-
1
-
-
84870829895
-
Referenceindependent comparative metagenomics using cross-assembly: CrAss
-
Dutilh BE, Schmieder R, Nulton J, Felts B, Salamon P, et al. (2012) Referenceindependent comparative metagenomics using cross-assembly: crAss. Bioinformatics 28: 3225-3231.
-
(2012)
Bioinformatics
, vol.28
, pp. 3225-3231
-
-
Dutilh, B.E.1
Schmieder, R.2
Nulton, J.3
Felts, B.4
Salamon, P.5
-
2
-
-
84869998312
-
Current opportunities and challenges in microbial metagenome analysis - A bioinformatic perspective
-
Teeling H, Glöckner FO (2012) Current opportunities and challenges in microbial metagenome analysis - a bioinformatic perspective. Brief Bioinform 13: 728-742.
-
(2012)
Brief Bioinform
, vol.13
, pp. 728-742
-
-
Teeling, H.1
Glöckner, F.O.2
-
3
-
-
78751527447
-
Networks of gene sharing among 329 proteobacterial genomes reveal differences in lateral gene transfer frequency at different phylogenetic depths
-
Kloesges T, Popa O, Martin W, Dagan T (2010) Networks of gene sharing among 329 proteobacterial genomes reveal differences in lateral gene transfer frequency at different phylogenetic depths. Mol Biol Evol 28: 1057-1074.
-
(2010)
Mol Biol Evol
, vol.28
, pp. 1057-1074
-
-
Kloesges, T.1
Popa, O.2
Martin, W.3
Dagan, T.4
-
4
-
-
83055186603
-
Ecology drives a global network of gene exchange connecting the human microbiome
-
Smillie CS, Smith MB, Friedman J, Cordero OX, David LA, et al. (2011) Ecology drives a global network of gene exchange connecting the human microbiome. Nature 480: 241-244.
-
(2011)
Nature
, vol.480
, pp. 241-244
-
-
Smillie, C.S.1
Smith, M.B.2
Friedman, J.3
Cordero, O.X.4
David, L.A.5
-
5
-
-
84865531061
-
The shared antibiotic resistome of soil bacteria and human pathogens
-
Forsberg KJ, Reyes A, Wang B, Selleck EM, Sommer MO, et al. (2012) The shared antibiotic resistome of soil bacteria and human pathogens. Science 337: 1107-1111.
-
(2012)
Science
, vol.337
, pp. 1107-1111
-
-
Forsberg, K.J.1
Reyes, A.2
Wang, B.3
Selleck, E.M.4
Sommer, M.O.5
-
6
-
-
79952422304
-
Quality control and preprocessing of metagenomic datasets
-
Schmieder R, Edwards R (2011) Quality control and preprocessing of metagenomic datasets. Bioinformatics 27: 863-86.
-
(2011)
Bioinformatics
, vol.27
, pp. 863-886
-
-
Schmieder, R.1
Edwards, R.2
-
7
-
-
77953727646
-
TagCleaner: Identification and removal of tag sequences from genomic and metagenomic datasets
-
Schmieder R, Lim YW, Rohwer F, Edwards R (2010) TagCleaner: Identification and removal of tag sequences from genomic and metagenomic datasets. BMC Bioinformatics 11: 341.
-
(2010)
BMC Bioinformatics
, vol.11
, pp. 341
-
-
Schmieder, R.1
Lim, Y.W.2
Rohwer, F.3
Edwards, R.4
-
8
-
-
53549118607
-
The metagenomics RAST server - A public resource for the automatic phylogenetic and functional analysis of metagenomes
-
Meyer F, Paarmann D, D'Souza M, Olson R, Glass EM, et al. (2008) The metagenomics RAST server - a public resource for the automatic phylogenetic and functional analysis of metagenomes. BMC Bioinformatics 9: 386.
-
(2008)
BMC Bioinformatics
, vol.9
, pp. 386
-
-
Meyer, F.1
Paarmann, D.2
D'Souza, M.3
Olson, R.4
Glass, E.M.5
-
10
-
-
80054911634
-
Metavir: A web server dedicated to virome analysis
-
Roux S, Faubladier M, Mahul A, Paulhe N, Bernard A, et al. (2011) Metavir: a web server dedicated to virome analysis. Bioinformatics 27: 3074-3075.
-
(2011)
Bioinformatics
, vol.27
, pp. 3074-3075
-
-
Roux, S.1
Faubladier, M.2
Mahul, A.3
Paulhe, N.4
Bernard, A.5
-
11
-
-
66249145772
-
Statistical methods for detecting differentially abundant features in clinical metagenomic samples
-
White JR, Nagarajan N, Pop M (2009) Statistical methods for detecting differentially abundant features in clinical metagenomic samples. PLOS Comput Biol 5: e1000352.
-
(2009)
PLOS Comput Biol
, vol.5
, pp. e1000352
-
-
White, J.R.1
Nagarajan, N.2
Pop, M.3
-
12
-
-
84865075440
-
ModuLand plug-in for Cytoscape: Determination of hierarchical layers of overlapping network modules and community centrality
-
Szalay-Beko M, Palotai R, Szappanos B, Kovács IA, Papp B, et al. (2012) ModuLand plug-in for Cytoscape: determination of hierarchical layers of overlapping network modules and community centrality. Bioinformatics 28: 2202-2204.
-
(2012)
Bioinformatics
, vol.28
, pp. 2202-2204
-
-
Szalay-Beko, M.1
Palotai, R.2
Szappanos, B.3
Kovács, I.A.4
Papp, B.5
-
13
-
-
84857357891
-
Rapidly expanding genetic diversity and host range of the Circoviridae viral family and other Rep encoding small circular ssDNA genomes
-
Delwart E, Li L (2012) Rapidly expanding genetic diversity and host range of the Circoviridae viral family and other Rep encoding small circular ssDNA genomes. Virus Res 164: 114-121.
-
(2012)
Virus Res
, vol.164
, pp. 114-121
-
-
Delwart, E.1
Li, L.2
-
14
-
-
79955894106
-
Microviridae goes temperate: Microvirus-related proviruses reside in the genomes of Bacteroidetes
-
Krupovic M, Forterre P (2011) Microviridae goes temperate: microvirus-related proviruses reside in the genomes of Bacteroidetes. PLOS One 10: e19893.
-
(2011)
PLOS One
, vol.10
, pp. e19893
-
-
Krupovic, M.1
Forterre, P.2
-
15
-
-
84892152977
-
Metagenomic and whole-genome analysis reveals new lineages of gokushoviruses and biogeographic separation in the sea
-
Labonté JM, Suttle CA (2013) Metagenomic and whole-genome analysis reveals new lineages of gokushoviruses and biogeographic separation in the sea. Front Microbiol 4: 404.
-
(2013)
Front Microbiol
, vol.4
, pp. 404
-
-
Labonté, J.M.1
Suttle, C.A.2
-
16
-
-
33751059692
-
The marine viromes of four oceanic regions
-
Angly FE, Felts B, Breitbart M, Salamon P, Edwards RA, et al. (2006) The marine viromes of four oceanic regions. PLOS Biol 4: e368.
-
(2006)
PLOS Biol
, vol.4
, pp. e368
-
-
Angly, F.E.1
Felts, B.2
Breitbart, M.3
Salamon, P.4
Edwards, R.A.5
-
17
-
-
77956275741
-
Bacterial acquisition in juveniles of several broadcast spawning coral species
-
Sharp KH, Ritchie KB, Schupp PJ, Ritson-Williams R, Paul VJ (2010) Bacterial acquisition in juveniles of several broadcast spawning coral species. PLOS One 5: e10898.
-
(2010)
PLOS One
, vol.5
, pp. e10898
-
-
Sharp, K.H.1
Ritchie, K.B.2
Schupp, P.J.3
Ritson-Williams, R.4
Paul, V.J.5
-
18
-
-
80052156440
-
Bacterial community assembly based on functional genes rather than species
-
Burke C, Steinberg P, Rusch D, Kjelleberg S, Thomas T (2011) Bacterial community assembly based on functional genes rather than species. Proc Natl Acad Sci USA 108: 14288-93.
-
(2011)
Proc Natl Acad Sci USA
, vol.108
, pp. 14288-14293
-
-
Burke, C.1
Steinberg, P.2
Rusch, D.3
Kjelleberg, S.4
Thomas, T.5
-
19
-
-
84915826443
-
Bacterial communities and speciesspecific associations with the mucus of Brazilian coral species
-
Carlos C, Torres TT, Ottoboni LM (2013) Bacterial communities and speciesspecific associations with the mucus of Brazilian coral species. Sci Rep 2013: 31624.
-
(2013)
Sci Rep
, vol.2013
, pp. 31624
-
-
Carlos, C.1
Torres, T.T.2
Ottoboni, L.M.3
-
20
-
-
84857711499
-
Spatial scales of bacterial diversity in cold-water coral reef ecosystems
-
Schöttner S, Wild C, Hoffmann F, Boetius A, Ramette A (2012) Spatial scales of bacterial diversity in cold-water coral reef ecosystems. PLOS One 7: e32093.
-
(2012)
PLOS One
, vol.7
, pp. e32093
-
-
Schöttner, S.1
Wild, C.2
Hoffmann, F.3
Boetius, A.4
Ramette, A.5
-
21
-
-
67549142694
-
Inter- and intra-habitat bacterial diversity associated with cold-water corals
-
Schöttner S, Hoffmann F, Wild C, Rapp HT, Boetius A, et al. (2009) Inter- and intra-habitat bacterial diversity associated with cold-water corals. ISME J 3: 156-759.
-
(2009)
ISME J
, vol.3
, pp. 156-759
-
-
Schöttner, S.1
Hoffmann, F.2
Wild, C.3
Rapp, H.T.4
Boetius, A.5
-
22
-
-
84876927827
-
Metagenomic analysis of healthy and white plague-affected Mussismilia braziliensis corals
-
Garcia GD, Gregoracci GB, Santos Ede O, Meirelles PM, Silva GG, et al. (2013) Metagenomic analysis of healthy and white plague-affected Mussismilia braziliensis corals. Microb Ecol 65: 1076-1086.
-
(2013)
Microb Ecol
, vol.65
, pp. 1076-1086
-
-
Garcia, G.D.1
Gregoracci, G.B.2
Santos Ede, O.3
Meirelles, P.M.4
Silva, G.G.5
-
23
-
-
68249143124
-
Metagenomic analysis of stressed coral holobionts
-
Vega Thurber R, Willner-Hall D, Rodriguez-Mueller B, Desnues C, Edwards RA, et al. (2009) Metagenomic analysis of stressed coral holobionts. Environ Microbiol 11: 2148-2163.
-
(2009)
Environ Microbiol
, vol.11
, pp. 2148-2163
-
-
Vega Thurber, R.1
Willner-Hall, D.2
Rodriguez-Mueller, B.3
Desnues, C.4
Edwards, R.A.5
-
24
-
-
35148876440
-
Metagenomic analysis of the microbial community associated with the coral Porites astreoides
-
Wegley L, Edwards R, Rodriguez-Brito B, Liu H, Rohwer F (2007) Metagenomic analysis of the microbial community associated with the coral Porites astreoides. Environ Microbiol 9: 2707-2719.
-
(2007)
Environ Microbiol
, vol.9
, pp. 2707-2719
-
-
Wegley, L.1
Edwards, R.2
Rodriguez-Brito, B.3
Liu, H.4
Rohwer, F.5
-
25
-
-
0024401931
-
Characterization of a purF operon mutation which affects colicin v production
-
Fath MJ, Mahanty HK, Kolter R (1989) Characterization of a purF operon mutation which affects colicin V production. J Bacteriol 171:3158-3161.
-
(1989)
J Bacteriol
, vol.171
, pp. 3158-3161
-
-
Fath, M.J.1
Mahanty, H.K.2
Kolter, R.3
-
26
-
-
84455190878
-
A genomic reappraisal of symbiotic function in the aphid/Buchnera symbiosis: Reduced transporter sets and variable membrane organisations
-
Charles H, Balmand S, Lamelas A, Cottret L, Pérez-Brocal V, et al. (2011) A genomic reappraisal of symbiotic function in the aphid/Buchnera symbiosis: reduced transporter sets and variable membrane organisations. PLOS One 6: e29096.
-
(2011)
PLOS One
, vol.6
, pp. e29096
-
-
Charles, H.1
Balmand, S.2
Lamelas, A.3
Cottret, L.4
Pérez-Brocal, V.5
-
27
-
-
84858860295
-
Physiological homogeneity among the endosymbionts of Riftia pachyptila and Tevnia jerichonana revealed by proteogenomics
-
Gardebrecht A, Markert S, Sievert SM, Felbeck H, Thürmer A, et al. (2012) Physiological homogeneity among the endosymbionts of Riftia pachyptila and Tevnia jerichonana revealed by proteogenomics. ISME J 6: 766-776.
-
(2012)
ISME J
, vol.6
, pp. 766-776
-
-
Gardebrecht, A.1
Markert, S.2
Sievert, S.M.3
Felbeck, H.4
Thürmer, A.5
-
28
-
-
84869137864
-
Transposon mutagenesis identifies uropathogenic Escherichia coli biofilm factors
-
Hadjifrangiskou M, Gu AP, Pinkner JS, Kostakioti M, Zhang EW, et al. (2012) Transposon mutagenesis identifies uropathogenic Escherichia coli biofilm factors. J Bacteriol 2012, 194: 6195-6205.
-
(2012)
J Bacteriol 2012
, vol.194
, pp. 6195-6205
-
-
Hadjifrangiskou, M.1
Gu, A.P.2
Pinkner, J.S.3
Kostakioti, M.4
Zhang, E.W.5
-
29
-
-
31144449168
-
Structures and mechanisms of glycosyltransferases
-
Breton C (2006) Structures and mechanisms of glycosyltransferases. Glycobiology 16: 29-37.
-
(2006)
Glycobiology
, vol.16
, pp. 29-37
-
-
Breton, C.1
-
30
-
-
0037387036
-
Bacterial glycoproteins: Functions, biosynthesis and applications
-
Upreti RK, Kumar M, Shankar V (2003) Bacterial glycoproteins: functions, biosynthesis and applications. Proteomics 3: 363-379.
-
(2003)
Proteomics
, vol.3
, pp. 363-379
-
-
Upreti, R.K.1
Kumar, M.2
Shankar, V.3
-
31
-
-
23844545192
-
A novel conserved cluster of genes promotes symbiotic colonization and sigma-dependent biofilm formation by Vibrio fischeri
-
Yip ES, Grublesky BT, Hussa EA, Visick KL (2005) A novel conserved cluster of genes promotes symbiotic colonization and sigma-dependent biofilm formation by Vibrio fischeri. Mol Microbiol 57: 1485-1498.
-
(2005)
Mol Microbiol
, vol.57
, pp. 1485-1498
-
-
Yip, E.S.1
Grublesky, B.T.2
Hussa, E.A.3
Visick, K.L.4
-
32
-
-
84859474080
-
Insights into the bovine rumen plasmidome
-
Brown Kav A, Sasson G, Jami E, Doron-Faigenboim A, Benhar I, et al. (2012) Insights into the bovine rumen plasmidome. Proc Natl Acad Aci USA 109: 5452-5457.
-
(2012)
Proc Natl Acad Aci USA
, vol.109
, pp. 5452-5457
-
-
Brown Kav, A.1
Sasson, G.2
Jami, E.3
Doron-Faigenboim, A.4
Benhar, I.5
-
33
-
-
60849116153
-
Protein secretion systems in bacterialhost associations, and their description in the Gene Ontology
-
Tseng TT, Tyler BM, Setubal JC (2009) Protein secretion systems in bacterialhost associations, and their description in the Gene Ontology. BMC Microbiol 9: S2.
-
(2009)
BMC Microbiol
, vol.9
, pp. S2
-
-
Tseng, T.T.1
Tyler, B.M.2
Setubal, J.C.3
-
34
-
-
0141430076
-
Bacterial type III secretion systems are ancient and evolved by multiple horizontal-transfer events
-
Gophna U, Ron EZ, Graur D (2003) Bacterial type III secretion systems are ancient and evolved by multiple horizontal-transfer events. Gene 312: 151-63.
-
(2003)
Gene
, vol.312
, pp. 151-163
-
-
Gophna, U.1
Ron, E.Z.2
Graur, D.3
-
35
-
-
84873324025
-
Distribution and diversity of bacterial secretion systems across metagenomic datasets
-
Barret M, Egan F, O'Gara F (2013) Distribution and diversity of bacterial secretion systems across metagenomic datasets. Environ Microbiol 5: 117-126.
-
(2013)
Environ Microbiol
, vol.5
, pp. 117-126
-
-
Barret, M.1
Egan, F.2
O'Gara, F.3
-
36
-
-
84880045850
-
The genus Pseudovibrio contains metabolically versatile bacteria adapted for symbiosis
-
Bondarev V, Richter M, Romano S, Piel J, Schwedt A, et al. (2013) The genus Pseudovibrio contains metabolically versatile bacteria adapted for symbiosis. Environ Microbiol 15: 2095-2113.
-
(2013)
Environ Microbiol
, vol.15
, pp. 2095-2113
-
-
Bondarev, V.1
Richter, M.2
Romano, S.3
Piel, J.4
Schwedt, A.5
-
37
-
-
84863611362
-
Taxonomic and functional microbial signatures of the endemic marine sponge Arenosclera brasiliensis
-
Trindade-Silva AE, Rua C, Silva GG, Dutilh BE, Moreira AP, et al. (2012) Taxonomic and functional microbial signatures of the endemic marine sponge Arenosclera brasiliensis. PLOS One 7: e39905.
-
(2012)
PLOS One
, vol.7
, pp. e39905
-
-
Trindade-Silva, A.E.1
Rua, C.2
Silva, G.G.3
Dutilh, B.E.4
Moreira, A.P.5
-
38
-
-
58749112734
-
A core gut microbiome in obese and lean twins
-
Turnbaugh PJ, Hamady M, Yatsunenko T, Cantarel BL, Duncan A, et al. (2009) A core gut microbiome in obese and lean twins. Nature 457: 480-484.
-
(2009)
Nature
, vol.457
, pp. 480-484
-
-
Turnbaugh, P.J.1
Hamady, M.2
Yatsunenko, T.3
Cantarel, B.L.4
Duncan, A.5
-
39
-
-
51449108782
-
Comparative metagenomics reveals host specific metavirulomes and horizontal gene transfer elements in the chicken cecum microbiome
-
Qu A, Brulc JM, Wilson MK, Law BF, Theoret JR, et al. (2008) Comparative metagenomics reveals host specific metavirulomes and horizontal gene transfer elements in the chicken cecum microbiome. PLoS One 3: e2945.
-
(2008)
PLoS One
, vol.3
, pp. e2945
-
-
Qu, A.1
Brulc, J.M.2
Wilson, M.K.3
Law, B.F.4
Theoret, J.R.5
-
40
-
-
84858406041
-
Large-scale analysis of plasmid relationships through gene-sharing networks
-
Tamminen M, Virta M, Fani R, Fondi M (2011) Large-scale analysis of plasmid relationships through gene-sharing networks. Mol Biol Evol 29: 1225-1240.
-
(2011)
Mol Biol Evol
, vol.29
, pp. 1225-1240
-
-
Tamminen, M.1
Virta, M.2
Fani, R.3
Fondi, M.4
-
41
-
-
0346186108
-
Rates of spread of marine pathogens
-
McCallum H, Harvell D, Dobson A (2003) Rates of spread of marine pathogens. Ecol Lett 6: 1062-1067.
-
(2003)
Ecol Lett
, vol.6
, pp. 1062-1067
-
-
McCallum, H.1
Harvell, D.2
Dobson, A.3
-
42
-
-
66149151286
-
Viruses manipulate the marine environment
-
Rohwer F, Thurber RV (2009) Viruses manipulate the marine environment. Nature 459: 207-212.
-
(2009)
Nature
, vol.459
, pp. 207-212
-
-
Rohwer, F.1
Thurber, R.V.2
-
43
-
-
84878305117
-
Potential impact of environmental bacteriophages in spreading antibiotic resistance genes
-
Muniesa M, Colomer-Lluch M, Jofre J (2013) Potential impact of environmental bacteriophages in spreading antibiotic resistance genes. Future Microbiol 8: 739-751.
-
(2013)
Future Microbiol
, vol.8
, pp. 739-751
-
-
Muniesa, M.1
Colomer-Lluch, M.2
Jofre, J.3
-
44
-
-
3142570537
-
Global distribution of nearly identical phage-encoded DNA sequences
-
Breitbart M, Miyake JH, Rohwer F (2004) Global distribution of nearly identical phage-encoded DNA sequences. FEMS Microbiol Lett 236: 249-256.
-
(2004)
FEMS Microbiol Lett
, vol.236
, pp. 249-256
-
-
Breitbart, M.1
Miyake, J.H.2
Rohwer, F.3
-
45
-
-
12244252269
-
Nearly identical bacteriophage structural gene sequences are widely distributed in both marine and freshwater environments
-
Short CM, Suttle CA (2005) Nearly identical bacteriophage structural gene sequences are widely distributed in both marine and freshwater environments. Appl Environ Microbiol 71: 480-486.
-
(2005)
Appl Environ Microbiol
, vol.71
, pp. 480-486
-
-
Short, C.M.1
Suttle, C.A.2
|