-
1
-
-
84994257227
-
-
World Health Organization
-
Global Tuberculosis Report (World Health Organization, 2016).
-
(2016)
Global Tuberculosis Report
-
-
-
2
-
-
84923206660
-
What can immunology contribute to the control of the world's leading cause of death from bacterial infection?
-
Nathan, C. What can immunology contribute to the control of the world's leading cause of death from bacterial infection? Immunol Rev 264, 2-5, doi:10. 1111/imr. 12277 (2015).
-
(2015)
Immunol Rev
, vol.264
, pp. 2-5
-
-
Nathan, C.1
-
3
-
-
84900330164
-
Human genetics of tuberculosis: A long and winding road
-
Abel, L., El-Baghdadi, J., Bousfiha, A. A., Casanova, J. L. & Schurr, E. Human genetics of tuberculosis: a long and winding road. Philos Trans R Soc Lond B Biol Sci 369, 20130428, doi:10. 1098/rstb. 2013. 0428 (2014).
-
(2014)
Philos Trans R Soc Lond B Biol Sci
, vol.369
, pp. 20130428
-
-
Abel, L.1
El-Baghdadi, J.2
Bousfiha, A.A.3
Casanova, J.L.4
Schurr, E.5
-
4
-
-
84978431877
-
The microbiota in adaptive immune homeostasis and disease
-
Honda, K. & Littman, D. R. The microbiota in adaptive immune homeostasis and disease. Nature 535, 75-84, doi:10. 1038/ nature18848 (2016).
-
(2016)
Nature
, vol.535
, pp. 75-84
-
-
Honda, K.1
Littman, D.R.2
-
5
-
-
84890564250
-
Commensal microbe-derived butyrate induces the differentiation of colonic regulatory T cells
-
Furusawa, Y. et al. Commensal microbe-derived butyrate induces the differentiation of colonic regulatory T cells. Nature 504, 446-450, doi:10. 1038/nature12721 (2013).
-
(2013)
Nature
, vol.504
, pp. 446-450
-
-
Furusawa, Y.1
-
6
-
-
84890550163
-
Metabolites produced by commensal bacteria promote peripheral regulatory T-cell generation
-
Arpaia, N. et al. Metabolites produced by commensal bacteria promote peripheral regulatory T-cell generation. Nature 504, 451-455, doi:10. 1038/nature12726 (2013).
-
(2013)
Nature
, vol.504
, pp. 451-455
-
-
Arpaia, N.1
-
7
-
-
84893704050
-
Gut microbiota metabolism of dietary fiber influences allergic airway disease and hematopoiesis
-
Trompette, A. et al. Gut microbiota metabolism of dietary fiber influences allergic airway disease and hematopoiesis. Nat Med 20, 159-166, doi:10. 1038/nm. 3444 (2014).
-
(2014)
Nat Med
, vol.20
, pp. 159-166
-
-
Trompette, A.1
-
8
-
-
84942874856
-
Early infancy microbial and metabolic alterations affect risk of childhood asthma
-
Arrieta, M. C. et al. Early infancy microbial and metabolic alterations affect risk of childhood asthma. Sci Transl Med 7, 307ra152, doi:10. 1126/scitranslmed. aab2271 (2015).
-
(2015)
Sci Transl Med
, vol.7
, pp. 307ra152
-
-
Arrieta, M.C.1
-
9
-
-
85016474563
-
Anaerobic bacterial fermentation products increase tuberculosis risk in antiretroviral-drug-treated HIV patients
-
Segal, L. N. et al. Anaerobic Bacterial Fermentation Products Increase Tuberculosis Risk in Antiretroviral-Drug-Treated HIV Patients. Cell Host Microbe 21, 530-537, e534, doi:10. 1016/j. chom. 2017. 03. 003 (2017).
-
(2017)
Cell Host Microbe
, vol.21
, pp. 530-537e534
-
-
Segal, L.N.1
-
10
-
-
84961223855
-
Functional redundancy-induced stability of gut microbiota subjected to disturbance
-
Moya, A. & Ferrer, M. Functional Redundancy-Induced Stability of Gut Microbiota Subjected to Disturbance. Trends Microbiol 24, 402-413, doi:10. 1016/j. tim. 2016. 02. 002 (2016).
-
(2016)
Trends Microbiol
, vol.24
, pp. 402-413
-
-
Moya, A.1
Ferrer, M.2
-
11
-
-
84969921123
-
Antibiotic-induced changes in the intestinal microbiota and disease
-
Becattini, S., Taur, Y. & Pamer, E. G. Antibiotic-Induced Changes in the Intestinal Microbiota and Disease. Trends Mol Med 22, 458-478, doi:10. 1016/j. molmed. 2016. 04. 003 (2016).
-
(2016)
Trends Mol Med
, vol.22
, pp. 458-478
-
-
Becattini, S.1
Taur, Y.2
Pamer, E.G.3
-
12
-
-
0025055132
-
Ciprofloxacin concentrations and impact of the colon microflora in patients undergoing colorectal surgery
-
Brismar, B., Edlund, C., Malmborg, A. S. & Nord, C. E. Ciprofloxacin concentrations and impact of the colon microflora in patients undergoing colorectal surgery. Antimicrob Agents Chemother 34, 481-483 (1990).
-
(1990)
Antimicrob Agents Chemother
, vol.34
, pp. 481-483
-
-
Brismar, B.1
Edlund, C.2
Malmborg, A.S.3
Nord, C.E.4
-
13
-
-
56849106496
-
The pervasive effects of an antibiotic on the human gut microbiota, as revealed by deep 16S rRNA sequencing
-
Dethlefsen, L., Huse, S., Sogin, M. L. & Relman, D. A. The pervasive effects of an antibiotic on the human gut microbiota, as revealed by deep 16S rRNA sequencing. PLoS Biol 6, e280, doi:10. 1371/journal. pbio. 0060280 (2008).
-
(2008)
PLoS Biol
, vol.6
, pp. e280
-
-
Dethlefsen, L.1
Huse, S.2
Sogin, M.L.3
Relman, D.A.4
-
14
-
-
84880453978
-
Functional consequences of microbial shifts in the human gastrointestinal tract linked to antibiotic treatment and obesity
-
Hernandez, E. et al. Functional consequences of microbial shifts in the human gastrointestinal tract linked to antibiotic treatment and obesity. Gut Microbes 4, 306-315, doi:10. 4161/gmic. 25321 (2013).
-
(2013)
Gut Microbes
, vol.4
, pp. 306-315
-
-
Hernandez, E.1
-
15
-
-
84892894991
-
Antibiotic-induced shifts in the mouse gut microbiome and metabolome increase susceptibility to Clostridium difficile infection
-
Theriot, C. M. et al. Antibiotic-induced shifts in the mouse gut microbiome and metabolome increase susceptibility to Clostridium difficile infection. Nat Commun 5, 3114, doi:10. 1038/ncomms4114 (2014).
-
(2014)
Nat Commun
, vol.5
, pp. 3114
-
-
Theriot, C.M.1
-
16
-
-
84865175815
-
Intestinal domination and the risk of bacteremia in patients undergoing allogeneic hematopoietic stem cell transplantation
-
Taur, Y. et al. Intestinal domination and the risk of bacteremia in patients undergoing allogeneic hematopoietic stem cell transplantation. Clin Infect Dis 55, 905-914, doi:10. 1093/cid/cis580 (2012).
-
(2012)
Clin Infect Dis
, vol.55
, pp. 905-914
-
-
Taur, Y.1
-
17
-
-
79952756960
-
Incomplete recovery and individualized responses of the human distal gut microbiota to repeated antibiotic perturbation
-
Dethlefsen, L. & Relman, D. A. Incomplete recovery and individualized responses of the human distal gut microbiota to repeated antibiotic perturbation. Proc Natl Acad Sci USA 108(Suppl 1), 4554-4561, doi:10. 1073/pnas. 1000087107 (2011).
-
(2011)
Proc Natl Acad Sci USA
, vol.108
, pp. 4554-4561
-
-
Dethlefsen, L.1
Relman, D.A.2
-
18
-
-
85029034077
-
Longitudinal profiling reveals a persistent intestinal dysbiosis triggered by conventional anti-tuberculosis therapy
-
Namasivayam, S. et al. Longitudinal profiling reveals a persistent intestinal dysbiosis triggered by conventional anti-tuberculosis therapy. Microbiome 5, 71, doi:10. 1186/s40168-017-0286-2 (2017).
-
(2017)
Microbiome
, vol.5
, pp. 71
-
-
Namasivayam, S.1
-
19
-
-
84924629414
-
Moderated estimation of fold change and dispersion for RNA-seq data with DESeq
-
Love, M. I., Huber, W. & Anders, S. Moderated estimation of fold change and dispersion for RNA-seq data with DESeq. 2. Genome Biol 15, 550, doi:10. 1186/s13059-014-0550-8 (2014).
-
(2014)
2. Genome Biol
, vol.15
, pp. 550
-
-
Love, M.I.1
Huber, W.2
Anders, S.3
-
20
-
-
79959383523
-
Metagenomic biomarker discovery and explanation
-
Segata, N. et al. Metagenomic biomarker discovery and explanation. Genome Biol 12, R60, doi:10. 1186/gb-2011-12-6-r60 (2011).
-
(2011)
Genome Biol
, vol.12
, pp. R60
-
-
Segata, N.1
-
21
-
-
84908409938
-
Membership and behavior of ultra-low-diversity pathogen communities present in the gut of humans during prolonged critical illness
-
Zaborin, A. et al. Membership and behavior of ultra-low-diversity pathogen communities present in the gut of humans during prolonged critical illness. MBio 5, e01361-01314, doi:10. 1128/mBio. 01361-14 (2014).
-
(2014)
MBio
, vol.5
, pp. e01361-01314
-
-
Zaborin, A.1
-
22
-
-
84864037467
-
Metabolic reconstruction for metagenomic data and its application to the human microbiome
-
Abubucker, S. et al. Metabolic reconstruction for metagenomic data and its application to the human microbiome. PLoS Comput Biol 8, e1002358, doi:10. 1371/journal. pcbi. 1002358 (2012).
-
(2012)
PLoS Comput Biol
, vol.8
, pp. e1002358
-
-
Abubucker, S.1
-
23
-
-
34248152283
-
Long-term ecological impacts of antibiotic administration on the human intestinal microbiota
-
Jernberg, C., Lofmark, S., Edlund, C. & Jansson, J. K. Long-term ecological impacts of antibiotic administration on the human intestinal microbiota. ISME J 1, 56-66, doi:10. 1038/ismej. 2007. 3 (2007).
-
(2007)
ISME J
, vol.1
, pp. 56-66
-
-
Jernberg, C.1
Lofmark, S.2
Edlund, C.3
Jansson, J.K.4
-
24
-
-
84896118638
-
Harnessing microbiota to kill a pathogen: Fixing the microbiota to treat clostridium difficile infections
-
Taur, Y. & Pamer, E. G. Harnessing microbiota to kill a pathogen: Fixing the microbiota to treat Clostridium difficile infections. Nat Med 20, 246-247, doi:10. 1038/nm. 3492 (2014).
-
(2014)
Nat Med
, vol.20
, pp. 246-247
-
-
Taur, Y.1
Pamer, E.G.2
-
25
-
-
84867656021
-
Outer membrane vesicles of a human commensal mediate immune regulation and disease protection
-
Shen, Y. et al. Outer membrane vesicles of a human commensal mediate immune regulation and disease protection. Cell Host Microbe 12, 509-520, doi:10. 1016/j. chom. 2012. 08. 004 (2012).
-
(2012)
Cell Host Microbe
, vol.12
, pp. 509-520
-
-
Shen, Y.1
-
26
-
-
85006106370
-
Linking the human gut microbiome to inflammatory cytokine production capacity
-
Schirmer, M. et al. Linking the Human Gut Microbiome to Inflammatory Cytokine Production Capacity. Cell 167, 1897, doi:10. 1016/j. cell. 2016. 11. 046 (2016).
-
(2016)
Cell
, vol.167
, pp. 1897
-
-
Schirmer, M.1
-
27
-
-
85003426944
-
Identifying species of symbiont bacteria from the human gut that, alone, can induce intestinal Th17 cells in mice
-
Tan, T. G. et al. Identifying species of symbiont bacteria from the human gut that, alone, can induce intestinal Th17 cells in mice. Proc Natl Acad Sci USA 113, E8141-E8150, doi:10. 1073/pnas. 1617460113 (2016).
-
(2016)
Proc Natl Acad Sci USA
, vol.113
, pp. E8141-E8150
-
-
Tan, T.G.1
-
28
-
-
20444401506
-
Rate of reinfection tuberculosis after successful treatment is higher than rate of new tuberculosis
-
Verver, S. et al. Rate of reinfection tuberculosis after successful treatment is higher than rate of new tuberculosis. Am J Respir Crit Care Med 171, 1430-1435, doi:10. 1164/rccm. 200409-1200OC (2005).
-
(2005)
Am J Respir Crit Care Med
, vol.171
, pp. 1430-1435
-
-
Verver, S.1
-
29
-
-
76449113203
-
High rates of recurrence in HIV-infected and HIV-uninfected patients with tuberculosis
-
Glynn, J. R. et al. High rates of recurrence in HIV-infected and HIV-uninfected patients with tuberculosis. J Infect Dis 201, 704-711, doi:10. 1086/650529 (2010).
-
(2010)
J Infect Dis
, vol.201
, pp. 704-711
-
-
Glynn, J.R.1
-
30
-
-
33644850653
-
Health insurance portability and accountability act of 1996
-
United, S. Health Insurance Portability and Accountability Act of 1996. Public Law 104-191. US Statut Large 110, 1936-2103 (1996).
-
(1996)
Public Law 104-191. US Statut Large
, vol.110
, pp. 1936-2103
-
-
United, S.1
-
31
-
-
62049084378
-
Research electronic data capture (REDCap)-a metadata-driven methodology and workflow process for providing translational research informatics support
-
Harris, P. A. et al. Research electronic data capture (REDCap)-a metadata-driven methodology and workflow process for providing translational research informatics support. J Biomed Inform 42, 377-381, doi:10. 1016/j. jbi. 2008. 08. 010 (2009).
-
(2009)
J Biomed Inform
, vol.42
, pp. 377-381
-
-
Harris, P.A.1
-
32
-
-
84862141704
-
Human gut microbiome viewed across age and geography
-
Yatsunenko, T. et al. Human gut microbiome viewed across age and geography. Nature 486, 222-227, doi:10. 1038/nature11053 (2012).
-
(2012)
Nature
, vol.486
, pp. 222-227
-
-
Yatsunenko, T.1
-
33
-
-
84884904719
-
UPARSE: Highly accurate OTU sequences from microbial amplicon reads
-
Edgar, R. C. UPARSE: highly accurate OTU sequences from microbial amplicon reads. Nat Methods 10, 996-998, doi:10. 1038/ nmeth. 2604 (2013).
-
(2013)
Nat Methods
, vol.10
, pp. 996-998
-
-
Edgar, R.C.1
-
34
-
-
79952006773
-
Chimeric 16S rRNA sequence formation and detection in Sanger and 454-pyrosequenced PCR amplicons
-
Haas, B. J. et al. Chimeric 16S rRNA sequence formation and detection in Sanger and 454-pyrosequenced PCR amplicons. Genome Res 21, 494-504, doi:10. 1101/gr. 112730. 110 (2011).
-
(2011)
Genome Res
, vol.21
, pp. 494-504
-
-
Haas, B.J.1
-
35
-
-
74049108922
-
BLAST+: Architecture and applications
-
Camacho, C. et al. BLAST+: architecture and applications. BMC Bioinformatics 10, 421, doi:10. 1186/1471-2105-10-421 (2009).
-
(2009)
BMC Bioinformatics
, vol.10
, pp. 421
-
-
Camacho, C.1
-
36
-
-
75549088021
-
The NCBI BioSystems database
-
Geer, L. Y. et al. The NCBI BioSystems database. Nucleic Acids Res 38, D492-496, doi:10. 1093/nar/gkp858 (2010).
-
(2010)
Nucleic Acids Res
, vol.38
, pp. D492-496
-
-
Geer, L.Y.1
-
37
-
-
84868270724
-
The Biological Observation Matrix (BIOM) format or: How i learned to stop worrying and love the ome-ome
-
McDonald, D. et al. The Biological Observation Matrix (BIOM) format or: how I learned to stop worrying and love the ome-ome. Gigascience 1, 7, doi:10. 1186/2047-217X-1-7 (2012).
-
(2012)
Gigascience
, vol.1
, pp. 7
-
-
McDonald, D.1
-
39
-
-
84876427223
-
Phyloseq: An R package for reproducible interactive analysis and graphics of microbiome census data
-
McMurdie, P. J. & Holmes, S. phyloseq: an R package for reproducible interactive analysis and graphics of microbiome census data. PLoS One 8, e61217, doi:10. 1371/journal. pone. 0061217 (2013).
-
(2013)
PLoS One
, vol.8
, pp. e61217
-
-
McMurdie, P.J.1
Holmes, S.2
-
41
-
-
84905049901
-
Trimmomatic: A flexible trimmer for Illumina sequence data
-
Bolger, A. M., Lohse, M. & Usadel, B. Trimmomatic: a flexible trimmer for Illumina sequence data. Bioinformatics 30, 2114-2120, doi:10. 1093/bioinformatics/btu170 (2014).
-
(2014)
Bioinformatics
, vol.30
, pp. 2114-2120
-
-
Bolger, A.M.1
Lohse, M.2
Usadel, B.3
-
42
-
-
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, doi:10. 1038/nmeth. 1923 (2012).
-
(2012)
Nat Methods
, vol.9
, pp. 357-359
-
-
Langmead, B.1
Salzberg, S.L.2
-
43
-
-
84964994621
-
MetaPhlAn2 for enhanced metagenomic taxonomic profiling
-
Truong, D. T. et al. MetaPhlAn2 for enhanced metagenomic taxonomic profiling. Nat Methods 12, 902-903, doi:10. 1038/nmeth. 3589 (2015).
-
(2015)
Nat Methods
, vol.12
, pp. 902-903
-
-
Truong, D.T.1
|