-
1
-
-
0036782279
-
Interactions among strategies associated with bacterial infection: Pathogenicity, epidemicity, and antibiotic resistance
-
Martinez J, Baquero F. Interactions among strategies associated with bacterial infection: pathogenicity, epidemicity, and antibiotic resistance. Clin. Microbiol. Rev. 15(4), 647-679 (2002).
-
(2002)
Clin. Microbiol. Rev
, vol.15
, Issue.4
, pp. 647-679
-
-
Martinez, J.1
Baquero, F.2
-
2
-
-
0034035284
-
Molecular basis of antibiotic resistance and β-lactamase inhibition by mechanism-based inactivators: Perspectives and future directions
-
Therrien C, Levesque RC. Molecular basis of antibiotic resistance and β-lactamase inhibition by mechanism-based inactivators: perspectives and future directions. FEMS Microbiol. Rev. 24, 251-262 (2000).
-
(2000)
FEMS Microbiol. Rev
, vol.24
, pp. 251-262
-
-
Therrien, C.1
Levesque, R.C.2
-
3
-
-
23444440823
-
Inactivation of antibiotics and the dissemination of resistance genes
-
Davies J. Inactivation of antibiotics and the dissemination of resistance genes. Science 264(5157), 375-382 (1994).
-
(1994)
Science
, vol.264
, Issue.5157
, pp. 375-382
-
-
Davies, J.1
-
4
-
-
0030790687
-
Common themes in microbial pathogenicity revisited
-
Finlay BB, Falkow S. Common themes in microbial pathogenicity revisited. Microbiol. Mol. Biol. Rev. 61(2), 136-169 (1997).
-
(1997)
Microbiol. Mol. Biol. Rev
, vol.61
, Issue.2
, pp. 136-169
-
-
Finlay, B.B.1
Falkow, S.2
-
5
-
-
0000277421
-
History of opportunistic infection in the immunocompromised host
-
Armstrong D. History of opportunistic infection in the immunocompromised host. Clin. Inf. Dis. 17 (Suppl. 2) S318-S321 (1993).
-
(1993)
Clin. Inf. Dis
, vol.17
, Issue.SUPPL. 2
-
-
Armstrong, D.1
-
6
-
-
0034444550
-
Host-pathogen interactions: Basic concepts of microbial commensalism, colonization, infection, and disease
-
Casadevall A, Pirofski LA. Host-pathogen interactions: basic concepts of microbial commensalism, colonization, infection, and disease. Infect. Immun. 68(12), 6511-6518 (2000).
-
(2000)
Infect. Immun
, vol.68
, Issue.12
, pp. 6511-6518
-
-
Casadevall, A.1
Pirofski, L.A.2
-
7
-
-
0028213878
-
Hospital-acquired infections: Diseases with increasingly limited therapies
-
Swartz MN. Hospital-acquired infections: diseases with increasingly limited therapies, Proc. Natl Acad. Sci. USA 91, 2420-2427 (1994).
-
(1994)
Proc. Natl Acad. Sci. USA
, vol.91
, pp. 2420-2427
-
-
Swartz, M.N.1
-
8
-
-
0032862511
-
Plasmid mediated resistance to thrombin-induced platelet microbicidal protein in staphylococci: Role of qacA locus
-
Kupperwasser LI, Skurray RA, Brown MH et al. Plasmid mediated resistance to thrombin-induced platelet microbicidal protein in staphylococci: role of qacA locus. Antimicrob. Agents Chemother. 43(10), 2395-2399 (1999).
-
(1999)
Antimicrob. Agents Chemother
, vol.43
, Issue.10
, pp. 2395-2399
-
-
Kupperwasser, L.I.1
Skurray, R.A.2
Brown, M.H.3
-
9
-
-
0025239739
-
Intracellular and cell-to-cell spread of Listeria monocytogens involve interaction with F-actin enterocytelike cell line Caco-2
-
Mounier JA, Ryter M, Ciquis-Rondon M, Sansonetti PJ. Intracellular and cell-to-cell spread of Listeria monocytogens involve interaction with F-actin enterocytelike cell line Caco-2. Infect. Immun. 58, 1048-1058 (1990).
-
(1990)
Infect. Immun
, vol.58
, pp. 1048-1058
-
-
Mounier, J.A.1
Ryter, M.2
Ciquis-Rondon, M.3
Sansonetti, P.J.4
-
10
-
-
0035843908
-
Genes lost and genes found: Evolution of bacterial pathogenesis and symbiosis
-
Ochman H, Mora NA. Genes lost and genes found: evolution of bacterial pathogenesis and symbiosis. Science 292, 1096-1098 (2001).
-
(2001)
Science
, vol.292
, pp. 1096-1098
-
-
Ochman, H.1
Mora, N.A.2
-
11
-
-
0031037207
-
The search for antimicrobial agents effective against bacteria resistant to multiple antibiotics
-
Chopra I, Hodgson J, Metcalf B, Poste G, The search for antimicrobial agents effective against bacteria resistant to multiple antibiotics. Antimicrob. Agents Chemother. 41, 497-503 (1997).
-
(1997)
Antimicrob. Agents Chemother
, vol.41
, pp. 497-503
-
-
Chopra, I.1
Hodgson, J.2
Metcalf, B.3
Poste, G.4
-
12
-
-
0029860724
-
High mutation frequencies among Escherichia coli and Salmonella pathogens
-
Leclerc JE, Li B, Payne WL, Cédula TA. High mutation frequencies among Escherichia coli and Salmonella pathogens. Science 274, 1208-1211 (1996).
-
(1996)
Science
, vol.274
, pp. 1208-1211
-
-
Leclerc, J.E.1
Li, B.2
Payne, W.L.3
Cédula, T.A.4
-
13
-
-
0030071463
-
The challenges of emerging infectious diseases: Development and spread of multiple-resistant bacterial pathogens
-
Tenover FC, Hughes JM. The challenges of emerging infectious diseases: development and spread of multiple-resistant bacterial pathogens. Science 275, 300 (1996).
-
(1996)
Science
, vol.275
, pp. 300
-
-
Tenover, F.C.1
Hughes, J.M.2
-
14
-
-
33947638029
-
Vaccines in the era of genomics: The pneumococcal challenge
-
Barocchi MA, Censini S, Rappuoli R. Vaccines in the era of genomics: the pneumococcal challenge. Vaccine 25, 2963-2973 (2007).
-
(2007)
Vaccine
, vol.25
, pp. 2963-2973
-
-
Barocchi, M.A.1
Censini, S.2
Rappuoli, R.3
-
15
-
-
0035859982
-
From genome to vaccine: In silico predictions, ex vivo verification
-
DeGroot AS, Bosma A, Chinai N et al. From genome to vaccine: in silico predictions, ex vivo verification. Vaccine 19(31), 4385-4395 (2001).
-
(2001)
Vaccine
, vol.19
, Issue.31
, pp. 4385-4395
-
-
DeGroot, A.S.1
Bosma, A.2
Chinai, N.3
-
16
-
-
0036334571
-
From genetic footprinting to antimicrobial drug targets: Examples in cofactor biosynthetic pathways
-
Gerdes SY, Scholle MD, D'Souza M, Bernal A et al. From genetic footprinting to antimicrobial drug targets: examples in cofactor biosynthetic pathways. J. Bacteriol. 184(16), 4555-4572 (2002).
-
(2002)
J. Bacteriol
, vol.184
, Issue.16
, pp. 4555-4572
-
-
Gerdes, S.Y.1
Scholle, M.D.2
D'Souza, M.3
Bernal, A.4
-
17
-
-
33646839796
-
A review of vaccine research and development: Meningococcal disease
-
Girard MP, Prezioski M, Aguado M et al. A review of vaccine research and development: meningococcal disease. Vaccine 24, 4692-4700 (2006).
-
(2006)
Vaccine
, vol.24
, pp. 4692-4700
-
-
Girard, M.P.1
Prezioski, M.2
Aguado, M.3
-
18
-
-
0742323372
-
Antimicrobial drug discovery through bacteriophage genomics
-
Liu J, Dehbi M, Moeck G et al. Antimicrobial drug discovery through bacteriophage genomics. Nat. Biotechnol. 22(2), 185-191 (2004).
-
(2004)
Nat. Biotechnol
, vol.22
, Issue.2
, pp. 185-191
-
-
Liu, J.1
Dehbi, M.2
Moeck, G.3
-
19
-
-
0036606483
-
Principles of docking: An overview of search algorithms and a guide to scoring functions
-
Halperin I, Ma B, Wolfson H, Nussinov R. Principles of docking: An overview of search algorithms and a guide to scoring functions. Proteins 47(4), 409-43 (2002).
-
(2002)
Proteins
, vol.47
, Issue.4
, pp. 409-443
-
-
Halperin, I.1
Ma, B.2
Wolfson, H.3
Nussinov, R.4
-
20
-
-
0035812694
-
Protein structure prediction and structural genomics
-
Baker D, Sali A. Protein structure prediction and structural genomics. Science 294, 93-96 (2001).
-
(2001)
Science
, vol.294
, pp. 93-96
-
-
Baker, D.1
Sali, A.2
-
22
-
-
0029787712
-
Triggering bacterial virulence
-
Cotter PA, Miller JF. Triggering bacterial virulence. Science 273, 1183-1184 (1996).
-
(1996)
Science
, vol.273
, pp. 1183-1184
-
-
Cotter, P.A.1
Miller, J.F.2
-
23
-
-
0030901705
-
Pathogenicity islands of virulent bacteria: Structure, function, and impact on microbial evolution
-
Hacker J, Blum-Oehler G, Muhldorfer I, Tschape H. Pathogenicity islands of virulent bacteria: structure, function, and impact on microbial evolution. Mol. Microbiol. 23, 1089-1097(1997).
-
(1997)
Mol. Microbiol
, vol.23
, pp. 1089-1097
-
-
Hacker, J.1
Blum-Oehler, G.2
Muhldorfer, I.3
Tschape, H.4
-
24
-
-
0035910029
-
Computational study of protein specificity, the molecular basis of HIV-1 protease drug resistance
-
Wang W, Kollman PA. Computational study of protein specificity, the molecular basis of HIV-1 protease drug resistance. Proc. Natl Acad. Sci. USA 98, 14937-14942 (2001).
-
(2001)
Proc. Natl Acad. Sci. USA
, vol.98
, pp. 14937-14942
-
-
Wang, W.1
Kollman, P.A.2
-
25
-
-
27244444060
-
-
Wiley, NJ, USA
-
Zhou J, Thompson DK, Xu, Y, Tiedje JM, Microbial Functional Genomics. Wiley, NJ, USA (2004).
-
(2004)
Microbial Functional Genomics
-
-
Zhou, J.1
Thompson, D.K.2
Xu, Y.3
Tiedje, J.M.4
-
26
-
-
0029078189
-
Transcriptional control of the mtr efflux system of Neisseria gonorrhoeae
-
Hagman KE, Shafer WE. Transcriptional control of the mtr efflux system of Neisseria gonorrhoeae. J. Bacteriol. 177(14), 4162-4165 (1995).
-
(1995)
J. Bacteriol
, vol.177
, Issue.14
, pp. 4162-4165
-
-
Hagman, K.E.1
Shafer, W.E.2
-
27
-
-
0029845913
-
Multidrug efflux pumps of Gram negative bacteria
-
Nikaido H. Multidrug efflux pumps of Gram negative bacteria. J. Bacteriol. 178(20), 5853-5859 (1996).
-
(1996)
J. Bacteriol
, vol.178
, Issue.20
, pp. 5853-5859
-
-
Nikaido, H.1
-
28
-
-
0028889420
-
Conjugative transposons: An unusual and diverse set of gene transfer elements
-
Salyers AA et al. Conjugative transposons: an unusual and diverse set of gene transfer elements. Microbiol. Rev. 59, 579 (1995).
-
(1995)
Microbiol. Rev
, vol.59
, pp. 579
-
-
Salyers, A.A.1
-
29
-
-
0034680167
-
Molecular mechanisms that confer antibacterial drug resistance
-
Walsh C. Molecular mechanisms that confer antibacterial drug resistance. Nature 406, 775-781 (2000).
-
(2000)
Nature
, vol.406
, pp. 775-781
-
-
Walsh, C.1
-
31
-
-
0032584169
-
Black holes and bacterial pathogenicity: A large genomic deletion that enhances the virulence of Shigella spp and enteroinvasive Escherichia coli
-
Maurelli AT, Fernandez RE, Bloch CA et al. Black holes and bacterial pathogenicity: a large genomic deletion that enhances the virulence of Shigella spp and enteroinvasive Escherichia coli. Proc. Natl Acad. Sci. USA 95, 3943-3948 (1998).
-
(1998)
Proc. Natl Acad. Sci. USA
, vol.95
, pp. 3943-3948
-
-
Maurelli, A.T.1
Fernandez, R.E.2
Bloch, C.A.3
-
32
-
-
0021958759
-
Large plasmids associated with virulence in Shigella species have a common function necessary for epithelial cell penetration
-
Watanbe H, Nakamura A. Large plasmids associated with virulence in Shigella species have a common function necessary for epithelial cell penetration. Infect. Immun. 48(1), 260-262 (1985).
-
(1985)
Infect. Immun
, vol.48
, Issue.1
, pp. 260-262
-
-
Watanbe, H.1
Nakamura, A.2
-
33
-
-
0027494050
-
Multiple antibiotic resistance in Pseudomonas aeruginosa: Evidence for involvement of an efflux operon
-
Poole K, Krebes K, McNally C, Neshat S. Multiple antibiotic resistance in Pseudomonas aeruginosa: evidence for involvement of an efflux operon. J. Bacteriol. 175(22), 7363-7372 (1993).
-
(1993)
J. Bacteriol
, vol.175
, Issue.22
, pp. 7363-7372
-
-
Poole, K.1
Krebes, K.2
McNally, C.3
Neshat, S.4
-
34
-
-
0035118974
-
Second order selection in bacterial evolution: Selection acting on mutation and recombination rates in the course of adaptation
-
Tenaillon O, Taddei F, Radman M, Matic I. Second order selection in bacterial evolution: selection acting on mutation and recombination rates in the course of adaptation. Res. Microbiol. 152, 11-16 (2001).
-
(2001)
Res. Microbiol
, vol.152
, pp. 11-16
-
-
Tenaillon, O.1
Taddei, F.2
Radman, M.3
Matic, I.4
-
35
-
-
0033591467
-
Bacterial biofilms: A common cause of persistent infections
-
Costerton JW, Stewart PS, Greenberg EP. Bacterial biofilms: a common cause of persistent infections. Science 284, 1318-1322 (1999).
-
(1999)
Science
, vol.284
, pp. 1318-1322
-
-
Costerton, J.W.1
Stewart, P.S.2
Greenberg, E.P.3
-
36
-
-
0042706146
-
Moonlighting proteins: Old proteins learning new tricks
-
Jeffrey CJ. Moonlighting proteins: old proteins learning new tricks. Trend Genet. 19, 415-417 (2003).
-
(2003)
Trend Genet
, vol.19
, pp. 415-417
-
-
Jeffrey, C.J.1
-
37
-
-
0021349548
-
Characterization of common virulence plasmids in Yersinia species and their role in the expression of outer membrane proteins
-
Portnoy DA, Wolf-Watz H, Bolin I et al. Characterization of common virulence plasmids in Yersinia species and their role in the expression of outer membrane proteins. Infect. Immun. 43(1), 108-114 (1984).
-
(1984)
Infect. Immun
, vol.43
, Issue.1
, pp. 108-114
-
-
Portnoy, D.A.1
Wolf-Watz, H.2
Bolin, I.3
-
38
-
-
33746319625
-
Enzyme isoselective inhibitors: A tool for binding trend analysis
-
Ozeri R, Khazanov N, Perlman N, Shokhen M, Albeck A. Enzyme isoselective inhibitors: a tool for binding trend analysis. ChemMedChem. 1, 631-638 (2006).
-
(2006)
ChemMedChem
, vol.1
, pp. 631-638
-
-
Ozeri, R.1
Khazanov, N.2
Perlman, N.3
Shokhen, M.4
Albeck, A.5
-
39
-
-
33746315974
-
Enzyme isoselective inhibitors: Application to drug design
-
Shokhen M, Khazanov N, Albeck A. Enzyme isoselective inhibitors: application to drug design. ChemMedChem 1, 639-643 (2006).
-
(2006)
ChemMedChem
, vol.1
, pp. 639-643
-
-
Shokhen, M.1
Khazanov, N.2
Albeck, A.3
-
40
-
-
40749153636
-
Enzyme inhibition trend analysis - a new method for drug design
-
Shokhen M, Khazanov N, Albeck A. Enzyme inhibition trend analysis - a new method for drug design. FEBS J. 272(Suppl. 1), B1-007 (2006).
-
(2006)
FEBS J
, vol.272
, Issue.SUPPL. 1
-
-
Shokhen, M.1
Khazanov, N.2
Albeck, A.3
-
41
-
-
0029809576
-
PhoP-PhoQ activates transcription of pmrAB encoding a two-component regulatory system involved in Salmonella typhirium antimicrobial peptide resistance
-
Gunn JS, Miller SI. PhoP-PhoQ activates transcription of pmrAB encoding a two-component regulatory system involved in Salmonella typhirium antimicrobial peptide resistance. J. Bacteriol. 178(23), 6857-6864 (1996).
-
(1996)
J. Bacteriol
, vol.178
, Issue.23
, pp. 6857-6864
-
-
Gunn, J.S.1
Miller, S.I.2
-
42
-
-
0033003281
-
PhoP-PhoQ regulated loci are required for enhanced bile resistance in Salmonella spp
-
Van Velkinburgh JC, Gunn JS. PhoP-PhoQ regulated loci are required for enhanced bile resistance in Salmonella spp. Infect. Immun. 67(4), 1614-1622 (1999).
-
(1999)
Infect. Immun
, vol.67
, Issue.4
, pp. 1614-1622
-
-
Van Velkinburgh, J.C.1
Gunn, J.S.2
-
43
-
-
0033384634
-
An automated comparative analysis of seventeen complete microbial genomes
-
Bansal AK. An automated comparative analysis of seventeen complete microbial genomes. Bioinformatics 15(11), 900-908 (1999).
-
(1999)
Bioinformatics
, vol.15
, Issue.11
, pp. 900-908
-
-
Bansal, A.K.1
-
45
-
-
0031966808
-
Reconstruction of amino acid biosynthesis pathways from the complete genome sequence
-
Bono H, Ogata H, Goto S, Kanehisa M. Reconstruction of amino acid biosynthesis pathways from the complete genome sequence. Genome Res 8(3), 203-210 (1998).
-
(1998)
Genome Res
, vol.8
, Issue.3
, pp. 203-210
-
-
Bono, H.1
Ogata, H.2
Goto, S.3
Kanehisa, M.4
-
46
-
-
0031715499
-
LIGAND: Chemical database for enzyme reactions
-
Goto S, Nishioka T, Kanehisa M. LIGAND: chemical database for enzyme reactions. Bioinformatics 14 (7), 591-599 (1998).
-
(1998)
Bioinformatics
, vol.14
, Issue.7
, pp. 591-599
-
-
Goto, S.1
Nishioka, T.2
Kanehisa, M.3
-
47
-
-
0141593601
-
Conserved pathways within bacteria and yeast as revealed by global protein network alignment
-
Kelley BP, Sharan R, Karp RM et al. Conserved pathways within bacteria and yeast as revealed by global protein network alignment. Proc. Natl Acad. Sci. USA 100(20), 11394-11399 (2003).
-
(2003)
Proc. Natl Acad. Sci. USA
, vol.100
, Issue.20
, pp. 11394-11399
-
-
Kelley, B.P.1
Sharan, R.2
Karp, R.M.3
-
48
-
-
0028236290
-
Transfer of antibiotic resistant genes between Gram-positive and Gram-negative bacteria
-
Courvalin P. Transfer of antibiotic resistant genes between Gram-positive and Gram-negative bacteria. Antimicrob. Agents Chemother. 38, 1447 (1994).
-
(1994)
Antimicrob. Agents Chemother
, vol.38
, pp. 1447
-
-
Courvalin, P.1
-
49
-
-
0034682335
-
Lateral gene-transfer and the nature of bacterial innovation
-
Ochman H, Lawrence JG, Groisman EA. Lateral gene-transfer and the nature of bacterial innovation. Nature 405, 299-304 (2000).
-
(2000)
Nature
, vol.405
, pp. 299-304
-
-
Ochman, H.1
Lawrence, J.G.2
Groisman, E.A.3
-
50
-
-
0342460609
-
Why are antibiotic resistance genes so resistant to elimination?
-
Salyers AA, CF Amabile-Cuevas. Why are antibiotic resistance genes so resistant to elimination? Antimicrob. Agents Chemother. 41, 2321-2325 (1997).
-
(1997)
Antimicrob. Agents Chemother
, vol.41
, pp. 2321-2325
-
-
Salyers, A.A.1
Amabile-Cuevas, C.F.2
-
51
-
-
4043062916
-
De novo drug design: Integration of structure-based and ligand-based methods
-
Dean PM, Lloyd DG, Todorov NP. De novo drug design: integration of structure-based and ligand-based methods. Curr. Opin. Drug Disc. Dev. 7, 347-353 (2006).
-
(2006)
Curr. Opin. Drug Disc. Dev
, vol.7
, pp. 347-353
-
-
Dean, P.M.1
Lloyd, D.G.2
Todorov, N.P.3
-
54
-
-
0034491031
-
Interpro: An integrated documentation resource for protein families, domains and functional sites
-
Mulder NJ, Apweiler R, Attwood TK et al. Interpro: an integrated documentation resource for protein families, domains and functional sites. Bioinformatics 16, 1145-50 (2001).
-
(2001)
Bioinformatics
, vol.16
, pp. 1145-1150
-
-
Mulder, N.J.1
Apweiler, R.2
Attwood, T.K.3
-
56
-
-
0036084258
-
-
Chen X, Ji ZL, Chen YZ. TTD: Therapeutic target database. Nucleic Acids Res. 30(1), 412-415 (2002).
-
Chen X, Ji ZL, Chen YZ. TTD: Therapeutic target database. Nucleic Acids Res. 30(1), 412-415 (2002).
-
-
-
-
57
-
-
33644874819
-
From genomics to chemical genomics: New developments in KEGG
-
Kanehisa M, Goto S, Hattori M et al. From genomics to chemical genomics: new developments in KEGG. Nucleic Acids Res. 34, D354-357 (2006).
-
(2006)
Nucleic Acids Res
, vol.34
-
-
Kanehisa, M.1
Goto, S.2
Hattori, M.3
-
58
-
-
0031850628
-
Computation with the KEGG pathway database
-
Ogata H, Goto S, Fujibuchi W, Kanehisa M. Computation with the KEGG pathway database. Biosystems 47, 119-128 (1996).
-
(1996)
Biosystems
, vol.47
, pp. 119-128
-
-
Ogata, H.1
Goto, S.2
Fujibuchi, W.3
Kanehisa, M.4
-
59
-
-
0141506108
-
Protein Ligand Database (PLD): Additional understandhig of the nature and specificity of protein-ligand complexes
-
Puvanendrampillai D, Mitchell JBO. Protein Ligand Database (PLD): additional understandhig of the nature and specificity of protein-ligand complexes. Bioinformatics 19(14), 1856-1857 (2003).
-
(2003)
Bioinformatics
, vol.19
, Issue.14
, pp. 1856-1857
-
-
Puvanendrampillai, D.1
Mitchell, J.B.O.2
-
60
-
-
9144270496
-
-
Salgado H, Gama-Castro S, Martínez-Antonio, A et al. RegulonDB (version 4.0, transcriptional regulation, operon organization and growth conditions in Escherichia coli K, 12. Nucleic Acids Res. 32, 303-306 2004
-
Salgado H, Gama-Castro S, Martínez-Antonio, A et al. RegulonDB (version 4.0): transcriptional regulation, operon organization and growth conditions in Escherichia coli K - 12. Nucleic Acids Res. 32, 303-306 (2004).
-
-
-
-
61
-
-
0035162592
-
The COG Database: New developments in phylogenetic classifications from complete genome
-
Tatusov RL, Natale DA, Garkavtsev IV et al. The COG Database: new developments in phylogenetic classifications from complete genome. Nucleic Acids Res. 29(1), 22-28 (2001).
-
(2001)
Nucleic Acids Res
, vol.29
, Issue.1
, pp. 22-28
-
-
Tatusov, R.L.1
Natale, D.A.2
Garkavtsev, I.V.3
-
62
-
-
0033918228
-
Conservation of DNA regulatory motifs and discovery of new motifs in microbial genomes
-
McGuire AM, Hughes JD, Church GM. Conservation of DNA regulatory motifs and discovery of new motifs in microbial genomes. Genome Res. 10(6), 744-757 (2000).
-
(2000)
Genome Res
, vol.10
, Issue.6
, pp. 744-757
-
-
McGuire, A.M.1
Hughes, J.D.2
Church, G.M.3
-
64
-
-
0003512471
-
-
Chapman & Hall, London, UK
-
Waterman MS. Introduction to Computational Biology, Maps, Sequence, and Genomes. Chapman & Hall, London, UK (1995).
-
(1995)
Introduction to Computational Biology, Maps, Sequence, and Genomes
-
-
Waterman, M.S.1
-
65
-
-
0033485517
-
Improved microbial gene identification with GLIMMER
-
Delcher AL, Harmon D, Kasif S, White O, Salzberg SL. Improved microbial gene identification with GLIMMER. Nucleic Acids Res. 27(23), 4636-4641 (1999).
-
(1999)
Nucleic Acids Res
, vol.27
, Issue.23
, pp. 4636-4641
-
-
Delcher, A.L.1
Harmon, D.2
Kasif, S.3
White, O.4
Salzberg, S.L.5
-
66
-
-
16644401595
-
Probabilistic methods of identifying genes in prokaryotic genomes: Connections to the HMM theory
-
Azad RK, Borodovsky M. Probabilistic methods of identifying genes in prokaryotic genomes: connections to the HMM theory. Brief Bioinformatics 5 (2), 118-130 (2004).
-
(2004)
Brief Bioinformatics
, vol.5
, Issue.2
, pp. 118-130
-
-
Azad, R.K.1
Borodovsky, M.2
-
67
-
-
0032519353
-
GeneMark.hmm: New solutions for gene finding
-
Lukashin AV, Borodovsky M. GeneMark.hmm: new solutions for gene finding. Nucleic Acids Res. 26 (4), 1107-1115 (1998).
-
(1998)
Nucleic Acids Res
, vol.26
, Issue.4
, pp. 1107-1115
-
-
Lukashin, A.V.1
Borodovsky, M.2
-
68
-
-
0025183708
-
Basic alignment search tools
-
Altschul SF, Gish W, Miller W, Myers EW, Lipman DJ. Basic alignment search tools. J. Mol. Biol. 215, 403-410 (1990).
-
(1990)
J. Mol. Biol
, vol.215
, pp. 403-410
-
-
Altschul, S.F.1
Gish, W.2
Miller, W.3
Myers, E.W.4
Lipman, D.J.5
-
69
-
-
0030801002
-
Gapped BLAST and PSI-BLAST. a new generation of protein database search programs
-
Altschul SF, Madden TL, Schaffer AA et al. Gapped BLAST and PSI-BLAST. a new generation of protein database search programs. Nucleic Acids Res. 15(17), 3389-3402 (1997).
-
(1997)
Nucleic Acids Res
, vol.15
, Issue.17
, pp. 3389-3402
-
-
Altschul, S.F.1
Madden, T.L.2
Schaffer, A.A.3
-
70
-
-
0036137327
-
A probabilistic method for identifying start codons in bacterial genomes
-
Suzek BE, Ermolaeva MD, Schreiber M, Salzberg SL. A probabilistic method for identifying start codons in bacterial genomes. Bioinformatics 17(12), 1123-1130 (2001).
-
(2001)
Bioinformatics
, vol.17
, Issue.12
, pp. 1123-1130
-
-
Suzek, B.E.1
Ermolaeva, M.D.2
Schreiber, M.3
Salzberg, S.L.4
-
71
-
-
0028825276
-
Automated construction and graphical presentation of protein blocks from unaligned sequences
-
Henikoff S, Henikoff JG, Alford WJ, Pietrokovski S. Automated construction and graphical presentation of protein blocks from unaligned sequences Gene 163(2), GC17-GC26 (1995).
-
(1995)
Gene
, vol.163
, Issue.2
-
-
Henikoff, S.1
Henikoff, J.G.2
Alford, W.J.3
Pietrokovski, S.4
-
72
-
-
0042121237
-
Multiple sequence alignment with the clustal series of programs
-
Chenna R, Sugawaral H, Koike Lopez TR, Gibson TJ, Higgins DJ, Thompson JD. Multiple sequence alignment with the clustal series of programs. Nucleic Acids Res. 31(13), 3497-3500 (2003).
-
(2003)
Nucleic Acids Res
, vol.31
, Issue.13
, pp. 3497-3500
-
-
Chenna, R.1
Sugawaral, H.2
Koike Lopez, T.R.3
Gibson, T.J.4
Higgins, D.J.5
Thompson, J.D.6
-
73
-
-
0038634973
-
Do current sequence analysis algorithms disclose multifunctional (moonlighting) proteins?
-
Gomez A, Domedel N, Cedano J, Penol J, Querol E. Do current sequence analysis algorithms disclose multifunctional (moonlighting) proteins? Bioinformatics 19, 895-896 (2003).
-
(2003)
Bioinformatics
, vol.19
, pp. 895-896
-
-
Gomez, A.1
Domedel, N.2
Cedano, J.3
Penol, J.4
Querol, E.5
-
74
-
-
13444305296
-
The ProDom database of protein domain families: More emphasis on 3D
-
Catherine B, Emmanuel C, Sébastien C, Yoann B, Sandrine D, Daniel K. The ProDom database of protein domain families: more emphasis on 3D. Nucleic Acids Res. 33, D212-D215 (2000).
-
(2000)
Nucleic Acids Res
, vol.33
-
-
Catherine, B.1
Emmanuel, C.2
Sébastien, C.3
Yoann, B.4
Sandrine, D.5
Daniel, K.6
-
75
-
-
0031813130
-
Pfam: Multiple sequence alignments and HMM-profiles of protein domains
-
Sonnhammer EL, Eddy SR, Birney E, Batman A, Durbin R. Pfam: multiple sequence alignments and HMM-profiles of protein domains. Nucleic Acids Res. 26, 320-322 (1998).
-
(1998)
Nucleic Acids Res
, vol.26
, pp. 320-322
-
-
Sonnhammer, E.L.1
Eddy, S.R.2
Birney, E.3
Batman, A.4
Durbin, R.5
-
77
-
-
0030111235
-
Metabolism and evolution of Haemophilius influenzae deduced from a whole-genome comparison with Escherichia coli
-
Tatusov RL, Mushegian M, Bork P et al. Metabolism and evolution of Haemophilius influenzae deduced from a whole-genome comparison with Escherichia coli. Curr Biol. 6, 279-291 (1996).
-
(1996)
Curr Biol
, vol.6
, pp. 279-291
-
-
Tatusov, R.L.1
Mushegian, M.2
Bork, P.3
-
78
-
-
0036204458
-
Evolutionary analysis by whole genome comparisons
-
Bansal AK, Myer TE. Evolutionary analysis by whole genome comparisons. J. Bacteriol. 184(8), 2260-2272 (2002).
-
(2002)
J. Bacteriol
, vol.184
, Issue.8
, pp. 2260-2272
-
-
Bansal, A.K.1
Myer, T.E.2
-
79
-
-
10744231057
-
Protein micro arrays guide tolerizing DNA vaccine treatment of autoimmune encephalomyelitis
-
Robinson WH, Fontoura P, Lee BJ et al. Protein micro arrays guide tolerizing DNA vaccine treatment of autoimmune encephalomyelitis. Nat. Biotechnol. 21(9), 1033-1039 (2003).
-
(2003)
Nat. Biotechnol
, vol.21
, Issue.9
, pp. 1033-1039
-
-
Robinson, W.H.1
Fontoura, P.2
Lee, B.J.3
-
80
-
-
0037833535
-
Bioinformatics: How it is being used to identify bacterial vaccine candidates
-
Zagursky RJ, Olmsted SB, Russell DP, Wooters JL. Bioinformatics: how it is being used to identify bacterial vaccine candidates. Vaccines 2(3), 417-436 (2003).
-
(2003)
Vaccines
, vol.2
, Issue.3
, pp. 417-436
-
-
Zagursky, R.J.1
Olmsted, S.B.2
Russell, D.P.3
Wooters, J.L.4
-
81
-
-
0242606435
-
Tests for gene clustering
-
Durand D, Sankoff D. Tests for gene clustering. J. Comput. Biol. 10(3/4), 453-482 (2003).
-
(2003)
J. Comput. Biol
, vol.10
, Issue.3-4
, pp. 453-482
-
-
Durand, D.1
Sankoff, D.2
-
83
-
-
0036330798
-
Genome-scale metabolic model of Helicobacter pylori 26695
-
Schilling CH, Covert MW, Famili I, Church GM, Edwards JS, Palsson BØ. Genome-scale metabolic model of Helicobacter pylori 26695. J. Bacteriol. 184(6), 4582-4593(2002).
-
(2002)
J. Bacteriol
, vol.184
, Issue.6
, pp. 4582-4593
-
-
Schilling, C.H.1
Covert, M.W.2
Famili, I.3
Church, G.M.4
Edwards, J.S.5
Palsson, B.6
-
84
-
-
0033080396
-
Detection of elementary flux modes in biochemical networks: A promising tool for pathway analysis and metabolic engineering
-
Schuster S, Dandekar T, Fell DA. Detection of elementary flux modes in biochemical networks: a promising tool for pathway analysis and metabolic engineering. Trends Biotechnol. 17(2), 53-60 (1999).
-
(1999)
Trends Biotechnol
, vol.17
, Issue.2
, pp. 53-60
-
-
Schuster, S.1
Dandekar, T.2
Fell, D.A.3
-
85
-
-
0036916269
-
Extreme pathway lengths and reaction participation in genome-scale metabolic networks
-
Papin JA, Price ND, Palsson BØ. Extreme pathway lengths and reaction participation in genome-scale metabolic networks. Genome Res. 12(12), 1889-1900 (2002).
-
(2002)
Genome Res
, vol.12
, Issue.12
, pp. 1889-1900
-
-
Papin, J.A.1
Price, N.D.2
Palsson, B.3
-
86
-
-
0035393302
-
Amino acid base interactions: A three dimensional analysis of protein-DNA interactions at an atomic level
-
Luscombe NM, Laskowski RA, Thornton JM. Amino acid base interactions: a three dimensional analysis of protein-DNA interactions at an atomic level. Nucleic Acid Res. 29(13), 2860-2874 (2001).
-
(2001)
Nucleic Acid Res
, vol.29
, Issue.13
, pp. 2860-2874
-
-
Luscombe, N.M.1
Laskowski, R.A.2
Thornton, J.M.3
-
87
-
-
17444430052
-
Dynamic network reconstruction from gene expression data applied to immune response during bacterial infection
-
Guthke R, Ulrich M, Hoffman M et al. Dynamic network reconstruction from gene expression data applied to immune response during bacterial infection. Bioinformatics. 21(8), 1626-1634 (2005).
-
(2005)
Bioinformatics
, vol.21
, Issue.8
, pp. 1626-1634
-
-
Guthke, R.1
Ulrich, M.2
Hoffman, M.3
-
88
-
-
0028806048
-
Quantitative monitoring of gene expression patterns with a complementary DNA micro array
-
Schena M, Shalon D, Davis RW, Brown PO. Quantitative monitoring of gene expression patterns with a complementary DNA micro array. Science 270, 467-470. (1995).
-
(1995)
Science
, vol.270
, pp. 467-470
-
-
Schena, M.1
Shalon, D.2
Davis, R.W.3
Brown, P.O.4
-
89
-
-
28644451737
-
Analysis of host response to bacterial infection using error model based gene expression micro array experiments
-
Stekel DJ, Sarti D, Trevino V. Analysis of host response to bacterial infection using error model based gene expression micro array experiments. Nucelic Acids Res. 33(6), 1-13 (2005).
-
(2005)
Nucelic Acids Res
, vol.33
, Issue.6
, pp. 1-13
-
-
Stekel, D.J.1
Sarti, D.2
Trevino, V.3
-
90
-
-
0034575477
-
Cluster inference methods and graphical models evaluated on NCI60 micro array gene expression data
-
Waddell PJ, Kishino H. Cluster inference methods and graphical models evaluated on NCI60 micro array gene expression data. Genome Inform. 11, 129-140 (2000).
-
(2000)
Genome Inform
, vol.11
, pp. 129-140
-
-
Waddell, P.J.1
Kishino, H.2
-
91
-
-
0344376570
-
Finding composite regulatory patterns in DNA sequences
-
Eskin E, Pevzner PA. Finding composite regulatory patterns in DNA sequences. Bioinformatics 18(1), 354-363 (2002).
-
(2002)
Bioinformatics
, vol.18
, Issue.1
, pp. 354-363
-
-
Eskin, E.1
Pevzner, P.A.2
-
92
-
-
0033565546
-
Computer analysis of transcription regulatory patterns in completely sequenced bacterial genomes
-
Mironov AA, Koonin EV, Roytberg MA, Gelfand MS. Computer analysis of transcription regulatory patterns in completely sequenced bacterial genomes. Nucleic Acids Res. 27, 2981-2989 (1999).
-
(1999)
Nucleic Acids Res
, vol.27
, pp. 2981-2989
-
-
Mironov, A.A.1
Koonin, E.V.2
Roytberg, M.A.3
Gelfand, M.S.4
-
93
-
-
10744226222
-
Computational discovery of gene modules and regulatory networks
-
Bar-Joseph Z, Gerber GK, Lee TI, et al. Computational discovery of gene modules and regulatory networks. Nat. Biotechnol: 21(11), 1337-1342 (2003).
-
(2003)
Nat. Biotechnol
, vol.21
, Issue.11
, pp. 1337-1342
-
-
Bar-Joseph, Z.1
Gerber, G.K.2
Lee, T.I.3
-
94
-
-
0033655775
-
Mutual information relevance networks: Functional genomics clustering using pair-wise entropy measurements
-
Butte A, Kohan I. Mutual information relevance networks: functional genomics clustering using pair-wise entropy measurements. Pac. Symp. Biocomput. 418-429 (2000).
-
(2000)
Pac. Symp. Biocomput
, pp. 418-429
-
-
Butte, A.1
Kohan, I.2
-
95
-
-
0012722659
-
Nod2 is a general sensor of peptidoglycan through muramyl dipeptide (MDP) detection
-
Girardin SE, Boneca IG, Viala J et al. Nod2 is a general sensor of peptidoglycan through muramyl dipeptide (MDP) detection. J. Biol. Chem. 2003. 278, 8869-8872 (2003).
-
(2003)
J. Biol. Chem
, vol.2003
, Issue.278
, pp. 8869-8872
-
-
Girardin, S.E.1
Boneca, I.G.2
Viala, J.3
-
96
-
-
0642340506
-
Genome wide identification of regulatory motifs in Bacillus subtilis
-
Mwangi MM, Siggia ED. Genome wide identification of regulatory motifs in Bacillus subtilis BMC. Bioinformatics 4(1), 18-20 (2003).
-
(2003)
BMC. Bioinformatics
, vol.4
, Issue.1
, pp. 18-20
-
-
Mwangi, M.M.1
Siggia, E.D.2
-
97
-
-
0347444723
-
MicroRNAs: Genomics, biogenesis, mechanism, and function
-
116, 281-297
-
Bartel DP. MicroRNAs: genomics, biogenesis, mechanism, and function. Cell 116, 281-297 (2004).
-
(2004)
Cell
-
-
Bartel, D.P.1
-
98
-
-
3042767202
-
MicroRNAs: Small RNAs with a big role in gene regulation
-
He L, Hannon GJ. MicroRNAs: small RNAs with a big role in gene regulation. Genetics 5, 522-532 (2004).
-
(2004)
Genetics
, vol.5
, pp. 522-532
-
-
He, L.1
Hannon, G.J.2
-
99
-
-
33644857025
-
Gene regulation by microRNAs
-
Carthew RW. Gene regulation by microRNAs. Curr. Opin. Genet. Dev. 16(2), 203-208 (2006):
-
(2006)
Curr. Opin. Genet. Dev
, vol.16
, Issue.2
, pp. 203-208
-
-
Carthew, R.W.1
-
100
-
-
33645967758
-
A plant miRNA contributes to antibacterial resistance by repressing auxin signaling
-
Navarro L, Dunoyer P, Jay F et al. A plant miRNA contributes to antibacterial resistance by repressing auxin signaling. Science 312(5772), 436-439 (2006).
-
(2006)
Science
, vol.312
, Issue.5772
, pp. 436-439
-
-
Navarro, L.1
Dunoyer, P.2
Jay, F.3
-
101
-
-
0033859844
-
Plasmid copy number control: An ever-growing story
-
del Solar G, Espinosa M. Plasmid copy number control: an ever-growing story. Mol. Microbiol. 37, 492-500(2001).
-
(2001)
Mol. Microbiol
, vol.37
, pp. 492-500
-
-
del Solar, G.1
Espinosa, M.2
-
102
-
-
0034649647
-
X inactivation: Tsix and Xist as yin and yang
-
Mlynarczyk SK, Panning B. X inactivation: Tsix and Xist as yin and yang. Curr. Biol. 10, R899-R903(2000).
-
(2000)
Curr. Biol
, vol.10
-
-
Mlynarczyk, S.K.1
Panning, B.2
-
103
-
-
1542297345
-
Computational Identification of microRNA targets
-
Rajewsky N, Socci ND. Computational Identification of microRNA targets. Dev. Biol. 267, 529-535 (2003).
-
(2003)
Dev. Biol
, vol.267
, pp. 529-535
-
-
Rajewsky, N.1
Socci, N.D.2
-
104
-
-
0037162702
-
Prediction of plant microRNA targets
-
Rhoades MW, Reinhart BJ, Lim LP, Burge CB, Bartel B, Bartel DP. Prediction of plant microRNA targets. Cell 110, 513-520 (2002).
-
(2002)
Cell
, vol.110
, pp. 513-520
-
-
Rhoades, M.W.1
Reinhart, B.J.2
Lim, L.P.3
Burge, C.B.4
Bartel, B.5
Bartel, D.P.6
-
105
-
-
33644750115
-
miRBase: MicroRNA sequences, targets and gene nomenclature
-
Griffiths-Jones S, Grocock RJ, van Dongen S, Bateman A, Enright AJ. miRBase: microRNA sequences, targets and gene nomenclature Nucleic Acid Res. 34, D140-D144(2006).
-
(2006)
Nucleic Acid Res
, vol.34
-
-
Griffiths-Jones, S.1
Grocock, R.J.2
van Dongen, S.3
Bateman, A.4
Enright, A.J.5
-
107
-
-
0027291015
-
Prediction of protein secondary structure at better than 70 percent accuracy
-
Rost B, Sander C. Prediction of protein secondary structure at better than 70 percent accuracy J. Mol. Biol. 232, 584-599 (1995).
-
(1995)
J. Mol. Biol
, vol.232
, pp. 584-599
-
-
Rost, B.1
Sander, C.2
-
108
-
-
0346799108
-
Prediction of protein function from protein sequence and structure
-
Whisstock JC, Lesk AM. Prediction of protein function from protein sequence and structure. Q. Rev. Biophys. 36(3), 307-340 (2003).
-
(2003)
Q. Rev. Biophys
, vol.36
, Issue.3
, pp. 307-340
-
-
Whisstock, J.C.1
Lesk, A.M.2
-
110
-
-
0034629284
-
Identification of vaccine candidates against Serogroup B meningococcus by whole genome sequencing
-
Pizza M. Identification of vaccine candidates against Serogroup B meningococcus by whole genome sequencing, Science 287, 1816-1820 (2000).
-
(2000)
Science
, vol.287
, pp. 1816-1820
-
-
Pizza, M.1
-
111
-
-
33748307473
-
Novel surface polypeptides of Campylobacter jejuni as traveler's diarrhea vaccine candidates discovered by proteomics
-
Prokhorva TA, Nielsen PN, Petersen J et al. Novel surface polypeptides of Campylobacter jejuni as traveler's diarrhea vaccine candidates discovered by proteomics. Vaccine 24, 6446-6455 (2006).
-
(2006)
Vaccine
, vol.24
, pp. 6446-6455
-
-
Prokhorva, T.A.1
Nielsen, P.N.2
Petersen, J.3
-
112
-
-
34147191723
-
Comparative in silico analysis of two vaccine candidates for group A streptococcus predicts that they both may have similar profiles
-
Shaila MS, Nayak R, Prakash SS et al. Comparative in silico analysis of two vaccine candidates for group A streptococcus predicts that they both may have similar profiles. Vaccine 25, 3567-3573 (2007).
-
(2007)
Vaccine
, vol.25
, pp. 3567-3573
-
-
Shaila, M.S.1
Nayak, R.2
Prakash, S.S.3
-
113
-
-
0012314060
-
Antigen discovery and tuberculosis vaccine development in the post-genomic era
-
Skjøt RLV, Agger EM, Andersen P. Antigen discovery and tuberculosis vaccine development in the post-genomic era. Scand. J. Infect. Dis. 33(9), 643-647 (2001).
-
(2001)
Scand. J. Infect. Dis
, vol.33
, Issue.9
, pp. 643-647
-
-
Skjøt, R.L.V.1
Agger, E.M.2
Andersen, P.3
-
115
-
-
0034280221
-
Tuberculosis vaccine design: Influenee of the completed genome sequence
-
Montgomery DL. Tuberculosis vaccine design: influenee of the completed genome sequence. Briefing in Bioinformatics 1(3), 289-296 (2000).
-
(2000)
Briefing in Bioinformatics
, vol.1
, Issue.3
, pp. 289-296
-
-
Montgomery, D.L.1
-
116
-
-
0033613170
-
DNA adenine methylase mutants of Saimonella typhimurium show defects in protein secretion, cell invasion, and M cell cytotoxicity
-
Garcia-del PF, Pucciarelli, MG, Casadesus J. DNA adenine methylase mutants of Saimonella typhimurium show defects in protein secretion, cell invasion, and M cell cytotoxicity. Proc. Natl. Acad. Sci. USA 96, 11578-11583 (1999).
-
(1999)
Proc. Natl. Acad. Sci. USA
, vol.96
, pp. 11578-11583
-
-
Garcia-del, P.F.1
Pucciarelli, M.G.2
Casadesus, J.3
-
117
-
-
1942537114
-
A DNA adenine methylase mutant of Shigella flexneri shows no significant attenuation of virulence
-
Honma Y, Fernández RE, Maurelli AT. A DNA adenine methylase mutant of Shigella flexneri shows no significant attenuation of virulence. Microbiology 150, 1973-1978 (2004).
-
(2004)
Microbiology
, vol.150
, pp. 1973-1978
-
-
Honma, Y.1
Fernández, R.E.2
Maurelli, A.T.3
-
118
-
-
0032979077
-
Genomics and antimicrobial drug discovery
-
Moir DT, Shaw KJ, Hare RS, Vovis GF. Genomics and antimicrobial drug discovery. Antimicrob. Agents Chemother. 43(3), 439-446 (1999).
-
(1999)
Antimicrob. Agents Chemother
, vol.43
, Issue.3
, pp. 439-446
-
-
Moir, D.T.1
Shaw, K.J.2
Hare, R.S.3
Vovis, G.F.4
-
119
-
-
0034678055
-
Harnessing the power of the genome in the search for new antibiotics
-
Rosamond J, Allsop A. Harnessing the power of the genome in the search for new antibiotics. Science 287, 1973-1976 (2000).
-
(2000)
Science
, vol.287
, pp. 1973-1976
-
-
Rosamond, J.1
Allsop, A.2
-
120
-
-
20444478991
-
Riboswitches as versatile gene control elements
-
Tucker BJ, Breaker RR. Riboswitches as versatile gene control elements. Curr. Opin. Struct. Biol. 15, 342-348 (2005).
-
(2005)
Curr. Opin. Struct. Biol
, vol.15
, pp. 342-348
-
-
Tucker, B.J.1
Breaker, R.R.2
-
121
-
-
0036792830
-
-
Marck C, Grosjean H. tRNAomics: Analysis of tRNA genes from 5-genomes of eukarya, archaea, and bacteria reveals anti-codon-sparing strategies and domain-specific features. RNA 8, 1189-1232 (2002).
-
Marck C, Grosjean H. tRNAomics: Analysis of tRNA genes from 5-genomes of eukarya, archaea, and bacteria reveals anti-codon-sparing strategies and domain-specific features. RNA 8, 1189-1232 (2002).
-
-
-
|