-
1
-
-
53349173070
-
Specific microbiota direct the differentiation of IL-17-producing T-helper cells in the mucosa of the small intestine
-
10.1016/j.chom.2008.09.009, 2597589, 18854238
-
Ivanov II, Frutos Rde L, Manel N, Yoshinaga K, Rifkin DB, Sartor RB, Finlay BB, Littman DR. Specific microbiota direct the differentiation of IL-17-producing T-helper cells in the mucosa of the small intestine. Cell Host Microbe 2008, 4:337-349. 10.1016/j.chom.2008.09.009, 2597589, 18854238.
-
(2008)
Cell Host Microbe
, vol.4
, pp. 337-349
-
-
Ivanov, I.I.1
Frutos Rde, L.2
Manel, N.3
Yoshinaga, K.4
Rifkin, D.B.5
Sartor, R.B.6
Finlay, B.B.7
Littman, D.R.8
-
2
-
-
84862637797
-
Gut immune maturation depends on colonization with a host-specific microbiota
-
10.1016/j.cell.2012.04.037, 3442780, 22726443
-
Chung H, Pamp SJ, Hill JA, Surana NK, Edelman SM, Troy EB, Reading NC, Villablanca EJ, Wang S, Mora JR, Umesaki Y, Mathis D, Benoist C, Relman DA, Kasper DL. Gut immune maturation depends on colonization with a host-specific microbiota. Cell 2012, 149:1578-1593. 10.1016/j.cell.2012.04.037, 3442780, 22726443.
-
(2012)
Cell
, vol.149
, pp. 1578-1593
-
-
Chung, H.1
Pamp, S.J.2
Hill, J.A.3
Surana, N.K.4
Edelman, S.M.5
Troy, E.B.6
Reading, N.C.7
Villablanca, E.J.8
Wang, S.9
Mora, J.R.10
Umesaki, Y.11
Mathis, D.12
Benoist, C.13
Relman, D.A.14
Kasper, D.L.15
-
3
-
-
65549109517
-
Studying bacteria in respiratory specimens by using conventional and molecular microbiological approaches
-
10.1186/1471-2466-9-14, 2678980, 19368727
-
Rogers GB, Daniels TW, Tuck A, Carroll MP, Connett GJ, David GJ, Bruce KD. Studying bacteria in respiratory specimens by using conventional and molecular microbiological approaches. BMC Pulm Med 2009, 9:14. 10.1186/1471-2466-9-14, 2678980, 19368727.
-
(2009)
BMC Pulm Med
, vol.9
, pp. 14
-
-
Rogers, G.B.1
Daniels, T.W.2
Tuck, A.3
Carroll, M.P.4
Connett, G.J.5
David, G.J.6
Bruce, K.D.7
-
4
-
-
0030923196
-
Bacterial colonization of distal airways in healthy subjects and chronic lung disease: a bronchoscopic study
-
10.1183/09031936.97.10051137, 9163659
-
Cabello H, Torres A, Celis R, El-Ebiary M, Puig de la Bellacasa J, Xaubet A, Gonzalez J, Agusti C, Soler N. Bacterial colonization of distal airways in healthy subjects and chronic lung disease: a bronchoscopic study. Eur Respir J 1997, 10:1137-1144. 10.1183/09031936.97.10051137, 9163659.
-
(1997)
Eur Respir J
, vol.10
, pp. 1137-1144
-
-
Cabello, H.1
Torres, A.2
Celis, R.3
El-Ebiary, M.4
Puig de la Bellacasa, J.5
Xaubet, A.6
Gonzalez, J.7
Agusti, C.8
Soler, N.9
-
5
-
-
84866126809
-
Assessing bacterial populations in the lung by replicate analysis of samples from the upper and lower respiratory tracts
-
10.1371/journal.pone.0042786, 3435383, 22970118
-
Charlson ES, Bittinger K, Chen J, Diamond JM, Li H, Collman RG, Bushman FD. Assessing bacterial populations in the lung by replicate analysis of samples from the upper and lower respiratory tracts. PLoS One 2012, 7:e42786. 10.1371/journal.pone.0042786, 3435383, 22970118.
-
(2012)
PLoS One
, vol.7
-
-
Charlson, E.S.1
Bittinger, K.2
Chen, J.3
Diamond, J.M.4
Li, H.5
Collman, R.G.6
Bushman, F.D.7
-
6
-
-
80053122563
-
Topographical continuity of bacterial populations in the healthy human respiratory tract
-
10.1164/rccm.201104-0655OC, 3208663, 21680950
-
Charlson ES, Bittinger K, Haas AR, Fitzgerald AS, Frank I, Yadav A, Bushman FD, Collman RG. Topographical continuity of bacterial populations in the healthy human respiratory tract. Am J Respir Crit Care Med 2011, 184:957-963. 10.1164/rccm.201104-0655OC, 3208663, 21680950.
-
(2011)
Am J Respir Crit Care Med
, vol.184
, pp. 957-963
-
-
Charlson, E.S.1
Bittinger, K.2
Haas, A.R.3
Fitzgerald, A.S.4
Frank, I.5
Yadav, A.6
Bushman, F.D.7
Collman, R.G.8
-
7
-
-
79952063902
-
Analysis of the lung microbiome in the " healthy" smoker and in COPD
-
10.1371/journal.pone.0016384, 3043049, 21364979
-
Erb-Downward JR, Thompson DL, Han MK, Freeman CM, McCloskey L, Schmidt LA, Young VB, Toews GB, Curtis JL, Sundaram B, Martinez FJ, Huffnagle GB. Analysis of the lung microbiome in the " healthy" smoker and in COPD. PLoS One 2011, 6:e16384. 10.1371/journal.pone.0016384, 3043049, 21364979.
-
(2011)
PLoS One
, vol.6
-
-
Erb-Downward, J.R.1
Thompson, D.L.2
Han, M.K.3
Freeman, C.M.4
McCloskey, L.5
Schmidt, L.A.6
Young, V.B.7
Toews, G.B.8
Curtis, J.L.9
Sundaram, B.10
Martinez, F.J.11
Huffnagle, G.B.12
-
8
-
-
77649119443
-
Disordered microbial communities in asthmatic airways
-
10.1371/journal.pone.0008578, 2798952, 20052417
-
Hilty M, Burke C, Pedro H, Cardenas P, Bush A, Bossley C, Davies J, Ervine A, Poulter L, Pachter L, Moffatt MF, Cookson WO. Disordered microbial communities in asthmatic airways. PLoS One 2010, 5:e8578. 10.1371/journal.pone.0008578, 2798952, 20052417.
-
(2010)
PLoS One
, vol.5
-
-
Hilty, M.1
Burke, C.2
Pedro, H.3
Cardenas, P.4
Bush, A.5
Bossley, C.6
Davies, J.7
Ervine, A.8
Poulter, L.9
Pachter, L.10
Moffatt, M.F.11
Cookson, W.O.12
-
9
-
-
84867427320
-
The lung microbiome in moderate and severe chronic obstructive pulmonary disease
-
10.1371/journal.pone.0047305, 3469539, 23071781
-
Pragman AA, Kim HB, Reilly CS, Wendt C, Isaacson RE. The lung microbiome in moderate and severe chronic obstructive pulmonary disease. PLoS One 2012, 7:e47305. 10.1371/journal.pone.0047305, 3469539, 23071781.
-
(2012)
PLoS One
, vol.7
-
-
Pragman, A.A.1
Kim, H.B.2
Reilly, C.S.3
Wendt, C.4
Isaacson, R.E.5
-
10
-
-
84877878844
-
Widespread colonization of the lung by Tropheryma whipplei in HIV infection
-
10.1164/rccm.201211-2145OC, 23392441, Lung HIV Microbiome Project
-
Lozupone C, Cota-Gomez A, Palmer BE, Linderman DJ, Charlson ES, Sodergren E, Mitreva M, Abubucker S, Martin J, Yao G, Campbell TB, Flores SC, Ackerman G, Stombaugh J, Ursell L, Beck JM, Curtis JL, Young VB, Lynch SV, Huang L, Weinstock GM, Knox KS, Twigg H, Morris A, Ghedin E, Bushman FD, Collman RG, Knight R, Fontenot AP. Lung HIV Microbiome Project Widespread colonization of the lung by Tropheryma whipplei in HIV infection. Am J Respir Crit Care Med 2013, 187:1110-1117. 10.1164/rccm.201211-2145OC, 23392441, Lung HIV Microbiome Project.
-
(2013)
Am J Respir Crit Care Med
, vol.187
, pp. 1110-1117
-
-
Lozupone, C.1
Cota-Gomez, A.2
Palmer, B.E.3
Linderman, D.J.4
Charlson, E.S.5
Sodergren, E.6
Mitreva, M.7
Abubucker, S.8
Martin, J.9
Yao, G.10
Campbell, T.B.11
Flores, S.C.12
Ackerman, G.13
Stombaugh, J.14
Ursell, L.15
Beck, J.M.16
Curtis, J.L.17
Young, V.B.18
Lynch, S.V.19
Huang, L.20
Weinstock, G.M.21
Knox, K.S.22
Twigg, H.23
Morris, A.24
Ghedin, E.25
Bushman, F.D.26
Collman, R.G.27
Knight, R.28
Fontenot, A.P.29
more..
-
11
-
-
84877899252
-
Comparison of the respiratory microbiome in healthy nonsmokers and smokers
-
10.1164/rccm.201210-1913OC, 23491408, Lung HIV Microbiome Project
-
Morris A, Beck JM, Schloss PD, Campbell TB, Crothers K, Curtis JL, Flores SC, Fontenot AP, Ghedin E, Huang L, Jablonski K, Kleerup E, Lynch SV, Sodergren E, Twigg H, Young VB, Bassis CM, Venkataraman A, Schmidt TM, Weinstock GM. Lung HIV Microbiome Project Comparison of the respiratory microbiome in healthy nonsmokers and smokers. Am J Respir Crit Care Med 2013, 187:1067-1075. 10.1164/rccm.201210-1913OC, 23491408, Lung HIV Microbiome Project.
-
(2013)
Am J Respir Crit Care Med
, vol.187
, pp. 1067-1075
-
-
Morris, A.1
Beck, J.M.2
Schloss, P.D.3
Campbell, T.B.4
Crothers, K.5
Curtis, J.L.6
Flores, S.C.7
Fontenot, A.P.8
Ghedin, E.9
Huang, L.10
Jablonski, K.11
Kleerup, E.12
Lynch, S.V.13
Sodergren, E.14
Twigg, H.15
Young, V.B.16
Bassis, C.M.17
Venkataraman, A.18
Schmidt, T.M.19
Weinstock, G.M.20
more..
-
12
-
-
0033053411
-
Risk factors for lower airway bacterial colonization in chronic bronchitis
-
10.1034/j.1399-3003.1999.13b20.x, 10065678
-
Monso E, Rosell A, Bonet G, Manterola J, Cardona PJ, Ruiz J, Morera J. Risk factors for lower airway bacterial colonization in chronic bronchitis. Eur Respir J 1999, 13:338-342. 10.1034/j.1399-3003.1999.13b20.x, 10065678.
-
(1999)
Eur Respir J
, vol.13
, pp. 338-342
-
-
Monso, E.1
Rosell, A.2
Bonet, G.3
Manterola, J.4
Cardona, P.J.5
Ruiz, J.6
Morera, J.7
-
13
-
-
0029085092
-
Bacterial infection in chronic obstructive pulmonary disease. A study of stable and exacerbated outpatients using the protected specimen brush
-
10.1164/ajrccm.152.4.7551388, 7551388
-
Monso E, Ruiz J, Rosell A, Manterola J, Fiz J, Morera J, Ausina V. Bacterial infection in chronic obstructive pulmonary disease. A study of stable and exacerbated outpatients using the protected specimen brush. Am J Respir Crit Care Med 1995, 152:1316-1320. 10.1164/ajrccm.152.4.7551388, 7551388.
-
(1995)
Am J Respir Crit Care Med
, vol.152
, pp. 1316-1320
-
-
Monso, E.1
Ruiz, J.2
Rosell, A.3
Manterola, J.4
Fiz, J.5
Morera, J.6
Ausina, V.7
-
14
-
-
0033018960
-
Predisposing factors to bacterial colonization in chronic obstructive pulmonary disease
-
10.1034/j.1399-3003.1999.13b21.x, 10065679
-
Zalacain R, Sobradillo V, Amilibia J, Barron J, Achotegui V, Pijoan JI, Llorente JL. Predisposing factors to bacterial colonization in chronic obstructive pulmonary disease. Eur Respir J 1999, 13:343-348. 10.1034/j.1399-3003.1999.13b21.x, 10065679.
-
(1999)
Eur Respir J
, vol.13
, pp. 343-348
-
-
Zalacain, R.1
Sobradillo, V.2
Amilibia, J.3
Barron, J.4
Achotegui, V.5
Pijoan, J.I.6
Llorente, J.L.7
-
15
-
-
81255157031
-
The emerging relationship between the airway microbiota and chronic respiratory disease: clinical implications
-
10.1586/ers.11.76, 3359942, 22082166
-
Huang YJ, Lynch SV. The emerging relationship between the airway microbiota and chronic respiratory disease: clinical implications. Expert Rev Respir Med 2011, 5:809-821. 10.1586/ers.11.76, 3359942, 22082166.
-
(2011)
Expert Rev Respir Med
, vol.5
, pp. 809-821
-
-
Huang, Y.J.1
Lynch, S.V.2
-
16
-
-
79551495183
-
Airway microbiota and bronchial hyperresponsiveness in patients with suboptimally controlled asthma
-
e371-373, 10.1016/j.jaci.2010.10.048, 3037020, 21194740, National Heart, Lung, and Blood Institute's Asthma Clinical Research Network
-
Huang YJ, Nelson CE, Brodie EL, Desantis TZ, Baek MS, Liu J, Woyke T, Allgaier M, Bristow J, Wiener-Kronish JP, Sutherland ER, King TS, Icitovic N, Martin RJ, Calhoun WJ, Castro M, Denlinger LC, Dimango E, Kraft M, Peters SP, Wasserman SI, Wechsler ME, Boushey HA, Lynch SV. National Heart, Lung, and Blood Institute's Asthma Clinical Research Network Airway microbiota and bronchial hyperresponsiveness in patients with suboptimally controlled asthma. J Allergy Clin Immunol 2011, 127:372-381. e371-373, 10.1016/j.jaci.2010.10.048, 3037020, 21194740, National Heart, Lung, and Blood Institute's Asthma Clinical Research Network.
-
(2011)
J Allergy Clin Immunol
, vol.127
, pp. 372-381
-
-
Huang, Y.J.1
Nelson, C.E.2
Brodie, E.L.3
Desantis, T.Z.4
Baek, M.S.5
Liu, J.6
Woyke, T.7
Allgaier, M.8
Bristow, J.9
Wiener-Kronish, J.P.10
Sutherland, E.R.11
King, T.S.12
Icitovic, N.13
Martin, R.J.14
Calhoun, W.J.15
Castro, M.16
Denlinger, L.C.17
Dimango, E.18
Kraft, M.19
Peters, S.P.20
Wasserman, S.I.21
Wechsler, M.E.22
Boushey, H.A.23
Lynch, S.V.24
more..
-
17
-
-
0030988811
-
Quantitative aspiration during sleep in normal subjects
-
10.1378/chest.111.5.1266, 9149581
-
Gleeson K, Eggli DF, Maxwell SL. Quantitative aspiration during sleep in normal subjects. Chest 1997, 111:1266-1272. 10.1378/chest.111.5.1266, 9149581.
-
(1997)
Chest
, vol.111
, pp. 1266-1272
-
-
Gleeson, K.1
Eggli, D.F.2
Maxwell, S.L.3
-
18
-
-
79551569573
-
Laryngeal penetration and aspiration in individuals with stable COPD
-
10.1111/j.1440-1843.2010.01875.x, 21054669
-
Cvejic L, Harding R, Churchward T, Turton A, Finlay P, Massey D, Bardin PG, Guy P. Laryngeal penetration and aspiration in individuals with stable COPD. Respirology 2011, 16:269-275. 10.1111/j.1440-1843.2010.01875.x, 21054669.
-
(2011)
Respirology
, vol.16
, pp. 269-275
-
-
Cvejic, L.1
Harding, R.2
Churchward, T.3
Turton, A.4
Finlay, P.5
Massey, D.6
Bardin, P.G.7
Guy, P.8
-
19
-
-
33750065102
-
Role of gastroesophageal reflux symptoms in exacerbations of COPD
-
Rascon-Aguilar IE, Pamer M, Wludyka P, Cury J, Coultas D, Lambiase LR, Nahman NS, Vega KJ. Role of gastroesophageal reflux symptoms in exacerbations of COPD. Ches 2006, 130:1096-1101.
-
(2006)
Ches
, vol.130
, pp. 1096-1101
-
-
Rascon-Aguilar, I.E.1
Pamer, M.2
Wludyka, P.3
Cury, J.4
Coultas, D.5
Lambiase, L.R.6
Nahman, N.S.7
Vega, K.J.8
-
20
-
-
84861399683
-
The lung tissue microbiome in chronic obstructive pulmonary disease
-
10.1164/rccm.201111-2075OC, 3359894, 22427533
-
Sze MA, Dimitriu PA, Hayashi S, Elliott WM, McDonough JE, Gosselink JV, Cooper J, Sin DD, Mohn WW, Hogg JC. The lung tissue microbiome in chronic obstructive pulmonary disease. Am J Respir Crit Care Med 2012, 185:1073-1080. 10.1164/rccm.201111-2075OC, 3359894, 22427533.
-
(2012)
Am J Respir Crit Care Med
, vol.185
, pp. 1073-1080
-
-
Sze, M.A.1
Dimitriu, P.A.2
Hayashi, S.3
Elliott, W.M.4
McDonough, J.E.5
Gosselink, J.V.6
Cooper, J.7
Sin, D.D.8
Mohn, W.W.9
Hogg, J.C.10
-
21
-
-
77049098120
-
A persistent and diverse airway microbiota present during chronic obstructive pulmonary disease exacerbations
-
10.1089/omi.2009.0100, 3116451, 20141328
-
Huang YJ, Kim E, Cox MJ, Brodie EL, Brown R, Wiener-Kronish JP, Lynch SV. A persistent and diverse airway microbiota present during chronic obstructive pulmonary disease exacerbations. OMICS 2010, 14:9-59. 10.1089/omi.2009.0100, 3116451, 20141328.
-
(2010)
OMICS
, vol.14
, pp. 9-59
-
-
Huang, Y.J.1
Kim, E.2
Cox, M.J.3
Brodie, E.L.4
Brown, R.5
Wiener-Kronish, J.P.6
Lynch, S.V.7
-
22
-
-
79953646075
-
Innate immune responses are increased in chronic obstructive pulmonary disease
-
10.1371/journal.pone.0018426, 3069087, 21483784
-
Baines KJ, Simpson JL, Gibson PG. Innate immune responses are increased in chronic obstructive pulmonary disease. PLoS One 2011, 6:e18426. 10.1371/journal.pone.0018426, 3069087, 21483784.
-
(2011)
PLoS One
, vol.6
-
-
Baines, K.J.1
Simpson, J.L.2
Gibson, P.G.3
-
23
-
-
44849090900
-
Cigarette smoke increases toll-like receptor 4 and modifies lipopolysaccharide-mediated responses in airway epithelial cells
-
10.1111/j.1365-2567.2007.02788.x, 2440834, 18217953
-
Pace E, Ferraro M, Siena L, Melis M, Montalbano AM, Johnson M, Bonsignore MR, Bonsignore G, Gjomarkaj M. Cigarette smoke increases toll-like receptor 4 and modifies lipopolysaccharide-mediated responses in airway epithelial cells. Immunology 2008, 124:401-411. 10.1111/j.1365-2567.2007.02788.x, 2440834, 18217953.
-
(2008)
Immunology
, vol.124
, pp. 401-411
-
-
Pace, E.1
Ferraro, M.2
Siena, L.3
Melis, M.4
Montalbano, A.M.5
Johnson, M.6
Bonsignore, M.R.7
Bonsignore, G.8
Gjomarkaj, M.9
-
24
-
-
56749157688
-
Long-term erythromycin therapy is associated with decreased chronic obstructive pulmonary disease exacerbations
-
10.1164/rccm.200801-145OC, 18723437
-
Seemungal TA, Wilkinson TM, Hurst JR, Perera WR, Sapsford RJ, Wedzicha JA. Long-term erythromycin therapy is associated with decreased chronic obstructive pulmonary disease exacerbations. Am J Respir Crit Care Med 2008, 178:1139-1147. 10.1164/rccm.200801-145OC, 18723437.
-
(2008)
Am J Respir Crit Care Med
, vol.178
, pp. 1139-1147
-
-
Seemungal, T.A.1
Wilkinson, T.M.2
Hurst, J.R.3
Perera, W.R.4
Sapsford, R.J.5
Wedzicha, J.A.6
-
25
-
-
80052157895
-
Azithromycin for prevention of exacerbations of COPD
-
10.1056/NEJMoa1104623, 3220999, 21864166, COPD Clinical Research Network
-
Albert RK, Connett J, Bailey WC, Casaburi R, Cooper JA, Criner GJ, Curtis JL, Dransfield MT, Han MK, Lazarus SC, Make B, Marchetti N, Martinez FJ, Madinger NE, McEvoy C, Niewoehner DE, Porsasz J, Price CS, Reilly J, Scanlon PD, Sciurba FC, Scharf SM, Washko GR, Woodruff PG, Anthonisen NR. COPD Clinical Research Network Azithromycin for prevention of exacerbations of COPD. N Engl J Med 2011, 365:689-698. 10.1056/NEJMoa1104623, 3220999, 21864166, COPD Clinical Research Network.
-
(2011)
N Engl J Med
, vol.365
, pp. 689-698
-
-
Albert, R.K.1
Connett, J.2
Bailey, W.C.3
Casaburi, R.4
Cooper, J.A.5
Criner, G.J.6
Curtis, J.L.7
Dransfield, M.T.8
Han, M.K.9
Lazarus, S.C.10
Make, B.11
Marchetti, N.12
Martinez, F.J.13
Madinger, N.E.14
McEvoy, C.15
Niewoehner, D.E.16
Porsasz, J.17
Price, C.S.18
Reilly, J.19
Scanlon, P.D.20
Sciurba, F.C.21
Scharf, S.M.22
Washko, G.R.23
Woodruff, P.G.24
Anthonisen, N.R.25
more..
-
26
-
-
17644363081
-
ATS/ERS recommendations for standardized procedures for the online and offline measurement of exhaled lower respiratory nitric oxide and nasal nitric oxide, 2005
-
Documents ATS. ATS/ERS recommendations for standardized procedures for the online and offline measurement of exhaled lower respiratory nitric oxide and nasal nitric oxide, 2005. Am J Respir Crit Care Med 2005, 171:912-930.
-
(2005)
Am J Respir Crit Care Med
, vol.171
, pp. 912-930
-
-
Documents, A.T.S.1
-
27
-
-
80051738661
-
HIV-1 and bacterial pneumonia in the era of antiretroviral therapy
-
10.1513/pats.201006-044WR, 3132786, 21653529
-
Segal LN, Methe BA, Nolan A, Hoshino Y, Rom WN, Dawson R, Bateman E, Weiden MD. HIV-1 and bacterial pneumonia in the era of antiretroviral therapy. Proc Am Thorac Soc 2011, 8:282-287. 10.1513/pats.201006-044WR, 3132786, 21653529.
-
(2011)
Proc Am Thorac Soc
, vol.8
, pp. 282-287
-
-
Segal, L.N.1
Methe, B.A.2
Nolan, A.3
Hoshino, Y.4
Rom, W.N.5
Dawson, R.6
Bateman, E.7
Weiden, M.D.8
-
28
-
-
56649124715
-
The influence of sex, handedness, and washing on the diversity of hand surface bacteria
-
10.1073/pnas.0807920105, 2584711, 19004758
-
Fierer N, Hamady M, Lauber CL, Knight R. The influence of sex, handedness, and washing on the diversity of hand surface bacteria. Proc Natl Acad Sci USA 2008, 105:17994-17999. 10.1073/pnas.0807920105, 2584711, 19004758.
-
(2008)
Proc Natl Acad Sci USA
, vol.105
, pp. 17994-17999
-
-
Fierer, N.1
Hamady, M.2
Lauber, C.L.3
Knight, R.4
-
29
-
-
77952243141
-
QIIME allows analysis of high-throughput community sequencing data
-
10.1038/nmeth.f.303, 3156573, 20383131
-
Caporaso JG, Kuczynski J, Stombaugh J, Bittinger K, Bushman FD, Costello EK, Fierer N, Pena 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. QIIME allows analysis of high-throughput community sequencing data. Nat Methods 2010, 7:335-336. 10.1038/nmeth.f.303, 3156573, 20383131.
-
(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
Pena, 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..
-
30
-
-
77957244650
-
Search and clustering orders of magnitude faster than BLAST
-
10.1093/bioinformatics/btq461, 20709691
-
Edgar RC. Search and clustering orders of magnitude faster than BLAST. Bioinformatics 2010, 26:2460-2461. 10.1093/bioinformatics/btq461, 20709691.
-
(2010)
Bioinformatics
, vol.26
, pp. 2460-2461
-
-
Edgar, R.C.1
-
31
-
-
34548293679
-
Naive Bayesian classifier for rapid assignment of rRNA sequences into the new bacterial taxonomy
-
10.1128/AEM.00062-07, 1950982, 17586664
-
Wang Q, Garrity GM, Tiedje JM, Cole JR. Naive Bayesian classifier for rapid assignment of rRNA sequences into the new bacterial taxonomy. Appl Environ Microbiol 2007, 73:5261-5267. 10.1128/AEM.00062-07, 1950982, 17586664.
-
(2007)
Appl Environ Microbiol
, vol.73
, pp. 5261-5267
-
-
Wang, Q.1
Garrity, G.M.2
Tiedje, J.M.3
Cole, J.R.4
-
32
-
-
75249107844
-
PyNAST: a flexible tool for aligning sequences to a template alignment
-
10.1093/bioinformatics/btp636, 2804299, 19914921
-
Caporaso JG, Bittinger K, Bushman FD, DeSantis TZ, Andersen GL, Knight R. PyNAST: a flexible tool for aligning sequences to a template alignment. Bioinformatics 2010, 26:266-267. 10.1093/bioinformatics/btp636, 2804299, 19914921.
-
(2010)
Bioinformatics
, vol.26
, pp. 266-267
-
-
Caporaso, J.G.1
Bittinger, K.2
Bushman, F.D.3
DeSantis, T.Z.4
Andersen, G.L.5
Knight, R.6
-
33
-
-
77949718257
-
FastTree 2-approximately maximum-likelihood trees for large alignments
-
10.1371/journal.pone.0009490, 2835736, 20224823
-
Price MN, Dehal PS, Arkin AP. FastTree 2-approximately maximum-likelihood trees for large alignments. PLoS One 2010, 5:e9490. 10.1371/journal.pone.0009490, 2835736, 20224823.
-
(2010)
PLoS One
, vol.5
-
-
Price, M.N.1
Dehal, P.S.2
Arkin, A.P.3
-
34
-
-
78751575501
-
UniFrac: an effective distance metric for microbial community comparison
-
10.1038/ismej.2010.133, 3105689, 20827291
-
Lozupone C, Lladser ME, Knights D, Stombaugh J, Knight R. UniFrac: an effective distance metric for microbial community comparison. ISME J 2011, 5:169-172. 10.1038/ismej.2010.133, 3105689, 20827291.
-
(2011)
ISME J
, vol.5
, pp. 169-172
-
-
Lozupone, C.1
Lladser, M.E.2
Knights, D.3
Stombaugh, J.4
Knight, R.5
-
35
-
-
0037433040
-
Identifying differentially expressed genes using false discovery rate controlling procedures
-
10.1093/bioinformatics/btf877, 12584122
-
Reiner A, Yekutieli D, Benjamini Y. Identifying differentially expressed genes using false discovery rate controlling procedures. Bioinformatics 2003, 19:368-375. 10.1093/bioinformatics/btf877, 12584122.
-
(2003)
Bioinformatics
, vol.19
, pp. 368-375
-
-
Reiner, A.1
Yekutieli, D.2
Benjamini, Y.3
-
36
-
-
29144464937
-
UniFrac: a new phylogenetic method for comparing microbial communities
-
10.1128/AEM.71.12.8228-8235.2005, 1317376, 16332807
-
Lozupone C, Knight R. UniFrac: a new phylogenetic method for comparing microbial communities. Appl Environ Microbiol 2005, 71:8228-8235. 10.1128/AEM.71.12.8228-8235.2005, 1317376, 16332807.
-
(2005)
Appl Environ Microbiol
, vol.71
, pp. 8228-8235
-
-
Lozupone, C.1
Knight, R.2
-
37
-
-
37649024043
-
The ade4 package: implementing the duality diagram for ecologists
-
Dray SaD AB. The ade4 package: implementing the duality diagram for ecologists. J Stat Softw 2007, 22:1-20.
-
(2007)
J Stat Softw
, vol.22
, pp. 1-20
-
-
Dray SaD, A.B.1
-
38
-
-
10044232061
-
The analytical solution of the additive constant problem
-
Cailliez F. The analytical solution of the additive constant problem. Psychometrika 1983, 48:305-310.
-
(1983)
Psychometrika
, vol.48
, pp. 305-310
-
-
Cailliez, F.1
-
39
-
-
33747827586
-
NAST: a multiple sequence alignment server for comparative analysis of 16S rRNA genes
-
10.1093/nar/gkl244, 1538769, 16845035
-
DeSantis TZ, Hugenholtz P, Keller K, Brodie EL, Larsen N, Piceno YM, Phan R, Andersen GL. NAST: a multiple sequence alignment server for comparative analysis of 16S rRNA genes. Nucleic Acids Res 2006, 34:W394-399. 10.1093/nar/gkl244, 1538769, 16845035.
-
(2006)
Nucleic Acids Res
, vol.34
-
-
DeSantis, T.Z.1
Hugenholtz, P.2
Keller, K.3
Brodie, E.L.4
Larsen, N.5
Piceno, Y.M.6
Phan, R.7
Andersen, G.L.8
-
40
-
-
78650857856
-
Comparative analyses of the bacterial microbiota of the human nostril and oropharynx
-
2925076, 20802827
-
Lemon KP, Klepac-Ceraj V, Schiffer HK, Brodie EL, Lynch SV, Kolter R. Comparative analyses of the bacterial microbiota of the human nostril and oropharynx. M Bio 2010, 1:e00129-10. 2925076, 20802827.
-
(2010)
M Bio
, vol.1
-
-
Lemon, K.P.1
Klepac-Ceraj, V.2
Schiffer, H.K.3
Brodie, E.L.4
Lynch, S.V.5
Kolter, R.6
-
41
-
-
78650868433
-
Disordered microbial communities in the upper respiratory tract of cigarette smokers
-
10.1371/journal.pone.0015216, 3004851, 21188149
-
Charlson ES, Chen J, Custers-Allen R, Bittinger K, Li H, Sinha R, Hwang J, Bushman FD, Collman RG. Disordered microbial communities in the upper respiratory tract of cigarette smokers. PLoS One 2010, 5:e15216. 10.1371/journal.pone.0015216, 3004851, 21188149.
-
(2010)
PLoS One
, vol.5
-
-
Charlson, E.S.1
Chen, J.2
Custers-Allen, R.3
Bittinger, K.4
Li, H.5
Sinha, R.6
Hwang, J.7
Bushman, F.D.8
Collman, R.G.9
-
42
-
-
80052301430
-
Bayesian community-wide culture-independent microbial source tracking
-
10.1038/nmeth.1650, 21765408
-
Knights D, Kuczynski J, Charlson ES, Zaneveld J, Mozer MC, Collman RG, Bushman FD, Knight R, Kelley ST. Bayesian community-wide culture-independent microbial source tracking. Nat Methods 2011, 8:761-763. 10.1038/nmeth.1650, 21765408.
-
(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
-
43
-
-
84865082160
-
Associating microbiome composition with environmental covariates using generalized UniFrac distances
-
10.1093/bioinformatics/bts342, 3413390, 22711789
-
Chen J, Bittinger K, Charlson ES, Hoffmann C, Lewis J, Wu GD, Collman RG, Bushman FD, Li H. Associating microbiome composition with environmental covariates using generalized UniFrac distances. Bioinformatics 2012, 28:2106-2113. 10.1093/bioinformatics/bts342, 3413390, 22711789.
-
(2012)
Bioinformatics
, vol.28
, pp. 2106-2113
-
-
Chen, J.1
Bittinger, K.2
Charlson, E.S.3
Hoffmann, C.4
Lewis, J.5
Wu, G.D.6
Collman, R.G.7
Bushman, F.D.8
Li, H.9
-
44
-
-
66649127821
-
Immunologic aspects of chronic obstructive pulmonary disease
-
10.1056/NEJMra0804752, 19494220
-
Cosio MG, Saetta M, Agusti A. Immunologic aspects of chronic obstructive pulmonary disease. N Engl J Med 2009, 360:2445-2454. 10.1056/NEJMra0804752, 19494220.
-
(2009)
N Engl J Med
, vol.360
, pp. 2445-2454
-
-
Cosio, M.G.1
Saetta, M.2
Agusti, A.3
-
45
-
-
0035028999
-
Exhaled and nasal nitric oxide as a marker of pneumonia in ventilated patients
-
10.1164/ajrccm.163.5.9906049, 11316650
-
Adrie C, Monchi M, Dinh-Xuan AT, Dall'Ava-Santucci J, Dhainaut JF, Pinsky MR. Exhaled and nasal nitric oxide as a marker of pneumonia in ventilated patients. Am J Respir Crit Care Med 2001, 163:1143-1149. 10.1164/ajrccm.163.5.9906049, 11316650.
-
(2001)
Am J Respir Crit Care Med
, vol.163
, pp. 1143-1149
-
-
Adrie, C.1
Monchi, M.2
Dinh-Xuan, A.T.3
Dall'Ava-Santucci, J.4
Dhainaut, J.F.5
Pinsky, M.R.6
-
46
-
-
44749088421
-
Exhaled nitric oxide: independent effects of atopy, smoking, respiratory tract infection, gender and height
-
10.1016/j.rmed.2008.02.012, 18396030
-
Dressel H, de la Motte D, Reichert J, Ochmann U, Petru R, Angerer P, Holz O, Nowak D, Jorres RA. Exhaled nitric oxide: independent effects of atopy, smoking, respiratory tract infection, gender and height. Respir Med 2008, 102:962-969. 10.1016/j.rmed.2008.02.012, 18396030.
-
(2008)
Respir Med
, vol.102
, pp. 962-969
-
-
Dressel, H.1
de la Motte, D.2
Reichert, J.3
Ochmann, U.4
Petru, R.5
Angerer, P.6
Holz, O.7
Nowak, D.8
Jorres, R.A.9
-
47
-
-
0037384348
-
Exhaled NO and plasma cGMP increase after endotoxin infusion in healthy volunteers
-
10.1183/09031936.03.00008603, 12762341
-
Soop A, Sollevi A, Weitzberg E, Lundberg JO, Palm J, Albert J. Exhaled NO and plasma cGMP increase after endotoxin infusion in healthy volunteers. Eur Respir J 2003, 21:594-599. 10.1183/09031936.03.00008603, 12762341.
-
(2003)
Eur Respir J
, vol.21
, pp. 594-599
-
-
Soop, A.1
Sollevi, A.2
Weitzberg, E.3
Lundberg, J.O.4
Palm, J.5
Albert, J.6
-
48
-
-
0029145012
-
Acute and chronic effects of cigarette smoking on exhaled nitric oxide
-
10.1164/ajrccm.152.2.7543345, 7543345
-
Kharitonov SA, Robbins RA, Yates D, Keatings V, Barnes PJ. Acute and chronic effects of cigarette smoking on exhaled nitric oxide. Am J Respir Crit Care Med 1995, 152:609-612. 10.1164/ajrccm.152.2.7543345, 7543345.
-
(1995)
Am J Respir Crit Care Med
, vol.152
, pp. 609-612
-
-
Kharitonov, S.A.1
Robbins, R.A.2
Yates, D.3
Keatings, V.4
Barnes, P.J.5
-
49
-
-
33845509479
-
Effect of smoking on exhaled nitric oxide and flow-independent nitric oxide exchange parameters
-
10.1183/09031936.06.00113705, 16641119
-
Malinovschi A, Janson C, Holmkvist T, Norback D, Merilainen P, Hogman M. Effect of smoking on exhaled nitric oxide and flow-independent nitric oxide exchange parameters. Eur Respir J 2006, 28:339-345. 10.1183/09031936.06.00113705, 16641119.
-
(2006)
Eur Respir J
, vol.28
, pp. 339-345
-
-
Malinovschi, A.1
Janson, C.2
Holmkvist, T.3
Norback, D.4
Merilainen, P.5
Hogman, M.6
-
50
-
-
84856557879
-
Cigarette smoke exposure induces CFTR internalization and insolubility, leading to airway surface liquid dehydration
-
10.1096/fj.11-192377, 3290447, 21990373
-
Clunes LA, Davies CM, Coakley RD, Aleksandrov AA, Henderson AG, Zeman KL, Worthington EN, Gentzsch M, Kreda SM, Cholon D, Bennett WD, Riordan JR, Boucher RC, Tarran R. Cigarette smoke exposure induces CFTR internalization and insolubility, leading to airway surface liquid dehydration. FASEB J 2012, 26:533-545. 10.1096/fj.11-192377, 3290447, 21990373.
-
(2012)
FASEB J
, vol.26
, pp. 533-545
-
-
Clunes, L.A.1
Davies, C.M.2
Coakley, R.D.3
Aleksandrov, A.A.4
Henderson, A.G.5
Zeman, K.L.6
Worthington, E.N.7
Gentzsch, M.8
Kreda, S.M.9
Cholon, D.10
Bennett, W.D.11
Riordan, J.R.12
Boucher, R.C.13
Tarran, R.14
-
51
-
-
78649744400
-
Long-term cigarette smoke exposure in a mouse model of ciliated epithelial cell function
-
10.1165/rcmb.2009-0297OC, 2993085, 20042711
-
Simet SM, Sisson JH, Pavlik JA, Devasure JM, Boyer C, Liu X, Kawasaki S, Sharp JG, Rennard SI, Wyatt TA. Long-term cigarette smoke exposure in a mouse model of ciliated epithelial cell function. Am J Respir Cell Mol Biol 2010, 43:635-640. 10.1165/rcmb.2009-0297OC, 2993085, 20042711.
-
(2010)
Am J Respir Cell Mol Biol
, vol.43
, pp. 635-640
-
-
Simet, S.M.1
Sisson, J.H.2
Pavlik, J.A.3
Devasure, J.M.4
Boyer, C.5
Liu, X.6
Kawasaki, S.7
Sharp, J.G.8
Rennard, S.I.9
Wyatt, T.A.10
-
52
-
-
0041346077
-
Alveolar macrophages from subjects with chronic obstructive pulmonary disease are deficient in their ability to phagocytose apoptotic airway epithelial cells
-
10.1046/j.1440-1711.2003.t01-1-01170.x, 12848850
-
Hodge S, Hodge G, Scicchitano R, Reynolds PN, Holmes M. Alveolar macrophages from subjects with chronic obstructive pulmonary disease are deficient in their ability to phagocytose apoptotic airway epithelial cells. Immunol Cell Biol 2003, 81:289-296. 10.1046/j.1440-1711.2003.t01-1-01170.x, 12848850.
-
(2003)
Immunol Cell Biol
, vol.81
, pp. 289-296
-
-
Hodge, S.1
Hodge, G.2
Scicchitano, R.3
Reynolds, P.N.4
Holmes, M.5
-
53
-
-
77951962615
-
Defective macrophage phagocytosis of bacteria in COPD
-
10.1183/09031936.00036709, 19897561
-
Taylor AE, Finney-Hayward TK, Quint JK, Thomas CM, Tudhope SJ, Wedzicha JA, Barnes PJ, Donnelly LE. Defective macrophage phagocytosis of bacteria in COPD. Eur Respir J 2010, 35:1039-1047. 10.1183/09031936.00036709, 19897561.
-
(2010)
Eur Respir J
, vol.35
, pp. 1039-1047
-
-
Taylor, A.E.1
Finney-Hayward, T.K.2
Quint, J.K.3
Thomas, C.M.4
Tudhope, S.J.5
Wedzicha, J.A.6
Barnes, P.J.7
Donnelly, L.E.8
|