-
1
-
-
1542377296
-
Community structure and metabolism through reconstruction of microbial genomes from the environment
-
DOI 10.1038/nature02340
-
Tyson, G. W. et al. Community structure and metabolism through reconstruction of microbial genomes from the environment. Nature 428, 37-43 (2004). (Pubitemid 38332350)
-
(2004)
Nature
, vol.428
, Issue.6978
, pp. 37-43
-
-
Tyson, G.W.1
Chapman, J.2
Hugenholtz, P.3
Allen, E.E.4
Ram, R.J.5
Richardson, P.M.6
Solovyev, V.V.7
Rubin, E.M.8
Rokhsar, D.S.9
Banfield, J.F.10
-
2
-
-
0037195156
-
Genomic analysis of uncultured marine viral communities
-
DOI 10.1073/pnas.202488399
-
Breitbart, M. et al. Genomic analysis of uncultured marine viral communities. Proc. Natl Acad. Sci. USA 99, 14250-14255 (2002). (Pubitemid 35257658)
-
(2002)
Proceedings of the National Academy of Sciences of the United States of America
, vol.99
, Issue.22
, pp. 14250-14255
-
-
Breitbart, M.1
Salamon, P.2
Andresen, B.3
Mahaffy, J.M.4
Segall, A.M.5
Mead, D.6
Azam, F.7
Rohwer, F.8
-
3
-
-
84867985452
-
Oxygen minimum zones harbour novel viral communities with low diversity
-
Cassman, N. et al. Oxygen minimum zones harbour novel viral communities with low diversity. Environ. Microbiol. 14, 3043-3065 (2012).
-
(2012)
Environ. Microbiol.
, vol.14
, pp. 3043-3065
-
-
Cassman, N.1
-
4
-
-
84880652104
-
Rapid evolution of the human gut virome
-
USA
-
Minot, S. et al. Rapid evolution of the human gut virome. Proc. Natl Acad. Sci. USA 110, 12450-12455 (2013).
-
(2013)
Proc. Natl Acad. Sci.
, vol.110
, pp. 12450-12455
-
-
Minot, S.1
-
5
-
-
84863393452
-
Hypervariable loci in the human gut virome
-
USA
-
Minot, S., Grunberg, S., Wu, G. D., Lewis, J. D. & Bushman, F. D. Hypervariable loci in the human gut virome. Proc. Natl Acad. Sci. USA 109, 3962-3966 (2012).
-
(2012)
Proc. Natl Acad. Sci.
, vol.109
, pp. 3962-3966
-
-
Minot, S.1
Grunberg, S.2
Wu, G.D.3
Lewis, J.D.4
Bushman, F.D.5
-
6
-
-
80053528043
-
The human gut virome: Inter-individual variation and dynamic response to diet
-
Minot, S. et al. The human gut virome: inter-individual variation and dynamic response to diet. Genome Res. 21, 1616-1625 (2011).
-
(2011)
Genome Res.
, vol.21
, pp. 1616-1625
-
-
Minot, S.1
-
7
-
-
84890281518
-
Gnotobiotic mouse model of phage-bacterial host dynamics in the human gut
-
USA
-
Reyes, A., Wu, M., McNulty, N. P., Rohwer, F. L. & Gordon, J. I. Gnotobiotic mouse model of phage-bacterial host dynamics in the human gut. Proc. Natl Acad. Sci. USA 110, 20236-20241 (2013).
-
(2013)
Proc. Natl Acad. Sci.
, vol.110
, pp. 20236-20241
-
-
Reyes, A.1
Wu, M.2
McNulty, N.P.3
Rohwer, F.L.4
Gordon, J.I.5
-
8
-
-
77954627922
-
Viruses in the faecal microbiota of monozygotic twins and their mothers
-
Reyes, A. et al. Viruses in the faecal microbiota of monozygotic twins and their mothers. Nature 466, 334-338 (2010).
-
(2010)
Nature
, vol.466
, pp. 334-338
-
-
Reyes, A.1
-
9
-
-
31144459030
-
RNA viral community in human feces: Prevalence of plant pathogenic viruses
-
Zhang, T. et al. RNA viral community in human feces: prevalence of plant pathogenic viruses. PLoS Biol. 4, e3 (2006).
-
(2006)
PLoS Biol.
, vol.4
-
-
Zhang, T.1
-
10
-
-
64149083137
-
Direct metagenomic detection of viral pathogens in nasal and faecal specimens using an unbiased high-throughput sequencing approach
-
Nakamura, S. et al. Direct metagenomic detection of viral pathogens in nasal and faecal specimens using an unbiased high-throughput sequencing approach. PLoS ONE 4, e4219 (2009).
-
(2009)
PLoS ONE
, vol.4
-
-
Nakamura, S.1
-
11
-
-
55549099265
-
Metagenomic diagnosis of bacterial infections
-
Nakamura, S. et al. Metagenomic diagnosis of bacterial infections. Emerg. Infect. Dis. 14, 1784-1786 (2008).
-
(2008)
Emerg. Infect. Dis.
, vol.14
, pp. 1784-1786
-
-
Nakamura, S.1
-
12
-
-
0141891348
-
Metagenomic analyses of an uncultured viral community from human feces
-
DOI 10.1128/JB.185.20.6220-6223.2003
-
Breitbart, M. et al. Metagenomic analyses of an uncultured viral community from human feces. J. Bacteriol. 185, 6220-6223 (2003). (Pubitemid 37248478)
-
(2003)
Journal of Bacteriology
, vol.185
, Issue.20
, pp. 6220-6223
-
-
Breitbart, M.1
Hewson, I.2
Felts, B.3
Mahaffy, J.M.4
Nulton, J.5
Salamon, P.6
Rohwer, F.7
-
13
-
-
83055177100
-
Diversity and abundance of single-stranded DNA viruses in human feces
-
Kim, M. S., Park, E. J., Roh, S. W. & Bae, J. W. Diversity and abundance of single-stranded DNA viruses in human feces. Appl. Environ. Microbiol. 77, 8062-8070 (2011).
-
(2011)
Appl. Environ. Microbiol.
, vol.77
, pp. 8062-8070
-
-
Kim, M.S.1
Park, E.J.2
Roh, S.W.3
Bae, J.W.4
-
14
-
-
33744804299
-
Metagenomic analysis of the human distal gut microbiome
-
DOI 10.1126/science.1124234
-
Gill, S. R. et al. Metagenomic analysis of the human distal gut microbiome. Science 312, 1355-1359 (2006). (Pubitemid 43839542)
-
(2006)
Science
, vol.312
, Issue.5778
, pp. 1355-1359
-
-
Gill, S.R.1
Pop, M.2
DeBoy, R.T.3
Eckburg, P.B.4
Turnbaugh, P.J.5
Samuel, B.S.6
Gordon, J.I.7
Relman, D.A.8
Fraser-Liggett, C.M.9
Nelson, K.E.10
-
15
-
-
85027927719
-
Enterotypes of the human gut microbiome
-
Arumugam, M. et al. Enterotypes of the human gut microbiome. Nature 473, 174-180 (2011).
-
(2011)
Nature
, vol.473
, pp. 174-180
-
-
Arumugam, M.1
-
16
-
-
70449713952
-
The NIH human microbiome project
-
Peterson, J. et al. The NIH Human Microbiome Project. Genome Res. 19, 2317-2323 (2009).
-
(2009)
Genome Res
, vol.19
, pp. 2317-2323
-
-
Peterson, J.1
-
17
-
-
77950251400
-
A human gut microbial gene catalogue established by metagenomic sequencing
-
Qin, J. et al. A human gut microbial gene catalogue established by metagenomic sequencing. Nature 464, 59-65 (2010).
-
(2010)
Nature
, vol.464
, pp. 59-65
-
-
Qin, J.1
-
18
-
-
84873510063
-
A guide to enterotypes across the human body: Meta-analysis of microbial community structures in human microbiome datasets
-
Koren, O. et al. A guide to enterotypes across the human body: meta-analysis of microbial community structures in human microbiome datasets. PLoS Comput. Biol. 9, e1002863 (2013).
-
(2013)
PLoS Comput. Biol.
, vol.9
-
-
Koren, O.1
-
19
-
-
33845874101
-
An obesity-associated gut microbiome with increased capacity for energy harvest
-
DOI 10.1038/nature05414, PII NATURE05414
-
Turnbaugh, P. J. et al. An obesity-associated gut microbiome with increased capacity for energy harvest. Nature 444, 1027-1031 (2006). (Pubitemid 46018515)
-
(2006)
Nature
, vol.444
, Issue.7122
, pp. 1027-1031
-
-
Turnbaugh, P.J.1
Ley, R.E.2
Mahowald, M.A.3
Magrini, V.4
Mardis, E.R.5
Gordon, J.I.6
-
20
-
-
84863989936
-
A bacterial driverpassenger model for colorectal cancer: Beyond the usual suspects
-
Tjalsma, H., Boleij, A., Marchesi, J. R. & Dutilh, B. E. A bacterial driverpassenger model for colorectal cancer: beyond the usual suspects. Nat. Rev. Microbiol. 10, 575-582 (2012).
-
(2012)
Nat. Rev. Microbiol.
, vol.10
, pp. 575-582
-
-
Tjalsma, H.1
Boleij, A.2
Marchesi, J.R.3
Dutilh, B.E.4
-
21
-
-
84857371051
-
Metagenomics and future perspectives in virus discovery
-
Mokili, J. L., Rohwer, F. & Dutilh, B. E. Metagenomics and future perspectives in virus discovery. Curr. Opin. Virol. 2, 63-77 (2012).
-
(2012)
Curr. Opin. Virol.
, vol.2
, pp. 63-77
-
-
Mokili, J.L.1
Rohwer, F.2
Dutilh, B.E.3
-
22
-
-
84865094411
-
Comparative (meta)genomic analysis and ecological profiling of human gut-specific bacteriophage phiB124-14
-
Ogilvie, L. A. et al. Comparative (meta)genomic analysis and ecological profiling of human gut-specific bacteriophage phiB124-14. PLoS ONE 7, e35053 (2012).
-
(2012)
PLoS ONE
, vol.7
-
-
Ogilvie, L.A.1
-
23
-
-
84875048145
-
Identification of a novel human papillomavirus by metagenomic analysis of samples from patients with febrile respiratory illness
-
Mokili, J. L. et al. Identification of a novel human papillomavirus by metagenomic analysis of samples from patients with febrile respiratory illness. PLoS ONE 8, e58404 (2013).
-
(2013)
PLoS ONE
, vol.8
-
-
Mokili, J.L.1
-
24
-
-
84884239907
-
Genome signature-based dissection of human gut metagenomes to extract subliminal viral sequences
-
Ogilvie, L. A. et al. Genome signature-based dissection of human gut metagenomes to extract subliminal viral sequences. Nat. Commun. 4, 2420 (2013).
-
(2013)
Nat. Commun.
, vol.4
, pp. 2420
-
-
Ogilvie, L.A.1
-
25
-
-
84903378191
-
Classification and quantification of bacteriophage taxa in human gut metagenomes
-
Waller, A. S. et al. Classification and quantification of bacteriophage taxa in human gut metagenomes. ISME J. 8, 1551-1552 (2014).
-
(2014)
ISME J.
, vol.8
, pp. 1551-1552
-
-
Waller, A.S.1
-
26
-
-
51649104135
-
Genome sequence of the Bacteroides fragilis phage ATCC 51477-B1
-
Hawkins, S. A., Layton, A. C., Ripp, S., Williams, D. & Sayler, G. S. Genome sequence of the Bacteroides fragilis phage ATCC 51477-B1. Virol. J. 5, 97 (2008).
-
(2008)
Virol. J.
, vol.5
, pp. 97
-
-
Hawkins, S.A.1
Layton, A.C.2
Ripp, S.3
Williams, D.4
Sayler, G.S.5
-
27
-
-
37249090179
-
Practical and theoretical advances in predicting the function of a protein by its phylogenetic distribution
-
DOI 10.1098/rsif.2007.1047, PII 73616Q08830171Q1
-
Kensche, P. R., van Noort, V., Dutilh, B. E. & Huynen, M. A. Practical and theoretical advances in predicting the function of a protein by its phylogenetic distribution. J R. Soc. Interface 5, 151-170 (2008). (Pubitemid 350274448)
-
(2008)
Journal of the Royal Society Interface
, vol.5
, Issue.19
, pp. 151-170
-
-
Kensche, P.R.1
Van Noort, V.2
Dutilh, B.E.3
Huynen, M.A.4
-
28
-
-
77954238817
-
A global network of coexisting microbes from environmental and whole-genome sequence data
-
Chaffron, S., Rehrauer, H., Pernthaler, J. & von Mering, C. A global network of coexisting microbes from environmental and whole-genome sequence data. Genome Res. 20, 947-959 (2010).
-
(2010)
Genome Res.
, vol.20
, pp. 947-959
-
-
Chaffron, S.1
Rehrauer, H.2
Pernthaler, J.3
Von Mering, C.4
-
29
-
-
84864579031
-
Microbial co-occurrence relationships in the human microbiome
-
Faust, K. et al. Microbial co-occurrence relationships in the human microbiome. PLoS Comput Biol. 8, e1002606 (2012).
-
(2012)
PLoS Comput Biol.
, vol.8
-
-
Faust, K.1
-
30
-
-
84866772472
-
Fermentation, hydrogen, and sulfur metabolism in multiple uncultivated bacterial phyla
-
Wrighton, K. C. et al. Fermentation, hydrogen, and sulfur metabolism in multiple uncultivated bacterial phyla. Science 337, 1661-1665 (2012).
-
(2012)
Science
, vol.337
, pp. 1661-1665
-
-
Wrighton, K.C.1
-
31
-
-
84879678051
-
Genome sequences of rare, uncultured bacteria obtained by differential coverage binning of multiple metagenomes
-
Albertsen, M. et al. Genome sequences of rare, uncultured bacteria obtained by differential coverage binning of multiple metagenomes. Nat. Biotechnol. 31, 533-538 (2013).
-
(2013)
Nat. Biotechnol.
, vol.31
, pp. 533-538
-
-
Albertsen, M.1
-
32
-
-
84870829895
-
Reference-independent comparative metagenomics using cross-assembly: CrAss
-
Dutilh, B. E. et al. Reference-independent comparative metagenomics using cross-assembly: crAss. Bioinformatics 28, 3225-3231 (2012).
-
(2012)
Bioinformatics
, vol.28
, pp. 3225-3231
-
-
Dutilh, B.E.1
-
33
-
-
33845957530
-
Accurate phylogenetic classification of variable-length DNA fragments
-
DOI 10.1038/nmeth976, PII NMETH976
-
McHardy, A. C., Martin, H. G., Tsirigos, A., Hugenholtz, P. & Rigoutsos, I. Accurate phylogenetic classification of variable-length DNA fragments. Nat. Methods 4, 63-72 (2007). (Pubitemid 46029478)
-
(2007)
Nature Methods
, vol.4
, Issue.1
, pp. 63-72
-
-
McHardy, A.C.1
Martin, H.G.2
Tsirigos, A.3
Hugenholtz, P.4
Rigoutsos, I.5
-
34
-
-
0025183708
-
Basic local alignment search tool
-
Altschul, S. F., Gish, W., Miller, W., Myers, E. W. & Lipman, D. J. Basic local alignment search tool. J. Mol. Biol. 215, 403-410 (1990).
-
(1990)
J. Mol. Biol.
, vol.215
, pp. 403-410
-
-
Altschul, S.F.1
Gish, W.2
Miller, W.3
Myers, E.W.4
Lipman, D.J.5
-
36
-
-
70350688130
-
Increasing the coverage of a metapopulation consensus genome by iterative read mapping and assembly
-
Dutilh, B. E., Huynen, M. A. & Strous, M. Increasing the coverage of a metapopulation consensus genome by iterative read mapping and assembly. Bioinformatics. 25, 2878-2881 (2009).
-
(2009)
Bioinformatics
, vol.25
, pp. 2878-2881
-
-
Dutilh, B.E.1
Huynen, M.A.2
Strous, M.3
-
37
-
-
84868099390
-
PhiSpy: A novel algorithm for finding prophages in bacterial genomes that combines similarity-and compositionbased strategies
-
Akhter, S., Aziz, R. K. & Edwards, R. A. PhiSpy: a novel algorithm for finding prophages in bacterial genomes that combines similarity-and compositionbased strategies. Nucleic Acids Res. 40, e126 (2012).
-
(2012)
Nucleic Acids Res.
, vol.40
-
-
Akhter, S.1
Aziz, R.K.2
Edwards, R.A.3
-
38
-
-
23144452044
-
The HHpred interactive server for protein homology detection and structure prediction
-
DOI 10.1093/nar/gki408
-
Soding, J., Biegert, A. & Lupas, A. N. The HHpred interactive server for protein homology detection and structure prediction. Nucleic Acids Res. 33, W244-W248 (2005). (Pubitemid 44529917)
-
(2005)
Nucleic Acids Research
, vol.33
-
-
Soding, J.1
Biegert, A.2
Lupas, A.N.3
-
39
-
-
84866069326
-
Artificial neural networks trained to detect viral and phage structural proteins
-
Seguritan, V. et al. Artificial neural networks trained to detect viral and phage structural proteins. PLoS Comput Biol. 8, e1002657 (2012).
-
(2012)
PLoS Comput Biol.
, vol.8
-
-
Seguritan, V.1
-
40
-
-
75549090603
-
The Pfam protein families database
-
Finn, R. D. et al. The Pfam protein families database. Nucleic Acids Res. 38, D211-D222 (2010).
-
(2010)
Nucleic Acids Res.
, vol.38
-
-
Finn, R.D.1
-
41
-
-
77952958875
-
Mining metagenomic data for novel domains: BACON, a new carbohydrate-binding module
-
Mello, L. V., Chen, X. & Rigden, D. J. Mining metagenomic data for novel domains: BACON, a new carbohydrate-binding module. FEBS Lett. 584, 2421-2426 (2010).
-
(2010)
FEBS Lett.
, vol.584
, pp. 2421-2426
-
-
Mello, L.V.1
Chen, X.2
Rigden, D.J.3
-
42
-
-
84879515171
-
Bacteriophage adhering to mucus provide a non-host-derived immunity
-
USA
-
Barr, J. J. et al. Bacteriophage adhering to mucus provide a non-host-derived immunity. Proc. Natl Acad. Sci. USA 110, 10771-10776 (2013).
-
(2013)
Proc. Natl Acad. Sci.
, vol.110
, pp. 10771-10776
-
-
Barr, J.J.1
-
43
-
-
79961015810
-
Statistical structure of host-phage interactions
-
USA
-
Flores, C. O., Meyer, J. R., Valverde, S., Farr, L. & Weitz, J. S. Statistical structure of host-phage interactions. Proc. Natl Acad. Sci. USA 108, E288-E297 (2011).
-
(2011)
Proc. Natl Acad. Sci.
, vol.108
-
-
Flores, C.O.1
Meyer, J.R.2
Valverde, S.3
Farr, L.4
Weitz, J.S.5
-
44
-
-
0036330981
-
The phage proteomic tree: A genome-based taxonomy for phage
-
DOI 10.1128/JB.184.16.4529-4535.2002
-
Rohwer, F. & Edwards, R. The phage proteomic tree: a genome-based taxonomy for phage. J. Bacteriol. 184, 4529-4535 (2002). (Pubitemid 34832581)
-
(2002)
Journal of Bacteriology
, vol.184
, Issue.16
, pp. 4529-4535
-
-
Rohwer, F.1
Edwards, R.2
-
45
-
-
34047118522
-
CRISPR provides acquired resistance against viruses in prokaryotes
-
DOI 10.1126/science.1138140
-
Barrangou, R. et al. CRISPR provides acquired resistance against viruses in prokaryotes. Science 315, 1709-1712 (2007). (Pubitemid 46515624)
-
(2007)
Science
, vol.315
, Issue.5819
, pp. 1709-1712
-
-
Barrangou, R.1
Fremaux, C.2
Deveau, H.3
Richards, M.4
Boyaval, P.5
Moineau, S.6
Romero, D.A.7
Horvath, P.8
-
46
-
-
84860513986
-
PILER: Identification and classification of genomic repeats
-
DOI 10.1093/bioinformatics/bti1003
-
Edgar, R. C. & Myers, E. W. PILER: identification and classification of genomic repeats. Bioinformatics 21(Suppl 1): i152-i158 (2005). (Pubitemid 41794485)
-
(2005)
Bioinformatics
, vol.21
, Issue.SUPPL. 1
-
-
Edgar, R.C.1
Myers, E.W.2
-
47
-
-
84899087750
-
Degenerate target sites mediate rapid primed CRISPR adaptation
-
USA
-
Fineran, P. C. et al. Degenerate target sites mediate rapid primed CRISPR adaptation. Proc. Natl Acad. Sci. USA 111, E1629-E1638 (2014).
-
(2014)
Proc. Natl Acad. Sci.
, vol.111
-
-
Fineran, P.C.1
-
48
-
-
84865169354
-
CRISPR targeting reveals a reservoir of common phages associated with the human gut microbiome
-
Stern, A., Mick, E., Tirosh, I., Sagy, O. & Sorek, R. CRISPR targeting reveals a reservoir of common phages associated with the human gut microbiome. Genome Res. 22, 1985-1994 (2012).
-
(2012)
Genome Res.
, vol.22
, pp. 1985-1994
-
-
Stern, A.1
Mick, E.2
Tirosh, I.3
Sagy, O.4
Sorek, R.5
-
49
-
-
53549118607
-
The metagenomics rast server-a public resource for the automatic phylogenetic and functional analysis of metagenomes
-
Meyer, F. et al. The metagenomics RAST server-a public resource for the automatic phylogenetic and functional analysis of metagenomes. BMC Bioinformatics 9, 386 (2008).
-
(2008)
BMC Bioinformatics
, vol.9
, pp. 386
-
-
Meyer, F.1
-
50
-
-
84897599619
-
Evidence for metaviromic islands in marine phages
-
Mizuno, C. M., Ghai, R. & Rodriguez-Valera, F. Evidence for metaviromic islands in marine phages. Front. Microbiol. 5, 27 (2014).
-
(2014)
Front. Microbiol.
, vol.5
, pp. 27
-
-
Mizuno, C.M.1
Ghai, R.2
Rodriguez-Valera, F.3
-
51
-
-
84863149571
-
UMARS: Un-MAppable reads solution
-
Li, S. C. et al. UMARS: Un-MAppable Reads Solution. BMC Bioinformatics 12(Suppl 1): S9 (2011).
-
(2011)
BMC Bioinformatics
, vol.12
, Issue.SUPPL. 1
-
-
Li, S.C.1
-
52
-
-
84874193410
-
Abundant SAR11 viruses in the ocean
-
Zhao, Y. et al. Abundant SAR11 viruses in the ocean. Nature 494, 357-360 (2013).
-
(2013)
Nature
, vol.494
, pp. 357-360
-
-
Zhao, Y.1
-
53
-
-
24044455869
-
Genome sequencing in microfabricated high-density picolitre reactors
-
DOI 10.1038/nature03959, PII N03959
-
Margulies, M. et al. Genome sequencing in microfabricated high-density picolitre reactors. Nature 437, 376-380 (2005). (Pubitemid 41613494)
-
(2005)
Nature
, vol.437
, Issue.7057
, pp. 376-380
-
-
Margulies, M.1
Egholm, M.2
Altman, W.E.3
Attiya, S.4
Bader, J.S.5
Bemben, L.A.6
Berka, J.7
Braverman, M.S.8
Chen, Y.-J.9
Chen, Z.10
Dewell, S.B.11
Du, L.12
Fierro, J.M.13
Gomes, X.V.14
Godwin, B.C.15
He, W.16
Helgesen, S.17
Ho, C.H.18
Irzyk, G.P.19
Jando, S.C.20
Alenquer, M.L.I.21
Jarvie, T.P.22
Jirage, K.B.23
Kim, J.-B.24
Knight, J.R.25
Lanza, J.R.26
Leamon, J.H.27
Lefkowitz, S.M.28
Lei, M.29
Li, J.30
Lohman, K.L.31
Lu, H.32
Makhijani, V.B.33
McDade, K.E.34
McKenna, M.P.35
Myers, E.W.36
Nickerson, E.37
Nobile, J.R.38
Plant, R.39
Puc, B.P.40
Ronan, M.T.41
Roth, G.T.42
Sarkis, G.J.43
Simons, J.F.44
Simpson, J.W.45
Srinivasan, M.46
Tartaro, K.R.47
Tomasz, A.48
Vogt, K.A.49
Volkmer, G.A.50
Wang, S.H.51
Wang, Y.52
Weiner, M.P.53
Yu, P.54
Begley, R.F.55
Rothberg, J.M.56
more..
-
54
-
-
79960696818
-
Java web tools for PCR, in silico PCR, and oligonucleotide assembly and analysis
-
Kalendar, R., Lee, D. & Schulman, A. H. Java web tools for PCR, in silico PCR, and oligonucleotide assembly and analysis. Genomics 98, 137-144 (2011).
-
(2011)
Genomics
, vol.98
, pp. 137-144
-
-
Kalendar, R.1
Lee, D.2
Schulman, A.H.3
-
55
-
-
84883478660
-
Gut microbiota from twins discordant for obesity modulate metabolism in mice
-
Ridaura, V. K. et al. Gut microbiota from twins discordant for obesity modulate metabolism in mice. Science 341, 1241214 (2013).
-
(2013)
Science
, vol.341
, pp. 1241214
-
-
Ridaura, V.K.1
-
56
-
-
34147132825
-
Identifying bacterial genes and endosymbiont DNA with Glimmer
-
DOI 10.1093/bioinformatics/btm009
-
Delcher, A. L., Bratke, K. A., Powers, E. C. & Salzberg, S. L. Identifying bacterial genes and endosymbiont DNA with Glimmer. Bioinformatics 23, 673-679 (2007). (Pubitemid 46554717)
-
(2007)
Bioinformatics
, vol.23
, Issue.6
, pp. 673-679
-
-
Delcher, A.L.1
Bratke, K.A.2
Powers, E.C.3
Salzberg, S.L.4
-
57
-
-
74049108922
-
BLAST\+: Architecture and applications
-
Camacho, C. et al. BLAST\+: architecture and applications. BMC Bioinformatics 10, 421 (2009).
-
(2009)
BMC Bioinformatics
, vol.10
, pp. 421
-
-
Camacho, C.1
-
58
-
-
80054078476
-
Fast, scalable generation of high-quality protein multiple sequence alignments using Clustal Omega
-
Sievers, F. et al. Fast, scalable generation of high-quality protein multiple sequence alignments using Clustal Omega. Mol. Syst. Biol. 7, 539 (2011).
-
(2011)
Mol. Syst. Biol.
, vol.7
, pp. 539
-
-
Sievers, F.1
-
59
-
-
42649099266
-
Conservation of divergent transcription in fungi
-
Kensche, P. R., Oti, M., Dutilh, B. E. & Huynen, M. A. Conservation of divergent transcription in fungi. Trends Genet. 24, 207-211 (2008).
-
(2008)
Trends Genet
, vol.24
, pp. 207-211
-
-
Kensche, P.R.1
Oti, M.2
Dutilh, B.E.3
Huynen, M.A.4
-
60
-
-
84859739224
-
Domain enhanced lookup time accelerated BLAST
-
Boratyn, G. M. et al. Domain enhanced lookup time accelerated BLAST. Biol. Direct. 7, 12 (2012).
-
(2012)
Biol. Direct.
, vol.7
, pp. 12
-
-
Boratyn, G.M.1
-
61
-
-
0034786532
-
The HMMTOP transmembrane topology prediction server
-
Tusnady, G. E. & Simon, I. The HMMTOP transmembrane topology prediction server. Bioinformatics 17, 849-850 (2001). (Pubitemid 32970487)
-
(2001)
Bioinformatics
, vol.17
, Issue.9
, pp. 849-850
-
-
Tusnady, G.E.1
Simon, I.2
-
62
-
-
2442713832
-
Genewise and genomewise
-
DOI 10.1101/gr.1865504
-
Birney, E., Clamp, M. & Durbin, R. GeneWise and Genomewise. Genome Res. 14, 988-995 (2004). (Pubitemid 38660520)
-
(2004)
Genome Research
, vol.14
, Issue.5
, pp. 988-995
-
-
Birney, E.1
Clamp, M.2
Durbin, R.3
-
63
-
-
33646191863
-
Ig-like domains on bacteriophages: A tale of promiscuity and deceit
-
Fraser, J. S., Yu, Z., Maxwell, K. L. & Davidson, A. R. Ig-like domains on bacteriophages: a tale of promiscuity and deceit. J.. Mol. Biol. 359, 496-507 (2006).
-
(2006)
J. Mol. Biol.
, vol.359
, pp. 496-507
-
-
Fraser, J.S.1
Yu, Z.2
Maxwell, K.L.3
Davidson, A.R.4
-
64
-
-
0000122573
-
PHYLIP-phylogeny inference package (Version 3.2)
-
Felsenstein, J. PHYLIP-Phylogeny Inference Package (Version 3.2). Cladistics 5, 164-166 (1989).
-
(1989)
Cladistics
, vol.5
, pp. 164-166
-
-
Felsenstein, J.1
-
65
-
-
62349130698
-
Ultrafast and memoryefficient alignment of short DNA sequences to the human genome
-
Langmead, B., Trapnell, C., Pop, M. & Salzberg, S. L. Ultrafast and memoryefficient alignment of short DNA sequences to the human genome. Genome Biol. 10, R25 (2009).
-
(2009)
Genome Biol.
, vol.10
-
-
Langmead, B.1
Trapnell, C.2
Pop, M.3
Salzberg, S.L.4
-
66
-
-
77953050946
-
A catalog of reference genomes from the human microbiome
-
Nelson, K. E. et al. A catalog of reference genomes from the human microbiome. Science 328, 994-999 (2010).
-
(2010)
Science
, vol.328
, pp. 994-999
-
-
Nelson, K.E.1
-
67
-
-
0030807655
-
BIONJ: An improved version of the NJ algorithm based on a simple model of sequence data
-
Gascuel, O. BIONJ: an improved version of the NJ algorithm based on a simple model of sequence data. Mol. Biol. Evol. 14, 685-695 (1997). (Pubitemid 27287289)
-
(1997)
Molecular Biology and Evolution
, vol.14
, Issue.7
, pp. 685-695
-
-
Gascuel, O.1
-
68
-
-
0023378298
-
Bacteriophages active against Bacteroides fragilis in sewage-polluted waters
-
Tartera, C. & Jofre, J. Bacteriophages active against Bacteroides fragilis in sewage-polluted waters. Appl. Environ. Microbiol. 53, 1632-1637 (1987).
-
(1987)
Appl. Environ. Microbiol.
, vol.53
, pp. 1632-1637
-
-
Tartera, C.1
Jofre, J.2
-
69
-
-
84862141704
-
Human gut microbiome viewed across age and geography
-
Yatsunenko, T. et al. Human gut microbiome viewed across age and geography. Nature 486, 222-227 (2012).
-
(2012)
Nature
, vol.486
, pp. 222-227
-
-
Yatsunenko, T.1
|