-
1
-
-
0033038809
-
Pseudomembranous colitis: Causes and cures
-
[CrossRef] [PubMed]
-
Surawicz,C.M.; McFarland,L.V. Pseudomembranous colitis: Causes and cures. Digestion 1999,60,91-100. [CrossRef] [PubMed]
-
(1999)
Digestion
, vol.60
, pp. 91-100
-
-
Surawicz, C.M.1
McFarland, L.V.2
-
2
-
-
84925311331
-
Clostridium difficile infection: Epidemiology,pathogenesis,risk factors,and therapeutic options
-
[CrossRef] [PubMed]
-
Goudarzi,M.; Seyedjavadi,S.S.; Goudarzi,H.; Mehdizadeh Aghdam,E.; Nazeri,S. Clostridium difficile infection: Epidemiology,pathogenesis,risk factors,and therapeutic options. Scientifica 2014,2014,9. [CrossRef] [PubMed]
-
(2014)
Scientifica
, vol.2014
, pp. 9
-
-
Goudarzi, M.1
Seyedjavadi, S.S.2
Goudarzi, H.3
Mehdizadeh Aghdam, E.4
Nazeri, S.5
-
3
-
-
84857067037
-
Profound alterations of intestinal microbiota following a single dose of clindamycin results in sustained susceptibility to Clostridium difficile-induced colitis
-
[CrossRef] [PubMed]
-
Buffie,C.G.; Jarchum,I.; Equinda,M.; Lipuma,L.; Gobourne,A.; Viale,A.; Ubeda,C.; Xavier,J.; Pamer,E.G. Profound alterations of intestinal microbiota following a single dose of clindamycin results in sustained susceptibility to Clostridium difficile-induced colitis. Infect. Immun. 2012,80,62-73. [CrossRef] [PubMed]
-
(2012)
Infect. Immun.
, vol.80
, pp. 62-73
-
-
Buffie, C.G.1
Jarchum, I.2
Equinda, M.3
Lipuma, L.4
Gobourne, A.5
Viale, A.6
Ubeda, C.7
Xavier, J.8
Pamer, E.G.9
-
4
-
-
84933505084
-
Diversity and evolution in the genome of Clostridium difficile
-
[CrossRef] [PubMed]
-
Knight,D.R.; Elliott,B.; Chang,B.J.; Perkins,T.T.; Riley,T.V. Diversity and evolution in the genome of Clostridium difficile. Clin. Microbiol. Rev. 2015,28,721-741. [CrossRef] [PubMed]
-
(2015)
Clin. Microbiol. Rev.
, vol.28
, pp. 721-741
-
-
Knight, D.R.1
Elliott, B.2
Chang, B.J.3
Perkins, T.T.4
Riley, T.V.5
-
5
-
-
84890463477
-
Variations in virulence and molecular biology among emerging strains of Clostridium difficile
-
[CrossRef] [PubMed]
-
Hunt,J.J.; Ballard,J.D. Variations in virulence and molecular biology among emerging strains of Clostridium difficile. Microbiol. Mol. Biol. Rev. 2013,77,567-581. [CrossRef] [PubMed]
-
(2013)
Microbiol. Mol. Biol. Rev.
, vol.77
, pp. 567-581
-
-
Hunt, J.J.1
Ballard, J.D.2
-
6
-
-
84957922991
-
Better together: Bacteriophage combinations significantly reduce Clostridium difficile growth in vitro and proliferation in vivo
-
[CrossRef] [PubMed]
-
Nale,J.Y.; Spencer,J.; Hargreaves,K.R.; Buckley,A.M.; Trzepinski,P.; Douce,G.R.; Clokie,M.R. Better together: Bacteriophage combinations significantly reduce Clostridium difficile growth in vitro and proliferation in vivo. Antimicrob. Agents Chemother. 2015,60,968-981. [CrossRef] [PubMed]
-
(2015)
Antimicrob. Agents Chemother.
, vol.60
, pp. 968-981
-
-
Nale, J.Y.1
Spencer, J.2
Hargreaves, K.R.3
Buckley, A.M.4
Trzepinski, P.5
Douce, G.R.6
Clokie, M.R.7
-
7
-
-
78650574888
-
Bacteriophage treatment significantly reduces viable Clostridium difficile and prevents toxin production in an in vitro model system
-
[CrossRef] [PubMed]
-
Meader,E.; Mayer,M.J.; Gasson,M.J.; Steverding,D.; Carding,S.R.; Narbad,A. Bacteriophage treatment significantly reduces viable Clostridium difficile and prevents toxin production in an in vitro model system. Anaerobe 2010,16,549-554. [CrossRef] [PubMed]
-
(2010)
Anaerobe
, vol.16
, pp. 549-554
-
-
Meader, E.1
Mayer, M.J.2
Gasson, M.J.3
Steverding, D.4
Carding, S.R.5
Narbad, A.6
-
8
-
-
0032844901
-
Prevention of Clostridium difficile-induced ileocecitis with bacteriophage
-
[CrossRef]
-
Ramesh,V.; Fralick,J.A.; Rolfe,R.D. Prevention of Clostridium difficile-induced ileocecitis with bacteriophage. Anaerobe 1999,5,69-78. [CrossRef]
-
(1999)
Anaerobe
, vol.5
, pp. 69-78
-
-
Ramesh, V.1
Fralick, J.A.2
Rolfe, R.D.3
-
9
-
-
33947403984
-
The complete genome sequence of Clostridium difficile phage FC2 and comparisons to FCD119 and inducible prophages of CD630
-
[CrossRef] [PubMed]
-
Goh,S.; Ong,P.F.; Song,K.P.; Riley,T.V.; Chang,B.J. The complete genome sequence of Clostridium difficile phage FC2 and comparisons to FCD119 and inducible prophages of CD630. Microbiology 2007,153,676-685. [CrossRef] [PubMed]
-
(2007)
Microbiology
, vol.153
, pp. 676-685
-
-
Goh, S.1
Ong, P.F.2
Song, K.P.3
Riley, T.V.4
Chang, B.J.5
-
10
-
-
33645226631
-
Genomic organization and molecular characterization of Clostridium difficile bacteriophage phicd119
-
[CrossRef] [PubMed]
-
Govind,R.; Fralick,J.A.; Rolfe,R.D. Genomic organization and molecular characterization of Clostridium difficile bacteriophage phicd119. J. Bacteriol. 2006,188,2568-2577. [CrossRef] [PubMed]
-
(2006)
J. Bacteriol.
, vol.188
, pp. 2568-2577
-
-
Govind, R.1
Fralick, J.A.2
Rolfe, R.D.3
-
11
-
-
84908432854
-
Abundant and diverse clustered regularly interspaced short palindromic repeat spacers in Clostridium difficile strains and prophages target multiple phage types within this pathogen
-
[CrossRef] [PubMed]
-
Hargreaves,K.R.; Flores,C.O.; Lawley,T.D.; Clokie,M.R. Abundant and diverse clustered regularly interspaced short palindromic repeat spacers in Clostridium difficile strains and prophages target multiple phage types within this pathogen. mBio 2014,5,e01045-e01013. [CrossRef] [PubMed]
-
(2014)
mBio
, vol.5
, pp. e01013-e01045
-
-
Hargreaves, K.R.1
Flores, C.O.2
Lawley, T.D.3
Clokie, M.R.4
-
12
-
-
84899692742
-
What does the talking? Quorum sensing signalling genes discovered in a bacteriophage genome
-
[CrossRef] [PubMed]
-
Hargreaves,K.R.; Kropinski,A.M.; Clokie,M.R.J. What does the talking? Quorum sensing signalling genes discovered in a bacteriophage genome. PLoS ONE 2014,9,e85131. [CrossRef] [PubMed]
-
(2014)
PLoS ONE
, vol.9
-
-
Hargreaves, K.R.1
Kropinski, A.M.2
Clokie, M.R.J.3
-
13
-
-
77954213225
-
Genome analysis of the Clostridium difficile phage FCD6356,a temperate phage of the Siphoviridae family
-
[CrossRef] [PubMed]
-
Horgan,M.; O’Sullivan,O.; Coffey,A.; Fitzgerald,G.F.; van Sinderen,D.; McAuliffe,O.; Ross,R.P. Genome analysis of the Clostridium difficile phage FCD6356,a temperate phage of the Siphoviridae family. Gene 2010,462,34-43. [CrossRef] [PubMed]
-
(2010)
Gene
, vol.462
, pp. 34-43
-
-
Horgan, M.1
O’Sullivan, O.2
Coffey, A.3
Fitzgerald, G.F.4
Van Sinderen, D.5
McAuliffe, O.6
Ross, R.P.7
-
14
-
-
53849135601
-
Molecular characterization of a Clostridium difficile bacteriophage and its cloned biologically active endolysin
-
[CrossRef] [PubMed]
-
Mayer,M.J.; Narbad,A.; Gasson,M.J. Molecular characterization of a Clostridium difficile bacteriophage and its cloned biologically active endolysin. J. Bacteriol. 2008,190,6734-6740. [CrossRef] [PubMed]
-
(2008)
J. Bacteriol.
, vol.190
, pp. 6734-6740
-
-
Mayer, M.J.1
Narbad, A.2
Gasson, M.J.3
-
15
-
-
84868623569
-
Evidence of in vivo prophage induction during Clostridium difficile infection
-
[CrossRef] [PubMed]
-
Meessen-Pinard,M.; Sekulovic,O.; Fortier,L.-C. Evidence of in vivo prophage induction during Clostridium difficile infection. Appl. Environ. Microbiol. 2012,78,7662-7670. [CrossRef] [PubMed]
-
(2012)
Appl. Environ. Microbiol.
, vol.78
, pp. 7662-7670
-
-
Meessen-Pinard, M.1
Sekulovic, O.2
Fortier, L.-C.3
-
16
-
-
84896992962
-
Characterization of temperate phages infecting Clostridium difficile isolates of human and animal origins
-
[CrossRef] [PubMed]
-
Sekulovic,O.; Garneau,J.R.; Neron,A.; Fortier,L.C. Characterization of temperate phages infecting Clostridium difficile isolates of human and animal origins. Appl. Environ. Microbiol. 2014,80,2555-2563. [CrossRef] [PubMed]
-
(2014)
Appl. Environ. Microbiol.
, vol.80
, pp. 2555-2563
-
-
Sekulovic, O.1
Garneau, J.R.2
Neron, A.3
Fortier, L.C.4
-
17
-
-
79958160416
-
Prophage-stimulated toxin production in Clostridium difficile NAP1/027 lysogens
-
[CrossRef] [PubMed]
-
Sekulovic,O.; Meessen-Pinard,M.; Fortier,L.C. Prophage-stimulated toxin production in Clostridium difficile NAP1/027 lysogens. J. Bacteriol. 2011,193,2726-2734. [CrossRef] [PubMed]
-
(2011)
J. Bacteriol.
, vol.193
, pp. 2726-2734
-
-
Sekulovic, O.1
Meessen-Pinard, M.2
Fortier, L.C.3
-
18
-
-
70449380104
-
Classification of myoviridae bacteriophages using protein sequence similarity
-
[CrossRef] [PubMed]
-
Lavigne,R.; Darius,P.; Summer,E.J.; Seto,D.;Mahadevan,P.; Nilsson,A.S.; Ackermann,H.W.; Kropinski,A.M. Classification of myoviridae bacteriophages using protein sequence similarity. BMC Microbiol. 2009,9,224. [CrossRef] [PubMed]
-
(2009)
BMC Microbiol.
, vol.9
, pp. 224
-
-
Lavigne, R.1
Darius, P.2
Summer, E.J.3
Seto, D.4
Mahadevan, P.5
Nilsson, A.S.6
Ackermann, H.W.7
Kropinski, A.M.8
-
19
-
-
84930958634
-
A taxonomic review of Clostridium difficile phages and proposal of a novel genus,"Phimmp04likevirus"
-
[CrossRef] [PubMed]
-
Hargreaves,K.R.; Clokie,M.R.J. A taxonomic review of Clostridium difficile phages and proposal of a novel genus,"Phimmp04likevirus". Viruses 2015,7,2534-2541. [CrossRef] [PubMed]
-
(2015)
Viruses
, vol.7
, pp. 2534-2541
-
-
Hargreaves, K.R.1
Clokie, M.R.J.2
-
21
-
-
84885070363
-
Genetically diverse Clostridium difficile strains harboring abundant prophages in an estuarine environment
-
[CrossRef] [PubMed]
-
Hargreaves,K.R.; Colvin,H.V.; Patel,K.V.; Clokie,J.J.; Clokie,M.R. Genetically diverse Clostridium difficile strains harboring abundant prophages in an estuarine environment. Appl. Environ. Microbiol. 2013,79,6236-6243. [CrossRef] [PubMed]
-
(2013)
Appl. Environ. Microbiol.
, vol.79
, pp. 6236-6243
-
-
Hargreaves, K.R.1
Colvin, H.V.2
Patel, K.V.3
Clokie, J.J.4
Clokie, M.R.5
-
22
-
-
13544256293
-
Isolation and characterization of temperate bacteriophages of Clostridium difficile
-
[CrossRef] [PubMed]
-
Goh,S.; Riley,T.V.; Chang,B.J. Isolation and characterization of temperate bacteriophages of Clostridium difficile. Appl. Environ. Microbiol. 2005,71,1079-1083. [CrossRef] [PubMed]
-
(2005)
Appl. Environ. Microbiol.
, vol.71
, pp. 1079-1083
-
-
Goh, S.1
Riley, T.V.2
Chang, B.J.3
-
26
-
-
75649124547
-
De novo assembly of human genomes with massively parallel short read sequencing
-
[CrossRef] [PubMed]
-
Li,R.; Zhu,H.; Ruan,J.; Qian,W.; Fang,X.; Shi,Z.; Li,Y.; Li,S.; Shan,G.; Kristiansen,K.; et al. De novo assembly of human genomes with massively parallel short read sequencing. Genome Res. 2010,20,265-272. [CrossRef] [PubMed]
-
(2010)
Genome Res.
, vol.20
, pp. 265-272
-
-
Li, R.1
Zhu, H.2
Ruan, J.3
Qian, W.4
Fang, X.5
Shi, Z.6
Li, Y.7
Li, S.8
Shan, G.9
Kristiansen, K.10
-
27
-
-
40049104732
-
SOAP: Short oligonucleotide alignment program
-
[CrossRef] [PubMed]
-
Li,R.; Li,Y.; Kristiansen,K.; Wang,J. SOAP: Short oligonucleotide alignment program. Bioinformatics 2008,24,713-714. [CrossRef] [PubMed]
-
(2008)
Bioinformatics
, vol.24
, pp. 713-714
-
-
Li, R.1
Li, Y.2
Kristiansen, K.3
Wang, J.4
-
28
-
-
84860771820
-
Spades: A new genome assembly algorithm and its applications to single-cell sequencing
-
[CrossRef] [PubMed]
-
Bankevich,A.; Nurk,S.; Antipov,D.; Gurevich,A.A.; Dvorkin,M.; Kulikov,A.S.; Lesin,V.M.; Nikolenko,S.I.; Pham,S.; Prjibelski,A.D.; et al. Spades: A new genome assembly algorithm and its applications to single-cell sequencing. J. Comput. Biol. 2012,19,455-477. [CrossRef] [PubMed]
-
(2012)
J. Comput. Biol.
, vol.19
, pp. 455-477
-
-
Bankevich, A.1
Nurk, S.2
Antipov, D.3
Gurevich, A.A.4
Dvorkin, M.5
Kulikov, A.S.6
Lesin, V.M.7
Nikolenko, S.I.8
Pham, S.9
Prjibelski, A.D.10
-
29
-
-
84863507534
-
Geneious basic: An integrated and extendable desktop software platform for the organization and analysis of sequence data
-
[CrossRef] [PubMed]
-
Kearse,M.; Moir,R.; Wilson,A.; Stones-Havas,S.; Cheung,M.; Sturrock,S.; Buxton,S.; Cooper,A.; Markowitz,S.; Duran,C.; et al. Geneious basic: An integrated and extendable desktop software platform for the organization and analysis of sequence data. Bioinformatics 2012,28,1647-1649. [CrossRef] [PubMed]
-
(2012)
Bioinformatics
, vol.28
, pp. 1647-1649
-
-
Kearse, M.1
Moir, R.2
Wilson, A.3
Stones-Havas, S.4
Cheung, M.5
Sturrock, S.6
Buxton, S.7
Cooper, A.8
Markowitz, S.9
Duran, C.10
-
30
-
-
23144452801
-
Genemark: Web software for gene finding in prokaryotes,eukaryotes and viruses
-
[CrossRef] [PubMed]
-
Besemer,J.; Borodovsky,M. Genemark: Web software for gene finding in prokaryotes,eukaryotes and viruses. Nucleic Acids Res. 2005,33,W451-W454. [CrossRef] [PubMed]
-
(2005)
Nucleic Acids Res.
, vol.33
, pp. W451-W454
-
-
Besemer, J.1
Borodovsky, M.2
-
31
-
-
34147132825
-
Identifying bacterial genes and endosymbiont DNA with Glimmer
-
[CrossRef] [PubMed]
-
Delcher,A.L.; Bratke,K.A.; Powers,E.C.; Salzberg,S.L. Identifying bacterial genes and endosymbiont DNA with Glimmer. Bioinformatics 2007,23,673-679. [CrossRef] [PubMed]
-
(2007)
Bioinformatics
, vol.23
, pp. 673-679
-
-
Delcher, A.L.1
Bratke, K.A.2
Powers, E.C.3
Salzberg, S.L.4
-
32
-
-
84891804612
-
The SEED and the Rapid Annotation of microbial genomes using subsystems technology (RAST)
-
[CrossRef] [PubMed]
-
Overbeek,R.; Olson,R.; Pusch,G.D.; Olsen,G.J.; Davis,J.J.; Disz,T.; Edwards,R.A.; Gerdes,S.; Parrello,B.; Shukla,M.; et al. The SEED and the Rapid Annotation of microbial genomes using subsystems technology (RAST). Nucleic Acids Res. 2014,42,D206-D214. [CrossRef] [PubMed]
-
(2014)
Nucleic Acids Res.
, vol.42
, pp. D206-D214
-
-
Overbeek, R.1
Olson, R.2
Pusch, G.D.3
Olsen, G.J.4
Davis, J.J.5
Disz, T.6
Edwards, R.A.7
Gerdes, S.8
Parrello, B.9
Shukla, M.10
-
33
-
-
77952299957
-
Prodigal: Prokaryotic gene recognition and translation initiation site identification
-
[CrossRef] [PubMed]
-
Hyatt,D.; Chen,G.L.; Locascio,P.F.; Land,M.L.; Larimer,F.W.; Hauser,L.J. Prodigal: Prokaryotic gene recognition and translation initiation site identification. BMC Bioinformatics 2010,11,119. [CrossRef] [PubMed]
-
(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
-
34
-
-
0030801002
-
Gapped BLAST and PSI-BLAST: A new generation of protein database search programs
-
[CrossRef] [PubMed]
-
Altschul,S.F.; Madden,T.L.; Schaffer,A.A.; Zhang,J.; Zhang,Z.; Miller,W.; Lipman,D.J. Gapped BLAST and PSI-BLAST: A new generation of protein database search programs. Nucleic Acids Res. 1997,25,3389-3402. [CrossRef] [PubMed]
-
(1997)
Nucleic Acids Res.
, vol.25
, pp. 3389-3402
-
-
Altschul, S.F.1
Madden, T.L.2
Schaffer, A.A.3
Zhang, J.4
Zhang, Z.5
Miller, W.6
Lipman, D.J.7
-
35
-
-
0025183708
-
Basic local alignment search tool
-
[CrossRef]
-
Altschul,S.F.; Gish,W.; Miller,W.; Myers,E.W.; Lipman,D.J. Basic local alignment search tool. J. Mol. Biol. 1990,215,403-410. [CrossRef]
-
(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
-
36
-
-
3242887157
-
CD-Search: Protein domain annotations on the fly
-
[CrossRef] [PubMed]
-
Marchler-Bauer,A.; Bryant,S.H. CD-Search: Protein domain annotations on the fly. Nucleic Acids Res. 2004,32,W327-W331. [CrossRef] [PubMed]
-
(2004)
Nucleic Acids Res.
, vol.32
, pp. W327-W331
-
-
Marchler-Bauer, A.1
Bryant, S.H.2
-
37
-
-
84899518211
-
Interproscan 5: Genome-scale protein function classification
-
[CrossRef] [PubMed]
-
Jones,P.; Binns,D.; Chang,H.Y.; Fraser,M.; Li,W.; McAnulla,C.; McWilliam,H.; Maslen,J.; Mitchell,A.; Nuka,G.; et al. Interproscan 5: Genome-scale protein function classification. Bioinformatics 2014,30,1236-1240. [CrossRef] [PubMed]
-
(2014)
Bioinformatics
, vol.30
, pp. 1236-1240
-
-
Jones, P.1
Binns, D.2
Chang, H.Y.3
Fraser, M.4
Li, W.5
McAnulla, C.6
McWilliam, H.7
Maslen, J.8
Mitchell, A.9
Nuka, G.10
-
38
-
-
23144460836
-
The tRNAscan-SE,snoscan and snoGPS web servers for the detection of tRNAs and snoRNAs
-
[CrossRef] [PubMed]
-
Schattner,P.; Brooks,A.N.; Lowe,T.M. The tRNAscan-SE,snoscan and snoGPS web servers for the detection of tRNAs and snoRNAs. Nucleic Acids Res. 2005,33,W686-W689. [CrossRef] [PubMed]
-
(2005)
Nucleic Acids Res.
, vol.33
, pp. W686-W689
-
-
Schattner, P.1
Brooks, A.N.2
Lowe, T.M.3
-
39
-
-
84890037468
-
Infernal 1.1: 100-fold faster RNA homology searches
-
[CrossRef] [PubMed]
-
Nawrocki,E.P.; Eddy,S.R. Infernal 1.1: 100-fold faster RNA homology searches. Bioinformatics 2013,29,2933-2935. [CrossRef] [PubMed]
-
(2013)
Bioinformatics
, vol.29
, pp. 2933-2935
-
-
Nawrocki, E.P.1
Eddy, S.R.2
-
40
-
-
33846975418
-
PILER-CR: Fast and accurate identification of CRISPR repeats
-
[CrossRef] [PubMed]
-
Edgar,R.C. PILER-CR: Fast and accurate identification of CRISPR repeats. BMC Bioinformatics 2007,8,18. [CrossRef] [PubMed]
-
(2007)
BMC Bioinformatics
, vol.8
, pp. 18
-
-
Edgar, R.C.1
-
41
-
-
34547579396
-
CRISPRFinder: A web tool to identify clustered regularly interspaced short palindromic repeats
-
[CrossRef] [PubMed]
-
Grissa,I.; Vergnaud,G.; Pourcel,C. CRISPRFinder: A web tool to identify clustered regularly interspaced short palindromic repeats. Nucleic Acids Res. 2007,35,W52-W57. [CrossRef] [PubMed]
-
(2007)
Nucleic Acids Res.
, vol.35
, pp. W52-W57
-
-
Grissa, I.1
Vergnaud, G.2
Pourcel, C.3
-
42
-
-
84879014174
-
Crisprtarget
-
[CrossRef] [PubMed]
-
Biswas,A.; Gagnon,J.N.; Brouns,S.J.J.; Fineran,P.C.; Brown,C.M. Crisprtarget. RNA Biol. 2013,10,817-827. [CrossRef] [PubMed]
-
(2013)
RNA Biol.
, vol.10
, pp. 817-827
-
-
Biswas, A.1
Gagnon, J.N.2
Brouns, S.J.J.3
Fineran, P.C.4
Brown, C.M.5
-
43
-
-
84862503656
-
Gegenees: Fragmented alignment of multiple genomes for determining phylogenomic distances and genetic signatures unique for specified target groups
-
[CrossRef] [PubMed]
-
Ågren,J.; Sundström,A.; Håfström,T.; Segerman,B. Gegenees: Fragmented alignment of multiple genomes for determining phylogenomic distances and genetic signatures unique for specified target groups. PLoS ONE 2012,7,e39107. [CrossRef] [PubMed]
-
(2012)
PLoS ONE
, vol.7
-
-
Ågren, J.1
Sundström, A.2
Håfström, T.3
Segerman, B.4
-
44
-
-
30744470609
-
Application of phylogenetic networks in evolutionary studies
-
[CrossRef] [PubMed]
-
Huson,D.H.; Bryant,D. Application of phylogenetic networks in evolutionary studies. Mol. Biol. Evolut. 2006,23,254-267. [CrossRef] [PubMed]
-
(2006)
Mol. Biol. Evolut.
, vol.23
, pp. 254-267
-
-
Huson, D.H.1
Bryant, D.2
-
45
-
-
77950806408
-
New algorithms and methods to estimate maximum-likelihood phylogenies: Assessing the performance of PhyML 3.0
-
[CrossRef] [PubMed]
-
Guindon,S.; Dufayard,J.-F.; Lefort,V.; Anisimova,M.; Hordijk,W.; Gascuel,O. New algorithms and methods to estimate maximum-likelihood phylogenies: Assessing the performance of PhyML 3.0. Syst. Biol. 2010,59,307-321. [CrossRef] [PubMed]
-
(2010)
Syst. Biol.
, vol.59
, pp. 307-321
-
-
Guindon, S.1
Dufayard, J.-F.2
Lefort, V.3
Anisimova, M.4
Hordijk, W.5
Gascuel, O.6
-
46
-
-
62449181292
-
Determining DNA packaging strategy by analysis of the termini of the chromosomes in tailed-bacteriophage virions
-
[PubMed]
-
Casjens,S.R.; Gilcrease,E.B. Determining DNA packaging strategy by analysis of the termini of the chromosomes in tailed-bacteriophage virions. Methods Mol. Biol. 2009,502,91-111. [PubMed]
-
(2009)
Methods Mol. Biol.
, vol.502
, pp. 91-111
-
-
Casjens, S.R.1
Gilcrease, E.B.2
-
47
-
-
77949718257
-
FastTree 2-Approximately maximum-likelihood trees for large alignments
-
[CrossRef] [PubMed]
-
Price,M.N.; Dehal,P.S.; Arkin,A.P. FastTree 2-Approximately maximum-likelihood trees for large alignments. PLoS ONE 2010,5,e9490. [CrossRef] [PubMed]
-
(2010)
PLoS ONE
, vol.5
-
-
Price, M.N.1
Dehal, P.S.2
Arkin, A.P.3
-
48
-
-
81455140612
-
RAxML and FastTree: Comparing two methods for large-scale maximum likelihood phylogeny estimation
-
[CrossRef] [PubMed]
-
Liu,K.; Linder,C.R.; Warnow,T. RAxML and FastTree: Comparing two methods for large-scale maximum likelihood phylogeny estimation. PLoS ONE 2011,6,e27731. [CrossRef] [PubMed]
-
(2011)
PLoS ONE
, vol.6
-
-
Liu, K.1
Linder, C.R.2
Warnow, T.3
-
49
-
-
79961109150
-
BLAST Ring Image Generator (BRIG): Simple prokaryote genome comparisons
-
[CrossRef] [PubMed]
-
Alikhan,N.F.; Petty,N.K.; Ben Zakour,N.L.; Beatson,S.A. BLAST Ring Image Generator (BRIG): simple prokaryote genome comparisons. BMC Genomics 2011,12,402. [CrossRef] [PubMed]
-
(2011)
BMC Genomics
, vol.12
, pp. 402
-
-
Alikhan, N.F.1
Petty, N.K.2
Ben Zakour, N.L.3
Beatson, S.A.4
-
50
-
-
79953306448
-
Easyfig: A genome comparison visualizer
-
[CrossRef] [PubMed]
-
Sullivan,M.J.; Petty,N.K.; Beatson,S.A. Easyfig: A genome comparison visualizer. Bioinformatics 2011,27,1009-1010. [CrossRef] [PubMed]
-
(2011)
Bioinformatics
, vol.27
, pp. 1009-1010
-
-
Sullivan, M.J.1
Petty, N.K.2
Beatson, S.A.3
-
51
-
-
33745634395
-
Cd-hit: A fast program for clustering and comparing large sets of protein or nucleotide sequences
-
[CrossRef] [PubMed]
-
Li,W.; Godzik,A. Cd-hit: A fast program for clustering and comparing large sets of protein or nucleotide sequences. Bioinformatics 2006,22,1658-1659. [CrossRef] [PubMed]
-
(2006)
Bioinformatics
, vol.22
, pp. 1658-1659
-
-
Li, W.1
Godzik, A.2
-
52
-
-
33745550745
-
The multidrug-resistant human pathogen Clostridium difficile has a highly mobile,mosaic genome
-
[CrossRef] [PubMed]
-
Sebaihia,M.;Wren,B.W.; Mullany,P.; Fairweather,N.F.; Minton,N.; Stabler,R.; Thomson,N.R.; Roberts,A.P.; Cerdeno-Tarraga,A.M.;Wang,H.; et al. The multidrug-resistant human pathogen Clostridium difficile has a highly mobile,mosaic genome. Nat. Genet. 2006,38,779-786. [CrossRef] [PubMed]
-
(2006)
Nat. Genet.
, vol.38
, pp. 779-786
-
-
Sebaihia, M.1
Wren, B.W.2
Mullany, P.3
Fairweather, N.F.4
Minton, N.5
Stabler, R.6
Thomson, N.R.7
Roberts, A.P.8
Cerdeno-Tarraga, A.M.9
Wang, H.10
-
53
-
-
84946593480
-
Function of the CRISPR-Cas System of the Human Pathogen Clostridium difficile
-
[PubMed]
-
Boudry,P.; Semenova,E.; Monot,M.; Datsenko,K.A.; Lopatina,A.; Sekulovic,O.; Ospina-Bedoya,M.; Fortier,L.C.; Severinov,K.; Dupuy,B.; et al. Function of the CRISPR-Cas System of the Human Pathogen Clostridium difficile. mBio 2015,6,e01112-e01115. [PubMed]
-
(2015)
mBio
, vol.6
, pp. e01112-e01115
-
-
Boudry, P.1
Semenova, E.2
Monot, M.3
Datsenko, K.A.4
Lopatina, A.5
Sekulovic, O.6
Ospina-Bedoya, M.7
Fortier, L.C.8
Severinov, K.9
Dupuy, B.10
-
54
-
-
84878502476
-
Genome-wide identification of regulatory RNAs in the human pathogen Clostridium difficile
-
[CrossRef] [PubMed]
-
Soutourina,O.A.; Monot,M.; Boudry,P.; Saujet,L.; Pichon,C.; Sismeiro,O.; Semenova,E.; Severinov,K.; Le Bouguenec,C.; Coppee,J.Y.; et al. Genome-wide identification of regulatory RNAs in the human pathogen Clostridium difficile. PLoS Genet. 2013,9,e1003493. [CrossRef] [PubMed]
-
(2013)
PLoS Genet.
, vol.9
-
-
Soutourina, O.A.1
Monot, M.2
Boudry, P.3
Saujet, L.4
Pichon, C.5
Sismeiro, O.6
Semenova, E.7
Severinov, K.8
Le Bouguenec, C.9
Coppee, J.Y.10
-
55
-
-
84898892172
-
Bacteriophage recombination systems and biotechnical applications
-
[CrossRef] [PubMed]
-
Nafissi,N.; Slavcev,R. Bacteriophage recombination systems and biotechnical applications. Appl. Microbiol. Biotechnol. 2014,98,2841-2851. [CrossRef] [PubMed]
-
(2014)
Appl. Microbiol. Biotechnol.
, vol.98
, pp. 2841-2851
-
-
Nafissi, N.1
Slavcev, R.2
-
56
-
-
84892930258
-
Genetic recombination in bacteriophage lambda
-
hzs001,[CrossRef]
-
Hillyar,C.R. Genetic recombination in bacteriophage lambda. Biosci. Horiz. 2012,5,hzs001. [CrossRef]
-
(2012)
Biosci. Horiz.
, vol.5
-
-
Hillyar, C.R.1
-
57
-
-
28844494086
-
An epidemic,toxin gene-variant strain of Clostridium difficile
-
[CrossRef] [PubMed]
-
McDonald,L.; Killgore,G.; Thompson,A.; Owens,R.; Kazakova,S.; Sambol,S.; Johnson,S.; Gerding,D. An epidemic,toxin gene-variant strain of Clostridium difficile. N. Engl. J. Med. 2005,353,2433-2441. [CrossRef] [PubMed]
-
(2005)
N. Engl. J. Med.
, vol.353
, pp. 2433-2441
-
-
McDonald, L.1
Killgore, G.2
Thompson, A.3
Owens, R.4
Kazakova, S.5
Sambol, S.6
Johnson, S.7
Gerding, D.8
-
58
-
-
84903191942
-
Epidemic Clostridium difficile strains demonstrate increased competitive fitness compared to nonepidemic isolates
-
[CrossRef] [PubMed]
-
Robinson,C.D.; Auchtung,J.M.; Collins,J.; Britton,R.A. Epidemic Clostridium difficile strains demonstrate increased competitive fitness compared to nonepidemic isolates. Infect. Immun. 2014,82,2815-2825. [CrossRef] [PubMed]
-
(2014)
Infect. Immun.
, vol.82
, pp. 2815-2825
-
-
Robinson, C.D.1
Auchtung, J.M.2
Collins, J.3
Britton, R.A.4
-
59
-
-
84903216693
-
Strain types and antimicrobial resistance patterns of Clostridium difficile isolates from the United States,2011 to 2013
-
[CrossRef] [PubMed]
-
Tickler,I.A.; Goering,R.V.; Whitmore,J.D.; Lynn,A.N.; Persing,D.H.; Tenover,F.C. Strain types and antimicrobial resistance patterns of Clostridium difficile isolates from the United States,2011 to 2013. Antimicrob. Agents Chemother. 2014,58,4214-4218. [CrossRef] [PubMed]
-
(2014)
Antimicrob. Agents Chemother.
, vol.58
, pp. 4214-4218
-
-
Tickler, I.A.1
Goering, R.V.2
Whitmore, J.D.3
Lynn, A.N.4
Persing, D.H.5
Tenover, F.C.6
-
60
-
-
36649034890
-
Morphological and genetic diversity of temperate phages in Clostridium difficile
-
[CrossRef] [PubMed]
-
Fortier,L.-C.; Moineau,S. Morphological and genetic diversity of temperate phages in Clostridium difficile. Appl. Environ. Microbiol. 2007,73,7358-7366. [CrossRef] [PubMed]
-
(2007)
Appl. Environ. Microbiol.
, vol.73
, pp. 7358-7366
-
-
Fortier, L.-C.1
Moineau, S.2
-
61
-
-
84995495686
-
CRISPR diversity and microevolution in Clostridium difficile
-
[CrossRef] [PubMed]
-
Andersen,J.M.; Shoup,M.; Robinson,C.; Britton,R.; Olsen,K.E.; Barrangou,R. CRISPR diversity and microevolution in Clostridium difficile. Genome Biol. Evol. 2016,8,2841-2855. [CrossRef] [PubMed]
-
(2016)
Genome Biol. Evol.
, vol.8
, pp. 2841-2855
-
-
Andersen, J.M.1
Shoup, M.2
Robinson, C.3
Britton, R.4
Olsen, K.E.5
Barrangou, R.6
-
62
-
-
80053528043
-
The human gut virome: Inter-individual variation and dynamic response to diet
-
[CrossRef] [PubMed]
-
Minot,S.; Sinha,R.; Chen,J.; Li,H.; Keilbaugh,S.A.;Wu,G.D.; Lewis,J.D.; Bushman,F.D. The human gut virome: Inter-individual variation and dynamic response to diet. Genome Res. 2011,21,1616-1625. [CrossRef] [PubMed]
-
(2011)
Genome Res.
, vol.21
, pp. 1616-1625
-
-
Minot, S.1
Sinha, R.2
Chen, J.3
Li, H.4
Keilbaugh, S.A.5
Wu, G.D.6
Lewis, J.D.7
Bushman, F.D.8
-
63
-
-
84875774723
-
Molecular aspects and comparative genomics of bacteriophage endolysins
-
[CrossRef] [PubMed]
-
Oliveira,H.; Melo,L.D.; Santos,S.B.; Nobrega,F.L.; Ferreira,E.C.; Cerca,N.; Azeredo,J.; Kluskens,L.D. Molecular aspects and comparative genomics of bacteriophage endolysins. J. Virol. 2013,87,4558-4570. [CrossRef] [PubMed]
-
(2013)
J. Virol.
, vol.87
, pp. 4558-4570
-
-
Oliveira, H.1
Melo, L.D.2
Santos, S.B.3
Nobrega, F.L.4
Ferreira, E.C.5
Cerca, N.6
Azeredo, J.7
Kluskens, L.D.8
-
64
-
-
0025843392
-
Electron microscopic investigation of lysogeny of clostridium difficile strains isolated from antibiotic-associated diarrhea cases and from healthy carriers
-
[CrossRef]
-
Nagy,E.; Foldes,J. Electron microscopic investigation of lysogeny of clostridium difficile strains isolated from antibiotic-associated diarrhea cases and from healthy carriers. Acta Pathol. Microbiol. Immunol. Scand. 1991,99,321-326. [CrossRef]
-
(1991)
Acta Pathol. Microbiol. Immunol. Scand.
, vol.99
, pp. 321-326
-
-
Nagy, E.1
Foldes, J.2
-
66
-
-
84866174355
-
Prophage carriage and diversity within clinically relevant strains of Clostridium difficile
-
[CrossRef] [PubMed]
-
Shan,J.; Patel,K.V.; Hickenbotham,P.T.; Nale,J.Y.; Hargreaves,K.R.; Clokie,M.R. Prophage carriage and diversity within clinically relevant strains of Clostridium difficile. Appl. Environ. Microbiol. 2012,78,6027-6034. [CrossRef] [PubMed]
-
(2012)
Appl. Environ. Microbiol.
, vol.78
, pp. 6027-6034
-
-
Shan, J.1
Patel, K.V.2
Hickenbotham, P.T.3
Nale, J.Y.4
Hargreaves, K.R.5
Clokie, M.R.6
-
67
-
-
19944434101
-
The generalized transducing Salmonella bacteriophage ES18: Complete genome sequence and DNA packaging strategy
-
[CrossRef] [PubMed]
-
Casjens,S.R.; Gilcrease,E.B.; Winn-Stapley,D.A.; Schicklmaier,P.; Schmieger,H.; Pedulla,M.L.; Ford,M.E.; Houtz,J.M.; Hatfull,G.F.; Hendrix,R.W. The generalized transducing Salmonella bacteriophage ES18: Complete genome sequence and DNA packaging strategy. J. Bacteriol. 2005,187,1091-1104. [CrossRef] [PubMed]
-
(2005)
J. Bacteriol.
, vol.187
, pp. 1091-1104
-
-
Casjens, S.R.1
Gilcrease, E.B.2
Winn-Stapley, D.A.3
Schicklmaier, P.4
Schmieger, H.5
Pedulla, M.L.6
Ford, M.E.7
Houtz, J.M.8
Hatfull, G.F.9
Hendrix, R.W.10
-
68
-
-
84928582552
-
Intra- and inter-generic transfer of pathogenicity island-encoded virulence genes by cos phages
-
[CrossRef] [PubMed]
-
Chen,J.; Carpena,N.; Quiles-Puchalt,N.; Ram,G.; Novick,R.P.; Penades,J.R. Intra- and inter-generic transfer of pathogenicity island-encoded virulence genes by cos phages. ISME J. 2015,9,1260-1263. [CrossRef] [PubMed]
-
(2015)
ISME J.
, vol.9
, pp. 1260-1263
-
-
Chen, J.1
Carpena, N.2
Quiles-Puchalt, N.3
Ram, G.4
Novick, R.P.5
Penades, J.R.6
-
69
-
-
84969257061
-
Mechanisms of DNA packaging by large double-stranded DNA viruses
-
[CrossRef] [PubMed]
-
Rao,V.B.; Feiss,M. Mechanisms of DNA packaging by large double-stranded DNA viruses. Annu. Rev. Virol. 2015,2,351-378. [CrossRef] [PubMed]
-
(2015)
Annu. Rev. Virol.
, vol.2
, pp. 351-378
-
-
Rao, V.B.1
Feiss, M.2
-
70
-
-
84891648569
-
Phage FC2 mediates transduction of Tn6215,encoding erythromycin resistance,between Clostridium difficile strains
-
[CrossRef] [PubMed]
-
Goh,S.; Hussain,H.; Chang,B.J.; Emmett,W.; Riley,T.V.; Mullany,P. Phage FC2 mediates transduction of Tn6215,encoding erythromycin resistance,between Clostridium difficile strains. mBio 2013,4,e00840-13. [CrossRef] [PubMed]
-
(2013)
mBio
, vol.4
, pp. e00840-e00913
-
-
Goh, S.1
Hussain, H.2
Chang, B.J.3
Emmett, W.4
Riley, T.V.5
Mullany, P.6
|