-
1
-
-
85041904945
-
-
National Transit Database. 2015. Monthly module raw data release. http://www.ntdprogram.gov/ntdprogram/data.htm.
-
(2015)
Monthly Module Raw Data Release
-
-
-
2
-
-
84907190237
-
Longitudinal analysis of microbial interaction between humans and the indoor environment
-
Lax S, Smith DP, Hampton-Marcell J, Owens SM, Handley KM, Scott NM, Gibbons SM, Larsen P, Shogan BD, Weiss S, Metcalf JL, Ursell LK, Vázquez-Baeza Y, Van Treuren W, Hasan NA, Gibson MK, Colwell R, Dantas G, Knight R, Gilbert JA. 2014. Longitudinal analysis of microbial interaction between humans and the indoor environment. Science 345:1048 -1052. http://dx.doi.org/10.1126/science.1254529.
-
(2014)
Science
, vol.345
, pp. 1048-1052
-
-
Lax, S.1
Smith, D.P.2
Hampton-Marcell, J.3
Owens, S.M.4
Handley, K.M.5
Scott, N.M.6
Gibbons, S.M.7
Larsen, P.8
Shogan, B.D.9
Weiss, S.10
Metcalf, J.L.11
Ursell, L.K.12
Vázquez-Baeza, Y.13
Van Treuren, W.14
Hasan, N.A.15
Gibson, M.K.16
Colwell, R.17
Dantas, G.18
Knight, R.19
Gilbert, J.A.20
more..
-
3
-
-
84903846612
-
Mobile phones carry the personal microbiome of their owners
-
Meadow JF, Altrichter AE, Green JL. 2014. Mobile phones carry the personal microbiome of their owners. PeerJ 2:e447. http://dx.doi.org/10.7717/peerj.447.
-
(2014)
PeerJ
, vol.2
, pp. e447
-
-
Meadow, J.F.1
Altrichter, A.E.2
Green, J.L.3
-
4
-
-
77950904616
-
Forensic identification using skin bacterial communities
-
Fierer N, Lauber CL, Zhou N, McDonald D, Costello EK, Knight R. 2010. Forensic identification using skin bacterial communities. Proc Natl Acad Sci U S A 107:6477-6481. http://dx.doi.org/10.1073/pnas.1000162107.
-
(2010)
Proc Natl Acad Sci U S A
, vol.107
, pp. 6477-6481
-
-
Fierer, N.1
Lauber, C.L.2
Zhou, N.3
McDonald, D.4
Costello, E.K.5
Knight, R.6
-
5
-
-
81755184089
-
Microbial biogeography of public restroom surfaces
-
Flores GE, Bates ST, Knights D, Lauber CL, Stombaugh J, Knight R, Fierer N. 2011. Microbial biogeography of public restroom surfaces. PLoS One 6:e28132. http://dx.doi.org/10.1371/journal.pone.0028132.
-
(2011)
PLoS One
, vol.6
, pp. e28132
-
-
Flores, G.E.1
Bates, S.T.2
Knights, D.3
Lauber, C.L.4
Stombaugh, J.5
Knight, R.6
Fierer, N.7
-
6
-
-
84927626197
-
Bacterial communities on classroom surfaces vary with human contact
-
Meadow JF, Altrichter AE, Kembel SW, Moriyama M, O’Connor TK, Womack AM, Brown GZ, Green JL, Bohannan BJ. 2014. Bacterial communities on classroom surfaces vary with human contact. Microbiome 2:7. http://dx.doi.org/10.1186/2049-2618-2-7.
-
(2014)
Microbiome
, vol.2
, pp. 7
-
-
Meadow, J.F.1
Altrichter, A.E.2
Kembel, S.W.3
Moriyama, M.4
O’Connor, T.K.5
Womack, A.M.6
Brown, G.Z.7
Green, J.L.8
Bohannan, B.J.9
-
7
-
-
84877153099
-
Culture-independent analysis of aerosol microbiology in a metropolitan subway system
-
Robertson CE, Baumgartner LK, Harris JK, Peterson KL, Stevens MJ, Frank DN, Pace NR. 2013. Culture-independent analysis of aerosol microbiology in a metropolitan subway system. Appl Environ Microbiol 79:3485-3493. http://dx.doi.org/10.1128/AEM.00331-13.
-
(2013)
Appl Environ Microbiol
, vol.79
, pp. 3485-3493
-
-
Robertson, C.E.1
Baumgartner, L.K.2
Harris, J.K.3
Peterson, K.L.4
Stevens, M.J.5
Frank, D.N.6
Pace, N.R.7
-
8
-
-
84914142515
-
Indoor-air microbiome in an urban subway network: Diversity and dynamics
-
Leung MH, Wilkins D, Li EK, Kong FK, Lee PK. 2014. Indoor-air microbiome in an urban subway network: diversity and dynamics. Appl Environ Microbiol 80:6760-6770. http://dx.doi.org/10.1128/AEM.02244-14.
-
(2014)
Appl Environ Microbiol
, vol.80
, pp. 6760-6770
-
-
Leung, M.H.1
Wilkins, D.2
Li, E.K.3
Kong, F.K.4
Lee, P.K.5
-
9
-
-
84925104897
-
Geospatial resolution of human and bacterial diversity with city-scale metagenomics
-
Afshinnekoo E, Meydan C, Chowdhury S, Jaroudi D, Boyer C, Bernstein N, Maritz JM, Reeves D, Gandara J, Chhangawala S, Ahsanud-din S, Simmons A, Nessel T, Sundaresh B, Pereira E, Jorgensen E, Kolokotronis S-O, Kirchberger N, Garcia I, Gandara D, Dhanraj S, Nawrin T, Saletore Y, Alexander N, Vijay P, Hénaff EM, Zumbo P, Walsh M, O’Mullan GD, Tighe S, Dudley JT, Dunaif A, Ennis S, O’Halloran E, Magalhaes TR, Boone B, Angela JL, Theodore MR, Paolantonio KS, Alter E, Schadt EE, Garbarino J, Robert PJ, Carlton JM, Levy S, Mason CE. 2015. Geospatial resolution of human and bacterial diversity with city-scale metagenomics. Cell Syst 1:72-87.
-
(2015)
Cell Syst
, vol.1
, pp. 72-87
-
-
Afshinnekoo, E.1
Meydan, C.2
Chowdhury, S.3
Jaroudi, D.4
Boyer, C.5
Bernstein, N.6
Maritz, J.M.7
Reeves, D.8
Gandara, J.9
Chhangawala, S.10
Ahsanud-Din, S.11
Simmons, A.12
Nessel, T.13
Sundaresh, B.14
Pereira, E.15
Jorgensen, E.16
Kolokotronis, S.-O.17
Kirchberger, N.18
Garcia, I.19
Gandara, D.20
Dhanraj, S.21
Nawrin, T.22
Saletore, Y.23
Alexander, N.24
Vijay, P.25
Hénaff, E.M.26
Zumbo, P.27
Walsh, M.28
O’Mullan, G.D.29
Tighe, S.30
Dudley, J.T.31
Dunaif, A.32
Ennis, S.33
O’Halloran, E.34
Magalhaes, T.R.35
Boone, B.36
Angela, J.L.37
Theodore, M.R.38
Paolantonio, K.S.39
Alter, E.40
Schadt, E.E.41
Garbarino, J.42
Robert, P.J.43
Carlton, J.M.44
Levy, S.45
Mason, C.E.46
more..
-
10
-
-
84938328887
-
Lack of evidence for plague or anthrax on the New York City subway
-
Ackelsberg J, Rakeman J, Hughes S, Petersen J, Mead P, Schriefer M, Kingry L, Hoffmaster A, Gee JE. 2015. Lack of evidence for plague or anthrax on the New York City subway. Cell Syst 1:4 -5.
-
(2015)
Cell Syst
, vol.1
, pp. 4-5
-
-
Ackelsberg, J.1
Rakeman, J.2
Hughes, S.3
Petersen, J.4
Mead, P.5
Schriefer, M.6
Kingry, L.7
Hoffmaster, A.8
Gee, J.E.9
-
11
-
-
79959383523
-
Metagenomic biomarker discovery and explanation
-
Segata N, Izard J, Waldron L, Gevers D, Miropolsky L, Garrett WS, Huttenhower C. 2011. Metagenomic biomarker discovery and explanation. Genome Biol 12:R60. http://dx.doi.org/10.1186/gb-2011-12-6-r60.
-
(2011)
Genome Biol
, vol.12
, pp. R60
-
-
Segata, N.1
Izard, J.2
Waldron, L.3
Gevers, D.4
Miropolsky, L.5
Garrett, W.S.6
Huttenhower, C.7
-
12
-
-
84862276328
-
Structure, function and diversity of the healthy human microbiome
-
Human Microbiome Project Consortium
-
Human Microbiome Project Consortium. 2012. Structure, function and diversity of the healthy human microbiome. Nature 486:207-214. http://dx.doi.org/10.1038/nature11234.
-
(2012)
Nature
, vol.486
, pp. 207-214
-
-
-
13
-
-
66349083859
-
Topographical and temporal diversity of the human skin microbiome
-
Grice EA, Kong HH, Conlan S, Deming CB, Davis J, Young AC, Bouffard GG, Blakesley RW, Murray PR, Green ED, Turner ML, Segre JA. 2009. Topographical and temporal diversity of the human skin microbiome. Science 324:1190 -1192. http://dx.doi.org/10.1126/science.1171700.
-
(2009)
Science
, vol.324
, pp. 1190-1192
-
-
Grice, E.A.1
Kong, H.H.2
Conlan, S.3
Deming, C.B.4
Davis, J.5
Young, A.C.6
Bouffard, G.G.7
Blakesley, R.W.8
Murray, P.R.9
Green, E.D.10
Turner, M.L.11
Segre, J.A.12
-
14
-
-
84899531657
-
Analysis, optimization and verification of Illumina-generated 16S rRNA gene amplicon surveys
-
Nelson MC, Morrison HG, Benjamino J, Grim SL, Graf J. 2014. Analysis, optimization and verification of Illumina-generated 16S rRNA gene amplicon surveys. PLoS One 9:e94249. http://dx.doi.org/10.1371/journal.pone.0094249.
-
(2014)
PLoS One
, vol.9
, pp. e94249
-
-
Nelson, M.C.1
Morrison, H.G.2
Benjamino, J.3
Grim, S.L.4
Graf, J.5
-
15
-
-
84862162269
-
Composition of the adult digestive tract bacterial microbiome based on seven mouth surfaces, tonsils, throat and stool samples
-
Segata N, Haake SK, Mannon P, Lemon KP, Waldron L, Gevers D, Huttenhower C, Izard J. 2012. Composition of the adult digestive tract bacterial microbiome based on seven mouth surfaces, tonsils, throat and stool samples. Genome Biol 13:R42. http://dx.doi.org/10.1186/gb-2012-13-6-r42.
-
(2012)
Genome Biol
, vol.13
, pp. R42
-
-
Segata, N.1
Haake, S.K.2
Mannon, P.3
Lemon, K.P.4
Waldron, L.5
Gevers, D.6
Huttenhower, C.7
Izard, J.8
-
16
-
-
58149142969
-
Molecular characteristics of xenobiotic-degrading sphingomonads
-
Stolz A. 2009. Molecular characteristics of xenobiotic-degrading sphingomonads. Appl Microbiol Biotechnol 81:793-811. http://dx.doi.org/10.1007/s00253-008-1752-3.
-
(2009)
Appl Microbiol Biotechnol
, vol.81
, pp. 793-811
-
-
Stolz, A.1
-
17
-
-
80755159333
-
Genome-scale reconstruction and system level investigation of the metabolic network of Methylobacterium extorquens AM1
-
Peyraud R, Schneider K, Kiefer P, Massou S, Vorholt JA, Portais JC. 2011. Genome-scale reconstruction and system level investigation of the metabolic network of Methylobacterium extorquens AM1. BMC Syst Biol 5:189. http://dx.doi.org/10.1186/1752-0509-5-189.
-
(2011)
BMC Syst Biol
, vol.5
, pp. 189
-
-
Peyraud, R.1
Schneider, K.2
Kiefer, P.3
Massou, S.4
Vorholt, J.A.5
Portais, J.C.6
-
18
-
-
84856845172
-
Genus Enhydrobacter Staley et al. 1987 should be recognized as a member of the family Rhodospirillaceae within the class Alphaproteobacteria
-
Kawamura Y, Fujiwara N, Naka T, Mitani A, Kubota H, Tomida J, Morita Y, Hitomi J. 2012. Genus Enhydrobacter Staley et al. 1987 should be recognized as a member of the family Rhodospirillaceae within the class Alphaproteobacteria. Microbiol Immunol 56:21-26. http:// dx.doi.org/10.1111/j.1348-0421.2011.00401.x.
-
(2012)
Microbiol Immunol
, vol.56
, pp. 21-26
-
-
Kawamura, Y.1
Fujiwara, N.2
Naka, T.3
Mitani, A.4
Kubota, H.5
Tomida, J.6
Morita, Y.7
Hitomi, J.8
-
19
-
-
72949091232
-
Bacterial community variation in human body habitats across space and time
-
Costello EK, Lauber CL, Hamady M, Fierer N, Gordon JI, Knight R. 2009. Bacterial community variation in human body habitats across space and time. Science 326:1694-1697. http://dx.doi.org/10.1126/science.1177486.
-
(2009)
Science
, vol.326
, pp. 1694-1697
-
-
Costello, E.K.1
Lauber, C.L.2
Hamady, M.3
Fierer, N.4
Gordon, J.I.5
Knight, R.6
-
20
-
-
84897846339
-
Architectural design drives the biogeography of indoor bacterial communities
-
Kembel SW, Meadow JF, O’Connor TK, Mhuireach G, Northcutt D, Kline J, Moriyama M, Brown GZ, Bohannan BJ, Green JL. 2014. Architectural design drives the biogeography of indoor bacterial communities. PLoS One 9:e87093. http://dx.doi.org/10.1371/journal.pone.0087093.
-
(2014)
PLoS One
, vol.9
, pp. e87093
-
-
Kembel, S.W.1
Meadow, J.F.2
O’Connor, T.K.3
Mhuireach, G.4
Northcutt, D.5
Kline, J.6
Moriyama, M.7
Brown, G.Z.8
Bohannan, B.J.9
Green, J.L.10
-
21
-
-
67651247607
-
Pyrosequencing-based assessment of soil pH as a predictor of soil bacterial community structure at the continental scale
-
Lauber CL, Hamady M, Knight R, Fierer N. 2009. Pyrosequencing-based assessment of soil pH as a predictor of soil bacterial community structure at the continental scale. Appl Environ Microbiol 75:5111-5120. http://dx.doi.org/10.1128/AEM.00335-09.
-
(2009)
Appl Environ Microbiol
, vol.75
, pp. 5111-5120
-
-
Lauber, C.L.1
Hamady, M.2
Knight, R.3
Fierer, N.4
-
22
-
-
80052301430
-
Bayesian community-wide culture-independent microbial source tracking
-
Knights D, Kuczynski J, Charlson ES, Zaneveld J, Mozer MC, Collman RG, Bushman FD, Knight R, Kelley ST. 2011. Bayesian community-wide culture-independent microbial source tracking. Nat Methods 8:761-763. http://dx.doi.org/10.1038/nmeth.1650.
-
(2011)
Nat Methods
, vol.8
, pp. 761-763
-
-
Knights, D.1
Kuczynski, J.2
Charlson, E.S.3
Zaneveld, J.4
Mozer, M.C.5
Collman, R.G.6
Bushman, F.D.7
Knight, R.8
Kelley, S.T.9
-
23
-
-
84872781401
-
Bacterial diversity in two neonatal intensive care units (NICUs)
-
Hewitt KM, Mannino FL, Gonzalez A, Chase JH, Caporaso JG, Knight R, Kelley ST. 2013. Bacterial diversity in two neonatal intensive care units (NICUs). PLoS One 8:e54703. http://dx.doi.org/10.1371/journal.pone.0054703.
-
(2013)
PLoS One
, vol.8
, pp. e54703
-
-
Hewitt, K.M.1
Mannino, F.L.2
Gonzalez, A.3
Chase, J.H.4
Caporaso, J.G.5
Knight, R.6
Kelley, S.T.7
-
24
-
-
46449124442
-
A diversity profile of the human skin microbiota
-
NISC Comparative Sequencing Program
-
Grice EA, Kong HH, Renaud G, Young AC, NISC Comparative Sequencing Program, Bouffard GG, Blakesley RW, Wolfsberg TG, Turner ML, Segre JA. 2008. A diversity profile of the human skin microbiota. Genome Res 18:1043-1050. http://dx.doi.org/10.1101/gr.075549.107.
-
(2008)
Genome Res
, vol.18
, pp. 1043-1050
-
-
Grice, E.A.1
Kong, H.H.2
Renaud, G.3
Young, A.C.4
Bouffard, G.G.5
Blakesley, R.W.6
Wolfsberg, T.G.7
Turner, M.L.8
Segre, J.A.9
-
25
-
-
36248986710
-
Malassezia globosa and restricta: Breakthrough understanding of the etiology and treatment of dandruff and seborrheic dermatitis through whole-genome analysis
-
Dawson TL, Jr. 2007. Malassezia globosa and restricta: breakthrough understanding of the etiology and treatment of dandruff and seborrheic dermatitis through whole-genome analysis. J Investig Dermatol Symp Proc 12:15-19. http://dx.doi.org/10.1038/sj.jidsymp.5650049.
-
(2007)
J Investig Dermatol Symp Proc
, vol.12
, pp. 15-19
-
-
Dawson, T.L.1
-
26
-
-
70349742410
-
Propionibacterium acnes and sebaceous lipogenesis: A love-hate relationship?
-
Zouboulis CC. 2009. Propionibacterium acnes and sebaceous lipogenesis: a love-hate relationship? J Invest Dermatol 129:2093-2096. http://dx.doi.org/10.1038/jid.2009.190.
-
(2009)
J Invest Dermatol
, vol.129
, pp. 2093-2096
-
-
Zouboulis, C.C.1
-
27
-
-
84866549438
-
Dysfunction of the intestinal microbiome in inflammatory bowel disease and treatment
-
Morgan XC, Tickle TL, Sokol H, Gevers D, Devaney KL, Ward DV, Reyes JA, Shah SA, LeLeiko N, Snapper SB, Bousvaros A, Korzenik J, Sands BE, Xavier RJ, Huttenhower C. 2012. Dysfunction of the intestinal microbiome in inflammatory bowel disease and treatment. Genome Biol 13:R79. http://dx.doi.org/10.1186/gb-2012-13-9-r79.
-
(2012)
Genome Biol
, vol.13
, pp. R79
-
-
Morgan, X.C.1
Tickle, T.L.2
Sokol, H.3
Gevers, D.4
Devaney, K.L.5
Ward, D.V.6
Reyes, J.A.7
Shah, S.A.8
LeLeiko, N.9
Snapper, S.B.10
Bousvaros, A.11
Korzenik, J.12
Sands, B.E.13
Xavier, R.J.14
Huttenhower, C.15
-
28
-
-
84855949949
-
Using network analysis to explore co-occurrence patterns in soil microbial communities
-
Barberán A, Bates ST, Casamayor EO, Fierer N. 2012. Using network analysis to explore co-occurrence patterns in soil microbial communities. ISME J 6:343-351. http://dx.doi.org/10.1038/ismej.2011.119.
-
(2012)
ISME J
, vol.6
, pp. 343-351
-
-
Barberán, A.1
Bates, S.T.2
Casamayor, E.O.3
Fierer, N.4
-
29
-
-
34347388470
-
UniRef: Comprehensive and non-redundant UniProt reference clusters
-
Suzek BE, Huang H, McGarvey P, Mazumder R, Wu CH. 2007. UniRef: comprehensive and non-redundant UniProt reference clusters. Bioinformatics 23:1282-1288. http://dx.doi.org/10.1093/bioinformatics/btm098.
-
(2007)
Bioinformatics
, vol.23
, pp. 1282-1288
-
-
Suzek, B.E.1
Huang, H.2
McGarvey, P.3
Mazumder, R.4
Wu, C.H.5
-
30
-
-
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. http://dx.doi.org/10.1093/nar/28.1.27.
-
(2000)
Nucleic Acids Res
, vol.28
, pp. 27-30
-
-
Kanehisa, M.1
Goto, S.2
-
31
-
-
3442895921
-
The complete genome sequence of Propionibacterium acnes, a commensal of human skin
-
Brüggemann H, Henne A, Hoster F, Liesegang H, Wiezer A, Stritt-matter A, Hujer S, Dürre P, Gottschalk G. 2004. The complete genome sequence of Propionibacterium acnes, a commensal of human skin. Science 305:671-673. http://dx.doi.org/10.1126/science.1100330.
-
(2004)
Science
, vol.305
, pp. 671-673
-
-
Brüggemann, H.1
Henne, A.2
Hoster, F.3
Liesegang, H.4
Wiezer, A.5
Stritt-Matter, A.6
Hujer, S.7
Dürre, P.8
Gottschalk, G.9
-
32
-
-
0017855942
-
Comparative studies of porphyrin production in Propionibacterium acnes and Propionibacterium granulosum
-
Lee WL, Shalita AR, Poh-Fitzpatrick MB. 1978. Comparative studies of porphyrin production in Propionibacterium acnes and Propionibacterium granulosum. J Bacteriol 133:811-815.
-
(1978)
J Bacteriol
, vol.133
, pp. 811-815
-
-
Lee, W.L.1
Shalita, A.R.2
Poh-Fitzpatrick, M.B.3
-
33
-
-
0031950791
-
Propionibacterium acnes and acne
-
Holland KT, Aldana O, Bojar RA, Cunliffe WJ, Eady EA, Holland DB, Ingham E, McGeown C, Till A, Walters C. 1998. Propionibacterium acnes and acne. Dermatology 196:67- 68. http://dx.doi.org/10.1159/000017870.
-
(1998)
Dermatology
, vol.196
, pp. 67-68
-
-
Holland, K.T.1
Aldana, O.2
Bojar, R.A.3
Cunliffe, W.J.4
Eady, E.A.5
Holland, D.B.6
Ingham, E.7
McGeown, C.8
Till, A.9
Walters, C.10
-
34
-
-
0035987288
-
Isolation and characterization of 14 additional genes specifying the anaerobic biosynthesis of cobalamin (vitamin B12) in Propionibacterium freudenreichii (P. Shermanii)
-
Roessner CA, Huang KX, Warren MJ, Raux E, Scott AI. 2002. Isolation and characterization of 14 additional genes specifying the anaerobic biosynthesis of cobalamin (vitamin B12) in Propionibacterium freudenreichii (P. shermanii). Microbiology 148:1845-1853. http://dx.doi.org/10.1099/00221287-148-6-1845.
-
(2002)
Microbiology
, vol.148
, pp. 1845-1853
-
-
Roessner, C.A.1
Huang, K.X.2
Warren, M.J.3
Raux, E.4
Scott, A.I.5
-
35
-
-
0030989127
-
The Propionibacterium freudenreichii hemYHBXRL gene cluster, which encodes enzymes and a regulator involved in the biosynthetic pathway from glutamate to pro-toheme
-
Hashimoto Y, Yamashita M, Murooka Y. 1997. The Propionibacterium freudenreichii hemYHBXRL gene cluster, which encodes enzymes and a regulator involved in the biosynthetic pathway from glutamate to pro-toheme. Appl Microbiol Biotechnol 47:385-392. http://dx.doi.org/10.1007/s002530050945.
-
(1997)
Appl Microbiol Biotechnol
, vol.47
, pp. 385-392
-
-
Hashimoto, Y.1
Yamashita, M.2
Murooka, Y.3
-
36
-
-
84953212097
-
High-specificity targeted functional profiling in microbial communities with ShortBRED
-
Kaminski J, Gibson MK, Franzosa EA, Segata N, Dantas G, Huttenhower C 2015. High-specificity targeted functional profiling in microbial communities with ShortBRED. PLOS Comput Biol. http://dx.doi.org/10.1371/journal.pcbi.1004557.
-
(2015)
PLOS Comput Biol
-
-
Kaminski, J.1
Gibson, M.K.2
Franzosa, E.A.3
Segata, N.4
Dantas, G.5
Huttenhower, C.6
-
37
-
-
84879017399
-
The comprehensive antibiotic resistance database
-
McArthur AG, Waglechner N, Nizam F, Yan A, Azad MA, Baylay AJ, Bhullar K, Canova MJ, De Pascale G, Ejim L, Kalan L, King AM, Koteva K, Morar M, Mulvey MR, O’Brien JS, Pawlowski AC, Piddock LJ, Spanogiannopoulos P, Sutherland AD, Tang I, Taylor PL, Thaker M, Wang W, Yan M, Yu T, Wright GD. 2013. The comprehensive antibiotic resistance database. Antimicrob Agents Chemother 57: 3348-3357. http://dx.doi.org/10.1128/AAC.00419-13.
-
(2013)
Antimicrob Agents Chemother
, vol.57
, pp. 3348-3357
-
-
McArthur, A.G.1
Waglechner, N.2
Nizam, F.3
Yan, A.4
Azad, M.A.5
Baylay, A.J.6
Bhullar, K.7
Canova, M.J.8
De Pascale, G.9
Ejim, L.10
Kalan, L.11
King, A.M.12
Koteva, K.13
Morar, M.14
Mulvey, M.R.15
O’Brien, J.S.16
Pawlowski, A.C.17
Piddock, L.J.18
Spanogiannopoulos, P.19
Sutherland, A.D.20
Tang, I.21
Taylor, P.L.22
Thaker, M.23
Wang, W.24
Yan, M.25
Yu, T.26
Wright, G.D.27
more..
-
38
-
-
84892572886
-
A metagenomic framework for the study of airborne microbial communities
-
Yooseph S, Andrews-Pfannkoch C, Tenney A, McQuaid J, Williamson S, Thiagarajan M, Brami D, Zeigler-Allen L, Hoffman J, Goll JB, Fadrosh D, Glass J, Adams MD, Friedman R, Venter JC. 2013. A metagenomic framework for the study of airborne microbial communities. PLoS One 8:e81862. http://dx.doi.org/10.1371/journal.pone.0081862.
-
(2013)
PLoS One
, vol.8
, pp. e81862
-
-
Yooseph, S.1
Andrews-Pfannkoch, C.2
Tenney, A.3
McQuaid, J.4
Williamson, S.5
Thiagarajan, M.6
Brami, D.7
Zeigler-Allen, L.8
Hoffman, J.9
Goll, J.B.10
Fadrosh, D.11
Glass, J.12
Adams, M.D.13
Friedman, R.14
Venter, J.C.15
-
39
-
-
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, Peng Y, Zhang D, Jie Z, Wu W, Qin Y, Xue W, Li J, Han L, Lu D, Wu P, Dai Y, Sun X, Li Z, Tang A, Zhong S, Li X, Chen W, Xu R, Wang M, Feng Q, Gong M, Yu J, Zhang Y, Zhang M, Hansen T, Sanchez G, Raes J, Falony G, Okuda S, Almeida M, LeChatelier E, Renault P, Pons N, Batto JM, Zhang Z, Chen H, Yang R, Zheng W, Li S, Yang H, Wang J, Ehrlich SD, Nielsen R, Pedersen O, Kristiansen K, Wang J. 2012. A metagenome-wide association study of gut microbiota in type 2 diabetes. Nature 490:55-60. http://dx.doi.org/10.1038/nature11450.
-
(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
Peng, Y.11
Zhang, D.12
Jie, Z.13
Wu, W.14
Qin, Y.15
Xue, W.16
Li, J.17
Han, L.18
Lu, D.19
Wu, P.20
Dai, Y.21
Sun, X.22
Li, Z.23
Tang, A.24
Zhong, S.25
Li, X.26
Chen, W.27
Xu, R.28
Wang, M.29
Feng, Q.30
Gong, M.31
Yu, J.32
Zhang, Y.33
Zhang, M.34
Hansen, T.35
Sanchez, G.36
Raes, J.37
Falony, G.38
Okuda, S.39
Almeida, M.40
LeChatelier, E.41
Renault, P.42
Pons, N.43
Batto, J.M.44
Zhang, Z.45
Chen, H.46
Yang, R.47
Zheng, W.48
Li, S.49
Yang, H.50
Wang, J.51
Ehrlich, S.D.52
Nielsen, R.53
Pedersen, O.54
Kristiansen, K.55
Wang, J.56
more..
-
40
-
-
84862141704
-
Human gut microbiome viewed across age and geography
-
Yatsunenko T, Rey FE, Manary MJ, Trehan I, Dominguez-Bello MG, Contreras M, Magris M, Hidalgo G, Baldassano RN, Anokhin AP, Heath AC, Warner B, Reeder J, Kuczynski J, Caporaso JG, Lozupone CA, Lauber C, Clemente JC, Knights D, Knight R, Gordon JI. 2012. Human gut microbiome viewed across age and geography. Nature 486:222-227. http://dx.doi.org/10.1038/nature11053.
-
(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
Heath, A.C.11
Warner, B.12
Reeder, J.13
Kuczynski, J.14
Caporaso, J.G.15
Lozupone, C.A.16
Lauber, C.17
Clemente, J.C.18
Knights, D.19
Knight, R.20
Gordon, J.I.21
more..
-
41
-
-
84880831180
-
Metagenome-wide analysis of antibiotic resistance genes in a large cohort of human gut microbiota
-
Hu Y, Yang X, Qin J, Lu N, Cheng G, Wu N, Pan Y, Li J, Zhu L, Wang X, Meng Z, Zhao F, Liu D, Ma J, Qin N, Xiang C, Xiao Y, Li L, Yang H, Wang J, Yang R, Gao GF, Wang J, Zhu B. 2013. Metagenome-wide analysis of antibiotic resistance genes in a large cohort of human gut microbiota. Nat Commun 4:2151. http://dx.doi.org/10.1038/ncomms3151.
-
(2013)
Nat Commun
, vol.4
, pp. 2151
-
-
Hu, Y.1
Yang, X.2
Qin, J.3
Lu, N.4
Cheng, G.5
Wu, N.6
Pan, Y.7
Li, J.8
Zhu, L.9
Wang, X.10
Meng, Z.11
Zhao, F.12
Liu, D.13
Ma, J.14
Qin, N.15
Xiang, C.16
Xiao, Y.17
Li, L.18
Yang, H.19
Wang, J.20
Yang, R.21
Gao, G.F.22
Wang, J.23
Zhu, B.24
more..
-
42
-
-
13444249995
-
VFDB: A reference database for bacterial virulence factors
-
Chen L, Yang J, Yu J, Yao Z, Sun L, Shen Y, Jin Q. 2005. VFDB: a reference database for bacterial virulence factors. Nucleic Acids Res 33:D325-D328. http://dx.doi.org/10.1093/nar/gki008.
-
(2005)
Nucleic Acids Res
, vol.33
, pp. D325-D328
-
-
Chen, L.1
Yang, J.2
Yu, J.3
Yao, Z.4
Sun, L.5
Shen, Y.6
Jin, Q.7
-
43
-
-
33846592867
-
Role of ventilation in airborne transmission of infectious agents in the built environment-a multidisciplinary systematic review
-
Li Y, Leung GM, Tang JW, Yang X, Chao CY, Lin JZ, Lu JW, Nielsen PV, Niu J, Qian H, Sleigh AC, Su HJ, Sundell J, Wong TW, Yuen PL. 2007. Role of ventilation in airborne transmission of infectious agents in the built environment-a multidisciplinary systematic review. Indoor Air 17:2-18. http://dx.doi.org/10.1111/j.1600-0668.2006.00445.x.
-
(2007)
Indoor Air
, vol.17
, pp. 2-18
-
-
Li, Y.1
Leung, G.M.2
Tang, J.W.3
Yang, X.4
Chao, C.Y.5
Lin, J.Z.6
Lu, J.W.7
Nielsen, P.V.8
Niu, J.9
Qian, H.10
Sleigh, A.C.11
Su, H.J.12
Sundell, J.13
Wong, T.W.14
Yuen, P.L.15
-
44
-
-
84920721220
-
Ecological succession and viability of human-associated microbiota on restroom surfaces
-
Gibbons SM, Schwartz T, Fouquier J, Mitchell M, Sangwan N, Gilbert JA, Kelley ST. 2015. Ecological succession and viability of human-associated microbiota on restroom surfaces. Appl Environ Microbiol 81:765-773. http://dx.doi.org/10.1128/AEM.03117-14.
-
(2015)
Appl Environ Microbiol
, vol.81
, pp. 765-773
-
-
Gibbons, S.M.1
Schwartz, T.2
Fouquier, J.3
Mitchell, M.4
Sangwan, N.5
Gilbert, J.A.6
Kelley, S.T.7
-
45
-
-
84862276328
-
Structure, function and diversity of the healthy human microbiome
-
Human Microbiome Project Consortium
-
Human Microbiome Project Consortium. 2012. Structure, function and diversity of the healthy human microbiome. Nature 486:207-214. http://dx.doi.org/10.1038/nature11234.
-
(2012)
Nature
, vol.486
, pp. 207-214
-
-
-
46
-
-
84891164163
-
MIxS-BE: A MIxS extension defining a minimum information standard for sequence data from the built environment
-
Glass EM, Dribinsky Y, Yilmaz P, Levin H, Van Pelt R, Wendel D, Wilke A, Eisen JA, Huse S, Shipanova A, Sogin M, Stajich J, Knight R, Meyer F, Schriml LM. 2014. MIxS-BE: a MIxS extension defining a minimum information standard for sequence data from the built environment. ISME J 8:1-3. http://dx.doi.org/10.1038/ismej.2013.176.
-
(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
Sogin, M.11
Stajich, J.12
Knight, R.13
Meyer, F.14
Schriml, L.M.15
-
47
-
-
84949535282
-
-
29 August
-
National Centers for Environmental Information and National Oceanic and Atmospheric Administration. 29 August 2015. Record of climatological observations. http://www.ncdc.noaa.gov/cdo-web/.
-
(2015)
Record of Climatological Observations
-
-
-
48
-
-
85041897384
-
-
Accessed 29 August 2015
-
Weather Underground. Weather history for KBOS. http://www.wunderground.com/history/. Accessed 29 August 2015.
-
Weather History for KBOS
-
-
-
49
-
-
33747175722
-
Molecular analysis of fungal microbiota in samples from healthy human skin and psoriatic lesions
-
Paulino LC, Tseng CH, Strober BE, Blaser MJ. 2006. Molecular analysis of fungal microbiota in samples from healthy human skin and psoriatic lesions. J Clin Microbiol 44:2933-2941. http://dx.doi.org/10.1128/JCM.00785-06.
-
(2006)
J Clin Microbiol
, vol.44
, pp. 2933-2941
-
-
Paulino, L.C.1
Tseng, C.H.2
Strober, B.E.3
Blaser, M.J.4
-
50
-
-
79952005915
-
Global patterns of 16S rRNA diversity at a depth of millions of sequences per sample
-
Caporaso JG, Lauber CL, Walters WA, Berg-Lyons D, Lozupone CA, Turnbaugh PJ, Fierer N, Knight R. 2011. Global patterns of 16S rRNA diversity at a depth of millions of sequences per sample. Proc Natl Acad Sci U S A 108(Suppl 1):4516-4522. http://dx.doi.org/10.1073/pnas.1000080107.
-
(2011)
Proc Natl Acad Sci U S A
, vol.108
, pp. 4516-4522
-
-
Caporaso, J.G.1
Lauber, C.L.2
Walters, W.A.3
Berg-Lyons, D.4
Lozupone, C.A.5
Turnbaugh, P.J.6
Fierer, N.7
Knight, R.8
-
51
-
-
77952243141
-
QIIME allows analysis of high-throughput community sequencing data
-
Caporaso JG, Kuczynski J, Stombaugh J, Bittinger K, Bushman FD, Costello EK, Fierer N, Peña AG, Goodrich JK, Gordon JI, Huttley GA, Kelley ST, Knights D, Koenig JE, Ley RE, Lozupone CA, McDonald D, Muegge BD, Pirrung M, Reeder J, Sevinsky JR, Turnbaugh PJ, Walters WA, Widmann J, Yatsunenko T, Zaneveld J, Knight R. 2010. QIIME allows analysis of high-throughput community sequencing data. Nat Methods 7:335-336. http://dx.doi.org/10.1038/nmeth.f.303.
-
(2010)
Nat Methods
, vol.7
, pp. 335-336
-
-
Caporaso, J.G.1
Kuczynski, J.2
Stombaugh, J.3
Bittinger, K.4
Bushman, F.D.5
Costello, E.K.6
Fierer, N.7
Peña, A.G.8
Goodrich, J.K.9
Gordon, J.I.10
Huttley, G.A.11
Kelley, S.T.12
Knights, D.13
Koenig, J.E.14
Ley, R.E.15
Lozupone, C.A.16
McDonald, D.17
Muegge, B.D.18
Pirrung, M.19
Reeder, J.20
Sevinsky, J.R.21
Turnbaugh, P.J.22
Walters, W.A.23
Widmann, J.24
Yatsunenko, T.25
Zaneveld, J.26
Knight, R.27
more..
-
52
-
-
70349255569
-
-
Oksanen J, Blanchet FG, Kindt R, Legendre P, Minchin P, O’Hara R, Simpson G, Solymos P, Stevens H, Wagner H. 2015. vegan: community ecology package. https://cran.r-project.org/web/packages/vegan/index.html.
-
(2015)
Vegan: Community Ecology Package
-
-
Oksanen, J.1
Blanchet, F.G.2
Kindt, R.3
Legendre, P.4
Minchin, P.5
O’Hara, R.6
Simpson, G.7
Solymos, P.8
Stevens, H.9
Wagner, H.10
-
53
-
-
84937442075
-
Compact graphical representation of phylogenetic data and metadata with GraPhlAn
-
Asnicar F, Weingart G, Tickle TL, Huttenhower C, Segata N. 2015. Compact graphical representation of phylogenetic data and metadata with GraPhlAn. PeerJ 3:e1029. http://dx.doi.org/10.7717/peerj.1029.
-
(2015)
PeerJ
, vol.3
, pp. e1029
-
-
Asnicar, F.1
Weingart, G.2
Tickle, T.L.3
Huttenhower, C.4
Segata, N.5
-
54
-
-
84864440400
-
Metagenomic microbial community profiling using unique clade-specific marker genes
-
Segata N, Waldron L, Ballarini A, Narasimhan V, Jousson O, Huttenhower C. 2012. Metagenomic microbial community profiling using unique clade-specific marker genes. Nat Methods 9:811-814. http://dx.doi.org/10.1038/nmeth.2066.
-
(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
-
55
-
-
84864037467
-
Metabolic reconstruction for metagenomic data and its application to the human microbiome
-
Abubucker S, Segata N, Goll J, Schubert AM, Izard J, Cantarel BL, Rodriguez-Mueller B, Zucker J, Thiagarajan M, Henrissat B, White O, Kelley ST, Methé B, Schloss PD, Gevers D, Mitreva M, Huttenhower C. 2012. Metabolic reconstruction for metagenomic data and its application to the human microbiome. PLOS Comput Biol 8:e1002358. http://dx.doi.org/10.1371/journal.pcbi.1002358.
-
(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
White, O.11
Kelley, S.T.12
Methé, B.13
Schloss, P.D.14
Gevers, D.15
Mitreva, M.16
Huttenhower, C.17
-
56
-
-
84891774001
-
The MetaCyc database of metabolic pathways and enzymes and the BioCyc collection of pathway/ genome databases
-
Caspi R, Altman T, Billington R, Dreher K, Foerster H, Fulcher CA, Holland TA, Keseler IM, Kothari A, Kubo A, Krummenacker M, La-tendresse M, Mueller LA, Ong Q, Paley S, Subhraveti P, Weaver DS, Weerasinghe D, Zhang P, Karp PD. 2014. The MetaCyc database of metabolic pathways and enzymes and the BioCyc collection of pathway/ genome databases. Nucleic Acids Res 42:D459 -D471. http://dx.doi.org/ 10.1093/nar/gkt1103.
-
(2014)
Nucleic Acids Res
, vol.42
, pp. D459-D471
-
-
Caspi, R.1
Altman, T.2
Billington, R.3
Dreher, K.4
Foerster, H.5
Fulcher, C.A.6
Holland, T.A.7
Keseler, I.M.8
Kothari, A.9
Kubo, A.10
Krummenacker, M.11
La-Tendresse, M.12
Mueller, L.A.13
Ong, Q.14
Paley, S.15
Subhraveti, P.16
Weaver, D.S.17
Weerasinghe, D.18
Zhang, P.19
Karp, P.D.20
more..
-
57
-
-
84859821563
-
UniPathway: A resource for the exploration and annotation of metabolic pathways
-
Morgat A, Coissac E, Coudert E, Axelsen KB, Keller G, Bairoch A, Bridge A, Bougueleret L, Xenarios I, Viari A. 2012. UniPathway: a resource for the exploration and annotation of metabolic pathways. Nucleic Acids Res 40:D761-D769. http://dx.doi.org/10.1093/nar/gkr1023.
-
(2012)
Nucleic Acids Res
, vol.40
, pp. D761-D769
-
-
Morgat, A.1
Coissac, E.2
Coudert, E.3
Axelsen, K.B.4
Keller, G.5
Bairoch, A.6
Bridge, A.7
Bougueleret, L.8
Xenarios, I.9
Viari, A.10
-
58
-
-
84891760956
-
Data, information, knowledge and principle: Back to metabolism in KEGG
-
Kanehisa M, Goto S, Sato Y, Kawashima M, Furumichi M, Tanabe M. 2014. Data, information, knowledge and principle: back to metabolism in KEGG. Nucleic Acids Res 42:D199-D205. http://dx.doi.org/10.1093/nar/gkt1076.
-
(2014)
Nucleic Acids Res
, vol.42
, pp. D199-D205
-
-
Kanehisa, M.1
Goto, S.2
Sato, Y.3
Kawashima, M.4
Furumichi, M.5
Tanabe, M.6
-
59
-
-
84925267288
-
UniRef clusters: A comprehensive and scalable alternative for improving sequence similarity searches
-
UniProt Consortium
-
Suzek BE, Wang Y, Huang H, McGarvey PB, Wu CH, UniProt Consortium. 2015. UniRef clusters: a comprehensive and scalable alternative for improving sequence similarity searches. Bioinformatics 31:926 -932. http://dx.doi.org/10.1093/bioinformatics/btu739.
-
(2015)
Bioinformatics
, vol.31
, pp. 926-932
-
-
Suzek, B.E.1
Wang, Y.2
Huang, H.3
McGarvey, P.B.4
Wu, C.H.5
-
60
-
-
58149183697
-
ARDB-Antibiotic Resistance Genes Database
-
Liu B, Pop M. 2009. ARDB-Antibiotic Resistance Genes Database. Nucleic Acids Res 37:D443-D447. http://dx.doi.org/10.1093/nar/gkn656.
-
(2009)
Nucleic Acids Res
, vol.37
, pp. D443-D447
-
-
Liu, B.1
Pop, M.2
|