-
1
-
-
79251587455
-
Metagenomic discovery of biomass-degrading genes and genomes from cow rumen
-
Hess, M. et al. Metagenomic discovery of biomass-degrading genes and genomes from cow rumen. Science (80-.). 331, 463-467 (2011).
-
(2011)
Science (80-.).
, vol.331
, pp. 463-467
-
-
Hess, M.1
-
2
-
-
84944894304
-
The rumen microbial metagenome associated with high methane production in cattle
-
Wallace, R. J. et al. The rumen microbial metagenome associated with high methane production in cattle. BMC Genom. 16, 839 (2015).
-
(2015)
BMC Genom.
, vol.16
, pp. 839
-
-
Wallace, R.J.1
-
3
-
-
84959914986
-
Bovine host genetic variation influences rumen microbial methane production with best selection criterion for low methane emitting and efficiently feed converting hosts based on metagenomic gene abundance
-
Roehe, R. et al. Bovine host genetic variation influences rumen microbial methane production with best selection criterion for low methane emitting and efficiently feed converting hosts based on metagenomic gene abundance. PLoS Genet. 12, e1005846 (2016).
-
(2016)
PLoS Genet.
, vol.12
, pp. e1005846
-
-
Roehe, R.1
-
4
-
-
85017132911
-
A review of bioinformatics tools for bio-prospecting from metagenomic sequence data
-
Roumpeka, D. D., Wallace, R. J., Escalettes, F., Fotheringham, I. & Watson, M. A review of bioinformatics tools for bio-prospecting from metagenomic sequence data. Front. Genet. 8, 23 (2017).
-
(2017)
Front. Genet.
, vol.8
, pp. 23
-
-
Roumpeka, D.D.1
Wallace, R.J.2
Escalettes, F.3
Fotheringham, I.4
Watson, M.5
-
5
-
-
1542377296
-
Community structure and metabolism through reconstruction of microbial genomes from the environment
-
Tyson, G. W. et al. Community structure and metabolism through reconstruction of microbial genomes from the environment. Nature 428, 37-43 (2004).
-
(2004)
Nature
, vol.428
, pp. 37-43
-
-
Tyson, G.W.1
-
6
-
-
84905387976
-
Methane yield phenotypes linked to differential gene expression in the sheep rumen microbiome
-
Shi, W. et al. Methane yield phenotypes linked to differential gene expression in the sheep rumen microbiome. Genome Res. 24, 1517-1525 (2014).
-
(2014)
Genome Res.
, vol.24
, pp. 1517-1525
-
-
Shi, W.1
-
7
-
-
85031798353
-
Ninety-nine de novo assembled genomes from the moose (Alces alces) rumen microbiome provide new insights into microbial plant biomass degradation
-
Svartström, O. et al. Ninety-nine de novo assembled genomes from the moose (Alces alces) rumen microbiome provide new insights into microbial plant biomass degradation. ISME J. https://doi.org/10.1038/ismej.2017.108 (2017).
-
(2017)
ISME J
-
-
Svartström, O.1
-
8
-
-
85029026923
-
Recovery of nearly 8, 000 metagenome-assembled genomes substantially expands the tree of life
-
Parks, D. H. et al. Recovery of nearly 8, 000 metagenome-assembled genomes substantially expands the tree of life. Nat. Microbiol. https://doi.org/10.1038/s41564-017-0012-7 (2017).
-
(2017)
Nat. Microbiol
-
-
Parks, D.H.1
-
9
-
-
84904548768
-
Species-level deconvolution of metagenome assemblies with Hi-C-based contact probability maps
-
Burton, J. N., Liachko, I., Dunham, M. J. & Shendure, J. Species-level deconvolution of metagenome assemblies with Hi-C-based contact probability maps. G3 Genes Genomes Genet. 4, 1339-1346 (2014).
-
(2014)
G3 Genes Genomes Genet.
, vol.4
, pp. 1339-1346
-
-
Burton, J.N.1
Liachko, I.2
Dunham, M.J.3
Shendure, J.4
-
10
-
-
84903835646
-
Strain-and plasmid-level deconvolution of a synthetic metagenome by sequencing proximity ligation products
-
Beitel, C. W. et al. Strain-and plasmid-level deconvolution of a synthetic metagenome by sequencing proximity ligation products. PeerJ 2, e415 (2014).
-
(2014)
PeerJ
, vol.2
, pp. e415
-
-
Beitel, C.W.1
-
11
-
-
85006217723
-
Insights into the role of Erysipelotrichaceae in the human host
-
Kaakoush, N. O. Insights into the role of Erysipelotrichaceae in the human host. Front. Cell. Infect. Microbiol. 5, 84 (2015).
-
(2015)
Front. Cell. Infect. Microbiol.
, vol.5
, pp. 84
-
-
Kaakoush, N.O.1
-
12
-
-
85027264358
-
Minimum information about a single amplified genome (MISAG) and a metagenome-assembled genome (MIMAG) of bacteria and archaea
-
Bowers, R. M. et al. Minimum information about a single amplified genome (MISAG) and a metagenome-assembled genome (MIMAG) of bacteria and archaea. Nat. Biotechnol. 35, 725-731 (2017).
-
(2017)
Nat. Biotechnol.
, vol.35
, pp. 725-731
-
-
Bowers, R.M.1
-
14
-
-
85016153986
-
UniProt: The universal protein knowledgebase
-
The UniProt Consortium
-
The UniProt Consortium. UniProt: the universal protein knowledgebase. Nucleic Acids Res. 45, D158-D169 (2017).
-
(2017)
Nucleic Acids Res.
, vol.45
, pp. D158-D169
-
-
-
15
-
-
0021064632
-
Bacillus spp. in the rumen ecosystem. Hemicellulose depolymerases and glycoside hydrolases of Bacillus spp. and rumen isolates grown under anaerobic conditions
-
Williams, A. G. & Withers, S. E. Bacillus spp. in the rumen ecosystem. Hemicellulose depolymerases and glycoside hydrolases of Bacillus spp. and rumen isolates grown under anaerobic conditions. J. Appl. Bacteriol. 55, 283-292 (1983).
-
(1983)
J. Appl. Bacteriol.
, vol.55
, pp. 283-292
-
-
Williams, A.G.1
Withers, S.E.2
-
16
-
-
80053636982
-
Reclassification of Lactobacillus catenaformis (Eggerth 1935) Moore and Holdeman 1970 and Lactobacillus vitulinus Sharpe et al. 1973 as Eggerthia catenaformis gen. nov., comb. nov. and Kandleria vitulina gen. nov., comb. nov., respectively
-
Salvetti, E. et al. Reclassification of Lactobacillus catenaformis (Eggerth 1935) Moore and Holdeman 1970 and Lactobacillus vitulinus Sharpe et al. 1973 as Eggerthia catenaformis gen. nov., comb. nov. and Kandleria vitulina gen. nov., comb. nov., respectively. Int. J. Syst. Evol. Microbiol. 61, 2520-2524 (2011).
-
(2011)
Int. J. Syst. Evol. Microbiol.
, vol.61
, pp. 2520-2524
-
-
Salvetti, E.1
-
17
-
-
84922032940
-
Prepartum and postpartum rumen fluid microbiomes: Characterization and correlation with production traits in dairy cows
-
Lima, F. S. et al. Prepartum and postpartum rumen fluid microbiomes: characterization and correlation with production traits in dairy cows. Appl. Environ. Microbiol. 81, 1327-1337 (2015).
-
(2015)
Appl. Environ. Microbiol.
, vol.81
, pp. 1327-1337
-
-
Lima, F.S.1
-
18
-
-
84995791150
-
Rumen metagenome and metatranscriptome analyses of low methane yield sheep reveals a Sharpea-enriched microbiome characterised by lactic acid formation and utilisation
-
Kamke, J. et al. Rumen metagenome and metatranscriptome analyses of low methane yield sheep reveals a Sharpea-enriched microbiome characterised by lactic acid formation and utilisation. Microbiome 4, 56 (2016).
-
(2016)
Microbiome
, vol.4
, pp. 56
-
-
Kamke, J.1
-
19
-
-
0028239570
-
Emendation of the description of Acidaminococcus fermentans, a trans-aconitate-and Cit rat e-oxidizing bacterium
-
Cook, G. M., Rainey, F. A., Chen, G., Stackebfulndt, E. & Russell, J. B. Emendation of the description of Acidaminococcus fermentans, a trans-aconitate-and Cit rat e-oxidizing bacterium. Int. J. Syst. Bacteriol. 44, 576-578 (1994).
-
(1994)
Int. J. Syst. Bacteriol.
, vol.44
, pp. 576-578
-
-
Cook, G.M.1
Rainey, F.A.2
Chen, G.3
Stackebfulndt, E.4
Russell, J.B.5
-
20
-
-
0028263531
-
Ability of Acidaminococcus fermentans to oxidize trans-aconitate and decrease the accumulation of tricarballylate, a toxic end product of ruminal fermentation
-
Cook, G. M., Wells, J. E. & Russell, J. B. Ability of Acidaminococcus fermentans to oxidize trans-aconitate and decrease the accumulation of tricarballylate, a toxic end product of ruminal fermentation. Appl. Environ. Microbiol. 60, 2533-2537 (1994).
-
(1994)
Appl. Environ. Microbiol.
, vol.60
, pp. 2533-2537
-
-
Cook, G.M.1
Wells, J.E.2
Russell, J.B.3
-
21
-
-
0001016571
-
Properties of a fatty acid forming organism isolated from the rumen of sheep
-
Elsden, S. R., Gilchrist, F. M., Lewis, D. & Volcani, B. E. Properties of a fatty acid forming organism isolated from the rumen of sheep. J. Bacteriol. 72, 681-689 (1956).
-
(1956)
J. Bacteriol.
, vol.72
, pp. 681-689
-
-
Elsden, S.R.1
Gilchrist, F.M.2
Lewis, D.3
Volcani, B.E.4
-
22
-
-
79956273780
-
Rumen pH and fermentation characteristics in dairy cows supplemented with Megasphaera elsdeniiNCIMB 41125 in early lactation
-
Aikman, P. C., Henning, P. H., Humphries, D. J. & Horn, C. H. Rumen pH and fermentation characteristics in dairy cows supplemented with Megasphaera elsdeniiNCIMB 41125 in early lactation. J. Dairy Sci. 94, 2840-2849 (2011).
-
(2011)
J. Dairy Sci.
, vol.94
, pp. 2840-2849
-
-
Aikman, P.C.1
Henning, P.H.2
Humphries, D.J.3
Horn, C.H.4
-
23
-
-
0026057070
-
Bifidobacterium ruminantium sp. nov. and Bifidobacterium merycicum sp. nov. from the rumens of cattle
-
Biavati, B. & Mattarelli, P. Bifidobacterium ruminantium sp. nov. and Bifidobacterium merycicum sp. nov. from the rumens of cattle. Int. J. Syst. Bacteriol. 41, 163-168 (1991).
-
(1991)
Int. J. Syst. Bacteriol.
, vol.41
, pp. 163-168
-
-
Biavati, B.1
Mattarelli, P.2
-
24
-
-
0004271150
-
-
Springer, Netherlands
-
Stewart, C. S., Flint, H. J. & Bryant, M. P. The Rumen Microbial Ecosystem 10-72 (Springer, Netherlands, 1997).
-
(1997)
The Rumen Microbial Ecosystem
, pp. 10-72
-
-
Stewart, C.S.1
Flint, H.J.2
Bryant, M.P.3
-
25
-
-
44249101121
-
The characterization of lactic acid producing bacteria from the rumen of dairy cattle grazing on improved pasture supplemented with wheat and barley grain
-
Hernandez, J. D., Scott, P. T., Shephard, R. W. & Al Jassim, R. A. M. The characterization of lactic acid producing bacteria from the rumen of dairy cattle grazing on improved pasture supplemented with wheat and barley grain. J. Appl. Microbiol. 104, 1754-1763 (2008).
-
(2008)
J. Appl. Microbiol.
, vol.104
, pp. 1754-1763
-
-
Hernandez, J.D.1
Scott, P.T.2
Shephard, R.W.3
Al Jassim, R.A.M.4
-
26
-
-
0842266507
-
Regulation of fermentation in a ruminal bacterium, Streptococcus bovis, with special reference to rumen acidosis
-
Asanuma, N. & Hino, T. Regulation of fermentation in a ruminal bacterium, Streptococcus bovis, with special reference to rumen acidosis. Anim. Sci. J. 73, 313-325 (2002).
-
(2002)
Anim. Sci. J.
, vol.73
, pp. 313-325
-
-
Asanuma, N.1
Hino, T.2
-
27
-
-
33947135278
-
Genome sequence and analysis of the soil cellulolytic actinomycete Thermobifida fusca YX
-
Lykidis, A. et al. Genome sequence and analysis of the soil cellulolytic actinomycete Thermobifida fusca YX. J. Bacteriol. 189, 2477-2486 (2007).
-
(2007)
J. Bacteriol.
, vol.189
, pp. 2477-2486
-
-
Lykidis, A.1
-
28
-
-
85016747721
-
Investigation and manipulation of metabolically active methanogen community composition during rumen development in black goats
-
Wang, Z. et al. Investigation and manipulation of metabolically active methanogen community composition during rumen development in black goats. Sci. Rep. 7, 422 (2017).
-
(2017)
Sci. Rep.
, vol.7
, pp. 422
-
-
Wang, Z.1
-
29
-
-
77952524936
-
The genome sequence of the rumen methanogen Methanobrevibacter ruminantium reveals new possibilities for controlling ruminant methane emissions
-
Leahy, S. C. et al The genome sequence of the rumen methanogen Methanobrevibacter ruminantium reveals new possibilities for controlling ruminant methane emissions. PLoS ONE 5, e8926 (2010).
-
(2010)
PLoS ONE
, vol.5
, pp. e8926
-
-
Leahy, S.C.1
-
30
-
-
33947319665
-
Methanobrevibacter millerae sp. nov. and Methanobrevibacter olleyae sp. nov., methanogens from the ovine and bovine rumen that can utilize formate for growth
-
Rea, S., Bowman, J. P., Popovski, S., Pimm, C. & Wright, A.-D. G. Methanobrevibacter millerae sp. nov. and Methanobrevibacter olleyae sp. nov., methanogens from the ovine and bovine rumen that can utilize formate for growth. Int. J. Syst. Evol. Microbiol. 57, 450-456 (2007).
-
(2007)
Int. J. Syst. Evol. Microbiol.
, vol.57
, pp. 450-456
-
-
Rea, S.1
Bowman, J.P.2
Popovski, S.3
Pimm, C.4
Wright, A.D.G.5
-
31
-
-
84887065544
-
Methanobrevibacter boviskoreani sp. nov., isolated from the rumen of Korean native cattle
-
Lee, J.-H. et al. Methanobrevibacter boviskoreani sp. nov., isolated from the rumen of Korean native cattle. Int. J. Syst. Evol. Microbiol. 63, 4196-4201 (2013).
-
(2013)
Int. J. Syst. Evol. Microbiol.
, vol.63
, pp. 4196-4201
-
-
Lee, J.H.1
-
32
-
-
84870675165
-
Genome sequence of 'Candidatus Methanomethylophilus alvus' Mx1201, a methanogenic archaeon from the human gut belonging to a seventh order of methanogens
-
Borrel, G. et al. Genome sequence of 'Candidatus Methanomethylophilus alvus' Mx1201, a methanogenic archaeon from the human gut belonging to a seventh order of methanogens. J. Bacteriol. 194, 6944-6945 (2012).
-
(2012)
J. Bacteriol.
, vol.194
, pp. 6944-6945
-
-
Borrel, G.1
-
33
-
-
84961912310
-
Differences down-under: Alcohol-fueled methanogenesis by archaea present in Australian macropodids
-
Hoedt, E. C. et al. Differences down-under: alcohol-fueled methanogenesis by archaea present in Australian macropodids. ISME J. 10, 2376-2388 (2016).
-
(2016)
ISME J.
, vol.10
, pp. 2376-2388
-
-
Hoedt, E.C.1
-
34
-
-
30744456055
-
The genome sequence of Methanosphaera stadtmanae reveals why this human intestinal archaeon is restricted to methanol and H2 for methane formation and ATP synthesis
-
Fricke, W. F. et al. The genome sequence of Methanosphaera stadtmanae reveals why this human intestinal archaeon is restricted to methanol and H2 for methane formation and ATP synthesis. J. Bacteriol. 188, 642-658 (2006).
-
(2006)
J. Bacteriol.
, vol.188
, pp. 642-658
-
-
Fricke, W.F.1
-
35
-
-
84891763855
-
The carbohydrate-active enzymes database (CAZy) in 2013
-
Lombard, V., Golaconda Ramulu, H., Drula, E., Coutinho, P. M. & Henrissat, B. The carbohydrate-active enzymes database (CAZy) in 2013. Nucleic Acids Res. 42, D490-D495 (2014).
-
(2014)
Nucleic Acids Res.
, vol.42
, pp. D490-D495
-
-
Lombard, V.1
Golaconda Ramulu, H.2
Drula, E.3
Coutinho, P.M.4
Henrissat, B.5
-
36
-
-
84864442502
-
DbCAN: A web resource for automated carbohydrate-active enzyme annotation
-
Yin, Y. et al. dbCAN: a web resource for automated carbohydrate-active enzyme annotation. Nucleic Acids Res. 40, W445-W451 (2012).
-
(2012)
Nucleic Acids Res.
, vol.40
, pp. W445-W451
-
-
Yin, Y.1
-
37
-
-
84862503319
-
The M5nr: A novel non-redundant database containing protein sequences and annotations from multiple sources and associated tools
-
Wilke, A. et al. The M5nr: a novel non-redundant database containing protein sequences and annotations from multiple sources and associated tools. BMC Bioinform. 13, 141 (2012).
-
(2012)
BMC Bioinform.
, vol.13
, pp. 141
-
-
Wilke, A.1
-
38
-
-
84891782659
-
Pfam: The protein families database
-
Finn, R. D. et al. Pfam: the protein families database. Nucleic Acids Res. 42, D222-D230 (2014).
-
(2014)
Nucleic Acids Res.
, vol.42
, pp. D222-D230
-
-
Finn, R.D.1
-
39
-
-
0027984011
-
The cellulosome-a treasure-trove for biotechnology
-
Bayer, E. A., Morag, E. & Lamed, R. The cellulosome-a treasure-trove for biotechnology. Trends Biotechnol. 12, 379-386 (1994).
-
(1994)
Trends Biotechnol.
, vol.12
, pp. 379-386
-
-
Bayer, E.A.1
Morag, E.2
Lamed, R.3
-
40
-
-
0035108208
-
Cellulosomal scaffoldin-like proteins from Ruminococcus flavefaciens
-
Ding, S. Y. et al. Cellulosomal scaffoldin-like proteins from Ruminococcus flavefaciens. J. Bacteriol. 183, 1945-1953 (2001).
-
(2001)
J. Bacteriol.
, vol.183
, pp. 1945-1953
-
-
Ding, S.Y.1
-
41
-
-
0035856590
-
Development and use of competitive PCR assays for the rumen cellulolytic bacteria: Fibrobacter succinogenes, Ruminococcus albus and Ruminococcus flavefaciens
-
Koike, S. et al. Development and use of competitive PCR assays for the rumen cellulolytic bacteria: Fibrobacter succinogenes, Ruminococcus albus and Ruminococcus flavefaciens. FEMS Microbiol. Lett. 204, 361-366 (2001).
-
(2001)
FEMS Microbiol. Lett.
, vol.204
, pp. 361-366
-
-
Koike, S.1
-
42
-
-
33947276676
-
Localization of ruminal cellulolytic bacteria on plant fibrous materials as determined by fluorescence in situ hybridization and real-time PCR
-
Shinkai, T. & Kobayashi, Y. Localization of ruminal cellulolytic bacteria on plant fibrous materials as determined by fluorescence in situ hybridization and real-time PCR. Appl. Environ. Microbiol. 73, 1646-1652 (2007).
-
(2007)
Appl. Environ. Microbiol.
, vol.73
, pp. 1646-1652
-
-
Shinkai, T.1
Kobayashi, Y.2
-
43
-
-
33846015876
-
Functional genomic and metabolic studies of the adaptations of a prominent adult human gut symbiont, Bacteroides thetaiotaomicron, to the suckling period
-
Bjursell, M. K., Martens, E. C. & Gordon, J. I. Functional genomic and metabolic studies of the adaptations of a prominent adult human gut symbiont, Bacteroides thetaiotaomicron, to the suckling period. J. Biol. Chem. 281, 36269-36279 (2006).
-
(2006)
J. Biol. Chem.
, vol.281
, pp. 36269-36279
-
-
Bjursell, M.K.1
Martens, E.C.2
Gordon, J.I.3
-
44
-
-
84928985213
-
Automatic prediction of polysaccharide utilization loci in Bacteroidetes species
-
Terrapon, N., Lombard, V., Gilbert, H. J. & Henrissat, B. Automatic prediction of polysaccharide utilization loci in Bacteroidetes species. Bioinformatics 31, 647-655 (2015).
-
(2015)
Bioinformatics
, vol.31
, pp. 647-655
-
-
Terrapon, N.1
Lombard, V.2
Gilbert, H.J.3
Henrissat, B.4
-
45
-
-
26244459142
-
Prevotella multisaccharivorax sp. nov., isolated from human subgingival plaque
-
Sakamoto, M., Umeda, M., Ishikawa, I. & Benno, Y. Prevotella multisaccharivorax sp. nov., isolated from human subgingival plaque. Int. J. Syst. Evol. Microbiol. 55, 1839-1843 (2005).
-
(2005)
Int. J. Syst. Evol. Microbiol.
, vol.55
, pp. 1839-1843
-
-
Sakamoto, M.1
Umeda, M.2
Ishikawa, I.3
Benno, Y.4
-
46
-
-
85020473832
-
Description of two novel members of the family Erysipelotrichaceae: Ileibacterium valens gen. nov., sp. nov. and Dubosiella newyorkensis gen. nov., sp. nov., from the murine intestine, and emendation to the description of Faecalibacterium rodentium
-
Cox, L. M. et al. Description of two novel members of the family Erysipelotrichaceae: Ileibacterium valens gen. nov., sp. nov. and Dubosiella newyorkensis gen. nov., sp. nov., from the murine intestine, and emendation to the description of Faecalibacterium rodentium. Int. J. Syst. Evol. Microbiol. 67, 1247-1254 (2017).
-
(2017)
Int. J. Syst. Evol. Microbiol.
, vol.67
, pp. 1247-1254
-
-
Cox, L.M.1
-
47
-
-
84971644054
-
Breznakia blatticola gen. nov. sp. nov. and Breznakia pachnodae sp. nov., two fermenting bacteria isolated from insect guts, and emended description of the family Erysipelotrichaceae
-
Tegtmeier, D., Riese, C., Geissinger, O., Radek, R. & Brune, A. Breznakia blatticola gen. nov. sp. nov. and Breznakia pachnodae sp. nov., two fermenting bacteria isolated from insect guts, and emended description of the family Erysipelotrichaceae. Syst. Appl. Microbiol. 39, 319-329 (2016).
-
(2016)
Syst. Appl. Microbiol.
, vol.39
, pp. 319-329
-
-
Tegtmeier, D.1
Riese, C.2
Geissinger, O.3
Radek, R.4
Brune, A.5
-
48
-
-
85010450365
-
Genome sequence of a novel multiple-antibiotic-resistant member of the Erysipelotrichaceae family isolated from a swine manure storage pit
-
Haley, B. J., Kim, S. W. & Whitehead, T. R. Genome sequence of a novel multiple-antibiotic-resistant member of the Erysipelotrichaceae family isolated from a swine manure storage pit. Genome Announc. 4, e00978-16 (2016).
-
(2016)
Genome Announc.
, vol.4
, pp. e00978-e001016
-
-
Haley, B.J.1
Kim, S.W.2
Whitehead, T.R.3
-
49
-
-
0034056803
-
Phylogenic and phenotypic characterization of some Eubacterium-like isolates from human feces: Description of Solobacterium moorei gen. nov., sp. nov
-
Kageyama, A. & Benno, Y. Phylogenic and phenotypic characterization of some Eubacterium-like isolates from human feces: description of Solobacterium moorei gen. nov., sp. nov. Microbiol. Immunol. 44, 223-227 (2000).
-
(2000)
Microbiol. Immunol.
, vol.44
, pp. 223-227
-
-
Kageyama, A.1
Benno, Y.2
-
50
-
-
84899090573
-
Kraken: Ultrafast metagenomic sequence classification using exact alignments
-
Wood, D. E. & Salzberg, S. L. Kraken: ultrafast metagenomic sequence classification using exact alignments. Genome Biol. 15, R46 (2014).
-
(2014)
Genome Biol.
, vol.15
, pp. R46
-
-
Wood, D.E.1
Salzberg, S.L.2
-
51
-
-
84946047645
-
Gene: A gene-centered information resource at NCBI
-
Brown, G. R. et al. Gene: a gene-centered information resource at NCBI. Nucleic Acids Res. 43, D36-D42 (2015).
-
(2015)
Nucleic Acids Res.
, vol.43
, pp. D36-D42
-
-
Brown, G.R.1
-
52
-
-
85024405108
-
1, 003 reference genomes of bacterial and archaeal isolates expand coverage of the tree of life
-
Mukherjee, S. et al. 1, 003 reference genomes of bacterial and archaeal isolates expand coverage of the tree of life. Nat. Biotechnol. https://doi.org/10.1038/nbt.3886 (2017).
-
(2017)
Nat. Biotechnol
-
-
Mukherjee, S.1
-
53
-
-
85042783307
-
-
The Hungate 1000 Accessed 28th June 2017
-
The Hungate 1000. A catalogue of reference genomes from the rumen microbiome. Available at: http://genome.jgi.doe.gov/TheHunmicrobiome/TheHunmicrobiome.info.html. Accessed 28th June 2017.
-
A Catalogue of Reference Genomes from the Rumen Microbiome
-
-
-
54
-
-
85002575175
-
Centrifuge: Rapid and sensitive classification of metagenomic sequences
-
Kim, D., Song, L., Breitwieser, F. P. & Salzberg, S. L. Centrifuge: rapid and sensitive classification of metagenomic sequences. Genome Res. 26, 1721-1729 (2016).
-
(2016)
Genome Res.
, vol.26
, pp. 1721-1729
-
-
Kim, D.1
Song, L.2
Breitwieser, F.P.3
Salzberg, S.L.4
-
55
-
-
74049108922
-
BLAST+: Architecture and applications
-
Camacho, C. et al. BLAST+: architecture and applications. BMC Bioinform. 10, 421 (2009).
-
(2009)
BMC Bioinform.
, vol.10
, pp. 421
-
-
Camacho, C.1
-
56
-
-
84903755330
-
Rumen cellulosomics: Divergent fiber-degrading strategies revealed by comparative genome-wide analysis of six ruminococcal strains
-
Dassa, B. et al Rumen cellulosomics: divergent fiber-degrading strategies revealed by comparative genome-wide analysis of six ruminococcal strains. PLoS ONE 9, e99221 (2014).
-
(2014)
PLoS ONE
, vol.9
, pp. e99221
-
-
Dassa, B.1
-
57
-
-
84976871272
-
Reference sequence (RefSeq) database at NCBI: Current status, taxonomic expansion, and functional annotation
-
O'Leary, N. A. et al. Reference sequence (RefSeq) database at NCBI: current status, taxonomic expansion, and functional annotation. Nucleic Acids Res. 44, D733-D745 (2016).
-
(2016)
Nucleic Acids Res.
, vol.44
, pp. D733-D745
-
-
O'Leary, N.A.1
-
58
-
-
84906233102
-
Illuminating the future of DNA sequencing
-
Watson, M. Illuminating the future of DNA sequencing. Genome Biol. 15, 108 (2014).
-
(2014)
Genome Biol.
, vol.15
, pp. 108
-
-
Watson, M.1
-
59
-
-
84996490489
-
Recovering complete and draft population genomes from metagenome datasets
-
Sangwan, N., Xia, F. & Gilbert, J. A. Recovering complete and draft population genomes from metagenome datasets. Microbiome 4, 8 (2016).
-
(2016)
Microbiome
, vol.4
, pp. 8
-
-
Sangwan, N.1
Xia, F.2
Gilbert, J.A.3
-
60
-
-
85011272688
-
Differential effects of monensin and a blend of essential oils on rumen microbiota composition of transition dairy cows
-
Schären, M. et al. Differential effects of monensin and a blend of essential oils on rumen microbiota composition of transition dairy cows. J. Dairy Sci. 100, 2765-2783 (2017).
-
(2017)
J. Dairy Sci.
, vol.100
, pp. 2765-2783
-
-
Schären, M.1
-
61
-
-
84927128279
-
High-grain feeding causes strong shifts in ruminal epithelial bacterial community and expression of Toll-like receptor genes in goats
-
Liu, J.-H., Bian, G.-R., Zhu, W.-Y. & Mao, S.-Y. High-grain feeding causes strong shifts in ruminal epithelial bacterial community and expression of Toll-like receptor genes in goats. Front. Microbiol. 6, 167 (2015).
-
(2015)
Front. Microbiol.
, vol.6
, pp. 167
-
-
Liu, J.H.1
Bian, G.R.2
Zhu, W.Y.3
Mao, S.Y.4
-
62
-
-
85014337689
-
Key bacterial families (Clostridiaceae, Erysipelotrichaceae and Bacteroidaceae) are related to the digestion of protein and energy in dogs
-
Bermingham, E. N., Maclean, P., Thomas, D. G., Cave, N. J. & Young, W. Key bacterial families (Clostridiaceae, Erysipelotrichaceae and Bacteroidaceae) are related to the digestion of protein and energy in dogs. PeerJ 5, e3019 (2017).
-
(2017)
PeerJ
, vol.5
, pp. e3019
-
-
Bermingham, E.N.1
MacLean, P.2
Thomas, D.G.3
Cave, N.J.4
Young, W.5
-
63
-
-
84926486633
-
Successful test launch for nanopore sequencing
-
Loman, N. J. & Watson, M. Successful test launch for nanopore sequencing. Nat. Methods 12, 303-304 (2015).
-
(2015)
Nat. Methods
, vol.12
, pp. 303-304
-
-
Loman, N.J.1
Watson, M.2
-
64
-
-
84991528128
-
A single chromosome assembly of Bacteroides fragilis strain BE1 from Illumina and MinION nanopore sequencing data
-
Risse, J. et al. A single chromosome assembly of Bacteroides fragilis strain BE1 from Illumina and MinION nanopore sequencing data. Gigascience 4, 60 (2015).
-
(2015)
Gigascience
, vol.4
, pp. 60
-
-
Risse, J.1
-
65
-
-
2442510059
-
Improved extraction of PCR-quality community DNA from digesta and fecal samples
-
Yu, Z. & Morrison, M. Improved extraction of PCR-quality community DNA from digesta and fecal samples. Biotechniques 36, 808-812 (2004).
-
(2004)
Biotechniques
, vol.36
, pp. 808-812
-
-
Yu, Z.1
Morrison, M.2
-
66
-
-
84905049901
-
Trimmomatic: A flexible trimmer for Illumina sequence data
-
Bolger, A. M., Lohse, M. & Usadel, B. Trimmomatic: a flexible trimmer for Illumina sequence data. Bioinformatics 30, 2114-2120 (2014).
-
(2014)
Bioinformatics
, vol.30
, pp. 2114-2120
-
-
Bolger, A.M.1
Lohse, M.2
Usadel, B.3
-
67
-
-
84929626808
-
MEGAHIT: An ultra-fast single-node solution for large and complex metagenomics assembly via succinct de Bruijn graph
-
Li, D., Liu, C.-M., Luo, R., Sadakane, K. & Lam, T.-W. MEGAHIT: an ultra-fast single-node solution for large and complex metagenomics assembly via succinct de Bruijn graph. Bioinformatics 31, 1674-1676 (2015).
-
(2015)
Bioinformatics
, vol.31
, pp. 1674-1676
-
-
Li, D.1
Liu, C.M.2
Luo, R.3
Sadakane, K.4
Lam, T.W.5
-
68
-
-
84861760530
-
IDBA-UD: A de novo assembler for single-cell and metagenomic sequencing data with highly uneven depth
-
Peng, Y., Leung, H. C. M., Yiu, S. M. & Chin, F. Y. L. IDBA-UD: a de novo assembler for single-cell and metagenomic sequencing data with highly uneven depth. Bioinformatics 28, 1420-1428 (2012).
-
(2012)
Bioinformatics
, vol.28
, pp. 1420-1428
-
-
Peng, Y.1
Leung, H.C.M.2
Yiu, S.M.3
Chin, F.Y.L.4
-
70
-
-
68549104404
-
The Sequence Alignment/Map format and SAMtools
-
Li, H. et al. The Sequence Alignment/Map format and SAMtools. Bioinformatics 25, 2078-2079 (2009).
-
(2009)
Bioinformatics
, vol.25
, pp. 2078-2079
-
-
Li, H.1
-
71
-
-
85034643980
-
DRep: A tool for fast and accurate genomic comparisons that enables improved genome recovery from metagenomes through de-replication
-
Olm, M. R., Brown, C. T., Brooks, B. & Banfield, J. F. dRep: a tool for fast and accurate genomic comparisons that enables improved genome recovery from metagenomes through de-replication. ISME J. https://doi.org/10.1038/ismej.2017.126 (2017).
-
(2017)
ISME J
-
-
Olm, M.R.1
Brown, C.T.2
Brooks, B.3
Banfield, J.F.4
-
72
-
-
85019133486
-
A. MetaSPAdes: A new versatile metagenomic assembler
-
Nurk, S., Meleshko, D., Korobeynikov, A. & Pevzner, P. A. metaSPAdes: a new versatile metagenomic assembler. Genome Res. 27, 824-834 (2017).
-
(2017)
Genome Res.
, vol.27
, pp. 824-834
-
-
Nurk, S.1
Meleshko, D.2
Korobeynikov, A.3
Pevzner, P.4
-
73
-
-
67649884743
-
Fast and accurate short read alignment with Burrows-Wheeler transform
-
Li, H. & Durbin, R. Fast and accurate short read alignment with Burrows-Wheeler transform. Bioinformatics 25, 1754-1760 (2009).
-
(2009)
Bioinformatics
, vol.25
, pp. 1754-1760
-
-
Li, H.1
Durbin, R.2
-
74
-
-
84925021592
-
Fast and sensitive protein alignment using DIAMOND
-
Buchfink, B., Xie, C. & Huson, D. H. Fast and sensitive protein alignment using DIAMOND. Nat. Methods 12, 59-60 (2015).
-
(2015)
Nat. Methods
, vol.12
, pp. 59-60
-
-
Buchfink, B.1
Xie, C.2
Huson, D.H.3
-
75
-
-
84962897215
-
ETE 3: Reconstruction, Analysis, and Visualization of Phylogenomic Data
-
Huerta-Cepas, J. et al. ETE 3: Reconstruction, Analysis, and Visualization of Phylogenomic Data. Mol. Biol. Evol. 33, 1635-1638 (2016).
-
(2016)
Mol. Biol. Evol.
, vol.33
, pp. 1635-1638
-
-
Huerta-Cepas, J.1
-
76
-
-
85042748001
-
-
bioRxiv
-
Stewart, R., Auffret, M., Snelling, T., Roehe, R. & Watson, M. MAGpy: a reproducible pipeline for the downstream analysis of metagenome-assembled genomes (MAGs). bioRxiv https://doi.org/10.1101/233544 (2017).
-
(2017)
MAGpy: A Reproducible Pipeline for the Downstream Analysis of Metagenome-assembled Genomes (MAGs)
-
-
Stewart, R.1
Auffret, M.2
Snelling, T.3
Roehe, R.4
Watson, M.5
-
77
-
-
84886013737
-
Meta4: A web-application for sharing and annotating metagenomic gene predictions using web-services
-
Richardson, E. J., Escalettes, F., Fotheringham, I., Wallace, R. J. & Watson, M. Meta4: a web-application for sharing and annotating metagenomic gene predictions using web-services. Front. Genet. 4, 168 (2013).
-
(2013)
Front. Genet.
, vol.4
, pp. 168
-
-
Richardson, E.J.1
Escalettes, F.2
Fotheringham, I.3
Wallace, R.J.4
Watson, M.5
-
78
-
-
85042800296
-
-
Welcome to sourmash!-sourmash 1.0 documentation Accessed 28th June 2017
-
Welcome to sourmash!-sourmash 1.0 documentation. Available at: https://sourmash.readthedocs.io/en/latest/. Accessed 28th June 2017.
-
-
-
-
79
-
-
84883116930
-
PhyloPhlAn is a new method for improved phylogenetic and taxonomic placement of microbes
-
Segata, N., Börnigen, D., Morgan, X. C. & Huttenhower, C. PhyloPhlAn is a new method for improved phylogenetic and taxonomic placement of microbes. Nat. Commun. 4, 2304 (2013).
-
(2013)
Nat. Commun.
, vol.4
, pp. 2304
-
-
Segata, N.1
Börnigen, D.2
Morgan, X.C.3
Huttenhower, C.4
-
80
-
-
84937442075
-
Compact graphical representation of phylogenetic data and metadata with GraPhlAn
-
Asnicar, F., Weingart, G., Tickle, T. L., Huttenhower, C. & Segata, N. Compact graphical representation of phylogenetic data and metadata with GraPhlAn. PeerJ 3, e1029 (2015).
-
(2015)
PeerJ
, vol.3
, pp. e1029
-
-
Asnicar, F.1
Weingart, G.2
Tickle, T.L.3
Huttenhower, C.4
Segata, N.5
-
81
-
-
65649092976
-
Biopython: Freely available Python tools for computational molecular biology and bioinformatics
-
Cock, P. J. A. et al. Biopython: freely available Python tools for computational molecular biology and bioinformatics. Bioinformatics 25, 1422-1423 (2009).
-
(2009)
Bioinformatics
, vol.25
, pp. 1422-1423
-
-
Cock, P.J.A.1
-
82
-
-
33644857839
-
GenomeDiagram: A python package for the visualization of large-scale genomic data
-
Pritchard, L., White, J. A., Birch, P. R. J. & Toth, I. K. GenomeDiagram: a python package for the visualization of large-scale genomic data. Bioinformatics 22, 616-617 (2006).
-
(2006)
Bioinformatics
, vol.22
, pp. 616-617
-
-
Pritchard, L.1
White, J.A.2
Birch, P.R.J.3
Toth, I.K.4
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