-
1
-
-
84859885188
-
Evidence of a robust resident bacteriophage population revealed through analysis of the human salivary virome
-
PMID: 22158393
-
Pride DT, Salzman J, Haynes M, Rohwer F, Davis-Long C, White RA 3rd, et al. (2012) Evidence of a robust resident bacteriophage population revealed through analysis of the human salivary virome. ISME J 6: 915-926. doi: 10.1038/ismej.2011.169 PMID: 22158393
-
(2012)
ISME J
, vol.6
, pp. 915-926
-
-
Pride, D.T.1
Salzman, J.2
Haynes, M.3
Rohwer, F.4
Davis-Long, C.5
White, R.A.6
-
2
-
-
0141891348
-
Metagenomic analyses of an uncultured viral community from human feces
-
PMID: 14526037
-
Breitbart M, Hewson I, Felts B, Mahaffy JM, Nulton J, Salamon P, et al. (2003) Metagenomic analyses of an uncultured viral community from human feces. J Bacteriol 185: 6220-6223. PMID: 14526037
-
(2003)
J Bacteriol
, vol.185
, pp. 6220-6223
-
-
Breitbart, M.1
Hewson, I.2
Felts, B.3
Mahaffy, J.M.4
Nulton, J.5
Salamon, P.6
-
3
-
-
77954627922
-
Viruses in the faecal microbiota of monozygotic twins and their mothers
-
PMID: 20631792
-
Reyes A, Haynes M, Hanson N, Angly FE, Heath AC, Rohwer F, et al. (2010) Viruses in the faecal microbiota of monozygotic twins and their mothers. Nature 466: 334-338. doi: 10.1038/nature09199 PMID: 20631792
-
(2010)
Nature
, vol.466
, pp. 334-338
-
-
Reyes, A.1
Haynes, M.2
Hanson, N.3
Angly, F.E.4
Heath, A.C.5
Rohwer, F.6
-
4
-
-
84862522999
-
Human skin microbiota: High diversity of DNA viruses identified on the human skin by high throughput sequencing
-
PMID: 22723863
-
Foulongne V, Sauvage V, Hebert C, Dereure O, Cheval J, Gouilh MA, et al. (2012) Human skin microbiota: high diversity of DNA viruses identified on the human skin by high throughput sequencing. PLoS One 7: e38499. doi: 10.1371/journal.pone.0038499 PMID: 22723863
-
(2012)
PLoS One
, vol.7
, pp. e38499
-
-
Foulongne, V.1
Sauvage, V.2
Hebert, C.3
Dereure, O.4
Cheval, J.5
Gouilh, M.A.6
-
5
-
-
84889594211
-
Temporal response of the human virome to immunosuppression and antiviral therapy
-
PMID: 24267896
-
De Vlaminck I, Khush KK, Strehl C, Kohli B, Luikart H, Neff NF, et al. (2013) Temporal response of the human virome to immunosuppression and antiviral therapy. Cell 155: 1178-1187. doi: 10.1016/j.cell.2013.10.034 PMID: 24267896
-
(2013)
Cell
, vol.155
, pp. 1178-1187
-
-
De Vlaminck, I.1
Khush, K.K.2
Strehl, C.3
Kohli, B.4
Luikart, H.5
Neff, N.F.6
-
6
-
-
70350545933
-
Metagenomic analysis of respiratory tract DNA viral communities in cystic fibrosis and non-cystic fibrosis individuals
-
PMID: 19816605
-
Willner D, Furlan M, Haynes M, Schmieder R, Angly FE, Silva J, et al. (2009) Metagenomic analysis of respiratory tract DNA viral communities in cystic fibrosis and non-cystic fibrosis individuals. PLoS One 4: e7370. doi: 10.1371/journal.pone.0007370 PMID: 19816605
-
(2009)
PLoS One
, vol.4
, pp. e7370
-
-
Willner, D.1
Furlan, M.2
Haynes, M.3
Schmieder, R.4
Angly, F.E.5
Silva, J.6
-
7
-
-
84880652104
-
Rapid evolution of the human gut virome
-
PMID:23836644
-
Minot S, Bryson A, Chehoud C, Wu GD, Lewis JD, Bushman FD (2013) Rapid evolution of the human gut virome. Proc Natl Acad Sci U S A 110: 12450-12455. doi: 10.1073/pnas.1300833110 PMID:23836644
-
(2013)
Proc Natl Acad Sci U S A
, vol.110
, pp. 12450-12455
-
-
Minot, S.1
Bryson, A.2
Chehoud, C.3
Wu, G.D.4
Lewis, J.D.5
Bushman, F.D.6
-
8
-
-
84879515171
-
Bacteriophage adhering to mucus provide a non-host-derived immunity
-
PMID: 23690590
-
Barr JJ, Auro R, Furlan M, Whiteson KL, Erb ML, Pogliano J, et al. (2013) Bacteriophage adhering to mucus provide a non-host-derived immunity. Proc Natl Acad Sci U S A 110: 10771-10776. doi: 10.1073/pnas.1305923110 PMID: 23690590
-
(2013)
Proc Natl Acad Sci U S A
, vol.110
, pp. 10771-10776
-
-
Barr, J.J.1
Auro, R.2
Furlan, M.3
Whiteson, K.L.4
Erb, M.L.5
Pogliano, J.6
-
9
-
-
84879373236
-
Resident viruses and their interactions with the immune system
-
PMID: 23778792
-
Duerkop BA, Hooper LV (2013) Resident viruses and their interactions with the immune system. Nat Immunol 14: 654-659. doi: 10.1038/ni.2614 PMID: 23778792
-
(2013)
Nat Immunol
, vol.14
, pp. 654-659
-
-
Duerkop, B.A.1
Hooper, L.V.2
-
10
-
-
84908222815
-
Phage and bacteria support mutual diversity in a narrowing staircase of coexistence
-
PMID: 24858781
-
Haerter JO, Mitarai N, Sneppen K (2014) Phage and bacteria support mutual diversity in a narrowing staircase of coexistence. ISME J 8: 2317-2326. doi: 10.1038/ismej.2014.80 PMID: 24858781
-
(2014)
ISME J
, vol.8
, pp. 2317-2326
-
-
Haerter, J.O.1
Mitarai, N.2
Sneppen, K.3
-
11
-
-
37249025333
-
Coevolution with viruses drives the evolution of bacterial mutation rates
-
PMID: 18059461
-
Pal C, Macia MD, Oliver A, Schachar I, Buckling A (2007) Coevolution with viruses drives the evolution of bacterial mutation rates. Nature 450: 1079-1081. PMID: 18059461
-
(2007)
Nature
, vol.450
, pp. 1079-1081
-
-
Pal, C.1
Macia, M.D.2
Oliver, A.3
Schachar, I.4
Buckling, A.5
-
12
-
-
34249740244
-
Experimental coevolution with bacteria and phage. The Pseudomonas fluorescens-Phi2 model system
-
PMID:17320489
-
Brockhurst MA, Morgan AD, Fenton A, Buckling A (2007) Experimental coevolution with bacteria and phage. The Pseudomonas fluorescens-Phi2 model system. Infect Genet Evol 7: 547-552. PMID:17320489
-
(2007)
Infect Genet Evol
, vol.7
, pp. 547-552
-
-
Brockhurst, M.A.1
Morgan, A.D.2
Fenton, A.3
Buckling, A.4
-
13
-
-
79953281735
-
Bacteria-phage antagonistic coevolution in soil
-
PMID: 21454789
-
Gomez P, Buckling A (2011) Bacteria-phage antagonistic coevolution in soil. Science 332: 106-109. doi: 10.1126/science.1198767 PMID: 21454789
-
(2011)
Science
, vol.332
, pp. 106-109
-
-
Gomez, P.1
Buckling, A.2
-
14
-
-
0033578311
-
Isolation of a temperate bacteriophage encoding the type III effector protein SopE from an epidemic Salmonella typhimurium strain
-
PMID: 10449782
-
Mirold S, Rabsch W, Rohde M, Stender S, Tschape H, Russmann H, et al. (1999) Isolation of a temperate bacteriophage encoding the type III effector protein SopE from an epidemic Salmonella typhimurium strain. Proc Natl Acad Sci U S A 96: 9845-9850. PMID: 10449782
-
(1999)
Proc Natl Acad Sci U S A
, vol.96
, pp. 9845-9850
-
-
Mirold, S.1
Rabsch, W.2
Rohde, M.3
Stender, S.4
Tschape, H.5
Russmann, H.6
-
15
-
-
84867903844
-
A composite bacteriophage alters colonization by an intestinal commensal bacterium
-
PMID: 23045666
-
Duerkop BA, Clements CV, Rollins D, Rodrigues JL, Hooper LV (2012) A composite bacteriophage alters colonization by an intestinal commensal bacterium. Proc Natl Acad Sci U S A 109: 17621-17626. doi: 10.1073/pnas.1206136109 PMID: 23045666
-
(2012)
Proc Natl Acad Sci U S A
, vol.109
, pp. 17621-17626
-
-
Duerkop, B.A.1
Clements, C.V.2
Rollins, D.3
Rodrigues, J.L.4
Hooper, L.V.5
-
16
-
-
69249152571
-
Bacteriophages encode factors required for protection in a symbiotic mutualism
-
PMID:19696350
-
Oliver KM, Degnan PH, Hunter MS, Moran NA (2009) Bacteriophages encode factors required for protection in a symbiotic mutualism. Science 325: 992-994. doi: 10.1126/science.1174463 PMID:19696350
-
(2009)
Science
, vol.325
, pp. 992-994
-
-
Oliver, K.M.1
Degnan, P.H.2
Hunter, M.S.3
Moran, N.A.4
-
17
-
-
33646559836
-
Environmental whole-genome amplification to access microbial populations in contaminated sediments
-
PMID: 16672469
-
Abulencia CB, Wyborski DL, Garcia JA, Podar M, Chen W, Chang SH, et al. (2006) Environmental whole-genome amplification to access microbial populations in contaminated sediments. Appl Environ Microbiol 72: 3291-3301. PMID: 16672469
-
(2006)
Appl Environ Microbiol
, vol.72
, pp. 3291-3301
-
-
Abulencia, C.B.1
Wyborski, D.L.2
Garcia, J.A.3
Podar, M.4
Chen, W.5
Chang, S.H.6
-
18
-
-
83155190998
-
Amplification methods bias metagenomic libraries of uncultured single-stranded and double-stranded DNA viruses
-
PMID: 21926223
-
Kim KH, Bae JW (2011) Amplification methods bias metagenomic libraries of uncultured single-stranded and double-stranded DNA viruses. Appl Environ Microbiol 77: 7663-7668. doi: 10.1128/AEM.00289-11 PMID: 21926223
-
(2011)
Appl Environ Microbiol
, vol.77
, pp. 7663-7668
-
-
Kim, K.H.1
Bae, J.W.2
-
19
-
-
77952243141
-
QIIME allows analysis of high-throughput community sequencing data
-
PMID: 20383131
-
Caporaso JG, Kuczynski J, Stombaugh J, Bittinger K, Bushman FD, Costello EK, et al. (2010) QIIME allows analysis of high-throughput community sequencing data. Nat Methods 7: 335-336. doi: 10.1038/nmeth.f.303 PMID: 20383131
-
(2010)
Nat Methods
, vol.7
, pp. 335-336
-
-
Caporaso, J.G.1
Kuczynski, J.2
Stombaugh, J.3
Bittinger, K.4
Bushman, F.D.5
Costello, E.K.6
-
20
-
-
72949107142
-
Introducing mothur: Open-source, platform-independent, community-supported software for describing and comparing microbial communities
-
PMID: 19801464
-
Schloss PD, Westcott SL, Ryabin T, Hall JR, Hartmann M, Hollister EB, et al. (2009) Introducing mothur: Open-Source, Platform-Independent, Community-Supported Software for Describing and Comparing Microbial Communities. Applied and Environmental Microbiology 75: 7537-7541. doi: 10.1128/AEM.01541-09 PMID: 19801464
-
(2009)
Applied and Environmental Microbiology
, vol.75
, pp. 7537-7541
-
-
Schloss, P.D.1
Westcott, S.L.2
Ryabin, T.3
Hall, J.R.4
Hartmann, M.5
Hollister, E.B.6
-
21
-
-
80054911634
-
Metavir: A web server dedicated to virome analysis
-
PMID:21911332
-
Roux S, Faubladier M, Mahul A, Paulhe N, Bernard A, Debroas D, et al. (2011) Metavir: a web server dedicated to virome analysis. Bioinformatics 27: 3074-3075. doi: 10.1093/bioinformatics/btr519 PMID:21911332
-
(2011)
Bioinformatics
, vol.27
, pp. 3074-3075
-
-
Roux, S.1
Faubladier, M.2
Mahul, A.3
Paulhe, N.4
Bernard, A.5
Debroas, D.6
-
22
-
-
19144363310
-
PHACCS, an online tool for estimating the structure and diversity of uncultured viral communities using metagenomic information
-
PMID: 15743531
-
Angly F, Rodriguez-Brito B, Bangor D, McNairnie P, Breitbart M, Salamon P, et al. (2005) PHACCS, an online tool for estimating the structure and diversity of uncultured viral communities using metagenomic information. BMC Bioinformatics 6: 41. PMID: 15743531
-
(2005)
BMC Bioinformatics
, vol.6
, pp. 41
-
-
Angly, F.1
Rodriguez-Brito, B.2
Bangor, D.3
McNairnie, P.4
Breitbart, M.5
Salamon, P.6
-
23
-
-
84880509968
-
Antibiotic treatment expands the resistance reservoir and ecological network of the phage metagenome
-
PMID: 23748443
-
Modi SR, Lee HH, Spina CS, Collins JJ (2013) Antibiotic treatment expands the resistance reservoir and ecological network of the phage metagenome. Nature 499: 219-222. doi: 10.1038/nature12212 PMID: 23748443
-
(2013)
Nature
, vol.499
, pp. 219-222
-
-
Modi, S.R.1
Lee, H.H.2
Spina, C.S.3
Collins, J.J.4
-
24
-
-
84855245603
-
Antibiotics in feed induce prophages in swine fecal microbiomes
-
Allen HK, Looft T, Bayles DO, Humphrey S, Levine UY, Alt D, et al. (2011) Antibiotics in feed induce prophages in swine fecal microbiomes. MBio 2.
-
(2011)
MBio
, vol.2
-
-
Allen, H.K.1
Looft, T.2
Bayles, D.O.3
Humphrey, S.4
Levine, U.Y.5
Alt, D.6
-
25
-
-
44249126241
-
Collateral effects of antibiotics: Carbadox and metronidazole induce VSH-1 and facilitate gene transfer among Brachyspira hyodysenteriae strains
-
PMID: 18359835
-
Stanton TB, Humphrey SB, Sharma VK, Zuerner RL (2008) Collateral effects of antibiotics: carbadox and metronidazole induce VSH-1 and facilitate gene transfer among Brachyspira hyodysenteriae strains. Appl Environ Microbiol 74: 2950-2956. doi: 10.1128/AEM.00189-08 PMID: 18359835
-
(2008)
Appl Environ Microbiol
, vol.74
, pp. 2950-2956
-
-
Stanton, T.B.1
Humphrey, S.B.2
Sharma, V.K.3
Zuerner, R.L.4
-
26
-
-
0023233136
-
Characterization of a bacteriophage that carries the genes for production of Shiga-like toxin 1 in Escherichia coli
-
PMID: 3040688
-
Huang A, Friesen J, Brunton JL (1987) Characterization of a bacteriophage that carries the genes for production of Shiga-like toxin 1 in Escherichia coli. J Bacteriol 169: 4308-4312. PMID: 3040688
-
(1987)
J Bacteriol
, vol.169
, pp. 4308-4312
-
-
Huang, A.1
Friesen, J.2
Brunton, J.L.3
-
27
-
-
0032932223
-
Induction of prophages of enterohe-morrhagic Escherichia coli O157:H7 with norfloxacin
-
PMID: 10094706
-
Matsushiro A, Sato K, Miyamoto H, Yamamura T, Honda T (1999) Induction of prophages of enterohe-morrhagic Escherichia coli O157:H7 with norfloxacin. J Bacteriol 181: 2257-2260. PMID: 10094706
-
(1999)
J Bacteriol
, vol.181
, pp. 2257-2260
-
-
Matsushiro, A.1
Sato, K.2
Miyamoto, H.3
Yamamura, T.4
Honda, T.5
-
28
-
-
0034056335
-
Quinolone antibiotics induce Shiga toxin-encoding bacteriophages, toxin production, and death in mice
-
PMID: 10669353
-
Zhang X, McDaniel AD, Wolf LE, Keusch GT, Waldor MK, Acheson DW (2000) Quinolone antibiotics induce Shiga toxin-encoding bacteriophages, toxin production, and death in mice. J Infect Dis 181: 664-670. PMID: 10669353
-
(2000)
J Infect Dis
, vol.181
, pp. 664-670
-
-
Zhang, X.1
McDaniel, A.D.2
Wolf, L.E.3
Keusch, G.T.4
Waldor, M.K.5
Acheson, D.W.6
-
29
-
-
0020662906
-
Escherichia coli O157:H7 strains associated with haemorrhagic colitis in the United States produce a Shigella dysenteriae 1 (SHIGA) like cytotoxin
-
O'Brien AO, Lively TA, Chen ME, Rothman SW, Formal SB (1983) Escherichia coli O157:H7 strains associated with haemorrhagic colitis in the United States produce a Shigella dysenteriae 1 (SHIGA) like cytotoxin. Lancet 1: 702.
-
(1983)
Lancet
, vol.1
, pp. 702
-
-
O'Brien, A.O.1
Lively, T.A.2
Chen, M.E.3
Rothman, S.W.4
Formal, S.B.5
-
30
-
-
22544461682
-
Hemolytic uremic syndrome
-
PMID: 15728781
-
Noris M, Remuzzi G (2005) Hemolytic uremic syndrome. J Am Soc Nephrol 16: 1035-1050. PMID: 15728781
-
(2005)
J Am Soc Nephrol
, vol.16
, pp. 1035-1050
-
-
Noris, M.1
Remuzzi, G.2
-
31
-
-
0003761043
-
-
Springer-Verlag, New York
-
Murphy FA, Fauquet C.M., Bishop D.H.L., Ghabrial S.A., Jarvis A.W., Martelli G.P., Mayo M.A., and Summers M.D. (1995) Virus Taxonomy: Sizth Report of the International Committee on Taxonomy of Viruses. Springer-Verlag, New York Vol. Supplement 10.
-
(1995)
Virus Taxonomy: Sizth Report of the International Committee on Taxonomy of Viruses
-
-
Murphy, F.A.1
Fauquet, C.M.2
Bishop, D.H.L.3
Ghabrial, S.A.4
Jarvis, A.W.5
Martelli, G.P.6
Mayo, M.A.7
Summers, M.D.8
-
32
-
-
79960597679
-
An integrated semiconductor device enabling non-optical genome sequencing
-
PMID: 21776081
-
Rothberg JM, Hinz W, Rearick TM, Schultz J, Mileski W, Davey M, et al. (2011) An integrated semiconductor device enabling non-optical genome sequencing. Nature 475: 348-352. doi: 10.1038/nature10242 PMID: 21776081
-
(2011)
Nature
, vol.475
, pp. 348-352
-
-
Rothberg, J.M.1
Hinz, W.2
Rearick, T.M.3
Schultz, J.4
Mileski, W.5
Davey, M.6
-
33
-
-
58149200948
-
The Ribosomal Database Project: Improved alignments and new tools for rRNA analysis
-
PMID: 19004872
-
Cole JR, Wang Q, Cardenas E, Fish J, Chai B, Farris RJ, et al. (2009) The Ribosomal Database Project: improved alignments and new tools for rRNA analysis. Nucleic Acids Res 37: D141-145. doi: 10.1093/nar/gkn879 PMID: 19004872
-
(2009)
Nucleic Acids Res
, vol.37
, pp. D141-145
-
-
Cole, J.R.1
Wang, Q.2
Cardenas, E.3
Fish, J.4
Chai, B.5
Farris, R.J.6
-
34
-
-
0037195156
-
Genomic analysis of uncultured marine viral communities
-
PMID: 12384570
-
Breitbart M, Salamon P, Andresen B, Mahaffy JM, Segall AM, Mead D, et al. (2002) Genomic analysis of uncultured marine viral communities. Proc Natl Acad Sci U S A 99: 14250-14255. PMID: 12384570
-
(2002)
Proc Natl Acad Sci U S A
, vol.99
, pp. 14250-14255
-
-
Breitbart, M.1
Salamon, P.2
Andresen, B.3
Mahaffy, J.M.4
Segall, A.M.5
Mead, D.6
-
35
-
-
53549118607
-
The metagenomics RAST server-A public resource for the automatic phylogenetic and functional analysis of metagenomes
-
PMID: 18803844
-
Meyer F, Paarmann D, D'Souza M, Olson R, Glass EM, Kubal M, et al. (2008) The metagenomics RAST server-a public resource for the automatic phylogenetic and functional analysis of metagenomes. BMC Bioinformatics 9: 386. doi: 10.1186/1471-2105-9-386 PMID: 18803844
-
(2008)
BMC Bioinformatics
, vol.9
, pp. 386
-
-
Meyer, F.1
Paarmann, D.2
D'Souza, M.3
Olson, R.4
Glass, E.M.5
Kubal, M.6
-
36
-
-
84879017399
-
The comprehensive antibiotic resistance database
-
PMID: 23650175
-
McArthur AG, Waglechner N, Nizam F, Yan A, Azad MA, Baylay AJ, et al. (2013) The comprehensive antibiotic resistance database. Antimicrob Agents Chemother 57: 3348-3357. doi: 10.1128/AAC.00419-13 PMID: 23650175
-
(2013)
Antimicrob Agents Chemother
, vol.57
, pp. 3348-3357
-
-
McArthur, A.G.1
Waglechner, N.2
Nizam, F.3
Yan, A.4
Azad, M.A.5
Baylay, A.J.6
-
37
-
-
84867613923
-
Microbial 16S rRNA Ion Tag and community metagenome sequencing using the Ion Torrent (PGM) Platform
-
PMID: 22849830
-
Whiteley AS, Jenkins S, Waite I, Kresoje N, Payne H, Mullan B, et al. (2012) Microbial 16S rRNA Ion Tag and community metagenome sequencing using the Ion Torrent (PGM) Platform. J Microbiol Methods 91: 80-88. doi: 10.1016/j.mimet.2012.07.008 PMID: 22849830
-
(2012)
J Microbiol Methods
, vol.91
, pp. 80-88
-
-
Whiteley, A.S.1
Jenkins, S.2
Waite, I.3
Kresoje, N.4
Payne, H.5
Mullan, B.6
-
38
-
-
77957244650
-
Search and clustering orders of magnitude faster than BLAST
-
PMID: 20709691
-
Edgar RC (2010) Search and clustering orders of magnitude faster than BLAST. Bioinformatics 26: 2460-2461. doi: 10.1093/bioinformatics/btq461 PMID: 20709691
-
(2010)
Bioinformatics
, vol.26
, pp. 2460-2461
-
-
Edgar, R.C.1
-
39
-
-
75249107844
-
PyNAST: A flexible tool for aligning sequences to a template alignment
-
PMID: 19914921
-
Caporaso JG, Bittinger K, Bushman FD, DeSantis TZ, Andersen GL, Knight R (2010) PyNAST: a flexible tool for aligning sequences to a template alignment. Bioinformatics 26: 266-267. doi: 10.1093/bioinformatics/btp636 PMID: 19914921
-
(2010)
Bioinformatics
, vol.26
, pp. 266-267
-
-
Caporaso, J.G.1
Bittinger, K.2
Bushman, F.D.3
DeSantis, T.Z.4
Andersen, G.L.5
Knight, R.6
-
40
-
-
33746061683
-
Greengenes, a chimera-checked 16S rRNA gene database and workbench compatible with ARB
-
PMID: 16820507
-
DeSantis TZ, Hugenholtz P, Larsen N, Rojas M, Brodie EL, Keller K, et al. (2006) Greengenes, a chimera-checked 16S rRNA gene database and workbench compatible with ARB. Appl Environ Microbiol 72: 5069-5072. PMID: 16820507
-
(2006)
Appl Environ Microbiol
, vol.72
, pp. 5069-5072
-
-
DeSantis, T.Z.1
Hugenholtz, P.2
Larsen, N.3
Rojas, M.4
Brodie, E.L.5
Keller, K.6
-
41
-
-
33745634395
-
Cd-hit: A fast program for clustering and comparing large sets of protein or nucleotide sequences
-
PMID: 16731699
-
Li W, Godzik A (2006) Cd-hit: a fast program for clustering and comparing large sets of protein or nucleotide sequences. Bioinformatics 22: 1658-1659. PMID: 16731699
-
(2006)
Bioinformatics
, vol.22
, pp. 1658-1659
-
-
Li, W.1
Godzik, A.2
-
42
-
-
67649327176
-
FastTree: Computing large minimum evolution trees with profiles instead of a distance matrix
-
PMID:19377059
-
Price MN, Dehal PS, Arkin AP (2009) FastTree: computing large minimum evolution trees with profiles instead of a distance matrix. Mol Biol Evol 26: 1641-1650. doi: 10.1093/molbev/msp077 PMID:19377059
-
(2009)
Mol Biol Evol
, vol.26
, pp. 1641-1650
-
-
Price, M.N.1
Dehal, P.S.2
Arkin, A.P.3
-
43
-
-
34548293679
-
Naive Bayesian classifier for rapid assignment of rRNA sequences into the new bacterial taxonomy
-
PMID:17586664
-
Wang Q, Garrity GM, Tiedje JM, Cole JR (2007) Naive Bayesian classifier for rapid assignment of rRNA sequences into the new bacterial taxonomy. Appl Environ Microbiol 73: 5261-5267. PMID:17586664
-
(2007)
Appl Environ Microbiol
, vol.73
, pp. 5261-5267
-
-
Wang, Q.1
Garrity, G.M.2
Tiedje, J.M.3
Cole, J.R.4
-
44
-
-
33748713890
-
UniFrac-an online tool for comparing microbial community diversity in a phylogenetic context
-
PMID: 16893466
-
Lozupone C, Hamady M, Knight R (2006) UniFrac-an online tool for comparing microbial community diversity in a phylogenetic context. BMC Bioinformatics 7: 371. PMID: 16893466
-
(2006)
BMC Bioinformatics
, vol.7
, pp. 371
-
-
Lozupone, C.1
Hamady, M.2
Knight, R.3
-
45
-
-
0034870192
-
Quantifying biodiversity: Procedures and pitfalls in the measurement and comparison of species richness
-
Gotelli NJ, Colwell RK (2001) Quantifying biodiversity: procedures and pitfalls in the measurement and comparison of species richness. Ecology Letters 4: 379-391.
-
(2001)
Ecology Letters
, vol.4
, pp. 379-391
-
-
Gotelli, N.J.1
Colwell, R.K.2
-
46
-
-
84906942533
-
Human oral viruses are personal, persistent and gender-consistent
-
Abeles SR, Robles-Sikisaka R, Ly M, Lum AG, Salzman J, Boehm TK, et al. (2014) Human oral viruses are personal, persistent and gender-consistent. ISME J 8: 1753-1767. doi:10.1038/ismej.2014.31PMID: 24646696
-
(2014)
ISME J
, vol.8
, pp. 1753-1767
-
-
Abeles, S.R.1
Robles-Sikisaka, R.2
Ly, M.3
Lum, A.G.4
Salzman, J.5
Boehm, T.K.6
-
47
-
-
84903975410
-
Altered oral viral ecology in association with periodontal disease
-
PMID: 24846382
-
Ly M, Abeles SR, Boehm TK, Robles-Sikisaka R, Naidu M, Santiago-Rodriguez T, et al. (2014) Altered oral viral ecology in association with periodontal disease. MBio 5: e01133-01114. doi: 10.1128/mBio.01133-14 PMID: 24846382
-
(2014)
MBio
, vol.5
, pp. e01133-01114
-
-
Ly, M.1
Abeles, S.R.2
Boehm, T.K.3
Robles-Sikisaka, R.4
Naidu, M.5
Santiago-Rodriguez, T.6
-
48
-
-
84903360551
-
Characterization of bacteriophage communities and CRISPR profiles from dental plaque
-
PMID: 24981669
-
Naidu M, Robles-Sikisaka R, Abeles SR, Boehm TK, Pride DT (2014) Characterization of bacteriophage communities and CRISPR profiles from dental plaque. BMC Microbiol 14: 175. doi: 10.1186/1471-2180-14-175 PMID: 24981669
-
(2014)
BMC Microbiol
, vol.14
, pp. 175
-
-
Naidu, M.1
Robles-Sikisaka, R.2
Abeles, S.R.3
Boehm, T.K.4
Pride, D.T.5
-
49
-
-
84883192222
-
Association between living environment and human oral viral ecology
-
PMID:23598790
-
Robles-Sikisaka R, Ly M, Boehm T, Naidu M, Salzman J, Pride DT (2013) Association between living environment and human oral viral ecology. ISME J 7: 1710-1724. doi: 10.1038/ismej.2013.63 PMID:23598790
-
(2013)
ISME J
, vol.7
, pp. 1710-1724
-
-
Robles-Sikisaka, R.1
Ly, M.2
Boehm, T.3
Naidu, M.4
Salzman, J.5
Pride, D.T.6
-
50
-
-
84903274696
-
Conservation of streptococcal CRISPRs on human skin and saliva
-
PMID: 24903519
-
Robles-Sikisaka R, Naidu M, Ly M, Salzman J, Abeles SR, Boehm TK, et al. (2014) Conservation of streptococcal CRISPRs on human skin and saliva. BMC Microbiol 14: 146. doi: 10.1186/1471-2180-14-146 PMID: 24903519
-
(2014)
BMC Microbiol
, vol.14
, pp. 146
-
-
Robles-Sikisaka, R.1
Naidu, M.2
Ly, M.3
Salzman, J.4
Abeles, S.R.5
Boehm, T.K.6
-
51
-
-
84927509899
-
The human urine virome in association with urinary tract infections
-
PMID: 25667584
-
Santiago-Rodriguez TM, Ly M, Bonilla N, Pride DT (2015) The human urine virome in association with urinary tract infections. Front Microbiol 6: 14. doi: 10.3389/fmicb.2015.00014 PMID: 25667584
-
(2015)
Front Microbiol
, vol.6
, pp. 14
-
-
Santiago-Rodriguez, T.M.1
Ly, M.2
Bonilla, N.3
Pride, D.T.4
-
52
-
-
72949091232
-
Bacterial community variation in human body habitats across space and time
-
PMID: 19892944
-
Costello EK, Lauber CL, Hamady M, Fierer N, Gordon JI, Knight R (2009) Bacterial community variation in human body habitats across space and time. Science 326: 1694-1697. doi:10.1126/science.1177486 PMID: 19892944
-
(2009)
Science
, vol.326
, pp. 1694-1697
-
-
Costello, E.K.1
Lauber, C.L.2
Hamady, M.3
Fierer, N.4
Gordon, J.I.5
Knight, R.6
-
53
-
-
84905041075
-
A highly abundant bacteriophage discovered in the unknown sequences of human faecal metagenomes
-
PMID: 25058116
-
Dutilh BE, Cassman N, McNair K, Sanchez SE, Silva GG, Boling L, et al. (2014) A highly abundant bacteriophage discovered in the unknown sequences of human faecal metagenomes. Nat Commun 5: 4498. doi: 10.1038/ncomms5498 PMID: 25058116
-
(2014)
Nat Commun
, vol.5
, pp. 4498
-
-
Dutilh, B.E.1
Cassman, N.2
McNair, K.3
Sanchez, S.E.4
Silva, G.G.5
Boling, L.6
-
54
-
-
0038781878
-
Unbiased whole-genome amplification directly from clinical samples
-
PMID: 12695328
-
Hosono S, Faruqi AF, Dean FB, Du Y, Sun Z, Wu X, et al. (2003) Unbiased whole-genome amplification directly from clinical samples. Genome Res 13: 954-964. PMID: 12695328
-
(2003)
Genome Res
, vol.13
, pp. 954-964
-
-
Hosono, S.1
Faruqi, A.F.2
Dean, F.B.3
Du, Y.4
Sun, Z.5
Wu, X.6
-
55
-
-
84862141704
-
Human gut microbiome viewed across age and geography
-
Yatsunenko T, Rey FE, Manary MJ, Trehan I, Dominguez-Bello MG, Contreras M, et al. (2012) Human gut microbiome viewed across age and geography. Nature 486: 222-227. doi:10.1038/nature11053PMID: 22699611
-
(2012)
Nature
, vol.486
, pp. 222-227
-
-
Yatsunenko, T.1
Rey, F.E.2
Manary, M.J.3
Trehan, I.4
Dominguez-Bello, M.G.5
Contreras, M.6
-
56
-
-
80053528043
-
The human gut virome: Inter-individual variation and dynamic response to diet
-
PMID: 21880779
-
Minot S, Sinha R, Chen J, Li H, Keilbaugh SA, Wu GD, et al. (2011) The human gut virome: inter-individual variation and dynamic response to diet. Genome Res 21: 1616-1625. doi:10.1101/gr.122705.111 PMID: 21880779
-
(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
-
57
-
-
84919835179
-
The human virome
-
Nelson K, editor. New York: Springer Science
-
Haynes Ma, R F (2011) The human virome. In: Nelson K, editor. Metagenomics of the human body. New York: Springer Science.
-
(2011)
Metagenomics of the Human Body
-
-
Haynes Ma, R.F.1
-
58
-
-
84912034784
-
Simulating distal gut mucosal and luminal communities using packed-column biofilm reactors and an in vitro chemostat model
-
PMID:25462016
-
McDonald JA, Fuentes S, Schroeter K, Heikamp-deJong I, Khursigara CM, de Vos WM, et al. (2015) Simulating distal gut mucosal and luminal communities using packed-column biofilm reactors and an in vitro chemostat model. J Microbiol Methods 108: 36-44. doi: 10.1016/j.mimet.2014.11.007 PMID:25462016
-
(2015)
J Microbiol Methods
, vol.108
, pp. 36-44
-
-
McDonald, J.A.1
Fuentes, S.2
Schroeter, K.3
Heikamp-DeJong, I.4
Khursigara, C.M.5
De Vos, W.M.6
-
59
-
-
84884168072
-
Evaluation of microbial community reproducibility, stability and composition in a human distal gut chemostat model
-
PMID: 23994646
-
McDonald JA, Schroeter K, Fuentes S, Heikamp-Dejong I, Khursigara CM, de Vos WM, et al. (2013) Evaluation of microbial community reproducibility, stability and composition in a human distal gut chemostat model. J Microbiol Methods 95: 167-174. doi: 10.1016/j.mimet.2013.08.008 PMID: 23994646
-
(2013)
J Microbiol Methods
, vol.95
, pp. 167-174
-
-
McDonald, J.A.1
Schroeter, K.2
Fuentes, S.3
Heikamp-Dejong, I.4
Khursigara, C.M.5
De Vos, W.M.6
-
60
-
-
47749126207
-
Coevolution drives temporal changes in fitness and diversity across environments in a bacteria-bacteriophage interaction
-
PMID: 18452575
-
Forde SE, Thompson JN, Holt RD, Bohannan BJ (2008) Coevolution drives temporal changes in fitness and diversity across environments in a bacteria-bacteriophage interaction. Evolution 62: 1830-1839. doi: 10.1111/j.1558-5646.2008.00411.x PMID: 18452575
-
(2008)
Evolution
, vol.62
, pp. 1830-1839
-
-
Forde, S.E.1
Thompson, J.N.2
Holt, R.D.3
Bohannan, B.J.4
|