-
1
-
-
84903759167
-
Microbes in the neonatal intensive care unit resemble those found in the gut of premature infants
-
Brooks, B. et al. Microbes in the neonatal intensive care unit resemble those found in the gut of premature infants. Microbiome 2, 1 (2014).
-
(2014)
Microbiome
, vol.2
, pp. 1
-
-
Brooks, B.1
-
2
-
-
84996559882
-
The first microbial environment of infants born by C-section: The operating room microbes
-
Shin, H. et al. The first microbial environment of infants born by C-section: the operating room microbes. Microbiome 3, 59 (2015).
-
(2015)
Microbiome
, vol.3
, pp. 59
-
-
Shin, H.1
-
3
-
-
84899792426
-
Strain/species identification in metagenomes using genome-specific markers
-
Tu, Q., He, Z. & Zhou, J. Strain/species identification in metagenomes using genome-specific markers. Nucleic Acids Res. 42, e67 (2014).
-
(2014)
Nucleic Acids Res.
, vol.42
, pp. e67
-
-
Tu, Q.1
He, Z.2
Zhou, J.3
-
4
-
-
84966430254
-
Characterization of the gut microbiome using 16S or shotgun metagenomics
-
Jovel, J. et al. Characterization of the gut microbiome using 16S or shotgun metagenomics. Front. Microbiol. 7, 459 (2016).
-
(2016)
Front. Microbiol.
, vol.7
, pp. 459
-
-
Jovel, J.1
-
5
-
-
76949094947
-
The population genetics of commensal
-
Tenaillon, O., Skurnik, D., Picard, B. & Denamur, E. The population genetics of commensal Escherichia coli. Nat. Rev. Microbiol. 8, 207-217 (2010).
-
(2010)
Escherichia coli. Nat. Rev. Microbiol.
, vol.8
, pp. 207-217
-
-
Tenaillon, O.1
Skurnik, D.2
Picard, B.3
Denamur, E.4
-
6
-
-
85006276920
-
Gut bacteria are rarely shared by co-hospitalized premature infants, regardless of necrotizing enterocolitis development
-
Raveh-Sadka, T. et al. Gut bacteria are rarely shared by co-hospitalized premature infants, regardless of necrotizing enterocolitis development. Elife 4, e05477 (2015).
-
(2015)
Elife
, vol.4
, pp. e05477
-
-
Raveh-Sadka, T.1
-
7
-
-
84976329731
-
Evidence for persistent and shared bacterial strains against a background of largely unique gut colonization in hospitalized premature infants
-
Raveh-Sadka, T. et al. Evidence for persistent and shared bacterial strains against a background of largely unique gut colonization in hospitalized premature infants. ISME J. 10, 2817-2830 (2016).
-
(2016)
ISME J.
, vol.10
, pp. 2817-2830
-
-
Raveh-Sadka, T.1
-
8
-
-
85017559090
-
Identical bacterial populations colonize premature infant gut, skin, and oral microbiomes and exhibit different in situ growth rates
-
Olm, M. R. et al. Identical bacterial populations colonize premature infant gut, skin, and oral microbiomes and exhibit different in situ growth rates. Genome Res. 27, 601-612 (2017).
-
(2017)
Genome Res.
, vol.27
, pp. 601-612
-
-
Olm, M.R.1
-
9
-
-
85034643980
-
DRep: A tool for fast and accurate genomic comparisons that enables improved genome recovery from metagenomes through de-replication
-
Olm, M. R., Brown, C. T., Brooks, B. & Banfield, J. F. dRep: a tool for fast and accurate genomic comparisons that enables improved genome recovery from metagenomes through de-replication. ISME J. doi: 10.1038/ismej.2017.126 (2017).
-
(2017)
ISME J.
-
-
Olm, M.R.1
Brown, C.T.2
Brooks, B.3
Banfield, J.F.4
-
10
-
-
84946034354
-
Microbial species delineation using whole genome sequences
-
Varghese, N. J. et al. Microbial species delineation using whole genome sequences. Nucleic Acids Res. 43, 6761-6771 (2015).
-
(2015)
Nucleic Acids Res.
, vol.43
, pp. 6761-6771
-
-
Varghese, N.J.1
-
11
-
-
84969862358
-
Concentrations and sources of airborne particles in a neonatal intensive care unit
-
Licina, D. et al. Concentrations and sources of airborne particles in a neonatal intensive care unit. PLoS ONE 11, e0154991 (2016).
-
(2016)
PLoS ONE
, vol.11
, pp. e0154991
-
-
Licina, D.1
-
12
-
-
84938484921
-
Development of the preterm infant gut microbiome: A research priority
-
Groer, M. W. et al. Development of the preterm infant gut microbiome: a research priority. Microbiome 2, 38 (2014).
-
(2014)
Microbiome
, vol.2
, pp. 38
-
-
Groer, M.W.1
-
13
-
-
84856448537
-
Assessing allergenic fungi in house dust by floor wipe sampling and quantitative PCR
-
Yamamoto, N., Shendell, D. G. & Peccia, J. Assessing allergenic fungi in house dust by floor wipe sampling and quantitative PCR. Indoor Air 21, 521-530 (2011).
-
(2011)
Indoor Air
, vol.21
, pp. 521-530
-
-
Yamamoto, N.1
Shendell, D.G.2
Peccia, J.3
-
15
-
-
84859210032
-
Fast gapped-read alignment with Bowtie 2
-
Langmead, B. & Salzberg, S. L. Fast gapped-read alignment with Bowtie 2. Nat. Methods 9, 357-359 (2012).
-
(2012)
Nat. Methods
, vol.9
, pp. 357-359
-
-
Langmead, B.1
Salzberg, S.L.2
-
16
-
-
84861760530
-
IDBA-UD: A de novo assembler for single-cell and metagenomic sequencing data with highly uneven depth
-
Peng, Y., Leung, H. C. M., Yiu, S. M. & Chin, F. Y. L. IDBA-UD: a de novo assembler for single-cell and metagenomic sequencing data with highly uneven depth. Bioinformatics 28, 1420-1428 (2012).
-
(2012)
Bioinformatics
, vol.28
, pp. 1420-1428
-
-
Peng, Y.1
Leung, H.C.M.2
Yiu, S.M.3
Chin, F.Y.L.4
-
17
-
-
77952299957
-
Prodigal: Prokaryotic gene recognition and translation initiation site identification
-
Hyatt, D. et al. Prodigal: prokaryotic gene recognition and translation initiation site identification. BMC Bioinformatics 11, 119 (2010).
-
(2010)
BMC Bioinformatics
, vol.11
, pp. 119
-
-
Hyatt, D.1
-
18
-
-
77957244650
-
Search and clustering orders of magnitude faster than BLAST
-
Edgar, R. C. Search and clustering orders of magnitude faster than BLAST. Bioinformatics 26, 2460-2461 (2010).
-
(2010)
Bioinformatics
, vol.26
, pp. 2460-2461
-
-
Edgar, R.C.1
-
19
-
-
84891760956
-
Data, information, knowledge and principle: Back to metabolism in KEGG
-
Kanehisa, M. et al. Data, information, knowledge and principle: back to metabolism in KEGG. Nucleic Acids Res. 42, 199-205 (2014).
-
(2014)
Nucleic Acids Res.
, vol.42
, pp. 199-205
-
-
Kanehisa, M.1
-
20
-
-
34347388470
-
UniRef: Comprehensive and non-redundant UniProt reference clusters
-
Suzek, B. E., Huang, H., McGarvey, P., Mazumder, R. & Wu, C. H. UniRef: comprehensive and non-redundant UniProt reference clusters. Bioinformatics 23, 1282-1288 (2007).
-
(2007)
Bioinformatics
, vol.23
, pp. 1282-1288
-
-
Suzek, B.E.1
Huang, H.2
McGarvey, P.3
Mazumder, R.4
Wu, C.H.5
-
21
-
-
84890037468
-
Infernal 1.1: 100-fold faster RNA homology searches
-
Nawrocki, E. P. & Eddy, S. R. Infernal 1.1: 100-fold faster RNA homology searches. Bioinformatics 29, 2933-2935 (2013).
-
(2013)
Bioinformatics
, vol.29
, pp. 2933-2935
-
-
Nawrocki, E.P.1
Eddy, S.R.2
-
22
-
-
0030854739
-
TRNAscan-SE: A program for improved detection of transfer RNA genes in genomic sequence
-
Lowe, T. M. & Eddy, S. R. TRNAscan-SE: a program for improved detection of transfer RNA genes in genomic sequence. Nucleic Acids Res. 25, 955-964 (1996).
-
(1996)
Nucleic Acids Res.
, vol.25
, pp. 955-964
-
-
Lowe, T.M.1
Eddy, S.R.2
-
23
-
-
84908597294
-
Binning metagenomic contigs by coverage and composition
-
Alneberg, J. et al. Binning metagenomic contigs by coverage and composition. Nat. Methods 11, 1144-1146 (2014).
-
(2014)
Nat. Methods
, vol.11
, pp. 1144-1146
-
-
Alneberg, J.1
-
24
-
-
84957911451
-
MaxBin 2.0: An automated binning algorithm to recover genomes from multiple metagenomic datasets
-
Wu, Y. W., Simmons, B. A. & Singer, S. W. MaxBin 2.0: an automated binning algorithm to recover genomes from multiple metagenomic datasets. Bioinformatics 32, 605-607 (2015).
-
(2015)
Bioinformatics
, vol.32
, pp. 605-607
-
-
Wu, Y.W.1
Simmons, B.A.2
Singer, S.W.3
-
25
-
-
84936942726
-
Unusual biology across a group comprising more than 15% of domain bacteria
-
Brown, C. T. et al. Unusual biology across a group comprising more than 15% of domain bacteria. Nature 523, 208-211 (2015).
-
(2015)
Nature
, vol.523
, pp. 208-211
-
-
Brown, C.T.1
|