Pubitemid 28158157)
-
(1998)
Nature Genetics
, vol.18
, Issue.4
, pp. 313-318
-
-
Bork, P.1
Koonin, E.V.2
-
5
-
-
50649112213
-
Activity-based protein profiling: From enzyme chemistry to proteomic chemistry
-
B.F. Cravatt, A.T. Wright, and J.W. Kozarich Activity-based protein profiling: from enzyme chemistry to proteomic chemistry Annu. Rev. Biochem. 77 2008 383 414
-
(2008)
Annu. Rev. Biochem.
, vol.77
, pp. 383-414
-
-
Cravatt, B.F.1
Wright, A.T.2
Kozarich, J.W.3
-
6
-
-
81755163097
-
Evidence-based annotation of gene function in Shewanella oneidensis MR-1 using genome-wide fitness profiling across 121 conditions
-
A. Deutschbauer, M.N. Price, K.M. Wetmore, W. Shao, J.K. Baumohl, Z. Xu, M. Nguyen, R. Tamse, R.W. Davis, and A.P. Arkin Evidence-based annotation of gene function in Shewanella oneidensis MR-1 using genome-wide fitness profiling across 121 conditions PLoS Genet. 7 2011 e1002385
-
(2011)
PLoS Genet.
, vol.7
, pp. 1002385
-
-
Deutschbauer, A.1
Price, M.N.2
Wetmore, K.M.3
Shao, W.4
Baumohl, J.K.5
Xu, Z.6
Nguyen, M.7
Tamse, R.8
Davis, R.W.9
Arkin, A.P.10
-
7
-
-
33847167237
-
Mechanism and catalysis of reactions of acyl phosphates. I. Nucleophilic reactions
-
G. DiSabato, and W.P. Jencks Mechanism and catalysis of reactions of acyl phosphates. I. Nucleophilic reactions J. Am. Chem. Soc. 83 1961 4393 4400
-
(1961)
J. Am. Chem. Soc.
, vol.83
, pp. 4393-4400
-
-
Disabato, G.1
Jencks, W.P.2
-
8
-
-
84859260583
-
Annotation of the M. tuberculosis hypothetical orfeome: Adding functional information to more than half of the uncharacterized proteins
-
T. Doerks, V. van Noort, P. Minguez, and P. Bork Annotation of the M. tuberculosis hypothetical orfeome: adding functional information to more than half of the uncharacterized proteins PLoS ONE 7 2012 e34302
-
(2012)
PLoS ONE
, vol.7
, pp. 34302
-
-
Doerks, T.1
Van Noort, V.2
Minguez, P.3
Bork, P.4
-
9
-
-
23044481526
-
Mutually dependent secretion of proteins required for mycobacterial virulence
-
DOI 10.1073/pnas.0504922102
-
S.M. Fortune, A. Jaeger, D.A. Sarracino, M.R. Chase, C.M. Sassetti, D.R. Sherman, B.R. Bloom, and E.J. Rubin Mutually dependent secretion of proteins required for mycobacterial virulence Proc. Natl. Acad. Sci. USA 102 2005 10676 10681 (Pubitemid 41061613)
-
(2005)
Proceedings of the National Academy of Sciences of the United States of America
, vol.102
, Issue.30
, pp. 10676-10681
-
-
Fortune, S.M.1
Jaeger, A.2
Sarracino, D.A.3
Chase, M.R.4
Sassetti, C.M.5
Sherman, D.R.6
Bloom, B.R.7
Rubin, E.J.8
-
10
-
-
77955042462
-
From complete genome sequence to 'complete' understanding?
-
M.Y. Galperin, and E.V. Koonin From complete genome sequence to 'complete' understanding? Trends Biotechnol. 28 2010 398 406
-
(2010)
Trends Biotechnol.
, vol.28
, pp. 398-406
-
-
Galperin, M.Y.1
Koonin, E.V.2
-
11
-
-
80855134793
-
PATRIC: The comprehensive bacterial bioinformatics resource with a focus on human pathogenic species
-
J.J. Gillespie, A.R. Wattam, S.A. Cammer, J.L. Gabbard, M.P. Shukla, O. Dalay, T. Driscoll, D. Hix, S.P. Mane, and C. Mao PATRIC: the comprehensive bacterial bioinformatics resource with a focus on human pathogenic species Infect. Immun. 79 2011 4286 4298
-
(2011)
Infect. Immun.
, vol.79
, pp. 4286-4298
-
-
Gillespie, J.J.1
Wattam, A.R.2
Cammer, S.A.3
Gabbard, J.L.4
Shukla, M.P.5
Dalay, O.6
Driscoll, T.7
Hix, D.8
Mane, S.P.9
Mao, C.10
-
12
-
-
78951489323
-
Probing bacterial pathogenesis with genetics, genomics, and chemical biology: Past, present, and future approaches
-
J.E. Gomez, A. Clatworthy, and D.T. Hung Probing bacterial pathogenesis with genetics, genomics, and chemical biology: past, present, and future approaches Crit. Rev. Biochem. Mol. Biol. 46 2011 41 66
-
(2011)
Crit. Rev. Biochem. Mol. Biol.
, vol.46
, pp. 41-66
-
-
Gomez, J.E.1
Clatworthy, A.2
Hung, D.T.3
-
13
-
-
34247588355
-
M. tuberculosis Ser/Thr protein kinase D phosphorylates an anti-anti-sigma factor homolog
-
A.E. Greenstein, J.A. MacGurn, C.E. Baer, A.M. Falick, J.S. Cox, and T. Alber M. tuberculosis Ser/Thr protein kinase D phosphorylates an anti-anti-sigma factor homolog PLoS Pathog. 3 2007 e49
-
(2007)
PLoS Pathog.
, vol.3
, pp. 49
-
-
Greenstein, A.E.1
MacGurn, J.A.2
Baer, C.E.3
Falick, A.M.4
Cox, J.S.5
Alber, T.6
-
14
-
-
0037249633
-
The TIGRFAMs database of protein families
-
DOI 10.1093/nar/gkg128
-
D.H. Haft, J.D. Selengut, and O. White The TIGRFAMs database of protein families Nucleic Acids Res. 31 2003 371 373 (Pubitemid 36150405)
-
(2003)
Nucleic Acids Research
, vol.31
, Issue.1
, pp. 371-373
-
-
Haft, D.H.1
Selengut, J.D.2
White, O.3
-
16
-
-
0033832615
-
Predicting protein function by genomic context: Quantitative evaluation and qualitative inferences
-
M. Huynen, B. Snel, W. Lathe 3rd, and P. Bork Predicting protein function by genomic context: quantitative evaluation and qualitative inferences Genome Res. 10 2000 1204 1210
-
(2000)
Genome Res.
, vol.10
, pp. 1204-1210
-
-
Huynen, M.1
Snel, B.2
Lathe III, W.3
Bork, P.4
-
17
-
-
83055173265
-
Proteogenomic analysis of Mycobacterium tuberculosis by high resolution mass spectrometry
-
M111.011627
-
D.S. Kelkar, D. Kumar, P. Kumar, L. Balakrishnan, B. Muthusamy, A.K. Yadav, P. Shrivastava, A. Marimuthu, S. Anand, and H. Sundaram Proteogenomic analysis of Mycobacterium tuberculosis by high resolution mass spectrometry Mol. Cell Proteomics 10 2011 M111.011627
-
(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
-
18
-
-
63849246525
-
Protein structure prediction on the Web: A case study using the Phyre server
-
L.A. Kelley, and M.J. Sternberg Protein structure prediction on the Web: a case study using the Phyre server Nat. Protoc. 4 2009 363 371
-
(2009)
Nat. Protoc.
, vol.4
, pp. 363-371
-
-
Kelley, L.A.1
Sternberg, M.J.2
-
19
-
-
78651281217
-
EcoCyc: A comprehensive database of Escherichia coli biology
-
I.M. Keseler, J. Collado-Vides, A. Santos-Zavaleta, M. Peralta-Gil, S. Gama-Castro, L. Muñiz-Rascado, C. Bonavides-Martinez, S. Paley, M. Krummenacker, and T. Altman EcoCyc: a comprehensive database of Escherichia coli biology Nucleic Acids Res. 39 Database issue 2011 D583 D590
-
(2011)
Nucleic Acids Res.
, vol.39
, Issue.DATABASE ISSUE
-
-
Keseler, I.M.1
Collado-Vides, J.2
Santos-Zavaleta, A.3
Peralta-Gil, M.4
Gama-Castro, S.5
Muñiz-Rascado, L.6
Bonavides-Martinez, C.7
Paley, S.8
Krummenacker, M.9
Altman, T.10
-
20
-
-
0034530012
-
Acyl phosphate esters: Charge-directed acylation and artificial blood
-
R. Kluger Acyl phosphate esters: charge-directed acylation and artificial blood Synlett 12 2000 1708 1720 (Pubitemid 32005583)
-
(2000)
Synlett
, Issue.12
, pp. 1708-1720
-
-
Kluger, R.1
-
21
-
-
78649790931
-
Allosteric activation mechanism of the Mycobacterium tuberculosis receptor Ser/Thr protein kinase, PknB
-
T.N. Lombana, N. Echols, M.C. Good, N.D. Thomsen, H.L. Ng, A.E. Greenstein, A.M. Falick, D.S. King, and T. Alber Allosteric activation mechanism of the Mycobacterium tuberculosis receptor Ser/Thr protein kinase, PknB Structure 18 2010 1667 1677
-
(2010)
Structure
, vol.18
, pp. 1667-1677
-
-
Lombana, T.N.1
Echols, N.2
Good, M.C.3
Thomsen, N.D.4
Ng, H.L.5
Greenstein, A.E.6
Falick, A.M.7
King, D.S.8
Alber, T.9
-
23
-
-
25144441735
-
A non-RD1 gene cluster is required for Snm secretion in Mycobacterium tuberculosis
-
DOI 10.1111/j.1365-2958.2005.04800.x
-
J.A. MacGurn, S. Raghavan, S.A. Stanley, and J.S. Cox A non-RD1 gene cluster is required for Snm secretion in Mycobacterium tuberculosis Mol. Microbiol. 57 2005 1653 1663 (Pubitemid 41337393)
-
(2005)
Molecular Microbiology
, vol.57
, Issue.6
, pp. 1653-1663
-
-
MacGurn, J.A.1
Raghavan, S.2
Stanley, S.A.3
Cox, J.S.4
-
24
-
-
78049483746
-
Leads for antitubercular compounds from kinase inhibitor library screens
-
S. Magnet, R.C. Hartkoorn, R. Székely, J. Pató, J.A. Triccas, P. Schneider, C. Szántai-Kis, L. Orfi, M. Chambon, and D. Banfi Leads for antitubercular compounds from kinase inhibitor library screens Tuberculosis (Edinb.) 90 2010 354 360
-
(2010)
Tuberculosis (Edinb.)
, vol.90
, pp. 354-360
-
-
Magnet, S.1
Hartkoorn, R.C.2
Székely, R.3
Pató, J.4
Triccas, J.A.5
Schneider, P.6
Szántai-Kis, C.7
Orfi, L.8
Chambon, M.9
Banfi, D.10
-
25
-
-
11144293517
-
Mycobacterium tuberculosis functional network analysis by global subcellular protein profiling
-
DOI 10.1091/mbc.E04-04-0329
-
K.G. Mawuenyega, C.V. Forst, K.M. Dobos, J.T. Belisle, J. Chen, E.M. Bradbury, A.R. Bradbury, and X. Chen Mycobacterium tuberculosis functional network analysis by global subcellular protein profiling Mol. Biol. Cell 16 2005 396 404 (Pubitemid 40024320)
-
(2005)
Molecular Biology of the Cell
, vol.16
, Issue.1
, pp. 396-404
-
-
Mawuenyega, K.G.1
Forst, C.V.2
Dobos, K.M.3
Belisle, J.T.4
Chen, J.5
Bradbury, E.M.6
Bradbury, A.R.M.7
Chen, X.8
-
26
-
-
82955194511
-
The DinB superfamily includes novel mycothiol, bacillithiol, and glutathione S-transferases
-
G.L. Newton, S.S. Leung, J.I. Wakabayashi, M. Rawat, and R.C. Fahey The DinB superfamily includes novel mycothiol, bacillithiol, and glutathione S-transferases Biochemistry 50 2011 10751 10760
-
(2011)
Biochemistry
, vol.50
, pp. 10751-10760
-
-
Newton, G.L.1
Leung, S.S.2
Wakabayashi, J.I.3
Rawat, M.4
Fahey, R.C.5
-
27
-
-
33846248354
-
Functional interrogation of the kinome using nucleotide acyl phosphates
-
DOI 10.1021/bi062142x
-
M.P. Patricelli, A.K. Szardenings, M. Liyanage, T.K. Nomanbhoy, M. Wu, H. Weissig, A. Aban, D. Chun, S. Tanner, and J.W. Kozarich Functional interrogation of the kinome using nucleotide acyl phosphates Biochemistry 46 2007 350 358 (Pubitemid 46105428)
-
(2007)
Biochemistry
, vol.46
, Issue.2
, pp. 350-358
-
-
Patricelli, M.P.1
Szardenings, A.K.2
Liyanage, M.3
Nomanbhoy, T.K.4
Wu, M.5
Weissig, H.6
Aban, A.7
Chun, D.8
Tanner, S.9
Kozarich, J.W.10
-
28
-
-
34848865681
-
Orthologous transcription factors in bacteria have different functions and regulate different genes
-
DOI 10.1371/journal.pcbi.0030175
-
M.N. Price, P.S. Dehal, and A.P. Arkin Orthologous transcription factors in bacteria have different functions and regulate different genes PLoS Comput. Biol. 3 2007 1739 1750 (Pubitemid 47502978)
-
(2007)
PLoS Computational Biology
, vol.3
, Issue.9
, pp. 1739-1750
-
-
Price, M.N.1
Dehal, P.S.2
Arkin, A.P.3
-
29
-
-
34547739476
-
Probing adenosine nucleotide-binding proteins with an affinity-labeled nucleotide probe and mass spectrometry
-
DOI 10.1021/ac0622375
-
H. Qiu, and Y. Wang Probing adenosine nucleotide-binding proteins with an affinity-labeled nucleotide probe and mass spectrometry Anal. Chem. 79 2007 5547 5556 (Pubitemid 47229799)
-
(2007)
Analytical Chemistry
, vol.79
, Issue.15
, pp. 5547-5556
-
-
Qiu, H.1
Wang, Y.2
-
30
-
-
58149182735
-
TB database: An integrated platform for tuberculosis research
-
T.B. Reddy, R. Riley, F. Wymore, P. Montgomery, D. DeCaprio, R. Engels, M. Gellesch, J. Hubble, D. Jen, and H. Jin TB database: an integrated platform for tuberculosis research Nucleic Acids Res. 37 Database issue 2009 D499 D508
-
(2009)
Nucleic Acids Res.
, vol.37
, Issue.DATABASE ISSUE
-
-
Reddy, T.B.1
Riley, R.2
Wymore, F.3
Montgomery, P.4
Decaprio, D.5
Engels, R.6
Gellesch, M.7
Hubble, J.8
Jen, D.9
Jin, H.10
-
31
-
-
55449113709
-
Comparative analyses of fundamental differences in membrane transport capabilities in prokaryotes and eukaryotes
-
Q. Ren, and I.T. Paulsen Comparative analyses of fundamental differences in membrane transport capabilities in prokaryotes and eukaryotes PLoS Comput. Biol. 1 2005 e27
-
(2005)
PLoS Comput. Biol.
, vol.1
, pp. 27
-
-
Ren, Q.1
Paulsen, I.T.2
-
32
-
-
0036308741
-
Enzyme function less conserved than anticipated
-
DOI 10.1016/S0022-2836(02)00016-5
-
B. Rost Enzyme function less conserved than anticipated J. Mol. Biol. 318 2002 595 608 (Pubitemid 34734850)
-
(2002)
Journal of Molecular Biology
, vol.318
, Issue.2
, pp. 595-608
-
-
Rost, B.1
-
33
-
-
33747894577
-
TM4 microarray software suite
-
A.I. Saeed, N.K. Bhagabati, J.C. Braisted, W. Liang, V. Sharov, E.A. Howe, J. Li, M. Thiagarajan, J.A. White, and J. Quackenbush TM4 microarray software suite Methods Enzymol. 411 2006 134 193
-
(2006)
Methods Enzymol.
, vol.411
, pp. 134-193
-
-
Saeed, A.I.1
Bhagabati, N.K.2
Braisted, J.C.3
Liang, W.4
Sharov, V.5
Howe, E.A.6
Li, J.7
Thiagarajan, M.8
White, J.A.9
Quackenbush, J.10
-
34
-
-
84868131974
-
Activity-based protein profiling reveals mitochondrial oxidative enzyme impairment and restoration in diet-induced obese mice
-
N.C. Sadler, T.E. Angel, M.P. Lewis, L.M. Pederson, L.M. Chauvigné-Hines, S.D. Wiedner, E.M. Zink, R.D. Smith, and A.T. Wright Activity-based protein profiling reveals mitochondrial oxidative enzyme impairment and restoration in diet-induced obese mice PLoS ONE 7 2012 e47996
-
(2012)
PLoS ONE
, vol.7
, pp. 47996
-
-
Sadler, N.C.1
Angel, T.E.2
Lewis, M.P.3
Pederson, L.M.4
Chauvigné-Hines, L.M.5
Wiedner, S.D.6
Zink, E.M.7
Smith, R.D.8
Wright, A.T.9
-
35
-
-
0345701347
-
Genes required for mycobacterial growth defined by high density mutagenesis
-
DOI 10.1046/j.1365-2958.2003.03425.x
-
C.M. Sassetti, D.H. Boyd, and E.J. Rubin Genes required for mycobacterial growth defined by high density mutagenesis Mol. Microbiol. 48 2003 77 84 (Pubitemid 36411469)
-
(2003)
Molecular Microbiology
, vol.48
, Issue.1
, pp. 77-84
-
-
Sassetti, C.M.1
Boyd, D.H.2
Rubin, E.J.3
-
38
-
-
77951216021
-
Activity-based proteomics of enzyme superfamilies: Serine hydrolases as a case study
-
G.M. Simon, and B.F. Cravatt Activity-based proteomics of enzyme superfamilies: serine hydrolases as a case study J. Biol. Chem. 285 2010 11051 11055
-
(2010)
J. Biol. Chem.
, vol.285
, pp. 11051-11055
-
-
Simon, G.M.1
Cravatt, B.F.2
-
39
-
-
22244445882
-
A tandem orthogonal proteolysis strategy for high-content chemical proteomics
-
DOI 10.1021/ja0532842
-
A.E. Speers, and B.F. Cravatt A tandem orthogonal proteolysis strategy for high-content chemical proteomics J. Am. Chem. Soc. 127 2005 10018 10019 (Pubitemid 40995443)
-
(2005)
Journal of the American Chemical Society
, vol.127
, Issue.28
, pp. 10018-10019
-
-
Speers, A.E.1
Cravatt, B.F.2
-
40
-
-
0037462106
-
Activity-based protein profiling in vivo using a copper(I)-catalyzed azide-alkyne [3 + 2] cycloaddition
-
DOI 10.1021/ja034490h
-
A.E. Speers, G.C. Adam, and B.F. Cravatt Activity-based protein profiling in vivo using a copper(i)-catalyzed azide-alkyne [3 + 2] cycloaddition J. Am. Chem. Soc. 125 2003 4686 4687 (Pubitemid 36505343)
-
(2003)
Journal of the American Chemical Society
, vol.125
, Issue.16
, pp. 4686-4687
-
-
Speers, A.E.1
Adam, G.C.2
Cravatt, B.F.3
-
41
-
-
84860575662
-
Proteogenomic analysis of bacteria and archaea: A 46 organism case study
-
E. Venter, R.D. Smith, and S.H. Payne Proteogenomic analysis of bacteria and archaea: a 46 organism case study PLoS ONE 6 2011 e27587
-
(2011)
PLoS ONE
, vol.6
, pp. 27587
-
-
Venter, E.1
Smith, R.D.2
Payne, S.H.3
-
42
-
-
33646264529
-
Advances in proteomics data analysis and display using an accurate mass and time tag approach
-
J.S. Zimmer, M.E. Monroe, W.J. Qian, and R.D. Smith Advances in proteomics data analysis and display using an accurate mass and time tag approach Mass Spectrom. Rev. 25 2006 450 482
-
(2006)
Mass Spectrom. Rev.
, vol.25
, pp. 450-482
-
-
Zimmer, J.S.1
Monroe, M.E.2
Qian, W.J.3
Smith, R.D.4
|