-
1
-
-
84866546211
-
Mind-altering microorganisms: the impact of the gut microbiota on brain and behaviour
-
COI: 1:CAS:528:DC%2BC38XhtlamurvN
-
Cryan, J. F. & Dinan, T. G. Mind-altering microorganisms: the impact of the gut microbiota on brain and behaviour. Nat. Rev. Neurosci. 13, 701–712 (2012).
-
(2012)
Nat. Rev. Neurosci.
, vol.13
, pp. 701-712
-
-
Cryan, J.F.1
Dinan, T.G.2
-
2
-
-
84912141027
-
Serotonin, tryptophan metabolism and the brain–gut–microbiome axis
-
O’Mahony, S. M., Clarke, G., Borre, Y. E., Dinan, T. G. & Cryan, J. F. Serotonin, tryptophan metabolism and the brain–gut–microbiome axis. Behav. Brain. Res. 277, 32–48 (2015).
-
(2015)
Behav. Brain. Res.
, vol.277
, pp. 32-48
-
-
O’Mahony, S.M.1
Clarke, G.2
Borre, Y.E.3
Dinan, T.G.4
Cryan, J.F.5
-
3
-
-
84911884131
-
The gut microbiota influences blood–brain barrier permeability in mice
-
Braniste, V. et al. The gut microbiota influences blood–brain barrier permeability in mice. Sci. Transl. Med. 6, 263ra158 (2014).
-
(2014)
Sci. Transl. Med.
, vol.6
, pp. 263ra158
-
-
Braniste, V.1
-
4
-
-
85040374820
-
Evidence for PMAT- and OCT-like biogenic amine transporters in a probiotic strain of Lactobacillus: implications for interkingdom communication within the microbiota–gut–brain axis
-
Lyte, M. & Brown, D. R. Evidence for PMAT- and OCT-like biogenic amine transporters in a probiotic strain of Lactobacillus: implications for interkingdom communication within the microbiota–gut–brain axis. PLoS ONE 13, e0191037 (2018).
-
(2018)
PLoS ONE
, vol.13
-
-
Lyte, M.1
Brown, D.R.2
-
5
-
-
85090848405
-
American Gut: an open platform for citizen science
-
Mcdonald, D. et al. American Gut: an open platform for citizen science. mSystems 3, e00031-18 (2018).
-
(2018)
mSystems
, vol.3
-
-
Mcdonald, D.1
-
6
-
-
84904411548
-
Correlation between the human fecal microbiota and depression
-
COI: 1:STN:280:DC%2BC2cjotlansg%3D%3D
-
Naseribafrouei, A. et al. Correlation between the human fecal microbiota and depression. Neurogastroenterol. Motil. 26, 1155–1162 (2014).
-
(2014)
Neurogastroenterol. Motil.
, vol.26
, pp. 1155-1162
-
-
Naseribafrouei, A.1
-
7
-
-
84942984411
-
Altered fecal microbiota composition in patients with major depressive disorder
-
Jiang, H. et al. Altered fecal microbiota composition in patients with major depressive disorder. Brain Behav. Immun. 48, 186–194 (2015).
-
(2015)
Brain Behav. Immun.
, vol.48
, pp. 186-194
-
-
Jiang, H.1
-
8
-
-
84963547235
-
Gut microbiome remodeling induces depressive-like behaviors through a pathway mediated by the host’s metabolism
-
COI: 1:CAS:528:DC%2BC28XmsVals78%3D
-
Zheng, P. et al. Gut microbiome remodeling induces depressive-like behaviors through a pathway mediated by the host’s metabolism. Mol. Psychiatry 21, 786–796 (2016).
-
(2016)
Mol. Psychiatry
, vol.21
, pp. 786-796
-
-
Zheng, P.1
-
9
-
-
84979955472
-
Transferring the blues: depression-associated gut microbiota induces neurobehavioural changes in the rat
-
Kelly, J. R. et al. Transferring the blues: depression-associated gut microbiota induces neurobehavioural changes in the rat. J. Psychiatr. Res. 82, 109–118 (2016).
-
(2016)
J. Psychiatr. Res.
, vol.82
, pp. 109-118
-
-
Kelly, J.R.1
-
10
-
-
84904567340
-
Pathogenic microbes, the microbiome, and Alzheimer’s disease (AD)
-
PID: 24982633
-
Hill, J. M., Clement, C., Pogue, A. I., Bhattacharjee, S. & Zhao, Y. et al. Pathogenic microbes, the microbiome, and Alzheimer’s disease (AD). Front. Aging Neurosci. 6, 127 (2014).
-
(2014)
Front. Aging Neurosci.
, vol.6
, pp. 127
-
-
Hill, J.M.1
Clement, C.2
Pogue, A.I.3
Bhattacharjee, S.4
Zhao, Y.5
-
11
-
-
84928204767
-
-
Burokas, A., Moloney, R. D., Dinan, T. G. & Cryan, J. F. Microbiota regulation of the mammalian gut–brain axis. 91, 1–62 (2015).
-
(2015)
Microbiota Regulation of the Mammalian gut–brain Axis.
, vol.91
, pp. 1-62
-
-
Burokas, A.1
Moloney, R.D.2
Dinan, T.G.3
Cryan, J.F.4
-
12
-
-
85045922618
-
Richness and ecosystem development across faecal snapshots of the gut microbiota
-
COI: 1:CAS:528:DC%2BC1cXotlGgsrc%3D
-
Falony, G., Vieira-Silva, S. & Raes, J. Richness and ecosystem development across faecal snapshots of the gut microbiota. Nat. Microbiol. 3, 526–528 (2018).
-
(2018)
Nat. Microbiol.
, vol.3
, pp. 526-528
-
-
Falony, G.1
Vieira-Silva, S.2
Raes, J.3
-
13
-
-
85007233429
-
Lost in translation? The potential psychobiotic Lactobacillus rhamnosus (JB-1) fails to modulate stress or cognitive performance in healthy male subjects
-
COI: 1:CAS:528:DC%2BC28XhvFKntr3N
-
Kelly, J. R. et al. Lost in translation? The potential psychobiotic Lactobacillus rhamnosus (JB-1) fails to modulate stress or cognitive performance in healthy male subjects. Brain Behav. Immun. 61, 50–59 (2017).
-
(2017)
Brain Behav. Immun.
, vol.61
, pp. 50-59
-
-
Kelly, J.R.1
-
14
-
-
85018307343
-
Functional implications of microbial and viral gut metagenome changes in early stage L-DOPA-naïve Parkinson’s disease patients
-
COI: 1:STN:280:DC%2BC1crhvVeltg%3D%3D
-
Bedarf, J. R. et al. Functional implications of microbial and viral gut metagenome changes in early stage L-DOPA-naïve Parkinson’s disease patients. Genome Med. 9, 39 (2017).
-
(2017)
Genome Med.
, vol.9
-
-
Bedarf, J.R.1
-
15
-
-
84968918909
-
Population-level analysis of gut microbiome variation
-
COI: 1:CAS:528:DC%2BC28Xms1Kisbo%3D
-
Falony, G. et al. Population-level analysis of gut microbiome variation. Science 352, 560–564 (2016).
-
(2016)
Science
, vol.352
, pp. 560-564
-
-
Falony, G.1
-
16
-
-
84968901892
-
Population-based metagenomics analysis reveals markers for gut microbiome composition and diversity
-
COI: 1:CAS:528:DC%2BC28Xms1KisL8%3D
-
Zhernakova, A. Population-based metagenomics analysis reveals markers for gut microbiome composition and diversity. Science 352, 565–569 (2016).
-
(2016)
Science
, vol.352
, pp. 565-569
-
-
Zhernakova, A.1
-
17
-
-
84941588145
-
Cohort profile: LifeLines DEEP, a prospective, general population cohort study in the northern Netherlands: study design and baseline characteristics
-
Tigchelaar, E. F. et al. Cohort profile: LifeLines DEEP, a prospective, general population cohort study in the northern Netherlands: study design and baseline characteristics. BMJ Open 5, e006772 (2015).
-
(2015)
BMJ Open
, vol.5
-
-
Tigchelaar, E.F.1
-
18
-
-
0027674811
-
The RAND 36-Item Health Survey 1.0
-
COI: 1:STN:280:DyaK2c7gtFSltQ%3D%3D
-
Hays, R. D., Sherbourne, C. D. & Mazel, R. M. The RAND 36-Item Health Survey 1.0. Health Econ. 2, 217–227 (1993).
-
(1993)
Health Econ.
, vol.2
, pp. 217-227
-
-
Hays, R.D.1
Sherbourne, C.D.2
Mazel, R.M.3
-
19
-
-
0034922874
-
The RAND-36 measure of health-related quality of life
-
COI: 1:STN:280:DC%2BD3MvksFWqsQ%3D%3D
-
Hays, R. D. & Morales, L. S. The RAND-36 measure of health-related quality of life. Ann. Med. 33, 350–357 (2001).
-
(2001)
Ann. Med.
, vol.33
, pp. 350-357
-
-
Hays, R.D.1
Morales, L.S.2
-
20
-
-
0003434672
-
-
New England Medical Center, Boston
-
Ware, J. E., Keller, S. D. & Kosinski, M. SF-36: Physical and Mental Health Summary Scales (Health Institute, New England Medical Center, Boston, 1994).
-
(1994)
SF-36: Physical and Mental Health Summary Scales (Health Institute
-
-
Ware, J.E.1
Keller, S.D.2
Kosinski, M.3
-
21
-
-
0030868530
-
Stool form scale as a useful guide to intestinal transit time
-
COI: 1:STN:280:DyaK2svksVCntw%3D%3D
-
Lewis, S. J. & Heaton, K. W. Stool form scale as a useful guide to intestinal transit time. Scand. J. Gastroenterol. 32, 920–924 (1997).
-
(1997)
Scand. J. Gastroenterol.
, vol.32
, pp. 920-924
-
-
Lewis, S.J.1
Heaton, K.W.2
-
22
-
-
84980335892
-
Bifidobacteria and butyrate-producing colon bacteria: importance and strategies for their stimulation in the human gut
-
Rivière, A., Selak, M., Lantin, D., Leroy, F. & De Vuyst, L. Bifidobacteria and butyrate-producing colon bacteria: importance and strategies for their stimulation in the human gut. Front. Microbiol. 7, 979 (2016).
-
(2016)
Front. Microbiol.
, vol.7
, pp. 979
-
-
Rivière, A.1
Selak, M.2
Lantin, D.3
Leroy, F.4
De Vuyst, L.5
-
23
-
-
84908608590
-
The gut microbiota, bacterial metabolites and colorectal cancer
-
COI: 1:CAS:528:DC%2BC2cXhsFKms7bL
-
Louis, P., Hold, G. L. & Flint, H. J. The gut microbiota, bacterial metabolites and colorectal cancer. Nat. Rev. Microbiol. 12, 661–672 (2014).
-
(2014)
Nat. Rev. Microbiol.
, vol.12
, pp. 661-672
-
-
Louis, P.1
Hold, G.L.2
Flint, H.J.3
-
24
-
-
84896092821
-
The treatment-naive microbiome in new-onset Crohn’s disease
-
COI: 1:CAS:528:DC%2BC2cXks1Omu7Y%3D
-
Gevers, D. et al. The treatment-naive microbiome in new-onset Crohn’s disease. Cell Host Microbe 15, 382–392 (2014).
-
(2014)
Cell Host Microbe
, vol.15
, pp. 382-392
-
-
Gevers, D.1
-
25
-
-
84978877862
-
Gut microbes in correlation with mood: case study in a closed experimental human life support system
-
COI: 1:STN:280:DC%2BC28fkvV2itw%3D%3D
-
Li, L. et al. Gut microbes in correlation with mood: case study in a closed experimental human life support system. Neurogastroenterol. Motil. 28, 1233–1240 (2016).
-
(2016)
Neurogastroenterol. Motil.
, vol.28
, pp. 1233-1240
-
-
Li, L.1
-
26
-
-
0040107893
-
Quality of life, intelligence and mood
-
Watten, R. G., Syversen, J. L. & Myhrer, T. Quality of life, intelligence and mood. Soc. Indic. Res. 36, 287–299 (1995).
-
(1995)
Soc. Indic. Res.
, vol.36
, pp. 287-299
-
-
Watten, R.G.1
Syversen, J.L.2
Myhrer, T.3
-
27
-
-
70350051602
-
-
British Psychological Society and Royal College of Psychiatrists, London
-
National Collaborating Centre for Mental Health, National Institute for Health and Clinical Excellence, Royal College of Psychiatrists, British Psychological Society Depression: the Treatment and Management of Depression in Adults (British Psychological Society and Royal College of Psychiatrists, London, 2010).
-
(2010)
Depression: The Treatment and Management of Depression in Adults
-
-
-
28
-
-
54349094991
-
The epidemiology of depression in Belgium. A review and some reflections for the future [Article in Dutch]
-
COI: 1:STN:280:DC%2BD1c1aisw%3D%3D, PID: 18951344
-
Bruffaerts, R., Bonnewyn, A. & Demyttenaere, K. The epidemiology of depression in Belgium. A review and some reflections for the future [Article in Dutch]. Tijdschr. Psychiatr. 50, 655–665 (2008).
-
(2008)
Tijdschr. Psychiatr.
, vol.50
, pp. 655-665
-
-
Bruffaerts, R.1
Bonnewyn, A.2
Demyttenaere, K.3
-
29
-
-
85043332830
-
Extensive impact of non-antibiotic drugs on human gut bacteria
-
COI: 1:CAS:528:DC%2BC1cXltVyqsLY%3D
-
Maier, L. et al. Extensive impact of non-antibiotic drugs on human gut bacteria. Nature 555, 623–628 (2018).
-
(2018)
Nature
, vol.555
, pp. 623-628
-
-
Maier, L.1
-
30
-
-
85053237031
-
Differential effects of psychotropic drugs on microbiome composition and gastrointestinal function
-
https://doi.org/10.1007/s00213-018-5006-5
-
Cussotto, S. et al. Differential effects of psychotropic drugs on microbiome composition and gastrointestinal function. Psychopharmacology 10.1007/s00213-018-5006-5 (2018).
-
(2018)
Psychopharmacology
-
-
Cussotto, S.1
-
31
-
-
84949772416
-
Disentangling type 2 diabetes and metformin treatment signatures in the human gut microbiota
-
COI: 1:CAS:528:DC%2BC2MXhvFemsbjN
-
Forslund, K. et al. Disentangling type 2 diabetes and metformin treatment signatures in the human gut microbiota. Nature 528, 262–266 (2015).
-
(2015)
Nature
, vol.528
, pp. 262-266
-
-
Forslund, K.1
-
32
-
-
84886724158
-
Psychobiotics: a novel class of psychotropic
-
COI: 1:CAS:528:DC%2BC3sXptFGktLw%3D
-
Dinan, T. G., Stanton, C. & Cryan, J. F. Psychobiotics: a novel class of psychotropic. Biol. Psychiatry 74, 720–726 (2013).
-
(2013)
Biol. Psychiatry
, vol.74
, pp. 720-726
-
-
Dinan, T.G.1
Stanton, C.2
Cryan, J.F.3
-
33
-
-
84856521514
-
Dirichlet multinomial mixtures: generative models for microbialmetagenomics
-
COI: 1:CAS:528:DC%2BC38Xis12nsLY%3D
-
Holmes, I., Harris, K. & Quince, C. Dirichlet multinomial mixtures: generative models for microbialmetagenomics. PLoS ONE 7, e30126 (2012).
-
(2012)
PLoS ONE
, vol.7
-
-
Holmes, I.1
Harris, K.2
Quince, C.3
-
34
-
-
85034861639
-
Quantitative microbiome profiling links gut community variation to microbial load
-
COI: 1:CAS:528:DC%2BC2sXhvVKqtb%2FM, PID: 29143816
-
Vandeputte, D. et al. Quantitative microbiome profiling links gut community variation to microbial load. Nature 551, 507–511 (2017).
-
(2017)
Nature
, vol.551
, pp. 507-511
-
-
Vandeputte, D.1
-
35
-
-
84891820094
-
IMG 4 version of the integrated microbial genomes comparative analysis system
-
COI: 1:CAS:528:DC%2BC2cXos1Sr
-
Markowitz, V. M. et al. IMG 4 version of the integrated microbial genomes comparative analysis system. Nucleic Acids Res. 42, D560–D567 (2014).
-
(2014)
Nucleic Acids Res.
, vol.42
, pp. D560-D567
-
-
Markowitz, V.M.1
-
36
-
-
0026555053
-
Catecholamine induced growth of gram negative bacteria
-
COI: 1:CAS:528:DyaK38XjslOltQ%3D%3D
-
Lyte, M. & Ernst, S. Catecholamine induced growth of gram negative bacteria. Life Sci. 50, 203–212 (1992).
-
(1992)
Life Sci.
, vol.50
, pp. 203-212
-
-
Lyte, M.1
Ernst, S.2
-
37
-
-
33845786505
-
5-HT in the enteric nervous system: gut function and neuropharmacology
-
COI: 1:CAS:528:DC%2BD2sXhsFWrtQ%3D%3D
-
McLean, P. G., Borman, R. A. & Lee, K. 5-HT in the enteric nervous system: gut function and neuropharmacology. Trends Neurosci. 30, 9–13 (2007).
-
(2007)
Trends Neurosci.
, vol.30
, pp. 9-13
-
-
McLean, P.G.1
Borman, R.A.2
Lee, K.3
-
38
-
-
84927131694
-
Indigenous bacteria from the gut microbiota regulate host serotonin biosynthesis
-
COI: 1:CAS:528:DC%2BC2MXmsVWqsLk%3D
-
Yano, J. M. et al. Indigenous bacteria from the gut microbiota regulate host serotonin biosynthesis. Cell 161, 264–276 (2015).
-
(2015)
Cell
, vol.161
, pp. 264-276
-
-
Yano, J.M.1
-
39
-
-
33747603715
-
Hormones and hormone-like substances of microorganisms: a review [Article in Russian]
-
COI: 1:STN:280:DC%2BD28vlsFalsQ%3D%3D, PID: 16878539
-
Tsavkelova, E. A., Klimova, S. Y., Cherdyntseva, T. A. & Netrusov, A. I. Hormones and hormone-like substances of microorganisms: a review [Article in Russian]. Prikl. Biokhim. Mikrobiol. 42, 261–268 (2006).
-
(2006)
Prikl. Biokhim. Mikrobiol.
, vol.42
, pp. 261-268
-
-
Tsavkelova, E.A.1
Klimova, S.Y.2
Cherdyntseva, T.A.3
Netrusov, A.I.4
-
41
-
-
85006741566
-
The neuro-endocrinological role of microbial glutamate and GABA signaling
-
Mazzoli, R. & Pessione, E. The neuro-endocrinological role of microbial glutamate and GABA signaling. Front. Microbiol. 7, 1934 (2016).
-
(2016)
Front. Microbiol.
, vol.7
, pp. 1934
-
-
Mazzoli, R.1
Pessione, E.2
-
42
-
-
84871860184
-
Functional γ-aminobutyrate shunt in Listeria monocytogenes: role in acid tolerance and succinate biosynthesis
-
COI: 1:CAS:528:DC%2BC3sXkvVKjs7o%3D
-
Feehily, C., O’Byrne, C. P. & Karatzas, K. A. G. Functional γ-aminobutyrate shunt in Listeria monocytogenes: role in acid tolerance and succinate biosynthesis. Appl. Environ. Microbiol. 79, 74–80 (2013).
-
(2013)
Appl. Environ. Microbiol.
, vol.79
, pp. 74-80
-
-
Feehily, C.1
O’Byrne, C.P.2
Karatzas, K.A.G.3
-
43
-
-
70350488795
-
Horizontal gene transfer of the secretome drives the evolution of bacterial cooperation and virulence
-
COI: 1:CAS:528:DC%2BD1MXhtlCrsrvM
-
Nogueira, T. et al. Horizontal gene transfer of the secretome drives the evolution of bacterial cooperation and virulence. Curr. Biol. 19, 1683–1691 (2009).
-
(2009)
Curr. Biol.
, vol.19
, pp. 1683-1691
-
-
Nogueira, T.1
-
44
-
-
31544445752
-
Of the major phenolic acids formed during human microbial fermentation of tea, citrus, and soy flavonoid supplements, only 3,4-dihydroxyphenylacetic acid has antiproliferative activity
-
COI: 1:CAS:528:DC%2BD28XivFSgtQ%3D%3D
-
Gao, K. et al. Of the major phenolic acids formed during human microbial fermentation of tea, citrus, and soy flavonoid supplements, only 3,4-dihydroxyphenylacetic acid has antiproliferative activity. J. Nutr. 136, 52–57 (2006).
-
(2006)
J. Nutr.
, vol.136
, pp. 52-57
-
-
Gao, K.1
-
45
-
-
85042200094
-
Cerebrospinal fluid biomarkers of central dopamine deficiency predict Parkinson’s disease
-
Goldstein, D. S., Holmes, C., Lopez, G. J., Wu, T. & Sharabi, Y. Cerebrospinal fluid biomarkers of central dopamine deficiency predict Parkinson’s disease. Parkinsonism Relat. Disord. 50, 108–112 (2018).
-
(2018)
Parkinsonism Relat. Disord.
, vol.50
, pp. 108-112
-
-
Goldstein, D.S.1
Holmes, C.2
Lopez, G.J.3
Wu, T.4
Sharabi, Y.5
-
46
-
-
75349092135
-
Neuroimmune aspects of food intake
-
COI: 1:CAS:528:DC%2BC3cXhs1amtr0%3D
-
Bienenstock, J., Forsythe, P., Karimi, K. & Kunze, W. Neuroimmune aspects of food intake. Int. Dairy J. 20, 253–258 (2010).
-
(2010)
Int. Dairy J.
, vol.20
, pp. 253-258
-
-
Bienenstock, J.1
Forsythe, P.2
Karimi, K.3
Kunze, W.4
-
47
-
-
0028323407
-
Plasma concentrations of gamma-aminobutyric acid (GABA) and mood disorders: a blood test for manic depressive disease?
-
COI: 1:CAS:528:DyaK2cXhvVygtbs%3D, PID: 8313610
-
Petty, F. Plasma concentrations of gamma-aminobutyric acid (GABA) and mood disorders: a blood test for manic depressive disease? Clin. Chem. 40, 296–302 (1994).
-
(1994)
Clin. Chem.
, vol.40
, pp. 296-302
-
-
Petty, F.1
-
48
-
-
85045521393
-
Elevated peripheral blood glutamate levels in major depressive disorder
-
Inoshita, M. et al. Elevated peripheral blood glutamate levels in major depressive disorder. Neuropsychiatr. Dis. Treat. 14, 945–953 (2018).
-
(2018)
Neuropsychiatr. Dis. Treat.
, vol.14
, pp. 945-953
-
-
Inoshita, M.1
-
49
-
-
21244472033
-
-
Chapman and Hall, Boca Raton
-
Chow, S., Shao, J. & Wang, H. Sample Size Calculations in Clinical Trial Research (Chapman and Hall, Boca Raton, 2008).
-
(2008)
Sample Size Calculations in Clinical Trial Research
-
-
Chow, S.1
Shao, J.2
Wang, H.3
-
50
-
-
0032211654
-
Translation, validation, and norming of the Dutch language version of the SF-36 Health Survey in community and chronic disease populations
-
COI: 1:STN:280:DyaK1M%2Fjt1SisQ%3D%3D
-
Aaronson, N. K. et al. Translation, validation, and norming of the Dutch language version of the SF-36 Health Survey in community and chronic disease populations. J. Clin. Epidemiol. 51, 1055–1068 (1998).
-
(1998)
J. Clin. Epidemiol.
, vol.51
, pp. 1055-1068
-
-
Aaronson, N.K.1
-
53
-
-
84974588700
-
A novel biomarker panel for irritable bowel syndrome and the application in the general population
-
COI: 1:CAS:528:DC%2BC28Xps1Sjsbs%3D
-
Mujagic, Z. et al. A novel biomarker panel for irritable bowel syndrome and the application in the general population. Sci. Rep. 6, 26420 (2016).
-
(2016)
Sci. Rep.
, vol.6
-
-
Mujagic, Z.1
-
54
-
-
85003546086
-
Brief report: D ialister as a microbial marker of disease activity in spondyloarthritis
-
COI: 1:CAS:528:DC%2BC2sXitlKj
-
Tito, R. Y. et al. Brief report: D ialister as a microbial marker of disease activity in spondyloarthritis. Arthritis Rheumatol. 69, 114–121 (2017).
-
(2017)
Arthritis Rheumatol.
, vol.69
, pp. 114-121
-
-
Tito, R.Y.1
-
55
-
-
84930000752
-
LotuS: an efficient and user-friendly OTU processing pipeline
-
Hildebrand, F., Tadeo, R., Voigt, A. Y., Bork, P. & Raes, J. LotuS: an efficient and user-friendly OTU processing pipeline. Microbiome 2, 30 (2014).
-
(2014)
Microbiome
, vol.2
-
-
Hildebrand, F.1
Tadeo, R.2
Voigt, A.Y.3
Bork, P.4
Raes, J.5
-
56
-
-
84969871954
-
DADA2: high-resolution sample inference from Illumina amplicon data
-
COI: 1:CAS:528:DC%2BC28XosVWitb4%3D
-
Callahan, B. J. et al. DADA2: high-resolution sample inference from Illumina amplicon data. Nat. Methods 13, 581–583 (2016).
-
(2016)
Nat. Methods
, vol.13
, pp. 581-583
-
-
Callahan, B.J.1
-
57
-
-
34548293679
-
Naive Bayesian classifier for rapid assignment of rRNA sequences into the new bacterial taxonomy
-
COI: 1:CAS:528:DC%2BD2sXpsleqtrc%3D
-
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, 5261–5267 (2007).
-
(2007)
Appl. Environ. Microbiol.
, vol.73
, pp. 5261-5267
-
-
Wang, Q.1
Garrity, G.M.2
Tiedje, J.M.3
Cole, J.R.4
-
58
-
-
84905049901
-
Trimmomatic: a flexible trimmer for Illumina sequence data
-
COI: 1:CAS:528:DC%2BC2cXht1Sqt7nP
-
Bolger, A. M., Lohse, M. & Usadel, B. Trimmomatic: a flexible trimmer for Illumina sequence data. Bioinformatics 30, 2114–2120 (2014).
-
(2014)
Bioinformatics
, vol.30
, pp. 2114-2120
-
-
Bolger, A.M.1
Lohse, M.2
Usadel, B.3
-
59
-
-
79952390994
-
Fast identification and removal of sequence contamination from genomic and metagenomic datasets
-
COI: 1:CAS:528:DC%2BC3MXjslSmtr4%3D
-
Schmieder, R. & Edwards, R. Fast identification and removal of sequence contamination from genomic and metagenomic datasets. PLoS ONE 6, e17288 (2011).
-
(2011)
PLoS ONE
, vol.6
-
-
Schmieder, R.1
Edwards, R.2
-
60
-
-
65649092976
-
Biopython: freely available Python tools for computational molecular biology and bioinformatics
-
COI: 1:CAS:528:DC%2BD1MXmtFeqt74%3D
-
Cock, P. J. A. et al. Biopython: freely available Python tools for computational molecular biology and bioinformatics. Bioinformatics 25, 1422–1423 (2009).
-
(2009)
Bioinformatics
, vol.25
, pp. 1422-1423
-
-
Cock, P.J.A.1
-
61
-
-
84905730165
-
An integrated catalog of reference genes in the human gut microbiome
-
COI: 1:CAS:528:DC%2BC2cXhtFSlsLjP
-
Li, J. et al. An integrated catalog of reference genes in the human gut microbiome. Nat. Biotechnol. 32, 834–841 (2014).
-
(2014)
Nat. Biotechnol.
, vol.32
, pp. 834-841
-
-
Li, J.1
-
62
-
-
67649884743
-
Fast and accurate short read alignment with Burrows–Wheeler transform
-
COI: 1:CAS:528:DC%2BD1MXot1Cjtbo%3D
-
Li, H. & Durbin, R. Fast and accurate short read alignment with Burrows–Wheeler transform. Bioinformatics 25, 1754–1760 (2009).
-
(2009)
Bioinformatics
, vol.25
, pp. 1754-1760
-
-
Li, H.1
Durbin, R.2
-
63
-
-
84897397058
-
featureCounts: an efficient general purpose program for assigning sequence reads to genomic features
-
COI: 1:CAS:528:DC%2BC2cXltFGqu7c%3D
-
Liao, Y., Smyth, G. K. & Shi, W. featureCounts: an efficient general purpose program for assigning sequence reads to genomic features. Bioinformatics 30, 923–930 (2014).
-
(2014)
Bioinformatics
, vol.30
, pp. 923-930
-
-
Liao, Y.1
Smyth, G.K.2
Shi, W.3
-
65
-
-
70349255569
-
-
R package version 2.4-2
-
Oksanen, J. et al. vegan: Community Ecology. R package version 2.4-2 http://CRAN.R-project.org/package=vegan (2017).
-
(2017)
Vegan: Community Ecology
-
-
Oksanen, J.1
-
66
-
-
84876427223
-
phyloseq: an R package for reproducible interactive analysis and graphics of microbiome census data
-
COI: 1:CAS:528:DC%2BC3sXntVWht7w%3D
-
McMurdie, P. J. & Holmes, S. phyloseq: an R package for reproducible interactive analysis and graphics of microbiome census data. PLoS ONE 8, e61217 (2013).
-
(2013)
PLoS ONE
, vol.8
-
-
McMurdie, P.J.1
Holmes, S.2
-
67
-
-
84982953236
-
Compositional analysis: a valid approach to analyze microbiome high-throughput sequencing data
-
COI: 1:CAS:528:DC%2BC28XhtVSgsLvK
-
Gloor, G. B. & Reid, G. Compositional analysis: a valid approach to analyze microbiome high-throughput sequencing data. Can. J. Microbiol. 62, 692–703 (2016).
-
(2016)
Can. J. Microbiol.
, vol.62
, pp. 692-703
-
-
Gloor, G.B.1
Reid, G.2
-
71
-
-
84867364321
-
phytools: an R package for phylogenetic comparative biology (and other things)
-
Revell, L. J. phytools: an R package for phylogenetic comparative biology (and other things). Methods Ecol. Evol. 3, 217–223 (2012).
-
(2012)
Methods Ecol. Evol.
, vol.3
, pp. 217-223
-
-
Revell, L.J.1
-
73
-
-
84891774001
-
The MetaCyc database of metabolic pathways and enzymes and the BioCyc collection of pathway/genome databases
-
Caspi, R. et al. The MetaCyc database of metabolic pathways and enzymes and the BioCyc collection of pathway/genome databases. Nucleic Acids Res. 42, 459–471 (2014).
-
(2014)
Nucleic Acids Res.
, vol.42
, pp. 459-471
-
-
Caspi, R.1
-
74
-
-
84891760956
-
Data, information, knowledge and principle: back to metabolism in KEGG
-
COI: 1:CAS:528:DC%2BC2cXoslej
-
Kanehisa, M. et al. Data, information, knowledge and principle: back to metabolism in KEGG. Nucleic Acids Res. 42, D199–D205 (2014).
-
(2014)
Nucleic Acids Res.
, vol.42
, pp. D199-D205
-
-
Kanehisa, M.1
-
75
-
-
84991204326
-
Species–function relationships shape ecological properties of the human gut microbiome
-
COI: 1:CAS:528:DC%2BC2sXkvF2ju74%3D
-
Vieira-Silva, S. et al. Species–function relationships shape ecological properties of the human gut microbiome. Nat. Microbiol. 1, 16088 (2016).
-
(2016)
Nat. Microbiol.
, vol.1
, pp. 16088
-
-
Vieira-Silva, S.1
-
76
-
-
84976907502
-
KEGG as a reference resource for gene and protein annotation
-
COI: 1:CAS:528:DC%2BC2sXhtV2nsrrI
-
Kanehisa, M., Sato, Y., Kawashima, M., Furumichi, M. & Tanabe, M. KEGG as a reference resource for gene and protein annotation. Nucleic Acids Res. 44, D457–D462 (2016).
-
(2016)
Nucleic Acids Res.
, vol.44
, pp. D457-D462
-
-
Kanehisa, M.1
Sato, Y.2
Kawashima, M.3
Furumichi, M.4
Tanabe, M.5
-
77
-
-
84876134492
-
TIGRFAMs and genome properties in 2013
-
COI: 1:CAS:528:DC%2BC38XhvV2ktrrE
-
Haft, D. H. et al. TIGRFAMs and genome properties in 2013. Nucleic Acids Res. 41, D387–D395 (2013).
-
(2013)
Nucleic Acids Res.
, vol.41
, pp. D387-D395
-
-
Haft, D.H.1
-
78
-
-
84861203603
-
eggNOG v3.0: orthologous groups covering 1133 organisms at 41 different taxonomic ranges
-
COI: 1:CAS:528:DC%2BC3MXhs12htbbM
-
Powell, S. et al. eggNOG v3.0: orthologous groups covering 1133 organisms at 41 different taxonomic ranges. Nucleic Acids Res. 40, D284–D289 (2012).
-
(2012)
Nucleic Acids Res.
, vol.40
, pp. D284-D289
-
-
Powell, S.1
-
79
-
-
84870017710
-
admetSAR: a comprehensive source and free tool for assessment of chemical ADMET properties
-
COI: 1:CAS:528:DC%2BC38XhsFGmtbnJ
-
Cheng, F. et al. admetSAR: a comprehensive source and free tool for assessment of chemical ADMET properties. J. Chem. Inf. Model. 52, 3099–3105 (2012).
-
(2012)
J. Chem. Inf. Model.
, vol.52
, pp. 3099-3105
-
-
Cheng, F.1
-
80
-
-
84856562355
-
The NCBI Taxonomy database
-
COI: 1:CAS:528:DC%2BC3MXhs12htb7M
-
Federhen, S. The NCBI Taxonomy database. Nucleic Acids Res. 40, D136–D143 (2012).
-
(2012)
Nucleic Acids Res.
, vol.40
, pp. D136-D143
-
-
Federhen, S.1
-
81
-
-
84873739311
-
The SILVA ribosomal RNA gene database project: improved data processing and web-based tools
-
Quast, C. et al. The SILVA ribosomal RNA gene database project: improved data processing and web-based tools. Nucleic Acids Res. 41, 590–596 (2013).
-
(2013)
Nucleic Acids Res.
, vol.41
, pp. 590-596
-
-
Quast, C.1
-
82
-
-
84937442075
-
Compact graphical representation of phylogenetic data and metadata with GraPhlAn
-
Asnicar, F., Weingart, G., Tickle, T. L., Huttenhower, C. & Segata, N. Compact graphical representation of phylogenetic data and metadata with GraPhlAn. PeerJ 3, e1029 (2015).
-
(2015)
PeerJ
, vol.3
-
-
Asnicar, F.1
Weingart, G.2
Tickle, T.L.3
Huttenhower, C.4
Segata, N.5
|