-
1
-
-
0025183708
-
Basic local alignment search tool
-
Altschul SF, Gish W, Miller W, Myers EW, Lipman DJ. 1990. Basic local alignment search tool. J Mol Biol 215: 403-410.
-
(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
-
2
-
-
0034069495
-
Gene ontology: Tool for the unification of biology
-
Ashburner M, Ball CA, Blake JA, Botstein D, Butler H, Cherry JM, Davis AP, Dolinski K, Dwight SS, Eppig JT, et al. 2000. Gene ontology: tool for the unification of biology. Nat Genet 25: 25-29.
-
(2000)
Nat Genet
, vol.25
, pp. 25-29
-
-
Ashburner, M.1
Ball, C.A.2
Blake, J.A.3
Botstein, D.4
Butler, H.5
Cherry, J.M.6
Davis, A.P.7
Dolinski, K.8
Dwight, S.S.9
Eppig, J.T.10
-
3
-
-
84929297936
-
Dynamics and stabilization of the human gut microbiome during the first year of life
-
Backhed F, Roswall J, Peng Y, Feng Q, Jia H, Kovatcheva-Datchary P, Li Y, Xia Y, Xie H, Zhong H, et al. 2015. Dynamics and stabilization of the human gut microbiome during the first year of life. Cell Host Microbe 17: 690-703.
-
(2015)
Cell Host Microbe
, vol.17
, pp. 690-703
-
-
Backhed, F.1
Roswall, J.2
Peng, Y.3
Feng, Q.4
Jia, H.5
Kovatcheva-Datchary, P.6
Li, Y.7
Xia, Y.8
Xie, H.9
Zhong, H.10
-
4
-
-
84975068696
-
Antibiotics, birth mode, and diet shape microbiome maturation during early life
-
Bokulich NA, Chung J, Battaglia T, Henderson N, Jay M, Li H, Lieber AD, Wu F, Perez-Perez GI, Chen Y, et al. 2016. Antibiotics, birth mode, and diet shape microbiome maturation during early life. Sci Transl Med 8: 343ra382.
-
(2016)
Sci Transl Med
, vol.8
, pp. 343ra382
-
-
Bokulich, N.A.1
Chung, J.2
Battaglia, T.3
Henderson, N.4
Jay, M.5
Li, H.6
Lieber, A.D.7
Wu, F.8
Perez-Perez, G.I.9
Chen, Y.10
-
5
-
-
84969704060
-
Culturing of 'unculturable' human microbiota reveals novel taxa and extensive sporulation
-
Browne HP, Forster SC, Anonye BO, Kumar N, Neville BA, Stares MD, Goulding D, Lawley TD. 2016. Culturing of 'unculturable' human microbiota reveals novel taxa and extensive sporulation. Nature 533: 543-546.
-
(2016)
Nature
, vol.533
, pp. 543-546
-
-
Browne, H.P.1
Forster, S.C.2
Anonye, B.O.3
Kumar, N.4
Neville, B.A.5
Stares, M.D.6
Goulding, D.7
Lawley, T.D.8
-
6
-
-
84942279620
-
High speed BLASTN: An accelerated MegaBLAST search tool
-
Chen Y, Ye W, Zhang Y, Xu Y. 2015. High speed BLASTN: an accelerated MegaBLAST search tool. Nucleic Acids Res 43: 7762-7768.
-
(2015)
Nucleic Acids Res
, vol.43
, pp. 7762-7768
-
-
Chen, Y.1
Ye, W.2
Zhang, Y.3
Xu, Y.4
-
7
-
-
84943595976
-
Detection of low-abundance bacterial strains in metagenomic datasets by eigengenome partitioning
-
Cleary B, Brito IL, Huang K, Gevers D, Shea T, Young S, Alm EJ. 2015. Detection of low-abundance bacterial strains in metagenomic datasets by eigengenome partitioning. Nat Biotechnol 33: 1053-1060.
-
(2015)
Nat Biotechnol
, vol.33
, pp. 1053-1060
-
-
Cleary, B.1
Brito, I.L.2
Huang, K.3
Gevers, D.4
Shea, T.5
Young, S.6
Alm, E.J.7
-
8
-
-
80055082271
-
Accelerated profile HMM searches
-
Eddy SR. 2011. Accelerated profile HMM searches. PLoS Comput Biol 7: e1002195.
-
(2011)
PLoS Comput Biol
, vol.7
, pp. e1002195
-
-
Eddy, S.R.1
-
9
-
-
77957244650
-
Search and clustering orders of magnitude faster than BLAST
-
Edgar RC. 2010. Search and clustering orders of magnitude faster than BLAST. Bioinformatics 26: 2460-2461.
-
(2010)
Bioinformatics
, vol.26
, pp. 2460-2461
-
-
Edgar, R.C.1
-
10
-
-
84879744885
-
The longterm stability of the human gut microbiota
-
Faith JJ, Guruge JL, Charbonneau M, Subramanian S, Seedorf H, Goodman AL, Clemente JC, Knight R, Heath AC, Leibel RL, et al. 2013. The longterm stability of the human gut microbiota. Science 341: 1237439.
-
(2013)
Science
, vol.341
, pp. 1237439
-
-
Faith, J.J.1
Guruge, J.L.2
Charbonneau, M.3
Subramanian, S.4
Seedorf, H.5
Goodman, A.L.6
Clemente, J.C.7
Knight, R.8
Heath, A.C.9
Leibel, R.L.10
-
11
-
-
84871826193
-
Cross-biome metagenomic analyses of soil microbial communities and their functional attributes
-
Fierer N, Leff JW, Adams BJ, Nielsen UN, Bates ST, Lauber CL, Owens S, Gilbert JA, Wall DH, Caporaso JG. 2012. Cross-biome metagenomic analyses of soil microbial communities and their functional attributes. Proc Natl Acad Sci 109: 21390-21395.
-
(2012)
Proc Natl Acad Sci
, vol.109
, pp. 21390-21395
-
-
Fierer, N.1
Leff, J.W.2
Adams, B.J.3
Nielsen, U.N.4
Bates, S.T.5
Lauber, C.L.6
Owens, S.7
Gilbert, J.A.8
Wall, D.H.9
Caporaso, J.G.10
-
12
-
-
84885070139
-
Pathoscope: Species identification and strain attribution with unassembled sequencing data
-
Francis OE, Bendall M, Manimaran S, Hong C, Clement NL, Castro-Nallar E, Snell Q, Schaalje GB, Clement MJ, Crandall KA, et al. 2013. Pathoscope: species identification and strain attribution with unassembled sequencing data. Genome Res 23: 1721-1729.
-
(2013)
Genome Res
, vol.23
, pp. 1721-1729
-
-
Francis, O.E.1
Bendall, M.2
Manimaran, S.3
Hong, C.4
Clement, N.L.5
Castro-Nallar, E.6
Snell, Q.7
Schaalje, G.B.8
Clement, M.J.9
Crandall, K.A.10
-
13
-
-
84969492201
-
Genetic determinants of the gut microbiome in UK twins
-
Goodrich JK, Davenport ER, Beaumont M, Jackson MA, Knight R, Ober C, Spector TD, Bell JT, Clark AG, Ley RE. 2016. Genetic determinants of the gut microbiome in UK twins. Cell Host Microbe 19: 731-743.
-
(2016)
Cell Host Microbe
, vol.19
, pp. 731-743
-
-
Goodrich, J.K.1
Davenport, E.R.2
Beaumont, M.3
Jackson, M.A.4
Knight, R.5
Ober, C.6
Spector, T.D.7
Bell, J.T.8
Clark, A.G.9
Ley, R.E.10
-
14
-
-
84922735613
-
Extensive strain-level copy-number variation across human gut microbiome species
-
Greenblum S, Carr R, Borenstein E. 2015. Extensive strain-level copy-number variation across human gut microbiome species. Cell 160: 583-594.
-
(2015)
Cell
, vol.160
, pp. 583-594
-
-
Greenblum, S.1
Carr, R.2
Borenstein, E.3
-
15
-
-
84862286169
-
A framework for human microbiome research
-
The Human Microbiome Project Consortium. 2012. A framework for human microbiome research. Nature 486: 215-221.
-
(2012)
Nature
, vol.486
, pp. 215-221
-
-
-
16
-
-
0033982936
-
KEGG: Kyoto encyclopedia of genes and genomes
-
Kanehisa M, Goto S. 2000. KEGG: Kyoto encyclopedia of genes and genomes. Nucleic Acids Res 28: 27-30.
-
(2000)
Nucleic Acids Res
, vol.28
, pp. 27-30
-
-
Kanehisa, M.1
Goto, S.2
-
17
-
-
84899559579
-
Single-cell genomics reveals hundreds of coexisting subpopulations in wild Prochlorococcus
-
Kashtan N, Roggensack SE, Rodrigue S, Thompson JW, Biller SJ, Coe A, Ding H, Marttinen P, Malmstrom RR, Stocker R, et al. 2014. Single-cell genomics reveals hundreds of coexisting subpopulations in wild Prochlorococcus. Science 344: 416-420.
-
(2014)
Science
, vol.344
, pp. 416-420
-
-
Kashtan, N.1
Roggensack, S.E.2
Rodrigue, S.3
Thompson, J.W.4
Biller, S.J.5
Coe, A.6
Ding, H.7
Marttinen, P.8
Malmstrom, R.R.9
Stocker, R.10
-
18
-
-
79952763661
-
Succession of microbial consortia in the developing infant gut microbiome
-
Koenig JE, Spora A, Scalfonea N, Frickera AD, Stombaugh J, Knight R, Angenent LT, Ley RE. 2011. Succession of microbial consortia in the developing infant gut microbiome. Proc Natl Acad Sci 108(Suppl 1): 4578-4585.
-
(2011)
Proc Natl Acad Sci
, vol.108
, pp. 4578-4585
-
-
Koenig, J.E.1
Spora, A.2
Scalfonea, N.3
Frickera, A.D.4
Stombaugh, J.5
Knight, R.6
Angenent, L.T.7
Ley, R.E.8
-
20
-
-
2942538300
-
Versatile and open software for comparing large genomes
-
Kurtz S, Phillippy A, Delcher AL, Smoot M, Shumway M, Antonescu C, Salzberg SL. 2004. Versatile and open software for comparing large genomes. Genome Biol 5: R12.
-
(2004)
Genome Biol
, vol.5
, pp. R12
-
-
Kurtz, S.1
Phillippy, A.2
Delcher, A.L.3
Smoot, M.4
Shumway, M.5
Antonescu, C.6
Salzberg, S.L.7
-
21
-
-
84883172257
-
Global marine bacterial diversity peaks at high latitudes in winter
-
Ladau J, Sharpton TJ, Finucane MM, Jospin G, Kembel SW, O'Dwyer J, Koeppel AF, Green JL, Pollard KS. 2013. Global marine bacterial diversity peaks at high latitudes in winter. ISME J 7: 1669-1677.
-
(2013)
ISME J
, vol.7
, pp. 1669-1677
-
-
Ladau, J.1
Sharpton, T.J.2
Finucane, M.M.3
Jospin, G.4
Kembel, S.W.5
O'Dwyer, J.6
Koeppel, A.F.7
Green, J.L.8
Pollard, K.S.9
-
22
-
-
84925517557
-
Insights from 20 years of bacterial genome sequencing
-
Land M, Hauser L, Jun SR, Nookaew I, Leuze MR, Ahn TH, Karpinets T, Lund O, Kora G, Wassenaar T, et al. 2015. Insights from 20 years of bacterial genome sequencing. Funct Integr Genomics 15: 141-161.
-
(2015)
Funct Integr Genomics
, vol.15
, pp. 141-161
-
-
Land, M.1
Hauser, L.2
Jun, S.R.3
Nookaew, I.4
Leuze, M.R.5
Ahn, T.H.6
Karpinets, T.7
Lund, O.8
Kora, G.9
Wassenaar, T.10
-
23
-
-
84859210032
-
Fast gapped-read alignment with Bowtie 2
-
Langmead B, Salzberg SL. 2012. Fast gapped-read alignment with Bowtie 2. Nat Methods 9: 357-359.
-
(2012)
Nat Methods
, vol.9
, pp. 357-359
-
-
Langmead, B.1
Salzberg, S.L.2
-
24
-
-
78651301328
-
The sequence read archive
-
(Database issue)
-
Leinonen R, Sugawara H, Shumway M, International Nucleotide Sequence Database Collaboration. 2011. The sequence read archive. Nucleic Acids Res 39(Database issue): D19-D21.
-
(2011)
Nucleic Acids Res
, vol.39
, pp. D19-D21
-
-
Leinonen, R.1
Sugawara, H.2
Shumway, M.3
-
25
-
-
68549104404
-
The Sequence Alignment/Map format and SAMtools
-
Li H, Handsaker B, Wysoker A, Fennell T, Ruan J, Homer N, Marth G, Abecasis G, Durbin R, Genome Project Data Processing Subgroup. 2009. The Sequence Alignment/Map format and SAMtools. Bioinformatics 25: 2078-2079.
-
(2009)
Bioinformatics
, vol.25
, pp. 2078-2079
-
-
Li, H.1
Handsaker, B.2
Wysoker, A.3
Fennell, T.4
Ruan, J.5
Homer, N.6
Marth, G.7
Abecasis, G.8
Durbin, R.9
-
26
-
-
84905730165
-
An integrated catalog of reference genes in the human gut microbiome
-
Li J, Jia H, Cai X, Zhong H, Feng Q, Sunagawa S, Arumugam M, Kultima JR, Prifti E, Nielsen T, et al. 2014. An integrated catalog of reference genes in the human gut microbiome. Nat Biotechnol 32: 834-841.
-
(2014)
Nat Biotechnol
, vol.32
, pp. 834-841
-
-
Li, J.1
Jia, H.2
Cai, X.3
Zhong, H.4
Feng, Q.5
Sunagawa, S.6
Arumugam, M.7
Kultima, J.R.8
Prifti, E.9
Nielsen, T.10
-
27
-
-
84968880438
-
Durable coexistence of donor and recipient strains after fecal microbiota transplantation
-
Li SS, Zhu A, Benes V, Costea PI, Hercog R, Hildebrand F, Huerta-Cepas J, Nieuwdorp M, Salojarvi J, Voigt AY, et al. 2016. Durable coexistence of donor and recipient strains after fecal microbiota transplantation. Science 352: 586-589.
-
(2016)
Science
, vol.352
, pp. 586-589
-
-
Li, S.S.1
Zhu, A.2
Benes, V.3
Costea, P.I.4
Hercog, R.5
Hildebrand, F.6
Huerta-Cepas, J.7
Nieuwdorp, M.8
Salojarvi, J.9
Voigt, A.Y.10
-
28
-
-
84891351800
-
Genetic variation of a bacterial pathogen within individuals with cystic fibrosis provides a record of selective pressures
-
Lieberman TD, Flett KB, Yelin I, Martin TR, McAdam AJ, Priebe GP, Kishony R. 2014. Genetic variation of a bacterial pathogen within individuals with cystic fibrosis provides a record of selective pressures. Nat Genet 46: 82-87.
-
(2014)
Nat Genet
, vol.46
, pp. 82-87
-
-
Lieberman, T.D.1
Flett, K.B.2
Yelin, I.3
Martin, T.R.4
McAdam, A.J.5
Priebe, G.P.6
Kishony, R.7
-
29
-
-
46249133773
-
Efficient algorithms for accurate hierarchical clustering of huge datasets: Tackling the entire protein space
-
Loewenstein Y, Portugaly E, Fromer M, Linial M. 2008. Efficient algorithms for accurate hierarchical clustering of huge datasets: tackling the entire protein space. Bioinformatics 24: i41-i49.
-
(2008)
Bioinformatics
, vol.24
, pp. i41-i49
-
-
Loewenstein, Y.1
Portugaly, E.2
Fromer, M.3
Linial, M.4
-
30
-
-
84943606160
-
ConStrains identifies microbial strains in metagenomic datasets
-
Luo C, Knight R, Siljander H, Knip M, Xavier RJ, Gevers D. 2015. ConStrains identifies microbial strains in metagenomic datasets. Nat Biotechnol 33: 1045-1052.
-
(2015)
Nat Biotechnol
, vol.33
, pp. 1045-1052
-
-
Luo, C.1
Knight, R.2
Siljander, H.3
Knip, M.4
Xavier, R.J.5
Gevers, D.6
-
31
-
-
84893685421
-
Mother-to-infant transmission of intestinal bifidobacterial strains has an impact on the early development of vaginally delivered infant's microbiota
-
Makino H, Kushiro A, Ishikawa E, Kubota H, Gawad A, Sakai T, Oishi K, Martin R, Ben-Amor K, Knol J, et al. 2013. Mother-to-infant transmission of intestinal bifidobacterial strains has an impact on the early development of vaginally delivered infant's microbiota. PLoS One 8: e78331.
-
(2013)
PLoS One
, vol.8
, pp. e78331
-
-
Makino, H.1
Kushiro, A.2
Ishikawa, E.3
Kubota, H.4
Gawad, A.5
Sakai, T.6
Oishi, K.7
Martin, R.8
Ben-Amor, K.9
Knol, J.10
-
32
-
-
84856085544
-
Sharing of bacterial strains between breast milk and infant feces
-
Martín V, Maldonado-Barragán A, Moles L, Rodriguez-Baños M, Campo RD, Fernández L, Rodríguez JM, Jiménez E. 2012. Sharing of bacterial strains between breast milk and infant feces. J Hum Lact 28: 36-44.
-
(2012)
J Hum Lact
, vol.28
, pp. 36-44
-
-
Martín, V.1
Maldonado-Barragán, A.2
Moles, L.3
Rodriguez-Baños, M.4
Campo, R.D.5
Fernández, L.6
Rodríguez, J.M.7
Jiménez, E.8
-
33
-
-
84883464181
-
Accurate and universal delineation of prokaryotic species
-
Mende DR, Sunagawa S, Zeller G, Bork P. 2013. Accurate and universal delineation of prokaryotic species. Nat Methods 10: 881-884.
-
(2013)
Nat Methods
, vol.10
, pp. 881-884
-
-
Mende, D.R.1
Sunagawa, S.2
Zeller, G.3
Bork, P.4
-
35
-
-
84943327494
-
Exploring vertical transmission of bifidobacteria from mother to child
-
Milani C, Mancabelli L, Lugli GA, Duranti S, Turroni F, Ferrario C, Mangifesta M, Viappiani A, Ferretti P, Gorfer V, et al. 2015. Exploring vertical transmission of bifidobacteria from mother to child. Appl Environ Microbiol 81: 7078-7087.
-
(2015)
Appl Environ Microbiol
, vol.81
, pp. 7078-7087
-
-
Milani, C.1
Mancabelli, L.2
Lugli, G.A.3
Duranti, S.4
Turroni, F.5
Ferrario, C.6
Mangifesta, M.7
Viappiani, A.8
Ferretti, P.9
Gorfer, V.10
-
36
-
-
84939141968
-
Average genome size estimation improves comparative metagenomics and sheds light on the functional ecology of the human microbiome
-
Nayfach S, Pollard KS. 2015. Average genome size estimation improves comparative metagenomics and sheds light on the functional ecology of the human microbiome. Genome Biol 16: 51.
-
(2015)
Genome Biol
, vol.16
, pp. 51
-
-
Nayfach, S.1
Pollard, K.S.2
-
37
-
-
84905730761
-
Identification and assembly of genomes and genetic elements in complex metagenomic samples without using reference genomes
-
Nielsen HB, Almeida M, Juncker AS, Rasmussen S, Li J, Sunagawa S, Plichta DR, Gautier L, Pedersen AG, Le Chatelier E, et al. 2014. Identification and assembly of genomes and genetic elements in complex metagenomic samples without using reference genomes. Nat Biotechnol 32: 822-828.
-
(2014)
Nat Biotechnol
, vol.32
, pp. 822-828
-
-
Nielsen, H.B.1
Almeida, M.2
Juncker, A.S.3
Rasmussen, S.4
Li, J.5
Sunagawa, S.6
Plichta, D.R.7
Gautier, L.8
Pedersen, A.G.9
Le-Chatelier, E.10
-
38
-
-
55549115654
-
Genes mirror geography within Europe
-
Novembre J, Johnson T, Bryc K, Kutalik Z, Boyko AR, Auton A, Indap A, King KS, Bergmann S, Nelson MR, et al. 2008. Genes mirror geography within Europe. Nature 456: 98-101.
-
(2008)
Nature
, vol.456
, pp. 98-101
-
-
Novembre, J.1
Johnson, T.2
Bryc, K.3
Kutalik, Z.4
Boyko, A.R.5
Auton, A.6
Indap, A.7
King, K.S.8
Bergmann, S.9
Nelson, M.R.10
-
39
-
-
84925708427
-
Subsistence strategies in traditional societies distinguish gut microbiomes
-
Obregon-Tito AJ, Tito RY, Metcalf J, Sankaranarayanan K, Clemente JC, Ursell LK, Zech Xu Z, Van Treuren W, Knight R, Gaffney PM, et al. 2015. Subsistence strategies in traditional societies distinguish gut microbiomes. Nat Commun 6: 6505.
-
(2015)
Nat Commun
, vol.6
, pp. 6505
-
-
Obregon-Tito, A.J.1
Tito, R.Y.2
Metcalf, J.3
Sankaranarayanan, K.4
Clemente, J.C.5
Ursell, L.K.6
Zech-Xu, Z.7
Van-Treuren, W.8
Knight, R.9
Gaffney, P.M.10
-
40
-
-
84867074831
-
A metagenome-wide association study of gut microbiota in type 2 diabetes
-
Qin J, Li Y, Cai Z, Li S, Zhu J, Zhang F, Liang S, Zhang W, Guan Y, Shen D, et al. 2012. A metagenome-wide association study of gut microbiota in type 2 diabetes. Nature 490: 55-60.
-
(2012)
Nature
, vol.490
, pp. 55-60
-
-
Qin, J.1
Li, Y.2
Cai, Z.3
Li, S.4
Zhu, J.5
Zhang, F.6
Liang, S.7
Zhang, W.8
Guan, Y.9
Shen, D.10
-
41
-
-
84937519881
-
Metagenome sequencing of the Hadza hunter-gatherer gut microbiota
-
Rampelli S, Schnorr SL, Consolandi C, Turroni S, Severgnini M, Peano C, Brigidi P, Crittenden AN, Henry AG, Candela M. 2015. Metagenome sequencing of the Hadza hunter-gatherer gut microbiota. Curr Biol 25: 1682-1693.
-
(2015)
Curr Biol
, vol.25
, pp. 1682-1693
-
-
Rampelli, S.1
Schnorr, S.L.2
Consolandi, C.3
Turroni, S.4
Severgnini, M.5
Peano, C.6
Brigidi, P.7
Crittenden, A.N.8
Henry, A.G.9
Candela, M.10
-
42
-
-
80052150179
-
Origins of the E. Coli strain causing an outbreak of hemolytic-uremic syndrome in Germany
-
Rasko DA, Webster DR, Sahl JW, Bashir A, Boisen N, Scheutz F, Paxinos EE, Sebra R, Chin CS, Iliopoulos D, et al. 2011. Origins of the E. coli strain causing an outbreak of hemolytic-uremic syndrome in Germany. N Engl J Med 365: 709-717.
-
(2011)
N Engl J Med
, vol.365
, pp. 709-717
-
-
Rasko, D.A.1
Webster, D.R.2
Sahl, J.W.3
Bashir, A.4
Boisen, N.5
Scheutz, F.6
Paxinos, E.E.7
Sebra, R.8
Chin, C.S.9
Iliopoulos, D.10
-
43
-
-
73149098333
-
Shifting the genomic gold standard for the prokaryotic species definition
-
Richter M, Rossello-Mora R. 2009. Shifting the genomic gold standard for the prokaryotic species definition. Proc Natl Acad Sci 106: 19126-19131.
-
(2009)
Proc Natl Acad Sci
, vol.106
, pp. 19126-19131
-
-
Richter, M.1
Rossello-Mora, R.2
-
44
-
-
84881138595
-
Insights into the phylogeny and coding potential of microbial dark matter
-
Rinke C, Schwientek P, Sczyrba A, Ivanova NN, Anderson IJ, Cheng JF, Darling A, Malfatti S, Swan BK, Gies EA, et al. 2013. Insights into the phylogeny and coding potential of microbial dark matter. Nature 499: 431-437.
-
(2013)
Nature
, vol.499
, pp. 431-437
-
-
Rinke, C.1
Schwientek, P.2
Sczyrba, A.3
Ivanova, N.N.4
Anderson, I.J.5
Cheng, J.F.6
Darling, A.7
Malfatti, S.8
Swan, B.K.9
Gies, E.A.10
-
45
-
-
84930626863
-
Fine-scale diversity and extensive recombination in a quasisexual bacterial population occupying a broad niche
-
Rosen MJ, Davison M, Bhaya D, Fisher DS. 2015. Fine-scale diversity and extensive recombination in a quasisexual bacterial population occupying a broad niche. Science 348: 1019-1023.
-
(2015)
Science
, vol.348
, pp. 1019-1023
-
-
Rosen, M.J.1
Davison, M.2
Bhaya, D.3
Fisher, D.S.4
-
46
-
-
84934275888
-
Phylogenetically typing bacterial strains from partial SNP genotypes observed from direct sequencing of clinical specimen metagenomic data
-
Sahl JW, Schupp JM, Rasko DA, Colman RE, Foster JT, Keim P. 2015. Phylogenetically typing bacterial strains from partial SNP genotypes observed from direct sequencing of clinical specimen metagenomic data. Genome Med 7: 52.
-
(2015)
Genome Med
, vol.7
, pp. 52
-
-
Sahl, J.W.1
Schupp, J.M.2
Rasko, D.A.3
Colman, R.E.4
Foster, J.T.5
Keim, P.6
-
47
-
-
84871732071
-
Genomic variation landscape of the human gut microbiome
-
Schloissnig S, Arumugam M, Sunagawa S, Mitreva M, Tap J, Zhu A, Waller A, Mende DR, Kultima JR, Martin J, et al. 2013. Genomic variation landscape of the human gut microbiome. Nature 493: 45-50.
-
(2013)
Nature
, vol.493
, pp. 45-50
-
-
Schloissnig, S.1
Arumugam, M.2
Sunagawa, S.3
Mitreva, M.4
Tap, J.5
Zhu, A.6
Waller, A.7
Mende, D.R.8
Kultima, J.R.9
Martin, J.10
-
48
-
-
84923080032
-
Gut microbiome of the Hadza hunter-gatherers
-
Schnorr SL, Candela M, Rampelli S, Centanni M, Consolandi C, Basaglia G, Turroni S, Biagi E, Peano C, Severgnini M, et al. 2014. Gut microbiome of the Hadza hunter-gatherers. Nat Commun 5: 3654.
-
(2014)
Nat Commun
, vol.5
, pp. 3654
-
-
Schnorr, S.L.1
Candela, M.2
Rampelli, S.3
Centanni, M.4
Consolandi, C.5
Basaglia, G.6
Turroni, S.7
Biagi, E.8
Peano, C.9
Severgnini, M.10
-
49
-
-
84961392884
-
Strain-level microbial epidemiology and population genomics from shotgun metagenomics
-
Scholz M, Ward DV, Pasolli E, Tolio T, Zolfo M, Asnicar F, Truong DT, Tett A, Morrow AL, Segata N. 2016. Strain-level microbial epidemiology and population genomics from shotgun metagenomics. Nat Methods 13: 435-438.
-
(2016)
Nat Methods
, vol.13
, pp. 435-438
-
-
Scholz, M.1
Ward, D.V.2
Pasolli, E.3
Tolio, T.4
Zolfo, M.5
Asnicar, F.6
Truong, D.T.7
Tett, A.8
Morrow, A.L.9
Segata, N.10
-
50
-
-
84859499489
-
Population genomics of early events in the ecological differentiation of bacteria
-
Shapiro BJ, Friedman J, Cordero OX, Preheim SP, Timberlake SC, Szabo G, Polz MF, Alm EJ. 2012. Population genomics of early events in the ecological differentiation of bacteria. Science 336: 48-51.
-
(2012)
Science
, vol.336
, pp. 48-51
-
-
Shapiro, B.J.1
Friedman, J.2
Cordero, O.X.3
Preheim, S.P.4
Timberlake, S.C.5
Szabo, G.6
Polz, M.F.7
Alm, E.J.8
-
51
-
-
80051985519
-
Genome-wide recombination drives diversification of epidemic strains of Acinetobacter baumannii
-
Snitkin ES, Zelazny AM, Montero CI, Stock F, Mijares L; NISC-Comparative-Sequence-Program, Murray PR, Segre JA. 2011. Genome-wide recombination drives diversification of epidemic strains of Acinetobacter baumannii. Proc Natl Acad Sci 108: 13758-13763.
-
(2011)
Proc Natl Acad Sci
, vol.108
, pp. 13758-13763
-
-
Snitkin, E.S.1
Zelazny, A.M.2
Montero, C.I.3
Stock, F.4
Mijares, L.5
Murray, P.R.6
Segre, J.A.7
-
52
-
-
84868098266
-
Single cell genomics: An individual look at microbes
-
Stepanauskas R. 2012. Single cell genomics: an individual look at microbes. Curr Opin Microbiol 15: 613-620.
-
(2012)
Curr Opin Microbiol
, vol.15
, pp. 613-620
-
-
Stepanauskas, R.1
-
53
-
-
84888884475
-
Metagenomic species profiling using universal phylogenetic marker genes
-
Sunagawa S, Mende DR, Zeller G, Izquierdo-Carrasco F, Berger SA, Kultima JR, Coelho LP, Arumugam M, Tap J, Nielsen HB, et al. 2013. Metagenomic species profiling using universal phylogenetic marker genes. Nat Methods 10: 1196-1199.
-
(2013)
Nat Methods
, vol.10
, pp. 1196-1199
-
-
Sunagawa, S.1
Mende, D.R.2
Zeller, G.3
Izquierdo-Carrasco, F.4
Berger, S.A.5
Kultima, J.R.6
Coelho, L.P.7
Arumugam, M.8
Tap, J.9
Nielsen, H.B.10
-
54
-
-
84929992013
-
Ocean plankton. Structure and function of the global ocean microbiome
-
Sunagawa S, Coelho LP, Chaffron S, Kultima JR, Labadie K, Salazar G, Djahanschiri B, Zeller G, Mende DR, Alberti A, et al. 2015. Ocean plankton. Structure and function of the global ocean microbiome. Science 348: 1261359.
-
(2015)
Science
, vol.348
, pp. 1261359
-
-
Sunagawa, S.1
Coelho, L.P.2
Chaffron, S.3
Kultima, J.R.4
Labadie, K.5
Salazar, G.6
Djahanschiri, B.7
Zeller, G.8
Mende, D.R.9
Alberti, A.10
-
55
-
-
0025281452
-
Plasmid profiling of members of the family Enterobacteriaceae, Lactobacilli, and Bifidobacteria to study the transmission of bacteria from mother to infant
-
Tannock GW, Fuller R, Smith SL, Hall MA. 1990. Plasmid profiling of members of the family Enterobacteriaceae, Lactobacilli, and Bifidobacteria to study the transmission of bacteria from mother to infant. J Clin Microbiol 28: 1225-1228.
-
(1990)
J Clin Microbiol
, vol.28
, pp. 1225-1228
-
-
Tannock, G.W.1
Fuller, R.2
Smith, S.L.3
Hall, M.A.4
-
56
-
-
84899792426
-
Strain/species identification in metagenomes using genome-specific markers
-
Tu Q, He Z, Zhou J. 2014. Strain/species identification in metagenomes using genome-specific markers. Nucleic Acids Res 42: e67.
-
(2014)
Nucleic Acids Res
, vol.42
, pp. e67
-
-
Tu, Q.1
He, Z.2
Zhou, J.3
-
57
-
-
84925002456
-
Social networks predict gut microbiome composition in wild baboons
-
Tung J, Barreiro LB, Burns MB, Grenier JC, Lynch J, Grieneisen LE, Altmann J, Alberts SC, Blekhman R, Archie EA. 2015. Social networks predict gut microbiome composition in wild baboons. eLife 4: e05224.
-
(2015)
ELife
, vol.4
, pp. e05224
-
-
Tung, J.1
Barreiro, L.B.2
Burns, M.B.3
Grenier, J.C.4
Lynch, J.5
Grieneisen, L.E.6
Altmann, J.7
Alberts, S.C.8
Blekhman, R.9
Archie, E.A.10
-
58
-
-
84946034354
-
Microbial species delineation using whole genome sequences
-
Varghese NJ, Mukherjee S, Ivanova N, Konstantinidis KT, Mavrommatis K, Kyrpides NC, Pati A. 2015. Microbial species delineation using whole genome sequences. Nucleic Acids Res 43: 6761-6771.
-
(2015)
Nucleic Acids Res
, vol.43
, pp. 6761-6771
-
-
Varghese, N.J.1
Mukherjee, S.2
Ivanova, N.3
Konstantinidis, K.T.4
Mavrommatis, K.5
Kyrpides, N.C.6
Pati, A.7
-
59
-
-
84891776599
-
PATRIC, the bacterial bioinformatics database and analysis resource
-
(Database issue)
-
Wattam AR, Abraham D, Dalay O, Disz TL, Driscoll T, Gabbard JL, Gillespie JJ, Gough R, Hix D, Kenyon R, et al. 2014. PATRIC, the bacterial bioinformatics database and analysis resource. Nucleic Acids Res 42(Database issue): D581-D591.
-
(2014)
Nucleic Acids Res
, vol.42
, pp. D581-D591
-
-
Wattam, A.R.1
Abraham, D.2
Dalay, O.3
Disz, T.L.4
Driscoll, T.5
Gabbard, J.L.6
Gillespie, J.J.7
Gough, R.8
Hix, D.9
Kenyon, R.10
-
60
-
-
72949101201
-
A phylogeny-driven genomic encyclopaedia of Bacteria and Archaea
-
Wu D, Hugenholtz P, Mavromatis K, Pukall R, Dalin E, Ivanova NN, Kunin V, Goodwin L, Wu M, Tindall BJ, et al. 2009. A phylogeny-driven genomic encyclopaedia of Bacteria and Archaea. Nature 462: 1056-1060.
-
(2009)
Nature
, vol.462
, pp. 1056-1060
-
-
Wu, D.1
Hugenholtz, P.2
Mavromatis, K.3
Pukall, R.4
Dalin, E.5
Ivanova, N.N.6
Kunin, V.7
Goodwin, L.8
Wu, M.9
Tindall, B.J.10
-
61
-
-
84885819796
-
Systematic identification of gene families for use as "markers" for phylogenetic and phylogeny-driven ecological studies of bacteria and archaea and their major subgroups
-
Wu D, Jospin G, Eisen JA. 2013. Systematic identification of gene families for use as "markers" for phylogenetic and phylogeny-driven ecological studies of bacteria and archaea and their major subgroups. PLoS One 8: e77033.
-
(2013)
PLoS One
, vol.8
, pp. e77033
-
-
Wu, D.1
Jospin, G.2
Eisen, J.A.3
-
62
-
-
84943607837
-
A catalog of the mouse gut metagenome
-
Xiao L, Feng Q, Liang S, Sonne SB, Xia Z, Qiu X, Li X, Long H, Zhang J, Zhang D, et al. 2015. A catalog of the mouse gut metagenome. Nat Biotechnol 33: 1103-1108.
-
(2015)
Nat Biotechnol
, vol.33
, pp. 1103-1108
-
-
Xiao, L.1
Feng, Q.2
Liang, S.3
Sonne, S.B.4
Xia, Z.5
Qiu, X.6
Li, X.7
Long, H.8
Zhang, J.9
Zhang, D.10
-
63
-
-
84975064151
-
Natural history of the infant gut microbiome and impact of antibiotic treatment on bacterial strain diversity and stability
-
Yassour M, Vatanen T, Siljander H, Hämäläinen AM, Härkönen T, Ryhänen SJ, Franzosa EA, Vlamakis H, Huttenhower C, Gevers D, et al. 2016. Natural history of the infant gut microbiome and impact of antibiotic treatment on bacterial strain diversity and stability. Sci Transl Med 8: 343ra81.
-
(2016)
Sci Transl Med
, vol.8
, pp. 343ra81
-
-
Yassour, M.1
Vatanen, T.2
Siljander, H.3
Hämäläinen, A.M.4
Härkönen, T.5
Ryhänen, S.J.6
Franzosa, E.A.7
Vlamakis, H.8
Huttenhower, C.9
Gevers, D.10
-
65
-
-
84939135810
-
Inter-individual differences in the gene content of human gut bacterial species
-
Zhu A, Sunagawa S, Mende DR, Bork P. 2015. Inter-individual differences in the gene content of human gut bacterial species. Genome Biol 16: 82.
-
(2015)
Genome Biol
, vol.16
, pp. 82
-
-
Zhu, A.1
Sunagawa, S.2
Mende, D.R.3
Bork, P.4
|