-
1
-
-
84864037467
-
Metabolic reconstruction for metagenomic data and its application to the human microbiome
-
Abubucker, S., Segata, N., Goll, J., Schubert, A.M., Izard, J., Cantarel, B.L., Rodriguez-Mueller, B., Zucker, J., Thiagarajan, M., Henrissat, B., et al. Metabolic reconstruction for metagenomic data and its application to the human microbiome. PLoS Comput. Biol., 8, 2012, e1002358.
-
(2012)
PLoS Comput. Biol.
, vol.8
, pp. e1002358
-
-
Abubucker, S.1
Segata, N.2
Goll, J.3
Schubert, A.M.4
Izard, J.5
Cantarel, B.L.6
Rodriguez-Mueller, B.7
Zucker, J.8
Thiagarajan, M.9
Henrissat, B.10
-
2
-
-
84890856205
-
The Statistical Analysis of Compositional Data
-
Blackburn Press Caldwell, N.J.
-
Aitchison, J., The Statistical Analysis of Compositional Data. 2003, Blackburn Press, Caldwell, N.J.
-
(2003)
-
-
Aitchison, J.1
-
3
-
-
84945537929
-
MICROBIOME. A unified initiative to harness Earth's microbiomes
-
Alivisatos, A.P., Blaser, M.J., Brodie, E.L., Chun, M., Dangl, J.L., Donohue, T.J., Dorrestein, P.C., Gilbert, J.A., Green, J.L., Jansson, J.K., et al., Unified Microbiome Initiative Consortium. MICROBIOME. A unified initiative to harness Earth's microbiomes. Science 350 (2015), 507–508.
-
(2015)
Science
, vol.350
, pp. 507-508
-
-
Alivisatos, A.P.1
Blaser, M.J.2
Brodie, E.L.3
Chun, M.4
Dangl, J.L.5
Donohue, T.J.6
Dorrestein, P.C.7
Gilbert, J.A.8
Green, J.L.9
Jansson, J.K.10
-
4
-
-
84908597294
-
Binning metagenomic contigs by coverage and composition
-
Alneberg, J., Bjarnason, B.S., de Bruijn, I., Schirmer, M., Quick, J., Ijaz, U.Z., Lahti, L., Loman, N.J., Andersson, A.F., Quince, C., Binning metagenomic contigs by coverage and composition. Nat. Methods 11 (2014), 1144–1146.
-
(2014)
Nat. Methods
, vol.11
, pp. 1144-1146
-
-
Alneberg, J.1
Bjarnason, B.S.2
de Bruijn, I.3
Schirmer, M.4
Quick, J.5
Ijaz, U.Z.6
Lahti, L.7
Loman, N.J.8
Andersson, A.F.9
Quince, C.10
-
5
-
-
84937040456
-
Using populations of human and microbial genomes for organism detection in metagenomes
-
Ames, S.K., Gardner, S.N., Marti, J.M., Slezak, T.R., Gokhale, M.B., Allen, J.E., Using populations of human and microbial genomes for organism detection in metagenomes. Genome Res. 25 (2015), 1056–1067.
-
(2015)
Genome Res.
, vol.25
, pp. 1056-1067
-
-
Ames, S.K.1
Gardner, S.N.2
Marti, J.M.3
Slezak, T.R.4
Gokhale, M.B.5
Allen, J.E.6
-
6
-
-
77958471357
-
Differential expression analysis for sequence count data
-
Anders, S., Huber, W., Differential expression analysis for sequence count data. Genome Biol., 11, 2010, R106.
-
(2010)
Genome Biol.
, vol.11
, pp. R106
-
-
Anders, S.1
Huber, W.2
-
7
-
-
84983786960
-
-
Command-line tools for processing biological sequencing data. ea-utils,.
-
Aronesty, E. (2011). Command-line tools for processing biological sequencing data. ea-utils, https://expressionanalysis.github.io/ea-utils/.
-
(2011)
-
-
Aronesty, E.1
-
8
-
-
85027927719
-
Enterotypes of the human gut microbiome
-
Arumugam, M., Raes, J., Pelletier, E., Le Paslier, D., Yamada, T., Mende, D.R., Fernandes, G.R., Tap, J., Bruls, T., Batto, J.M., et al., MetaHIT Consortium. Enterotypes of the human gut microbiome. Nature 473 (2011), 174–180.
-
(2011)
Nature
, vol.473
, pp. 174-180
-
-
Arumugam, M.1
Raes, J.2
Pelletier, E.3
Le Paslier, D.4
Yamada, T.5
Mende, D.R.6
Fernandes, G.R.7
Tap, J.8
Bruls, T.9
Batto, J.M.10
-
9
-
-
84862179132
-
BioProject and BioSample databases at NCBI: facilitating capture and organization of metadata
-
Barrett, T., Clark, K., Gevorgyan, R., Gorelenkov, V., Gribov, E., Karsch-Mizrachi, I., Kimelman, M., Pruitt, K.D., Resenchuk, S., Tatusova, T., et al. BioProject and BioSample databases at NCBI: facilitating capture and organization of metadata. Nucleic Acids Res. 40 (2012), D57–D63.
-
(2012)
Nucleic Acids Res.
, vol.40
, pp. D57-D63
-
-
Barrett, T.1
Clark, K.2
Gevorgyan, R.3
Gorelenkov, V.4
Gribov, E.5
Karsch-Mizrachi, I.6
Kimelman, M.7
Pruitt, K.D.8
Resenchuk, S.9
Tatusova, T.10
-
10
-
-
84861548193
-
Summarizing and correcting the GC content bias in high-throughput sequencing
-
Benjamini, Y., Speed, T.P., Summarizing and correcting the GC content bias in high-throughput sequencing. Nucleic Acids Res., 40, 2012, e72.
-
(2012)
Nucleic Acids Res.
, vol.40
, pp. e72
-
-
Benjamini, Y.1
Speed, T.P.2
-
11
-
-
77954834592
-
Average genome size: a potential source of bias in comparative metagenomics
-
Beszteri, B., Temperton, B., Frickenhaus, S., Giovannoni, S.J., Average genome size: a potential source of bias in comparative metagenomics. ISME J. 4 (2010), 1075–1077.
-
(2010)
ISME J.
, vol.4
, pp. 1075-1077
-
-
Beszteri, B.1
Temperton, B.2
Frickenhaus, S.3
Giovannoni, S.J.4
-
12
-
-
84871979584
-
Quality-filtering vastly improves diversity estimates from Illumina amplicon sequencing
-
Bokulich, N.A., Subramanian, S., Faith, J.J., Gevers, D., Gordon, J.I., Knight, R., Mills, D.A., Caporaso, J.G., Quality-filtering vastly improves diversity estimates from Illumina amplicon sequencing. Nat. Methods 10 (2013), 57–59.
-
(2013)
Nat. Methods
, vol.10
, pp. 57-59
-
-
Bokulich, N.A.1
Subramanian, S.2
Faith, J.J.3
Gevers, D.4
Gordon, J.I.5
Knight, R.6
Mills, D.A.7
Caporaso, J.G.8
-
13
-
-
84926500572
-
A reproducible approach to high-throughput biological data acquisition and integration
-
Börnigen, D., Moon, Y.S., Rahnavard, G., Waldron, L., McIver, L., Shafquat, A., Franzosa, E.A., Miropolsky, L., Sweeney, C., Morgan, X.C., et al. A reproducible approach to high-throughput biological data acquisition and integration. PeerJ, 3, 2015, e791.
-
(2015)
PeerJ
, vol.3
, pp. e791
-
-
Börnigen, D.1
Moon, Y.S.2
Rahnavard, G.3
Waldron, L.4
McIver, L.5
Shafquat, A.6
Franzosa, E.A.7
Miropolsky, L.8
Sweeney, C.9
Morgan, X.C.10
-
14
-
-
84864518203
-
Pacific biosciences sequencing technology for genotyping and variation discovery in human data
-
Carneiro, M.O., Russ, C., Ross, M.G., Gabriel, S.B., Nusbaum, C., DePristo, M.A., Pacific biosciences sequencing technology for genotyping and variation discovery in human data. BMC Genomics, 13, 2012, 375.
-
(2012)
BMC Genomics
, vol.13
, pp. 375
-
-
Carneiro, M.O.1
Russ, C.2
Ross, M.G.3
Gabriel, S.B.4
Nusbaum, C.5
DePristo, M.A.6
-
15
-
-
84922717073
-
Comparative analysis of functional metagenomic annotation and the mappability of short reads
-
Carr, R., Borenstein, E., Comparative analysis of functional metagenomic annotation and the mappability of short reads. PLoS ONE, 9, 2014, e105776.
-
(2014)
PLoS ONE
, vol.9
, pp. e105776
-
-
Carr, R.1
Borenstein, E.2
-
16
-
-
84887265124
-
Reconstructing the genomic content of microbiome taxa through shotgun metagenomic deconvolution
-
Carr, R., Shen-Orr, S.S., Borenstein, E., Reconstructing the genomic content of microbiome taxa through shotgun metagenomic deconvolution. PLoS Comput. Biol., 9, 2013, e1003292.
-
(2013)
PLoS Comput. Biol.
, vol.9
, pp. e1003292
-
-
Carr, R.1
Shen-Orr, S.S.2
Borenstein, E.3
-
17
-
-
85041931479
-
cual-id: globally unique, correctable, and human-friendly sample identifiers for comparative omics studies
-
Chase, J.H., Bolyen, E.T., Rideout, J.R., Caporaso, J.G., cual-id: globally unique, correctable, and human-friendly sample identifiers for comparative omics studies. mSystems 1 (2015), e00010–e00015.
-
(2015)
mSystems
, vol.1
, pp. e00010-e00015
-
-
Chase, J.H.1
Bolyen, E.T.2
Rideout, J.R.3
Caporaso, J.G.4
-
18
-
-
84943595976
-
Detection of low-abundance bacterial strains in metagenomic datasets by eigengenome partitioning
-
Cleary, B., Brito, I.L., Huang, K., Gevers, D., Shea, T., Young, S., Alm, E.J., Detection of low-abundance bacterial strains in metagenomic datasets by eigengenome partitioning. Nat. Biotechnol. 33 (2015), 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
-
19
-
-
84862286169
-
A framework for human microbiome research
-
Consortium, T.H.M.P., Human Microbiome Project Consortium. A framework for human microbiome research. Nature 486 (2012), 215–221.
-
(2012)
Nature
, vol.486
, pp. 215-221
-
-
Consortium, T.H.M.P.1
-
20
-
-
84938244327
-
Small molecules from the human microbiota
-
Donia, M.S., Fischbach, M.A., Small molecules from the human microbiota. Science, 349, 2015, 1254766.
-
(2015)
Science
, vol.349
, pp. 1254766
-
-
Donia, M.S.1
Fischbach, M.A.2
-
21
-
-
84945562524
-
Microbiology: Create a global microbiome effort
-
Dubilier, N., McFall-Ngai, M., Zhao, L., Microbiology: Create a global microbiome effort. Nature 526 (2015), 631–634.
-
(2015)
Nature
, vol.526
, pp. 631-634
-
-
Dubilier, N.1
McFall-Ngai, M.2
Zhao, L.3
-
22
-
-
84905041075
-
A highly abundant bacteriophage discovered in the unknown sequences of human faecal metagenomes
-
Dutilh, B.E., Cassman, N., McNair, K., Sanchez, S.E., Silva, G.G., Boling, L., Barr, J.J., Speth, D.R., Seguritan, V., Aziz, R.K., et al. A highly abundant bacteriophage discovered in the unknown sequences of human faecal metagenomes. Nat. Commun., 5, 2014, 4498.
-
(2014)
Nat. Commun.
, vol.5
, pp. 4498
-
-
Dutilh, B.E.1
Cassman, N.2
McNair, K.3
Sanchez, S.E.4
Silva, G.G.5
Boling, L.6
Barr, J.J.7
Speth, D.R.8
Seguritan, V.9
Aziz, R.K.10
-
23
-
-
84869998071
-
MetaHIT: The European Union Project on Metagenomics of the Human Intestinal Tract
-
E.K. Nelson Springer New York New York
-
Ehrlich, S.D., MetaHIT: The European Union Project on Metagenomics of the Human Intestinal Tract. Nelson, E.K., (eds.) Metagenomics of the Human Body, 2011, Springer New York, New York, 307–316.
-
(2011)
Metagenomics of the Human Body
, pp. 307-316
-
-
Ehrlich, S.D.1
-
24
-
-
84863920287
-
Microbial interactions: from networks to models
-
Faust, K., Raes, J., Microbial interactions: from networks to models. Nat. Rev. Microbiol. 10 (2012), 538–550.
-
(2012)
Nat. Rev. Microbiol.
, vol.10
, pp. 538-550
-
-
Faust, K.1
Raes, J.2
-
25
-
-
84897138661
-
A taxonomic signature of obesity in the microbiome? Getting to the guts of the matter
-
Finucane, M.M., Sharpton, T.J., Laurent, T.J., Pollard, K.S., A taxonomic signature of obesity in the microbiome? Getting to the guts of the matter. PLoS ONE, 9, 2014, e84689.
-
(2014)
PLoS ONE
, vol.9
, pp. e84689
-
-
Finucane, M.M.1
Sharpton, T.J.2
Laurent, T.J.3
Pollard, K.S.4
-
26
-
-
84904687373
-
Identifying keystone species in the human gut microbiome from metagenomic timeseries using sparse linear regression
-
Fisher, C.K., Mehta, P., Identifying keystone species in the human gut microbiome from metagenomic timeseries using sparse linear regression. PLoS ONE, 9, 2014, e102451.
-
(2014)
PLoS ONE
, vol.9
, pp. e102451
-
-
Fisher, C.K.1
Mehta, P.2
-
27
-
-
84864384245
-
The “most wanted” taxa from the human microbiome for whole genome sequencing
-
Fodor, A.A., DeSantis, T.Z., Wylie, K.M., Badger, J.H., Ye, Y., Hepburn, T., Hu, P., Sodergren, E., Liolios, K., Huot-Creasy, H., et al. The “most wanted” taxa from the human microbiome for whole genome sequencing. PLoS ONE, 7, 2012, e41294.
-
(2012)
PLoS ONE
, vol.7
, pp. e41294
-
-
Fodor, A.A.1
DeSantis, T.Z.2
Wylie, K.M.3
Badger, J.H.4
Ye, Y.5
Hepburn, T.6
Hu, P.7
Sodergren, E.8
Liolios, K.9
Huot-Creasy, H.10
-
28
-
-
84949772416
-
Disentangling type 2 diabetes and metformin treatment signatures in the human gut microbiota
-
Forslund, K., Hildebrand, F., Nielsen, T., Falony, G., Le Chatelier, E., Sunagawa, S., Prifti, E., Vieira-Silva, S., Gudmundsdottir, V., Krogh Pedersen, H., et al., MetaHIT consortium. Disentangling type 2 diabetes and metformin treatment signatures in the human gut microbiota. Nature 528 (2015), 262–266.
-
(2015)
Nature
, vol.528
, pp. 262-266
-
-
Forslund, K.1
Hildebrand, F.2
Nielsen, T.3
Falony, G.4
Le Chatelier, E.5
Sunagawa, S.6
Prifti, E.7
Vieira-Silva, S.8
Gudmundsdottir, V.9
Krogh Pedersen, H.10
-
29
-
-
84929512453
-
Sequencing and beyond: integrating molecular ‘omics’ for microbial community profiling
-
Franzosa, E.A., Hsu, T., Sirota-Madi, A., Shafquat, A., Abu-Ali, G., Morgan, X.C., Huttenhower, C., Sequencing and beyond: integrating molecular ‘omics’ for microbial community profiling. Nat. Rev. Microbiol. 13 (2015), 360–372.
-
(2015)
Nat. Rev. Microbiol.
, vol.13
, pp. 360-372
-
-
Franzosa, E.A.1
Hsu, T.2
Sirota-Madi, A.3
Shafquat, A.4
Abu-Ali, G.5
Morgan, X.C.6
Huttenhower, C.7
-
30
-
-
79959794996
-
The Earth Microbiome Project: meeting report of the “EMP meeting on sample selection and acquisition” at Argonne National Laboratory October 6 2010
-
Gilbert, J.A., Meyer, F., Jansson, J., Gordon, J., Pace, N., Tiedje, J., Ley, R., Fierer, N., Field, D., Kyrpides, N., et al. The Earth Microbiome Project: meeting report of the “EMP meeting on sample selection and acquisition” at Argonne National Laboratory October 6 2010. Stand. Genomic Sci. 3 (2010), 249–253.
-
(2010)
Stand. Genomic Sci.
, vol.3
, pp. 249-253
-
-
Gilbert, J.A.1
Meyer, F.2
Jansson, J.3
Gordon, J.4
Pace, N.5
Tiedje, J.6
Ley, R.7
Fierer, N.8
Field, D.9
Kyrpides, N.10
-
31
-
-
84891164163
-
MIxS-BE: a MIxS extension defining a minimum information standard for sequence data from the built environment
-
Glass, E.M., Dribinsky, Y., Yilmaz, P., Levin, H., Van Pelt, R., Wendel, D., Wilke, A., Eisen, J.A., Huse, S., Shipanova, A., et al. MIxS-BE: a MIxS extension defining a minimum information standard for sequence data from the built environment. ISME J. 8 (2014), 1–3.
-
(2014)
ISME J.
, vol.8
, pp. 1-3
-
-
Glass, E.M.1
Dribinsky, Y.2
Yilmaz, P.3
Levin, H.4
Van Pelt, R.5
Wendel, D.6
Wilke, A.7
Eisen, J.A.8
Huse, S.9
Shipanova, A.10
-
32
-
-
70350294348
-
Systematic artifacts in metagenomes from complex microbial communities
-
Gomez-Alvarez, V., Teal, T.K., Schmidt, T.M., Systematic artifacts in metagenomes from complex microbial communities. ISME J. 3 (2009), 1314–1317.
-
(2009)
ISME J.
, vol.3
, pp. 1314-1317
-
-
Gomez-Alvarez, V.1
Teal, T.K.2
Schmidt, T.M.3
-
33
-
-
84904569753
-
Conducting a microbiome study
-
Goodrich, J.K., Di Rienzi, S.C., Poole, A.C., Koren, O., Walters, W.A., Caporaso, J.G., Knight, R., Ley, R.E., Conducting a microbiome study. Cell 158 (2014), 250–262.
-
(2014)
Cell
, vol.158
, pp. 250-262
-
-
Goodrich, J.K.1
Di Rienzi, S.C.2
Poole, A.C.3
Koren, O.4
Walters, W.A.5
Caporaso, J.G.6
Knight, R.7
Ley, R.E.8
-
34
-
-
84880941320
-
Towards a predictive systems-level model of the human microbiome: progress, challenges, and opportunities
-
Greenblum, S., Chiu, H.C., Levy, R., Carr, R., Borenstein, E., Towards a predictive systems-level model of the human microbiome: progress, challenges, and opportunities. Curr. Opin. Biotechnol. 24 (2013), 810–820.
-
(2013)
Curr. Opin. Biotechnol.
, vol.24
, pp. 810-820
-
-
Greenblum, S.1
Chiu, H.C.2
Levy, R.3
Carr, R.4
Borenstein, E.5
-
35
-
-
84922735613
-
Extensive strain-level copy-number variation across human gut microbiome species
-
Greenblum, S., Carr, R., Borenstein, E., Extensive strain-level copy-number variation across human gut microbiome species. Cell 160 (2015), 583–594.
-
(2015)
Cell
, vol.160
, pp. 583-594
-
-
Greenblum, S.1
Carr, R.2
Borenstein, E.3
-
36
-
-
84883147815
-
Exploring nucleo-cytoplasmic large DNA viruses in Tara Oceans microbial metagenomes
-
Hingamp, P., Grimsley, N., Acinas, S.G., Clerissi, C., Subirana, L., Poulain, J., Ferrera, I., Sarmento, H., Villar, E., Lima-Mendez, G., et al. Exploring nucleo-cytoplasmic large DNA viruses in Tara Oceans microbial metagenomes. ISME J. 7 (2013), 1678–1695.
-
(2013)
ISME J.
, vol.7
, pp. 1678-1695
-
-
Hingamp, P.1
Grimsley, N.2
Acinas, S.G.3
Clerissi, C.4
Subirana, L.5
Poulain, J.6
Ferrera, I.7
Sarmento, H.8
Villar, E.9
Lima-Mendez, G.10
-
37
-
-
84897492912
-
Tackling soil diversity with the assembly of large, complex metagenomes
-
Howe, A.C., Jansson, J.K., Malfatti, S.A., Tringe, S.G., Tiedje, J.M., Brown, C.T., Tackling soil diversity with the assembly of large, complex metagenomes. Proc. Natl. Acad. Sci. USA 111 (2014), 4904–4909.
-
(2014)
Proc. Natl. Acad. Sci. USA
, vol.111
, pp. 4904-4909
-
-
Howe, A.C.1
Jansson, J.K.2
Malfatti, S.A.3
Tringe, S.G.4
Tiedje, J.M.5
Brown, C.T.6
-
38
-
-
84916886220
-
Advancing the microbiome research community
-
Huttenhower, C., Knight, R., Brown, C.T., Caporaso, J.G., Clemente, J.C., Gevers, D., Franzosa, E.A., Kelley, S.T., Knights, D., Ley, R.E., et al., Scientists for Advancement of Microbiome Research. Advancing the microbiome research community. Cell 159 (2014), 227–230.
-
(2014)
Cell
, vol.159
, pp. 227-230
-
-
Huttenhower, C.1
Knight, R.2
Brown, C.T.3
Caporaso, J.G.4
Clemente, J.C.5
Gevers, D.6
Franzosa, E.A.7
Kelley, S.T.8
Knights, D.9
Ley, R.E.10
-
39
-
-
84946781151
-
Library preparation methodology can influence genomic and functional predictions in human microbiome research
-
Jones, M.B., Highlander, S.K., Anderson, E.L., Li, W., Dayrit, M., Klitgord, N., Fabani, M.M., Seguritan, V., Green, J., Pride, D.T., et al. Library preparation methodology can influence genomic and functional predictions in human microbiome research. Proc. Natl. Acad. Sci. USA 112 (2015), 14024–14029.
-
(2015)
Proc. Natl. Acad. Sci. USA
, vol.112
, pp. 14024-14029
-
-
Jones, M.B.1
Highlander, S.K.2
Anderson, E.L.3
Li, W.4
Dayrit, M.5
Klitgord, N.6
Fabani, M.M.7
Seguritan, V.8
Green, J.9
Pride, D.T.10
-
40
-
-
84903517029
-
Direct amplification, sequencing and profiling of Chlamydia trachomatis strains in single and mixed infection clinical samples
-
Joseph, S.J., Li, B., Ghonasgi, T., Haase, C.P., Qin, Z.S., Dean, D., Read, T.D., Direct amplification, sequencing and profiling of Chlamydia trachomatis strains in single and mixed infection clinical samples. PLoS ONE, 9, 2014, e99290.
-
(2014)
PLoS ONE
, vol.9
, pp. e99290
-
-
Joseph, S.J.1
Li, B.2
Ghonasgi, T.3
Haase, C.P.4
Qin, Z.S.5
Dean, D.6
Read, T.D.7
-
41
-
-
84899559579
-
Single-cell genomics reveals hundreds of coexisting subpopulations in wild Prochlorococcus
-
Kashtan, N., Roggensack, S.E., Rodrigue, S., Thompson, J.W., Biller, S.J., Coe, A., Ding, H., Marttinen, P., Malmstrom, R.R., Stocker, R., et al. Single-cell genomics reveals hundreds of coexisting subpopulations in wild Prochlorococcus. Science 344 (2014), 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
-
42
-
-
84903286893
-
The Marine Microbial Eukaryote Transcriptome Sequencing Project (MMETSP): illuminating the functional diversity of eukaryotic life in the oceans through transcriptome sequencing
-
Keeling, P.J., Burki, F., Wilcox, H.M., Allam, B., Allen, E.E., Amaral-Zettler, L.A., Armbrust, E.V., Archibald, J.M., Bharti, A.K., Bell, C.J., et al. The Marine Microbial Eukaryote Transcriptome Sequencing Project (MMETSP): illuminating the functional diversity of eukaryotic life in the oceans through transcriptome sequencing. PLoS Biol., 12, 2014, e1001889.
-
(2014)
PLoS Biol.
, vol.12
, pp. e1001889
-
-
Keeling, P.J.1
Burki, F.2
Wilcox, H.M.3
Allam, B.4
Allen, E.E.5
Amaral-Zettler, L.A.6
Armbrust, E.V.7
Archibald, J.M.8
Bharti, A.K.9
Bell, C.J.10
-
43
-
-
84896089558
-
The impact of different DNA extraction kits and laboratories upon the assessment of human gut microbiota composition by 16S rRNA gene sequencing
-
Kennedy, N.A., Walker, A.W., Berry, S.H., Duncan, S.H., Farquarson, F.M., Louis, P., Thomson, J.M., Satsangi, J., Flint, H.J., Parkhill, J., et al., UK IBD Genetics Consortium. The impact of different DNA extraction kits and laboratories upon the assessment of human gut microbiota composition by 16S rRNA gene sequencing. PLoS ONE, 9, 2014, e88982.
-
(2014)
PLoS ONE
, vol.9
, pp. e88982
-
-
Kennedy, N.A.1
Walker, A.W.2
Berry, S.H.3
Duncan, S.H.4
Farquarson, F.M.5
Louis, P.6
Thomson, J.M.7
Satsangi, J.8
Flint, H.J.9
Parkhill, J.10
-
44
-
-
17144428129
-
Simpson diversity and the Shannon–Wiener index as special cases of a generalized entropy
-
Keylock, C.J., Simpson diversity and the Shannon–Wiener index as special cases of a generalized entropy. Oikos 109 (2005), 203–207.
-
(2005)
Oikos
, vol.109
, pp. 203-207
-
-
Keylock, C.J.1
-
45
-
-
84862024684
-
Unlocking the potential of metagenomics through replicated experimental design
-
Knight, R., Jansson, J., Field, D., Fierer, N., Desai, N., Fuhrman, J.A., Hugenholtz, P., van der Lelie, D., Meyer, F., Stevens, R., et al. Unlocking the potential of metagenomics through replicated experimental design. Nat. Biotechnol. 30 (2012), 513–520.
-
(2012)
Nat. Biotechnol.
, vol.30
, pp. 513-520
-
-
Knight, R.1
Jansson, J.2
Field, D.3
Fierer, N.4
Desai, N.5
Fuhrman, J.A.6
Hugenholtz, P.7
van der Lelie, D.8
Meyer, F.9
Stevens, R.10
-
46
-
-
84862198590
-
The Sequence Read Archive: explosive growth of sequencing data
-
Kodama, Y., Shumway, M., Leinonen, R., International Nucleotide Sequence Database Collaboration. The Sequence Read Archive: explosive growth of sequencing data. Nucleic Acids Res. 40 (2012), D54–D56.
-
(2012)
Nucleic Acids Res.
, vol.40
, pp. D54-D56
-
-
Kodama, Y.1
Shumway, M.2
Leinonen, R.3
-
47
-
-
84941368240
-
Growth dynamics of gut microbiota in health and disease inferred from single metagenomic samples
-
Korem, T., Zeevi, D., Suez, J., Weinberger, A., Avnit-Sagi, T., Pompan-Lotan, M., Matot, E., Jona, G., Harmelin, A., Cohen, N., et al. Growth dynamics of gut microbiota in health and disease inferred from single metagenomic samples. Science 349 (2015), 1101–1106.
-
(2015)
Science
, vol.349
, pp. 1101-1106
-
-
Korem, T.1
Zeevi, D.2
Suez, J.3
Weinberger, A.4
Avnit-Sagi, T.5
Pompan-Lotan, M.6
Matot, E.7
Jona, G.8
Harmelin, A.9
Cohen, N.10
-
48
-
-
84873510063
-
A guide to enterotypes across the human body: meta-analysis of microbial community structures in human microbiome datasets
-
Koren, O., Knights, D., Gonzalez, A., Waldron, L., Segata, N., Knight, R., Huttenhower, C., Ley, R.E., A guide to enterotypes across the human body: meta-analysis of microbial community structures in human microbiome datasets. PLoS Comput. Biol., 9, 2013, e1002863.
-
(2013)
PLoS Comput. Biol.
, vol.9
, pp. e1002863
-
-
Koren, O.1
Knights, D.2
Gonzalez, A.3
Waldron, L.4
Segata, N.5
Knight, R.6
Huttenhower, C.7
Ley, R.E.8
-
49
-
-
84953791854
-
Synthetic long-read sequencing reveals intraspecies diversity in the human microbiome
-
Kuleshov, V., Jiang, C., Zhou, W., Jahanbani, F., Batzoglou, S., Snyder, M., Synthetic long-read sequencing reveals intraspecies diversity in the human microbiome. Nat. Biotechnol. 34 (2016), 64–69.
-
(2016)
Nat. Biotechnol.
, vol.34
, pp. 64-69
-
-
Kuleshov, V.1
Jiang, C.2
Zhou, W.3
Jahanbani, F.4
Batzoglou, S.5
Snyder, M.6
-
50
-
-
84930608352
-
Sparse and compositionally robust inference of microbial ecological networks
-
Kurtz, Z.D., Müller, C.L., Miraldi, E.R., Littman, D.R., Blaser, M.J., Bonneau, R.A., Sparse and compositionally robust inference of microbial ecological networks. PLoS Comput. Biol., 11, 2015, e1004226.
-
(2015)
PLoS Comput. Biol.
, vol.11
, pp. e1004226
-
-
Kurtz, Z.D.1
Müller, C.L.2
Miraldi, E.R.3
Littman, D.R.4
Blaser, M.J.5
Bonneau, R.A.6
-
51
-
-
84883172257
-
Global marine bacterial diversity peaks at high latitudes in winter
-
Ladau, J., Sharpton, T.J., Finucane, M.M., Jospin, G., Kembel, S.W., O'Dwyer, J., Koeppel, A.F., Green, J.L., Pollard, K.S., Global marine bacterial diversity peaks at high latitudes in winter. ISME J. 7 (2013), 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
-
52
-
-
84919665956
-
Intraspecies competition for niches in the distal gut dictate transmission during persistent Salmonella infection
-
Lam, L.H., Monack, D.M., Intraspecies competition for niches in the distal gut dictate transmission during persistent Salmonella infection. PLoS Pathog., 10, 2014, e1004527.
-
(2014)
PLoS Pathog.
, vol.10
, pp. e1004527
-
-
Lam, L.H.1
Monack, D.M.2
-
53
-
-
84859210032
-
Fast gapped-read alignment with Bowtie 2
-
Langmead, B., Salzberg, S.L., Fast gapped-read alignment with Bowtie 2. Nat. Methods 9 (2012), 357–359.
-
(2012)
Nat. Methods
, vol.9
, pp. 357-359
-
-
Langmead, B.1
Salzberg, S.L.2
-
54
-
-
84881110826
-
Metabolic modeling of species interaction in the human microbiome elucidates community-level assembly rules
-
Levy, R., Borenstein, E., Metabolic modeling of species interaction in the human microbiome elucidates community-level assembly rules. Proc. Natl. Acad. Sci. USA 110 (2013), 12804–12809.
-
(2013)
Proc. Natl. Acad. Sci. USA
, vol.110
, pp. 12804-12809
-
-
Levy, R.1
Borenstein, E.2
-
55
-
-
84945484378
-
Metagenomic and network analysis reveal wide distribution and co-occurrence of environmental antibiotic resistance genes
-
Li, B., Yang, Y., Ma, L., Ju, F., Guo, F., Tiedje, J.M., Zhang, T., Metagenomic and network analysis reveal wide distribution and co-occurrence of environmental antibiotic resistance genes. ISME J. 9 (2015), 2490–2502.
-
(2015)
ISME J.
, vol.9
, pp. 2490-2502
-
-
Li, B.1
Yang, Y.2
Ma, L.3
Ju, F.4
Guo, F.5
Tiedje, J.M.6
Zhang, T.7
-
56
-
-
84983750196
-
-
(2014a). Data from: An integrated catalog of reference genes in the human gut microbiome. GigaScience Database.
-
Li, J., Jia, H., Cai, X., Zhong, H., Feng, Q., Sunagawa, S., Arumugam, M., Kultima, J.R., Prifti, E., Nielsen, T., et al. (2014a). Data from: An integrated catalog of reference genes in the human gut microbiome. GigaScience Database. http://gigadb.org/dataset/100064.
-
-
-
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
-
57
-
-
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, J.R., Prifti, E., Nielsen, T., et al. MetaHIT Consortium, MetaHIT Consortium. An integrated catalog of reference genes in the human gut microbiome. Nat. Biotechnol. 32 (2014), 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
-
58
-
-
84954556725
-
An evaluation of the accuracy and speed of metagenome analysis tools
-
Lindgreen, S., Adair, K.L., Gardner, P.P., An evaluation of the accuracy and speed of metagenome analysis tools. Sci Rep, 6, 2016, 19233.
-
(2016)
Sci Rep
, vol.6
, pp. 19233
-
-
Lindgreen, S.1
Adair, K.L.2
Gardner, P.P.3
-
59
-
-
79960869431
-
Accurate and fast estimation of taxonomic profiles from metagenomic shotgun sequences
-
Liu, B., Gibbons, T., Ghodsi, M., Treangen, T., Pop, M., Accurate and fast estimation of taxonomic profiles from metagenomic shotgun sequences. BMC Genomics, 12(2), 2011, S4.
-
(2011)
BMC Genomics
, vol.12
, Issue.2
, pp. S4
-
-
Liu, B.1
Gibbons, T.2
Ghodsi, M.3
Treangen, T.4
Pop, M.5
-
60
-
-
84859782215
-
BactQuant: an enhanced broad-coverage bacterial quantitative real-time PCR assay
-
Liu, C.M., Aziz, M., Kachur, S., Hsueh, P.R., Huang, Y.T., Keim, P., Price, L.B., BactQuant: an enhanced broad-coverage bacterial quantitative real-time PCR assay. BMC Microbiol., 12, 2012, 56.
-
(2012)
BMC Microbiol.
, vol.12
, pp. 56
-
-
Liu, C.M.1
Aziz, M.2
Kachur, S.3
Hsueh, P.R.4
Huang, Y.T.5
Keim, P.6
Price, L.B.7
-
61
-
-
84883864245
-
Meta-analyses of studies of the human microbiota
-
Lozupone, C.A., Stombaugh, J., Gonzalez, A., Ackermann, G., Wendel, D., Vázquez-Baeza, Y., Jansson, J.K., Gordon, J.I., Knight, R., Meta-analyses of studies of the human microbiota. Genome Res. 23 (2013), 1704–1714.
-
(2013)
Genome Res.
, vol.23
, pp. 1704-1714
-
-
Lozupone, C.A.1
Stombaugh, J.2
Gonzalez, A.3
Ackermann, G.4
Wendel, D.5
Vázquez-Baeza, Y.6
Jansson, J.K.7
Gordon, J.I.8
Knight, R.9
-
62
-
-
84943606160
-
ConStrains identifies microbial strains in metagenomic datasets
-
Luo, C., Knight, R., Siljander, H., Knip, M., Xavier, R.J., Gevers, D., ConStrains identifies microbial strains in metagenomic datasets. Nat. Biotechnol. 33 (2015), 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
-
63
-
-
34748848639
-
The NCBI dbGaP database of genotypes and phenotypes
-
Mailman, M.D., Feolo, M., Jin, Y., Kimura, M., Tryka, K., Bagoutdinov, R., Hao, L., Kiang, A., Paschall, J., Phan, L., et al. The NCBI dbGaP database of genotypes and phenotypes. Nat. Genet. 39 (2007), 1181–1186.
-
(2007)
Nat. Genet.
, vol.39
, pp. 1181-1186
-
-
Mailman, M.D.1
Feolo, M.2
Jin, Y.3
Kimura, M.4
Tryka, K.5
Bagoutdinov, R.6
Hao, L.7
Kiang, A.8
Paschall, J.9
Phan, L.10
-
64
-
-
84871375552
-
Ecology of uncultured Prochlorococcus clades revealed through single-cell genomics and biogeographic analysis
-
Malmstrom, R.R., Rodrigue, S., Huang, K.H., Kelly, L., Kern, S.E., Thompson, A., Roggensack, S., Berube, P.M., Henn, M.R., Chisholm, S.W., Ecology of uncultured Prochlorococcus clades revealed through single-cell genomics and biogeographic analysis. ISME J. 7 (2013), 184–198.
-
(2013)
ISME J.
, vol.7
, pp. 184-198
-
-
Malmstrom, R.R.1
Rodrigue, S.2
Huang, K.H.3
Kelly, L.4
Kern, S.E.5
Thompson, A.6
Roggensack, S.7
Berube, P.M.8
Henn, M.R.9
Chisholm, S.W.10
-
65
-
-
84939202778
-
MUSiCC: a marker genes based framework for metagenomic normalization and accurate profiling of gene abundances in the microbiome
-
Manor, O., Borenstein, E., MUSiCC: a marker genes based framework for metagenomic normalization and accurate profiling of gene abundances in the microbiome. Genome Biol., 16, 2015, 53.
-
(2015)
Genome Biol.
, vol.16
, pp. 53
-
-
Manor, O.1
Borenstein, E.2
-
66
-
-
84951567393
-
Metagenome analysis exploiting high-throughput chromosome conformation capture (3C) data
-
Marbouty, M., Koszul, R., Metagenome analysis exploiting high-throughput chromosome conformation capture (3C) data. Trends Genet. 31 (2015), 673–682.
-
(2015)
Trends Genet.
, vol.31
, pp. 673-682
-
-
Marbouty, M.1
Koszul, R.2
-
67
-
-
84872535919
-
Xenobiotics shape the physiology and gene expression of the active human gut microbiome
-
Maurice, C.F., Haiser, H.J., Turnbaugh, P.J., Xenobiotics shape the physiology and gene expression of the active human gut microbiome. Cell 152 (2013), 39–50.
-
(2013)
Cell
, vol.152
, pp. 39-50
-
-
Maurice, C.F.1
Haiser, H.J.2
Turnbaugh, P.J.3
-
68
-
-
84901363655
-
Waste not, want not: why rarefying microbiome data is inadmissible
-
McMurdie, P.J., Holmes, S., Waste not, want not: why rarefying microbiome data is inadmissible. PLoS Comput. Biol., 10, 2014, e1003531.
-
(2014)
PLoS Comput. Biol.
, vol.10
, pp. e1003531
-
-
McMurdie, P.J.1
Holmes, S.2
-
69
-
-
84857524013
-
Assessment of metagenomic assembly using simulated next generation sequencing data
-
Mende, D.R., Waller, A.S., Sunagawa, S., Järvelin, A.I., Chan, M.M., Arumugam, M., Raes, J., Bork, P., Assessment of metagenomic assembly using simulated next generation sequencing data. PLoS ONE, 7, 2012, e31386.
-
(2012)
PLoS ONE
, vol.7
, pp. e31386
-
-
Mende, D.R.1
Waller, A.S.2
Sunagawa, S.3
Järvelin, A.I.4
Chan, M.M.5
Arumugam, M.6
Raes, J.7
Bork, P.8
-
70
-
-
84883464181
-
Accurate and universal delineation of prokaryotic species
-
Mende, D.R., Sunagawa, S., Zeller, G., Bork, P., Accurate and universal delineation of prokaryotic species. Nat. Methods 10 (2013), 881–884.
-
(2013)
Nat. Methods
, vol.10
, pp. 881-884
-
-
Mende, D.R.1
Sunagawa, S.2
Zeller, G.3
Bork, P.4
-
71
-
-
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, E.M., Kubal, M., Paczian, T., Rodriguez, A., Stevens, R., Wilke, A., et al. The metagenomics RAST server - a public resource for the automatic phylogenetic and functional analysis of metagenomes. BMC Bioinformatics, 9, 2008, 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
Kubal, M.6
Paczian, T.7
Rodriguez, A.8
Stevens, R.9
Wilke, A.10
-
72
-
-
84892736640
-
Expanding the marine virosphere using metagenomics
-
Mizuno, C.M., Rodriguez-Valera, F., Kimes, N.E., Ghai, R., Expanding the marine virosphere using metagenomics. PLoS Genet., 9, 2013, e1003987.
-
(2013)
PLoS Genet.
, vol.9
, pp. e1003987
-
-
Mizuno, C.M.1
Rodriguez-Valera, F.2
Kimes, N.E.3
Ghai, R.4
-
73
-
-
84939141968
-
Average genome size estimation improves comparative metagenomics and sheds light on the functional ecology of the human microbiome
-
Nayfach, S., Pollard, K.S., Average genome size estimation improves comparative metagenomics and sheds light on the functional ecology of the human microbiome. Genome Biol., 16, 2015, 51.
-
(2015)
Genome Biol.
, vol.16
, pp. 51
-
-
Nayfach, S.1
Pollard, K.S.2
-
74
-
-
84949219026
-
Automated and accurate estimation of gene family abundance from shotgun metagenomes
-
Nayfach, S., Bradley, P.H., Wyman, S.K., Laurent, T.J., Williams, A., Eisen, J.A., Pollard, K.S., Sharpton, T.J., Automated and accurate estimation of gene family abundance from shotgun metagenomes. PLoS Comput. Biol., 11, 2015, e1004573.
-
(2015)
PLoS Comput. Biol.
, vol.11
, pp. e1004573
-
-
Nayfach, S.1
Bradley, P.H.2
Wyman, S.K.3
Laurent, T.J.4
Williams, A.5
Eisen, J.A.6
Pollard, K.S.7
Sharpton, T.J.8
-
75
-
-
84947772278
-
MetaQuery: a web server for rapid annotation and quantitative analysis of specific genes in the human gut microbiome
-
Nayfach, S., Fischbach, M.A., Pollard, K.S., MetaQuery: a web server for rapid annotation and quantitative analysis of specific genes in the human gut microbiome. Bioinformatics 31 (2015), 3368–3370.
-
(2015)
Bioinformatics
, vol.31
, pp. 3368-3370
-
-
Nayfach, S.1
Fischbach, M.A.2
Pollard, K.S.3
-
76
-
-
84983753753
-
An integrated metagenomics pipeline for strain profiling reveals novel patterns of transmission and global biogeography of bacteria
-
Nayfach, S., Rodriguez-Mueller, B., Garud, N., Pollard, K.S., An integrated metagenomics pipeline for strain profiling reveals novel patterns of transmission and global biogeography of bacteria. BioRxiv, 2016, 10.1101/031757.
-
(2016)
BioRxiv
-
-
Nayfach, S.1
Rodriguez-Mueller, B.2
Garud, N.3
Pollard, K.S.4
-
77
-
-
84922751927
-
TIPP: taxonomic identification and phylogenetic profiling
-
Nguyen, N.P., Mirarab, S., Liu, B., Pop, M., Warnow, T., TIPP: taxonomic identification and phylogenetic profiling. Bioinformatics 30 (2014), 3548–3555.
-
(2014)
Bioinformatics
, vol.30
, pp. 3548-3555
-
-
Nguyen, N.P.1
Mirarab, S.2
Liu, B.3
Pop, M.4
Warnow, T.5
-
78
-
-
84905730761
-
Identification and assembly of genomes and genetic elements in complex metagenomic samples without using reference genomes
-
Nielsen, H.B., Almeida, M., Juncker, A.S., Rasmussen, S., Li, J., Sunagawa, S., Plichta, D.R., Gautier, L., Pedersen, A.G., Le Chatelier, E., et al. MetaHIT Consortium, MetaHIT Consortium. Identification and assembly of genomes and genetic elements in complex metagenomic samples without using reference genomes. Nat. Biotechnol. 32 (2014), 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
-
79
-
-
84954354477
-
Assessing the accuracy of quantitative molecular microbial profiling
-
O'Sullivan, D.M., Laver, T., Temisak, S., Redshaw, N., Harris, K.A., Foy, C.A., Studholme, D.J., Huggett, J.F., Assessing the accuracy of quantitative molecular microbial profiling. Int. J. Mol. Sci. 15 (2014), 21476–21491.
-
(2014)
Int. J. Mol. Sci.
, vol.15
, pp. 21476-21491
-
-
O'Sullivan, D.M.1
Laver, T.2
Temisak, S.3
Redshaw, N.4
Harris, K.A.5
Foy, C.A.6
Studholme, D.J.7
Huggett, J.F.8
-
80
-
-
84908074440
-
Biogeography and individuality shape function in the human skin metagenome
-
Oh, J., Byrd, A.L., Deming, C., Conlan, S., Kong, H.H., Segre, J.A., Segre, J.A., NISC Comparative Sequencing Program. Biogeography and individuality shape function in the human skin metagenome. Nature 514 (2014), 59–64.
-
(2014)
Nature
, vol.514
, pp. 59-64
-
-
Oh, J.1
Byrd, A.L.2
Deming, C.3
Conlan, S.4
Kong, H.H.5
Segre, J.A.6
Segre, J.A.7
-
81
-
-
84888865593
-
Differential abundance analysis for microbial marker-gene surveys
-
Paulson, J.N., Stine, O.C., Bravo, H.C., Pop, M., Differential abundance analysis for microbial marker-gene surveys. Nat. Methods 10 (2013), 1200–1202.
-
(2013)
Nat. Methods
, vol.10
, pp. 1200-1202
-
-
Paulson, J.N.1
Stine, O.C.2
Bravo, H.C.3
Pop, M.4
-
82
-
-
84930214841
-
Open science resources for the discovery and analysis of Tara Oceans data
-
Pesant, S., Not, F., Picheral, M., Kandels-Lewis, S., Le Bescot, N., Gorsky, G., Iudicone, D., Karsenti, E., Speich, S., Troublé, R., et al., Tara Oceans Consortium Coordinators. Open science resources for the discovery and analysis of Tara Oceans data. Sci Data, 2, 2015, 150023.
-
(2015)
Sci Data
, vol.2
, pp. 150023
-
-
Pesant, S.1
Not, F.2
Picheral, M.3
Kandels-Lewis, S.4
Le Bescot, N.5
Gorsky, G.6
Iudicone, D.7
Karsenti, E.8
Speich, S.9
Troublé, R.10
-
83
-
-
70449713952
-
The NIH Human Microbiome Project
-
Peterson, J., Garges, S., Giovanni, M., McInnes, P., Wang, L., Schloss, J.A., Bonazzi, V., McEwen, J.E., Wetterstrand, K.A., Deal, C., et al., NIH HMP Working Group. The NIH Human Microbiome Project. Genome Res. 19 (2009), 2317–2323.
-
(2009)
Genome Res.
, vol.19
, pp. 2317-2323
-
-
Peterson, J.1
Garges, S.2
Giovanni, M.3
McInnes, P.4
Wang, L.5
Schloss, J.A.6
Bonazzi, V.7
McEwen, J.E.8
Wetterstrand, K.A.9
Deal, C.10
-
84
-
-
84897466729
-
Non-random DNA fragmentation in next-generation sequencing
-
Poptsova, M.S., Il'icheva, I.A., Nechipurenko, D.Y., Panchenko, L.A., Khodikov, M.V., Oparina, N.Y., Polozov, R.V., Nechipurenko, Y.D., Grokhovsky, S.L., Non-random DNA fragmentation in next-generation sequencing. Sci. Rep., 4, 2014, 4532.
-
(2014)
Sci. Rep.
, vol.4
, pp. 4532
-
-
Poptsova, M.S.1
Il'icheva, I.A.2
Nechipurenko, D.Y.3
Panchenko, L.A.4
Khodikov, M.V.5
Oparina, N.Y.6
Polozov, R.V.7
Nechipurenko, Y.D.8
Grokhovsky, S.L.9
-
85
-
-
84870006986
-
Functional assignment of metagenomic data: challenges and applications
-
Prakash, T., Taylor, T.D., Functional assignment of metagenomic data: challenges and applications. Brief. Bioinform. 13 (2012), 711–727.
-
(2012)
Brief. Bioinform.
, vol.13
, pp. 711-727
-
-
Prakash, T.1
Taylor, T.D.2
-
86
-
-
84886937146
-
Distribution-based clustering: using ecology to refine the operational taxonomic unit
-
Preheim, S.P., Perrotta, A.R., Martin-Platero, A.M., Gupta, A., Alm, E.J., Distribution-based clustering: using ecology to refine the operational taxonomic unit. Appl. Environ. Microbiol. 79 (2013), 6593–6603.
-
(2013)
Appl. Environ. Microbiol.
, vol.79
, pp. 6593-6603
-
-
Preheim, S.P.1
Perrotta, A.R.2
Martin-Platero, A.M.3
Gupta, A.4
Alm, E.J.5
-
87
-
-
84865591846
-
A tale of three next generation sequencing platforms: comparison of Ion Torrent, Pacific Biosciences and Illumina MiSeq sequencers
-
Quail, M.A., Smith, M., Coupland, P., Otto, T.D., Harris, S.R., Connor, T.R., Bertoni, A., Swerdlow, H.P., Gu, Y., A tale of three next generation sequencing platforms: comparison of Ion Torrent, Pacific Biosciences and Illumina MiSeq sequencers. BMC Genomics, 13, 2012, 341.
-
(2012)
BMC Genomics
, vol.13
, pp. 341
-
-
Quail, M.A.1
Smith, M.2
Coupland, P.3
Otto, T.D.4
Harris, S.R.5
Connor, T.R.6
Bertoni, A.7
Swerdlow, H.P.8
Gu, Y.9
-
88
-
-
80052150179
-
Origins of the E. coli strain causing an outbreak of hemolytic-uremic syndrome in Germany
-
Rasko, D.A., Webster, D.R., Sahl, J.W., Bashir, A., Boisen, N., Scheutz, F., Paxinos, E.E., Sebra, R., Chin, C.S., Iliopoulos, D., et al. Origins of the E. coli strain causing an outbreak of hemolytic-uremic syndrome in Germany. N. Engl. J. Med. 365 (2011), 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
-
89
-
-
84938484157
-
All hail reproducibility in microbiome research
-
Ravel, J., Wommack, K.E., All hail reproducibility in microbiome research. Microbiome, 2, 2014, 8.
-
(2014)
Microbiome
, vol.2
, pp. 8
-
-
Ravel, J.1
Wommack, K.E.2
-
90
-
-
84881138595
-
Insights into the phylogeny and coding potential of microbial dark matter
-
Rinke, C., Schwientek, P., Sczyrba, A., Ivanova, N.N., Anderson, I.J., Cheng, J.-F., Darling, A., Malfatti, S., Swan, B.K., Gies, E.A., et al. Insights into the phylogeny and coding potential of microbial dark matter. Nature 499 (2013), 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
-
91
-
-
79952709611
-
Improving RNA-Seq expression estimates by correcting for fragment bias
-
Roberts, A., Trapnell, C., Donaghey, J., Rinn, J.L., Pachter, L., Improving RNA-Seq expression estimates by correcting for fragment bias. Genome Biol., 12, 2011, R22.
-
(2011)
Genome Biol.
, vol.12
, pp. R22
-
-
Roberts, A.1
Trapnell, C.2
Donaghey, J.3
Rinn, J.L.4
Pachter, L.5
-
92
-
-
75249087100
-
edgeR: a Bioconductor package for differential expression analysis of digital gene expression data
-
Robinson, M.D., McCarthy, D.J., Smyth, G.K., edgeR: a Bioconductor package for differential expression analysis of digital gene expression data. Bioinformatics 26 (2010), 139–140.
-
(2010)
Bioinformatics
, vol.26
, pp. 139-140
-
-
Robinson, M.D.1
McCarthy, D.J.2
Smyth, G.K.3
-
93
-
-
84920644670
-
Reagent and laboratory contamination can critically impact sequence-based microbiome analyses
-
Salter, S.J., Cox, M.J., Turek, E.M., Calus, S.T., Cookson, W.O., Moffatt, M.F., Turner, P., Parkhill, J., Loman, N.J., Walker, A.W., Reagent and laboratory contamination can critically impact sequence-based microbiome analyses. BMC Biol., 12, 2014, 87.
-
(2014)
BMC Biol.
, vol.12
, pp. 87
-
-
Salter, S.J.1
Cox, M.J.2
Turek, E.M.3
Calus, S.T.4
Cookson, W.O.5
Moffatt, M.F.6
Turner, P.7
Parkhill, J.8
Loman, N.J.9
Walker, A.W.10
-
94
-
-
84884551538
-
Use of internal standards for quantitative metatranscriptome and metagenome analysis
-
Satinsky, B.M., Gifford, S.M., Crump, B.C., Moran, M.A., Use of internal standards for quantitative metatranscriptome and metagenome analysis. Methods Enzymol. 531 (2013), 237–250.
-
(2013)
Methods Enzymol.
, vol.531
, pp. 237-250
-
-
Satinsky, B.M.1
Gifford, S.M.2
Crump, B.C.3
Moran, M.A.4
-
95
-
-
84871732071
-
Genomic variation landscape of the human gut microbiome
-
Schloissnig, S., Arumugam, M., Sunagawa, S., Mitreva, M., Tap, J., Zhu, A., Waller, A., Mende, D.R., Kultima, J.R., Martin, J., et al. Genomic variation landscape of the human gut microbiome. Nature 493 (2013), 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
-
96
-
-
39049092823
-
A statistical toolbox for metagenomics: assessing functional diversity in microbial communities
-
Schloss, P.D., Handelsman, J., A statistical toolbox for metagenomics: assessing functional diversity in microbial communities. BMC Bioinformatics, 9, 2008, 34.
-
(2008)
BMC Bioinformatics
, vol.9
, pp. 34
-
-
Schloss, P.D.1
Handelsman, J.2
-
97
-
-
84864440400
-
Metagenomic microbial community profiling using unique clade-specific marker genes
-
Segata, N., Waldron, L., Ballarini, A., Narasimhan, V., Jousson, O., Huttenhower, C., Metagenomic microbial community profiling using unique clade-specific marker genes. Nat. Methods 9 (2012), 811–814.
-
(2012)
Nat. Methods
, vol.9
, pp. 811-814
-
-
Segata, N.1
Waldron, L.2
Ballarini, A.3
Narasimhan, V.4
Jousson, O.5
Huttenhower, C.6
-
98
-
-
84881548286
-
Computational meta'omics for microbial community studies
-
Segata, N., Boernigen, D., Tickle, T.L., Morgan, X.C., Garrett, W.S., Huttenhower, C., Computational meta'omics for microbial community studies. Mol. Syst. Biol., 9, 2013, 666.
-
(2013)
Mol. Syst. Biol.
, vol.9
, pp. 666
-
-
Segata, N.1
Boernigen, D.2
Tickle, T.L.3
Morgan, X.C.4
Garrett, W.S.5
Huttenhower, C.6
-
99
-
-
84859499489
-
Population genomics of early events in the ecological differentiation of bacteria
-
Shapiro, B.J., Friedman, J., Cordero, O.X., Preheim, S.P., Timberlake, S.C., Szabó, G., Polz, M.F., Alm, E.J., Population genomics of early events in the ecological differentiation of bacteria. Science 336 (2012), 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
Szabó, G.6
Polz, M.F.7
Alm, E.J.8
-
100
-
-
84979608055
-
An introduction to the analysis of shotgun metagenomic data
-
Sharpton, T.J., An introduction to the analysis of shotgun metagenomic data. Front. Plant Sci., 5, 2014, 209.
-
(2014)
Front. Plant Sci.
, vol.5
, pp. 209
-
-
Sharpton, T.J.1
-
101
-
-
79551562225
-
PhylOTU: a high-throughput procedure quantifies microbial community diversity and resolves novel taxa from metagenomic data
-
Sharpton, T.J., Riesenfeld, S.J., Kembel, S.W., Ladau, J., O'Dwyer, J.P., Green, J.L., Eisen, J.A., Pollard, K.S., PhylOTU: a high-throughput procedure quantifies microbial community diversity and resolves novel taxa from metagenomic data. PLoS Comput. Biol., 7, 2011, e1001061.
-
(2011)
PLoS Comput. Biol.
, vol.7
, pp. e1001061
-
-
Sharpton, T.J.1
Riesenfeld, S.J.2
Kembel, S.W.3
Ladau, J.4
O'Dwyer, J.P.5
Green, J.L.6
Eisen, J.A.7
Pollard, K.S.8
-
102
-
-
84949675208
-
The microbiome quality control project: baseline study design and future directions
-
Sinha, R., Abnet, C.C., White, O., Knight, R., Huttenhower, C., The microbiome quality control project: baseline study design and future directions. Genome Biol., 16, 2015, 276.
-
(2015)
Genome Biol.
, vol.16
, pp. 276
-
-
Sinha, R.1
Abnet, C.C.2
White, O.3
Knight, R.4
Huttenhower, C.5
-
103
-
-
84955180101
-
Massively parallel sequencing of single cells by epicPCR links functional genes with phylogenetic markers
-
Spencer, S.J., Tamminen, M.V., Preheim, S.P., Guo, M.T., Briggs, A.W., Brito, I.L., A Weitz, D., Pitkänen, L.K., Vigneault, F., Juhani Virta, M.P., Alm, E.J., Massively parallel sequencing of single cells by epicPCR links functional genes with phylogenetic markers. ISME J. 10 (2016), 427–436.
-
(2016)
ISME J.
, vol.10
, pp. 427-436
-
-
Spencer, S.J.1
Tamminen, M.V.2
Preheim, S.P.3
Guo, M.T.4
Briggs, A.W.5
Brito, I.L.6
A Weitz, D.7
Pitkänen, L.K.8
Vigneault, F.9
Juhani Virta, M.P.10
Alm, E.J.11
-
104
-
-
84923363366
-
Re-defining microbial diversity from its single-celled building blocks
-
Stepanauskas, R., Re-defining microbial diversity from its single-celled building blocks. Environ. Microbiol. Rep. 7 (2015), 36–37.
-
(2015)
Environ. Microbiol. Rep.
, vol.7
, pp. 36-37
-
-
Stepanauskas, R.1
-
105
-
-
84888884475
-
Metagenomic species profiling using universal phylogenetic marker genes
-
Sunagawa, S., Mende, D.R., Zeller, G., Izquierdo-Carrasco, F., Berger, S.A., Kultima, J.R., Coelho, L.P., Arumugam, M., Tap, J., Nielsen, H.B., et al. Metagenomic species profiling using universal phylogenetic marker genes. Nat. Methods 10 (2013), 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
-
106
-
-
84929992013
-
Ocean plankton. Structure and function of the global ocean microbiome
-
Sunagawa, S., Coelho, L.P., Chaffron, S., Kultima, J.R., Labadie, K., Salazar, G., Djahanschiri, B., Zeller, G., Mende, D.R., Alberti, A., et al., Tara Oceans coordinators. Ocean plankton. Structure and function of the global ocean microbiome. Science, 348, 2015, 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
-
107
-
-
0031904685
-
Specific ribosomal DNA sequences from diverse environmental settings correlate with experimental contaminants
-
Tanner, M.A., Goebel, B.M., Dojka, M.A., Pace, N.R., Specific ribosomal DNA sequences from diverse environmental settings correlate with experimental contaminants. Appl. Environ. Microbiol. 64 (1998), 3110–3113.
-
(1998)
Appl. Environ. Microbiol.
, vol.64
, pp. 3110-3113
-
-
Tanner, M.A.1
Goebel, B.M.2
Dojka, M.A.3
Pace, N.R.4
-
108
-
-
84923545661
-
Interpreting 16S metagenomic data without clustering to achieve sub-OTU resolution
-
Tikhonov, M., Leach, R.W., Wingreen, N.S., Interpreting 16S metagenomic data without clustering to achieve sub-OTU resolution. ISME J. 9 (2015), 68–80.
-
(2015)
ISME J.
, vol.9
, pp. 68-80
-
-
Tikhonov, M.1
Leach, R.W.2
Wingreen, N.S.3
-
109
-
-
84939179628
-
Temporal and technical variability of human gut metagenomes
-
Voigt, A.Y., Costea, P.I., Kultima, J.R., Li, S.S., Zeller, G., Sunagawa, S., Bork, P., Temporal and technical variability of human gut metagenomes. Genome Biol., 16, 2015, 73.
-
(2015)
Genome Biol.
, vol.16
, pp. 73
-
-
Voigt, A.Y.1
Costea, P.I.2
Kultima, J.R.3
Li, S.S.4
Zeller, G.5
Sunagawa, S.6
Bork, P.7
-
110
-
-
34548293679
-
Naive Bayesian classifier for rapid assignment of rRNA sequences into the new bacterial taxonomy
-
Wang, Q., Garrity, G.M., Tiedje, J.M., Cole, J.R., Naive Bayesian classifier for rapid assignment of rRNA sequences into the new bacterial taxonomy. Appl. Environ. Microbiol. 73 (2007), 5261–5267.
-
(2007)
Appl. Environ. Microbiol.
, vol.73
, pp. 5261-5267
-
-
Wang, Q.1
Garrity, G.M.2
Tiedje, J.M.3
Cole, J.R.4
-
111
-
-
84924580226
-
Tracking down the sources of experimental contamination in microbiome studies
-
Weiss, S., Amir, A., Hyde, E.R., Metcalf, J.L., Song, S.J., Knight, R., Tracking down the sources of experimental contamination in microbiome studies. Genome Biol., 15, 2014, 564.
-
(2014)
Genome Biol.
, vol.15
, pp. 564
-
-
Weiss, S.1
Amir, A.2
Hyde, E.R.3
Metcalf, J.L.4
Song, S.J.5
Knight, R.6
-
112
-
-
84945247885
-
Effects of library size variance, sparsity, and compositionality on the analysis of microbiome data
-
Weiss, S.J., Xu, Z., Amir, A., Peddada, S., Bittinger, K., Gonzalez, A., Lozupone, C., Zaneveld, J.R., Vazquez-Baeza, Y., Birmingham, A., et al. Effects of library size variance, sparsity, and compositionality on the analysis of microbiome data. PeerJ, 3, 2015, e1408.
-
(2015)
PeerJ
, vol.3
, pp. e1408
-
-
Weiss, S.J.1
Xu, Z.2
Amir, A.3
Peddada, S.4
Bittinger, K.5
Gonzalez, A.6
Lozupone, C.7
Zaneveld, J.R.8
Vazquez-Baeza, Y.9
Birmingham, A.10
-
113
-
-
84893542053
-
An environmental bacterial taxon with a large and distinct metabolic repertoire
-
Wilson, M.C., Mori, T., Rückert, C., Uria, A.R., Helf, M.J., Takada, K., Gernert, C., Steffens, U.A., Heycke, N., Schmitt, S., et al. An environmental bacterial taxon with a large and distinct metabolic repertoire. Nature 506 (2014), 58–62.
-
(2014)
Nature
, vol.506
, pp. 58-62
-
-
Wilson, M.C.1
Mori, T.2
Rückert, C.3
Uria, A.R.4
Helf, M.J.5
Takada, K.6
Gernert, C.7
Steffens, U.A.8
Heycke, N.9
Schmitt, S.10
-
114
-
-
84902602767
-
Actionable diagnosis of neuroleptospirosis by next-generation sequencing
-
Wilson, M.R., Naccache, S.N., Samayoa, E., Biagtan, M., Bashir, H., Yu, G., Salamat, S.M., Somasekar, S., Federman, S., Miller, S., et al. Actionable diagnosis of neuroleptospirosis by next-generation sequencing. N. Engl. J. Med. 370 (2014), 2408–2417.
-
(2014)
N. Engl. J. Med.
, vol.370
, pp. 2408-2417
-
-
Wilson, M.R.1
Naccache, S.N.2
Samayoa, E.3
Biagtan, M.4
Bashir, H.5
Yu, G.6
Salamat, S.M.7
Somasekar, S.8
Federman, S.9
Miller, S.10
-
115
-
-
40549141418
-
Metagenomics: read length matters
-
Wommack, K.E., Bhavsar, J., Ravel, J., Metagenomics: read length matters. Appl. Environ. Microbiol. 74 (2008), 1453–1463.
-
(2008)
Appl. Environ. Microbiol.
, vol.74
, pp. 1453-1463
-
-
Wommack, K.E.1
Bhavsar, J.2
Ravel, J.3
-
116
-
-
72949101201
-
A phylogeny-driven genomic encyclopaedia of Bacteria and Archaea
-
Wu, D., Hugenholtz, P., Mavromatis, K., Pukall, R., Dalin, E., Ivanova, N.N., Kunin, V., Goodwin, L., Wu, M., Tindall, B.J., et al. A phylogeny-driven genomic encyclopaedia of Bacteria and Archaea. Nature 462 (2009), 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
-
117
-
-
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, J.A., 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, 2013, e77033.
-
(2013)
PLoS ONE
, vol.8
, pp. e77033
-
-
Wu, D.1
Jospin, G.2
Eisen, J.A.3
-
118
-
-
82755170566
-
Accurate genome relative abundance estimation based on shotgun metagenomic reads
-
Xia, L.C., Cram, J.A., Chen, T., Fuhrman, J.A., Sun, F., Accurate genome relative abundance estimation based on shotgun metagenomic reads. PLoS ONE, 6, 2011, e27992.
-
(2011)
PLoS ONE
, vol.6
, pp. e27992
-
-
Xia, L.C.1
Cram, J.A.2
Chen, T.3
Fuhrman, J.A.4
Sun, F.5
-
119
-
-
84862141704
-
Human gut microbiome viewed across age and geography
-
Yatsunenko, T., Rey, F.E., Manary, M.J., Trehan, I., Dominguez-Bello, M.G., Contreras, M., Magris, M., Hidalgo, G., Baldassano, R.N., Anokhin, A.P., et al. Human gut microbiome viewed across age and geography. Nature 486 (2012), 222–227.
-
(2012)
Nature
, vol.486
, pp. 222-227
-
-
Yatsunenko, T.1
Rey, F.E.2
Manary, M.J.3
Trehan, I.4
Dominguez-Bello, M.G.5
Contreras, M.6
Magris, M.7
Hidalgo, G.8
Baldassano, R.N.9
Anokhin, A.P.10
-
120
-
-
79955749319
-
Minimum information about a marker gene sequence (MIMARKS) and minimum information about any (x) sequence (MIxS) specifications
-
Yilmaz, P., Kottmann, R., Field, D., Knight, R., Cole, J.R., Amaral-Zettler, L., Gilbert, J.A., Karsch-Mizrachi, I., Johnston, A., Cochrane, G., et al. Minimum information about a marker gene sequence (MIMARKS) and minimum information about any (x) sequence (MIxS) specifications. Nat. Biotechnol. 29 (2011), 415–420.
-
(2011)
Nat. Biotechnol.
, vol.29
, pp. 415-420
-
-
Yilmaz, P.1
Kottmann, R.2
Field, D.3
Knight, R.4
Cole, J.R.5
Amaral-Zettler, L.6
Gilbert, J.A.7
Karsch-Mizrachi, I.8
Johnston, A.9
Cochrane, G.10
-
121
-
-
84929440325
-
Metabolic dependencies drive species co-occurrence in diverse microbial communities
-
Zelezniak, A., Andrejev, S., Ponomarova, O., Mende, D.R., Bork, P., Patil, K.R., Metabolic dependencies drive species co-occurrence in diverse microbial communities. Proc. Natl. Acad. Sci. USA 112 (2015), 6449–6454.
-
(2015)
Proc. Natl. Acad. Sci. USA
, vol.112
, pp. 6449-6454
-
-
Zelezniak, A.1
Andrejev, S.2
Ponomarova, O.3
Mende, D.R.4
Bork, P.5
Patil, K.R.6
-
122
-
-
84872274753
-
SRAdb: query and use public next-generation sequencing data from within R
-
Zhu, Y., Stephens, R.M., Meltzer, P.S., Davis, S.R., SRAdb: query and use public next-generation sequencing data from within R. BMC Bioinformatics, 14, 2013, 19.
-
(2013)
BMC Bioinformatics
, vol.14
, pp. 19
-
-
Zhu, Y.1
Stephens, R.M.2
Meltzer, P.S.3
Davis, S.R.4
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