-
1
-
-
84857044523
-
Food fermentations: Microorganisms with technological beneficial use
-
Bourdichon F, Casaregola S, Farrokh C, Frisvad JC, Gerds ML, Hammes WP, Harnett J, Huys G, Laulund S, Ouwehand A, Powell IB, Prajapati JB, Seto Y, Ter Schure E, Van Boven A, Vankerckhoven V, Zgoda A, Tuijtelaars S, Hansen EB. 2012. Food fermentations: microorganisms with technological beneficial use. Int J Food Microbiol 154:87–97. https://doi.org/10.1016/j.ijfoodmicro.2011.12.030.
-
(2012)
Int J Food Microbiol
, vol.154
, pp. 87-97
-
-
Bourdichon, F.1
Casaregola, S.2
Farrokh, C.3
Frisvad, J.C.4
Gerds, M.L.5
Hammes, W.P.6
Harnett, J.7
Huys, G.8
Laulund, S.9
Ouwehand, A.10
Powell, I.B.11
Prajapati, J.B.12
Seto, Y.13
Ter Schure, E.14
van Boven, A.15
Vankerckhoven, V.16
Zgoda, A.17
Tuijtelaars, S.18
Hansen, E.B.19
-
2
-
-
85077716925
-
Fermented foods in a global age: East meets West
-
Tamang JP, Cotter PD, Endo A, Han NS, Kort R, Liu SQ, Mayo B, Westerik N, Hutkins R. 2020. Fermented foods in a global age: East meets West. Compr Rev Food Sci Food Saf 19:184–217. https://doi.org/10.1111/1541-4337.12520.
-
(2020)
Compr Rev Food Sci Food Saf
, vol.19
, pp. 184-217
-
-
Tamang, J.P.1
Cotter, P.D.2
Endo, A.3
Han, N.S.4
Kort, R.5
Liu, S.Q.6
Mayo, B.7
Westerik, N.8
Hutkins, R.9
-
3
-
-
84964350689
-
Review: Diversity of microorganisms in global fermented foods and beverages
-
Tamang JP, Watanabe K, Holzapfel WH. 2016. Review: diversity of microorganisms in global fermented foods and beverages. Front Microbiol 7:377. https://doi.org/10.3389/fmicb.2016.00377.
-
(2016)
Front Microbiol
, vol.7
, pp. 377
-
-
Tamang, J.P.1
Watanabe, K.2
Holzapfel, W.H.3
-
4
-
-
85052627801
-
Fermented foods as a dietary source of live organisms
-
Rezac S, Kok CR, Heermann M, Hutkins R. 2018. Fermented foods as a dietary source of live organisms. Front Microbiol 9:1785. https://doi.org/10.3389/fmicb.2018.01785.
-
(2018)
Front Microbiol
, vol.9
, pp. 1785
-
-
Rezac, S.1
Kok, C.R.2
Heermann, M.3
Hutkins, R.4
-
5
-
-
84892828465
-
Diet rapidly and reproducibly alters the human gut microbiome
-
David LA, Maurice CF, Carmody RN, Gootenberg DB, Button JE, Wolfe BE, Ling AV, Devlin AS, Varma Y, Fischbach MA, Biddinger SB, Dutton RJ, Turnbaugh PJ. 2014. Diet rapidly and reproducibly alters the human gut microbiome. Nature 505:559–563. https://doi.org/10.1038/nature12820.
-
(2014)
Nature
, vol.505
, pp. 559-563
-
-
David, L.A.1
Maurice, C.F.2
Carmody, R.N.3
Gootenberg, D.B.4
Button, J.E.5
Wolfe, B.E.6
Ling, A.V.7
Devlin, A.S.8
Varma, Y.9
Fischbach, M.A.10
Biddinger, S.B.11
Dutton, R.J.12
Turnbaugh, P.J.13
-
6
-
-
85006395736
-
Health benefits of fermented foods: Microbiota and beyond
-
Marco ML, Heeney D, Binda S, Cifelli CJ, Cotter PD, Foligné B, Gänzle M, Kort R, Pasin G, Pihlanto A, Smid EJ, Hutkins R. 2017. Health benefits of fermented foods: microbiota and beyond. Curr Opin Biotechnol 44: 94–102. https://doi.org/10.1016/j.copbio.2016.11.010.
-
(2017)
Curr Opin Biotechnol
, vol.44
, pp. 94-102
-
-
Marco, M.L.1
Heeney, D.2
Binda, S.3
Cifelli, C.J.4
Cotter, P.D.5
Foligné, B.6
Gänzle, M.7
Kort, R.8
Pasin, G.9
Pihlanto, A.10
Smid, E.J.11
Hutkins, R.12
-
7
-
-
85070788908
-
Metabolites of lactic acid bacteria present in fermented foods are highly potent agonists of human hydroxycarboxylic acid receptor 3
-
Peters A, Krumbholz P, Jäger E, Heintz-Buschart A, Çakir MV, Rothemund S, Gaudl A, Ceglarek U, Schöneberg T, Stäubert C. 2019. Metabolites of lactic acid bacteria present in fermented foods are highly potent agonists of human hydroxycarboxylic acid receptor 3. PLoS Genet 15: e1008145. https://doi.org/10.1371/journal.pgen.1008283.
-
(2019)
PLoS Genet
, vol.15
-
-
Peters, A.1
Krumbholz, P.2
Jäger, E.3
Heintz-Buschart, A.4
Çakir, M.V.5
Rothemund, S.6
Gaudl, A.7
Ceglarek, U.8
Schöneberg, T.9
Stäubert, C.10
-
8
-
-
79959478455
-
Changes in diet and lifestyle and long-term weight gain in women and men
-
Mozaffarian D, Hao T, Rimm EB, Willett WC, Hu FB. 2011. Changes in diet and lifestyle and long-term weight gain in women and men. N Engl J Med 364:2392–2404. https://doi.org/10.1056/NEJMoa1014296.
-
(2011)
N Engl J Med
, vol.364
, pp. 2392-2404
-
-
Mozaffarian, D.1
Hao, T.2
Rimm, E.B.3
Willett, W.C.4
Hu, F.B.5
-
9
-
-
84924333218
-
Dairy consumption and risk of type 2 diabetes: 3 cohorts of US adults and an updated meta-analysis
-
Chen M, Sun Q, Giovannucci E, Mozaffarian D, Manson JAE, Willett WC, Hu FB. 2014. Dairy consumption and risk of type 2 diabetes: 3 cohorts of US adults and an updated meta-analysis. BMC Med 12:215. https://doi.org/10.1186/s12916-014-0215-1.
-
(2014)
BMC Med
, vol.12
, pp. 215
-
-
Chen, M.1
Sun, Q.2
Giovannucci, E.3
Mozaffarian, D.4
Manson, J.A.E.5
Willett, W.C.6
Hu, F.B.7
-
10
-
-
84958044175
-
Fermented food intake is associated with a reduced likelihood of atopic dermatitis in an adult population (Korean National Health and Nutrition Examination Survey 2012-2013)
-
Park S, Bae JH. 2016. Fermented food intake is associated with a reduced likelihood of atopic dermatitis in an adult population (Korean National Health and Nutrition Examination Survey 2012-2013). Nutr Res 36: 125–133. https://doi.org/10.1016/j.nutres.2015.11.011.
-
(2016)
Nutr Res
, vol.36
, pp. 125-133
-
-
Park, S.1
Bae, J.H.2
-
11
-
-
85028616610
-
Fermented soy product intake is inversely associated with the development of high blood pressure: The Japan public health center-based prospective study
-
Nozue M, Shimazu T, Sasazuki S, Charvat H, Mori N, Mutoh M, Sawada N, Iwasaki M, Yamaji T, Inoue M, Kokubo Y, Yamagishi K, Iso H, Tsugane S. 2017. Fermented soy product intake is inversely associated with the development of high blood pressure: the Japan Public Health Center-Based Prospective Study. J Nutr 14:1749–1756. https://doi.org/10.3945/jn.117.250282.
-
(2017)
J Nutr
, vol.14
, pp. 1749-1756
-
-
Nozue, M.1
Shimazu, T.2
Sasazuki, S.3
Charvat, H.4
Mori, N.5
Mutoh, M.6
Sawada, N.7
Iwasaki, M.8
Yamaji, T.9
Inoue, M.10
Kokubo, Y.11
Yamagishi, K.12
Iso, H.13
Tsugane, S.14
-
12
-
-
80053618114
-
Linking long-term dietary patterns with gut microbial enterotypes
-
Wu GD, Chen J, Hoffmann C, Bittinger K, Chen YY, Keilbaugh SA, Bewtra M, Knights D, Walters WA, Knight R, Sinha R, Gilroy E, Gupta K, Baldassano R, Nessel L, Li H, Bushman FD, Lewis JD. 2011. Linking long-term dietary patterns with gut microbial enterotypes. Science 334:105–108. https://doi.org/10.1126/science.1208344.
-
(2011)
Science
, vol.334
, pp. 105-108
-
-
Wu, G.D.1
Chen, J.2
Hoffmann, C.3
Bittinger, K.4
Chen, Y.Y.5
Keilbaugh, S.A.6
Bewtra, M.7
Knights, D.8
Walters, W.A.9
Knight, R.10
Sinha, R.11
Gilroy, E.12
Gupta, K.13
Baldassano, R.14
Nessel, L.15
Li, H.16
Bushman, F.D.17
Lewis, J.D.18
-
13
-
-
79956301905
-
Diet drives convergence in gut microbiome functions across mammalian phylogeny and within humans
-
Muegge BD, Kuczynski J, Knights D, Clemente JC, González A, Fontana L, Henrissat B, Knight R, Gordon JI. 2011. Diet drives convergence in gut microbiome functions across mammalian phylogeny and within humans. Science 332:970–974. https://doi.org/10.1126/science.1198719.
-
(2011)
Science
, vol.332
, pp. 970-974
-
-
Muegge, B.D.1
Kuczynski, J.2
Knights, D.3
Clemente, J.C.4
González, A.5
Fontana, L.6
Henrissat, B.7
Knight, R.8
Gordon, J.I.9
-
14
-
-
33847233644
-
Reduced dietary intake of carbohydrates by obese subjects results in decreased concentrations of butyrate and butyrate-producing bacteria in feces
-
Duncan SH, Belenguer A, Holtrop G, Johnstone AM, Flint HJ, Lobley GE. 2007. Reduced dietary intake of carbohydrates by obese subjects results in decreased concentrations of butyrate and butyrate-producing bacteria in feces. Appl Environ Microbiol 73:1073–1078. https://doi.org/10.1128/AEM.02340-06.
-
(2007)
Appl Environ Microbiol
, vol.73
, pp. 1073-1078
-
-
Duncan, S.H.1
Belenguer, A.2
Holtrop, G.3
Johnstone, A.M.4
Flint, H.J.5
Lobley, G.E.6
-
15
-
-
33845901507
-
Microbial ecology: Human gut microbes associated with obesity
-
Ley RE, Turnbaugh PJ, Klein S, Gordon JI. 2006. Microbial ecology: human gut microbes associated with obesity. Nature 444:1022–1023. https://doi.org/10.1038/4441022a.
-
(2006)
Nature
, vol.444
, pp. 1022-1023
-
-
Ley, R.E.1
Turnbaugh, P.J.2
Klein, S.3
Gordon, J.I.4
-
16
-
-
78751580602
-
Dominant and diet-responsive groups of bacteria within the human colonic microbiota
-
Walker AW, Ince J, Duncan SH, Webster LM, Holtrop G, Ze X, Brown D, Stares MD, Scott P, Bergerat A, Louis P, McIntosh F, Johnstone AM, Lobley GE, Parkhill J, Flint HJ. 2011. Dominant and diet-responsive groups of bacteria within the human colonic microbiota. ISME J 5:220–230. https://doi.org/10.1038/ismej.2010.118.
-
(2011)
ISME J
, vol.5
, pp. 220-230
-
-
Walker, A.W.1
Ince, J.2
Duncan, S.H.3
Webster, L.M.4
Holtrop, G.5
Ze, X.6
Brown, D.7
Stares, M.D.8
Scott, P.9
Bergerat, A.10
Louis, P.11
McIntosh, F.12
Johnstone, A.M.13
Lobley, G.E.14
Parkhill, J.15
Flint, H.J.16
-
17
-
-
85070954719
-
Fermented foods: Definitions and characteristics, impact on the gut microbiota and effects on gastrointestinal health and disease
-
Dimidi E, Cox SR, Rossi M, Whelan K. 2019. Fermented foods: definitions and characteristics, impact on the gut microbiota and effects on gastrointestinal health and disease. Nutrients 11:E1806. https://doi.org/10.3390/nu11081806.
-
(2019)
Nutrients
, vol.11
, pp. E1806
-
-
Dimidi, E.1
Cox, S.R.2
Rossi, M.3
Whelan, K.4
-
18
-
-
85082542088
-
Crowdsourcing our national gut
-
Grieneisen LE, Blekhman R. 2018. Crowdsourcing our national gut. mSystems 3:e00060-18. https://doi.org/10.1128/mSystems.00060-18.
-
(2018)
mSystems
, vol.3
, pp. e00060-e00118
-
-
Grieneisen, L.E.1
Blekhman, R.2
-
19
-
-
84968918909
-
Population-level analysis of gut microbiome variation
-
Falony G, Joossens M, Vieira-Silva S, Wang J, Darzi Y, Faust K, Kurilshikov A, Bonder MJ, Valles-Colomer M, Vandeputte D, Tito RY, Chaffron S, Rymenans L, Verspecht C, Sutter LD, Lima-Mendez G, D’hoe K, Jonckheere K, Homola D, Garcia R, Tigchelaar EF, Eeckhaudt L, Fu J, Henckaerts L, Zhernakova A, Wijmenga C, Raes J. 2016. Population-level analysis of gut microbiome variation. Science 352:560 –564. https://doi.org/10.1126/science.aad3503.
-
(2016)
Science
, vol.352
, pp. 560-564
-
-
Falony, G.1
Joossens, M.2
Vieira-Silva, S.3
Wang, J.4
Darzi, Y.5
Faust, K.6
Kurilshikov, A.7
Bonder, M.J.8
Valles-Colomer, M.9
Vandeputte, D.10
Tito, R.Y.11
Chaffron, S.12
Rymenans, L.13
Verspecht, C.14
Sutter, L.D.15
Lima-Mendez, G.16
D’hoe, K.17
Jonckheere, K.18
Homola, D.19
Garcia, R.20
Tigchelaar, E.F.21
Eeckhaudt, L.22
Fu, J.23
Henckaerts, L.24
Zhernakova, A.25
Wijmenga, C.26
Raes, J.27
more..
-
20
-
-
84968901892
-
Population-based metagenomics analysis reveals markers for gut microbiome composition and diversity
-
Zhernakova A, Kurilshikov A, Bonder MJ, Tigchelaar EF, Schirmer M, Vatanen T, Mujagic Z, Vila AV, Falony G, Vieira-Silva S, Wang J, Imhann F, Brandsma E, Jankipersadsing SA, Joossens M, Cenit MC, Deelen P, Swertz MA, Weersma RK, Feskens EJM, Netea MG, Gevers D, Jonkers D, Franke L, Aulchenko YS, Huttenhower C, Raes J, Hofker MH, Xavier RJ, Wijmenga C, Fu J. 2016. Population-based metagenomics analysis reveals markers for gut microbiome composition and diversity. Science 352:565–569. https://doi.org/10.1126/science.aad3369.
-
(2016)
Science
, vol.352
, pp. 565-569
-
-
Zhernakova, A.1
Kurilshikov, A.2
Bonder, M.J.3
Tigchelaar, E.F.4
Schirmer, M.5
Vatanen, T.6
Mujagic, Z.7
Vila, A.V.8
Falony, G.9
Vieira-Silva, S.10
Wang, J.11
Imhann, F.12
Brandsma, E.13
Jankipersadsing, S.A.14
Joossens, M.15
Cenit, M.C.16
Deelen, P.17
Swertz, M.A.18
Weersma, R.K.19
Feskens, E.J.M.20
Netea, M.G.21
Gevers, D.22
Jonkers, D.23
Franke, L.24
Aulchenko, Y.S.25
Huttenhower, C.26
Raes, J.27
Hofker, M.H.28
Xavier, R.J.29
Wijmenga, C.30
Fu, J.31
more..
-
21
-
-
85043351358
-
Environment dominates over host genetics in shaping human gut microbiota
-
Rothschild D, Weissbrod O, Barkan E, Kurilshikov A, Korem T, Zeevi D, Costea PI, Godneva A, Kalka IN, Bar N, Shilo S, Lador D, Vila AV, Zmora N, Pevsner-Fischer M, Israeli D, Kosower N, Malka G, Wolf BC, Avnit-Sagi T, Lotan-Pompan M, Weinberger A, Halpern Z, Carmi S, Fu J, Wijmenga C, Zhernakova A, Elinav E, Segal E. 2018. Environment dominates over host genetics in shaping human gut microbiota. Nature 555:210 –215. https://doi.org/10.1038/nature25973.
-
(2018)
Nature
, vol.555
, pp. 210-215
-
-
Rothschild, D.1
Weissbrod, O.2
Barkan, E.3
Kurilshikov, A.4
Korem, T.5
Zeevi, D.6
Costea, P.I.7
Godneva, A.8
Kalka, I.N.9
Bar, N.10
Shilo, S.11
Lador, D.12
Vila, A.V.13
Zmora, N.14
Pevsner-Fischer, M.15
Israeli, D.16
Kosower, N.17
Malka, G.18
Wolf, B.C.19
Avnit-Sagi, T.20
Lotan-Pompan, M.21
Weinberger, A.22
Halpern, Z.23
Carmi, S.24
Fu, J.25
Wijmenga, C.26
Zhernakova, A.27
Elinav, E.28
Segal, E.29
more..
-
22
-
-
20544437650
-
-
Centers for Disease Control and Prevention. Centers for Disease Control and Prevention, Atlanta, GA
-
Centers for Disease Control and Prevention. 2018. National Health and Nutrition Examination Survey data, 2011–2012. Centers for Disease Control and Prevention, Atlanta, GA.
-
(2018)
National Health and Nutrition Examination Survey Data, 2011–2012
-
-
-
23
-
-
84907964491
-
Trends in dietary quality among adults in the United States, 1999 through 2010
-
Wang DD, Leung CW, Li Y, Ding EL, Chiuve SE, Hu FB, Willett WC. 2014. Trends in dietary quality among adults in the United States, 1999 through 2010. JAMA Intern Med 174:1587–1595. https://doi.org/10.1001/jamainternmed.2014.3422.
-
(2014)
JAMA Intern Med
, vol.174
, pp. 1587-1595
-
-
Wang, D.D.1
Leung, C.W.2
Li, Y.3
Ding, E.L.4
Chiuve, S.E.5
Hu, F.B.6
Willett, W.C.7
-
24
-
-
84951821453
-
Geographic disparities in Healthy Eating Index scores (HEI-2005 and 2010) by residential property values: Findings from Seattle Obesity Study (SOS)
-
Drewnowski A, Aggarwal A, Cook A, Stewart O, Moudon AV. 2016. Geographic disparities in Healthy Eating Index scores (HEI-2005 and 2010) by residential property values: findings from Seattle Obesity Study (SOS). Prev Med 83:46–55. https://doi.org/10.1016/j.ypmed.2015.11.021.
-
(2016)
Prev Med
, vol.83
, pp. 46-55
-
-
Drewnowski, A.1
Aggarwal, A.2
Cook, A.3
Stewart, O.4
Moudon, A.V.5
-
25
-
-
85049197113
-
American gut: An open platform for citizen science microbiome research
-
McDonald D, Hyde E, Debelius JW, Morton JT, Gonzalez A, Ackermann G, Aksenov AA, Behsaz B, Brennan C, Chen Y, DeRight Goldasich L, Dorrestein PC, Dunn RR, Fahimipour AK, Gaffney J, Gilbert JA, Gogul G, Green JL, Hugenholtz P, Humphrey G, Huttenhower C, Jackson MA, Janssen S, Jeste DV, Jiang L, Kelley ST, Knights D, Kosciolek T, Ladau J, Leach J, Marotz C, Meleshko D, Melnik AV, Metcalf JL, Mohimani H, Montassier E, Navas-Molina J, Nguyen TT, Peddada S, Pevzner P, Pollard KS, Rahnavard G, Robbins-Pianka A, Sangwan N, Shorenstein J, Smarr L, Song SJ, Spector T, Swafford AD, Thackray VG, Thompson LR, Tripathi A, Vázquez-Baeza Y, Vrbanac A, Wischmeyer P, Wolfe E, Zhu Q, Knight R, Mann AE, Amir A, Frazier A, Martino C, Lebrilla C, Lozupone C, Lewis CM, Raison C, Zhang C, Lauber CL, Warinner C, Lowry CA, Callewaert C, Bloss C, Willner D, Galzerani DD, Gonzalez DJ, Mills DA, Chopra D, Gevers D, Berg-Lyons D, Sears DD, Wendel D, Lovelace E, Pierce E, TerAvest E, Bolyen E, Bushman FD, Wu GD, Church GM, Saxe G, Holscher HD, Ugrina I, German JB, Caporaso JG, Wozniak JM, Kerr J, Ravel J, Lewis JD, Suchodolski JS, Jansson JK, Hampton-Marcell JT, Bobe J, Raes J, Chase JH, Eisen JA, Monk J, Clemente JC, Petrosino J, Goodrich J, Gauglitz J, Jacobs J, Zengler K, Swanson KS, Lewis K, Mayer K, Bittinger K, Dillon L, Zaramela LS, Schriml LM, Dominguez-Bello MG, Jankowska MM, Blaser M, Pirrung M, Minson M, Kurisu M, Ajami N, Gottel NR, Chia N, Fierer N, White O, Cani PD, Gajer P, Strandwitz P, Kashyap P, Dutton R, Park RS, Xavier RJ, Mills RH, Krajmalnik-Brown R, Ley R, Owens SM, Klemmer S, Matamoros S, Mirarab S, Moorman S, Holmes S, Schwartz T, Eshoo-Anton TW, Vigers T, Pandey V, Treuren WV, Fang X, Zech Xu Z, Jarmusch A, Geier J, Reeve N, Silva R, Kopylova E, Nguyen D, Sanders K, Salido Benitez RA, Heale AC, Abramson M, Waldispühl J, Butyaev A, Drogaris C, Nazarova E, Ball M, Gunderson B. 2018. American Gut: an open platform for citizen science microbiome research. mSystems 3:e00031-18. https://doi.org/10.1128/mSystems.00031-18.
-
(2018)
mSystems
, vol.3
-
-
McDonald, D.1
Hyde, E.2
Debelius, J.W.3
Morton, J.T.4
Gonzalez, A.5
Ackermann, G.6
Aksenov, A.A.7
Behsaz, B.8
Brennan, C.9
Chen, Y.10
DeRight Goldasich, L.11
Dorrestein, P.C.12
Dunn, R.R.13
Fahimipour, A.K.14
Gaffney, J.15
Gilbert, J.A.16
Gogul, G.17
Green, J.L.18
Hugenholtz, P.19
Humphrey, G.20
Huttenhower, C.21
Jackson, M.A.22
Janssen, S.23
Jeste, D.V.24
Jiang, L.25
Kelley, S.T.26
Knights, D.27
Kosciolek, T.28
Ladau, J.29
Leach, J.30
Marotz, C.31
Meleshko, D.32
Melnik, A.V.33
Metcalf, J.L.34
Mohimani, H.35
Montassier, E.36
Navas-Molina, J.37
Nguyen, T.T.38
Peddada, S.39
Pevzner, P.40
Pollard, K.S.41
Rahnavard, G.42
Robbins-Pianka, A.43
Sangwan, N.44
Shorenstein, J.45
Smarr, L.46
Song, S.J.47
Spector, T.48
Swafford, A.D.49
Thackray, V.G.50
Thompson, L.R.51
Tripathi, A.52
Vázquez-Baeza, Y.53
Vrbanac, A.54
Wischmeyer, P.55
Wolfe, E.56
Zhu, Q.57
Knight, R.58
Mann, A.E.59
Amir, A.60
Frazier, A.61
Martino, C.62
Lebrilla, C.63
Lozupone, C.64
Lewis, C.M.65
Raison, C.66
Zhang, C.67
Lauber, C.L.68
Warinner, C.69
Lowry, C.A.70
Callewaert, C.71
Bloss, C.72
Willner, D.73
Galzerani, D.D.74
Gonzalez, D.J.75
Mills, D.A.76
Chopra, D.77
Gevers, D.78
Berg-Lyons, D.79
Sears, D.D.80
Wendel, D.81
Lovelace, E.82
Pierce, E.83
TerAvest, E.84
Bolyen, E.85
Bushman, F.D.86
Wu, G.D.87
Church, G.M.88
Saxe, G.89
Holscher, H.D.90
Ugrina, I.91
German, J.B.92
Caporaso, J.G.93
Wozniak, J.M.94
Kerr, J.95
Ravel, J.96
Lewis, J.D.97
Suchodolski, J.S.98
Jansson, J.K.99
more..
-
26
-
-
33748713890
-
UniFrac—an online tool for comparing microbial community diversity in a phylogenetic context
-
Lozupone C, Hamady M, Knight R. 2006. UniFrac—an online tool for comparing microbial community diversity in a phylogenetic context. BMC Bioinformatics 7:371. https://doi.org/10.1186/1471-2105-7-371.
-
(2006)
BMC Bioinformatics
, vol.7
, pp. 371
-
-
Lozupone, C.1
Hamady, M.2
Knight, R.3
-
27
-
-
85067602734
-
Establishing microbial composition measurement standards with reference frames
-
Morton JT, Marotz C, Washburne A, Silverman J, Zaramela LS, Edlund A, Zengler K, Knight R. 2019. Establishing microbial composition measurement standards with reference frames. Nat Commun 10:2719. https://doi.org/10.1038/s41467-019-10656-5.
-
(2019)
Nat Commun
, vol.10
, pp. 2719
-
-
Morton, J.T.1
Marotz, C.2
Washburne, A.3
Silverman, J.4
Zaramela, L.S.5
Edlund, A.6
Zengler, K.7
Knight, R.8
-
28
-
-
85081991717
-
Qurro
-
Fedarko MW, Martino C, Morton JT, Marotz CA, Minich JJ, Allen EE, Knight R. 2019. Qurro. Zenodo https://doi.org/10.5281/zenodo.3369454.
-
(2019)
Zenodo
-
-
Fedarko, M.W.1
Martino, C.2
Morton, J.T.3
Marotz, C.A.4
Minich, J.J.5
Allen, E.E.6
Knight, R.7
-
29
-
-
84940644968
-
A mathematical theory of communication
-
Shannon CE. 1948. A mathematical theory of communication. Bell Syst Tech J 27:379–423. https://doi.org/10.1002/j.1538-7305.1948.tb01338.x.
-
(1948)
Bell Syst Tech J
, vol.27
, pp. 379-423
-
-
Shannon, C.E.1
-
30
-
-
0026499429
-
Conservation evaluation and phylogenetic diversity
-
Faith DP. 1992. Conservation evaluation and phylogenetic diversity. Biol Conserv 61:1–10. https://doi.org/10.1016/0006-3207(92)91201-3.
-
(1992)
Biol Conserv
, vol.61
, pp. 1-10
-
-
Faith, D.P.1
-
31
-
-
85082020472
-
Bayesian sparse functional principal components analysis models dynamic temporal changes in longitudinal microbiome studies, 1836 –1853
-
American Statistical Association, Alexandria, VA
-
Jiang L, Vazquez-Baeza Y, Gonzalez A, Natarajan L, Knight R, Thompson WK. 2019. Bayesian sparse functional principal components analysis models dynamic temporal changes in longitudinal microbiome studies, 1836 –1853. In JSM Proceedings, Statistics in Epidemiology Section. American Statistical Association, Alexandria, VA. https://ww2.amstat.org/membersonly/proceedings/2019/data/assets/pdf/1199578.pdf.
-
(2019)
JSM Proceedings, Statistics in Epidemiology Section
-
-
Jiang, L.1
Vazquez-Baeza, Y.2
Gonzalez, A.3
Natarajan, L.4
Knight, R.5
Thompson, W.K.6
-
32
-
-
85047965440
-
-
Heliyon
-
Wang X, Xiao J, Jia Y, Pan Y, Wang Y. 2018. Lactobacillus kefiranofaciens, the sole dominant and stable bacterial species, exhibits distinct morphotypes upon colonization in Tibetan kefir grains. Heliyon 4:e00649. https://doi.org/10.1016/j.heliyon.2018.e00649.
-
(2018)
Lactobacillus Kefiranofaciens, the Sole Dominant and Stable Bacterial Species, Exhibits Distinct Morphotypes upon Colonization in Tibetan Kefir Grains
, vol.4
-
-
Wang, X.1
Xiao, J.2
Jia, Y.3
Pan, Y.4
Wang, Y.5
-
33
-
-
84882870334
-
The effect of Lactobacillus buchneri and Lactobacillus parabuchneri on the eye formation of semi-hard cheese
-
Fröhlich-Wyder MT, Guggisberg D, Badertscher R, Wechsler D, Wittwer A, Irmler S. 2013. The effect of Lactobacillus buchneri and Lactobacillus parabuchneri on the eye formation of semi-hard cheese. Int Dairy J 33:120 –128. https://doi.org/10.1016/j.idairyj.2013.03.004.
-
(2013)
Int Dairy J
, vol.33
, pp. 120-128
-
-
Fröhlich-Wyder, M.T.1
Guggisberg, D.2
Badertscher, R.3
Wechsler, D.4
Wittwer, A.5
Irmler, S.6
-
34
-
-
84905396404
-
Lactobacillus helveticus: Importance in food and health
-
Giraffa G. 2014. Lactobacillus helveticus: importance in food and health. Front Microbiol 5:338. https://doi.org/10.3389/fmicb.2014.00338.
-
(2014)
Front Microbiol
, vol.5
, pp. 338
-
-
Giraffa, G.1
-
35
-
-
77951033002
-
Primary metabolism in Lactobacillus sakei food isolates by proteomic analysis
-
McLeod A, Zagorec M, Champomier-Vergès MC, Naterstad K, Axelsson L. 2010. Primary metabolism in Lactobacillus sakei food isolates by proteomic analysis. BMC Microbiol 10:120. https://doi.org/10.1186/1471-2180-10-120.
-
(2010)
BMC Microbiol
, vol.10
, pp. 120
-
-
McLeod, A.1
Zagorec, M.2
Champomier-Vergès, M.C.3
Naterstad, K.4
Axelsson, L.5
-
36
-
-
85075724305
-
Learning representations of microbe–metabolite interactions
-
Morton JT, Aksenov AA, Nothias LF, Foulds JR, Quinn RA, Badri MH, Swenson TL, Van Goethem MW, Northen TR, Vazquez-Baeza Y, Wang M, Bokulich NA, Watters A, Song SJ, Bonneau R, Dorrestein PC, Knight R. 2019. Learning representations of microbe–metabolite interactions. Nat Methods 16:1306–1314. https://doi.org/10.1038/s41592-019-0616-3.
-
(2019)
Nat Methods
, vol.16
, pp. 1306-1314
-
-
Morton, J.T.1
Aksenov, A.A.2
Nothias, L.F.3
Foulds, J.R.4
Quinn, R.A.5
Badri, M.H.6
Swenson, T.L.7
van Goethem, M.W.8
Northen, T.R.9
Vazquez-Baeza, Y.10
Wang, M.11
Bokulich, N.A.12
Watters, A.13
Song, S.J.14
Bonneau, R.15
Dorrestein, P.C.16
Knight, R.17
-
37
-
-
33947124087
-
Metabolism of linoleic acid by human gut bacteria: Different routes for biosynthesis of conjugated linoleic acid
-
Devillard E, McIntosh FM, Duncan SH, Wallace RJ. 2007. Metabolism of linoleic acid by human gut bacteria: different routes for biosynthesis of conjugated linoleic acid. J Bacteriol 189:2566–2570. https://doi.org/10.1128/JB.01359-06.
-
(2007)
J Bacteriol
, vol.189
, pp. 2566-2570
-
-
Devillard, E.1
McIntosh, F.M.2
Duncan, S.H.3
Wallace, R.J.4
-
38
-
-
0842268116
-
Impact of microbial cultures on conjugated linoleic acid in dairy products—a review
-
Sieber R, Collomb M, Aeschlimann A, Jelen P, Eyer H. 2004. Impact of microbial cultures on conjugated linoleic acid in dairy products—a review. Int Dairy J 14:1–15. https://doi.org/10.1016/S0958-6946(03)00151-1.
-
(2004)
Int Dairy J
, vol.14
, pp. 1-15
-
-
Sieber, R.1
Collomb, M.2
Aeschlimann, A.3
Jelen, P.4
Eyer, H.5
-
39
-
-
85029454538
-
Bacterial conjugated linoleic acid production and their applications
-
Yang B, Gao H, Stanton C, Ross RP, Zhang H, Chen YQ, Chen H, Chen W. 2017. Bacterial conjugated linoleic acid production and their applications. Prog Lipid Res 68:26–36. https://doi.org/10.1016/j.plipres.2017.09.002.
-
(2017)
Prog Lipid Res
, vol.68
, pp. 26-36
-
-
Yang, B.1
Gao, H.2
Stanton, C.3
Ross, R.P.4
Zhang, H.5
Chen, Y.Q.6
Chen, H.7
Chen, W.8
-
40
-
-
84923264498
-
Conjugated linoleic and linolenic acid production by bacteria: Development of functional foods
-
Rigobelo E ed, IntechOpen, London, United Kingdom
-
Van Nieuwenhove CP, Teran V, Gonzalez SN. 2012. Conjugated linoleic and linolenic acid production by bacteria: development of functional foods. In Rigobelo E (ed), Probiotics. IntechOpen, London, United Kingdom.
-
(2012)
Probiotics
-
-
van Nieuwenhove, C.P.1
Teran, V.2
Gonzalez, S.N.3
-
41
-
-
84920189634
-
Health benefits of conjugated linoleic acid (CLA)
-
Koba K, Yanagita T. 2014. Health benefits of conjugated linoleic acid (CLA). Obes Res Clin Pract 8:e525–532. https://doi.org/10.1016/j.orcp.2013.10.001.
-
(2014)
Obes Res Clin Pract
, vol.8
, pp. e525-e532
-
-
Koba, K.1
Yanagita, T.2
-
42
-
-
84862110789
-
Implication of conjugated linoleic acid (CLA) in human health
-
Dilzer A, Park Y. 2012. Implication of conjugated linoleic acid (CLA) in human health. Crit Rev Food Sci Nutr 52:488–513. https://doi.org/10.1080/10408398.2010.501409.
-
(2012)
Crit Rev Food Sci Nutr
, vol.52
, pp. 488-513
-
-
Dilzer, A.1
Park, Y.2
-
43
-
-
84887122496
-
Polyunsaturated fatty acid saturation by gut lactic acid bacteria affecting host lipid composition
-
Kishino S, Takeuchi M, Park SB, Hirata A, Kitamura N, Kunisawa J, Kiyono H, Iwamoto R, Isobe Y, Arita M, Arai H, Ueda K, Shima J, Takahashi S, Yokozeki K, Shimizu S, Ogawa J. 2013. Polyunsaturated fatty acid saturation by gut lactic acid bacteria affecting host lipid composition. Proc Natl Acad Sci U S A 110:17808–17813. https://doi.org/10.1073/pnas.1312937110.
-
(2013)
Proc Natl Acad Sci U S A
, vol.110
, pp. 17808-17813
-
-
Kishino, S.1
Takeuchi, M.2
Park, S.B.3
Hirata, A.4
Kitamura, N.5
Kunisawa, J.6
Kiyono, H.7
Iwamoto, R.8
Isobe, Y.9
Arita, M.10
Arai, H.11
Ueda, K.12
Shima, J.13
Takahashi, S.14
Yokozeki, K.15
Shimizu, S.16
Ogawa, J.17
-
44
-
-
84946397538
-
Production of conjugated dienoic and trienoic fatty acids by lactic acid bacteria and bifidobacteria
-
Terán V, Pizarro PL, Zacarías MF, Vinderola G, Medina R, Van Nieuwenhove C. 2015. Production of conjugated dienoic and trienoic fatty acids by lactic acid bacteria and bifidobacteria. J Funct Foods 19(Part A): 417–425. https://doi.org/10.1016/j.jff.2015.09.046.
-
(2015)
J Funct Foods
, vol.19
, pp. 417-425
-
-
Terán, V.1
Pizarro, P.L.2
Zacarías, M.F.3
Vinderola, G.4
Medina, R.5
van Nieuwenhove, C.6
-
45
-
-
44349180442
-
Synthesis of conjugated linoleic acid by human-derived Bifidobacterium breve LMC 017: Utilization as a functional starter culture for milk fermentation
-
Chung SH, Kim IH, Park HG, Kang HS, Yoon CS, Jeong HY, Choi NJ, Kwon EG, Kim YJ. 2008. Synthesis of conjugated linoleic acid by human-derived Bifidobacterium breve LMC 017: utilization as a functional starter culture for milk fermentation. J Agric Food Chem 56:3311–3316. https://doi.org/10.1021/jf0730789.
-
(2008)
J Agric Food Chem
, vol.56
, pp. 3311-3316
-
-
Chung, S.H.1
Kim, I.H.2
Park, H.G.3
Kang, H.S.4
Yoon, C.S.5
Jeong, H.Y.6
Choi, N.J.7
Kwon, E.G.8
Kim, Y.J.9
-
46
-
-
0037219436
-
Conjugated linoleic acid biosynthesis by human-derived Bifidobacterium species
-
Coakley M, Ross RP, Nordgren M, Fitzgerald G, Devery R, Stanton C. 2003. Conjugated linoleic acid biosynthesis by human-derived Bifidobacterium species. J Appl Microbiol 94:138 –145. https://doi.org/10.1046/j.1365-2672.2003.01814.x.
-
(2003)
J Appl Microbiol
, vol.94
, pp. 138-145
-
-
Coakley, M.1
Ross, R.P.2
Nordgren, M.3
Fitzgerald, G.4
Devery, R.5
Stanton, C.6
-
47
-
-
84951033733
-
Addressing current criticism regarding the value of self-report dietary data
-
Subar AF, Freedman LS, Tooze JA, Kirkpatrick SI, Boushey C, Neuhouser ML, Thompson FE, Potischman N, Guenther PM, Tarasuk V, Reedy J, Krebs-Smith SM. 2015. Addressing current criticism regarding the value of self-report dietary data. J Nutr 145:2639–2645. https://doi.org/10.3945/jn.115.219634.
-
(2015)
J Nutr
, vol.145
, pp. 2639-2645
-
-
Subar, A.F.1
Freedman, L.S.2
Tooze, J.A.3
Kirkpatrick, S.I.4
Boushey, C.5
Neuhouser, M.L.6
Thompson, F.E.7
Potischman, N.8
Guenther, P.M.9
Tarasuk, V.10
Reedy, J.11
Krebs-Smith, S.M.12
-
48
-
-
84894241797
-
The Healthy Eating Index-2010 Is a valid and reliable measure of diet quality according to the 2010 Dietary Guidelines for Americans
-
Guenther PM, Kirkpatrick SI, Reedy J, Krebs-Smith SM, Buckman DW, Dodd KW, Casavale KO, Carroll RJ. 2014. The Healthy Eating Index-2010 Is a valid and reliable measure of diet quality according to the 2010 Dietary Guidelines for Americans. J Nutr 144:399–407. https://doi.org/ 10.3945/jn.113.183079.
-
(2014)
J Nutr
, vol.144
, pp. 399-407
-
-
Guenther, P.M.1
Kirkpatrick, S.I.2
Reedy, J.3
Krebs-Smith, S.M.4
Buckman, D.W.5
Dodd, K.W.6
Casavale, K.O.7
Carroll, R.J.8
-
49
-
-
85020877465
-
DNA extraction for streamlined metagenomics of diverse environmental samples
-
Marotz C, Amir A, Humphrey G, Gaffney J, Gogul G, Knight R. 2017. DNA extraction for streamlined metagenomics of diverse environmental samples. Biotechniques 62:290–293. https://doi.org/10.2144/000114559.
-
(2017)
Biotechniques
, vol.62
, pp. 290-293
-
-
Marotz, C.1
Amir, A.2
Humphrey, G.3
Gaffney, J.4
Gogul, G.5
Knight, R.6
-
50
-
-
85054059754
-
Qiita: Rapid, web-enabled microbiome meta-analysis
-
Gonzalez A, Navas-Molina JA, Kosciolek T, McDonald D, Vázquez-Baeza Y, Ackermann G, DeReus J, Janssen S, Swafford AD, Orchanian SB, Sanders JG, Shorenstein J, Holste H, Petrus S, Robbins-Pianka A, Brislawn CJ, Wang M, Rideout JR, Bolyen E, Dillon M, Caporaso JG, Dorrestein PC, Knight R. 2018. Qiita: rapid, web-enabled microbiome meta-analysis. Nat Methods 15:796–798. https://doi.org/10.1038/s41592-018-0141-9.
-
(2018)
Nat Methods
, vol.15
, pp. 796-798
-
-
Gonzalez, A.1
Navas-Molina, J.A.2
Kosciolek, T.3
McDonald, D.4
Vázquez-Baeza, Y.5
Ackermann, G.6
DeReus, J.7
Janssen, S.8
Swafford, A.D.9
Orchanian, S.B.10
Sanders, J.G.11
Shorenstein, J.12
Holste, H.13
Petrus, S.14
Robbins-Pianka, A.15
Brislawn, C.J.16
Wang, M.17
Rideout, J.R.18
Bolyen, E.19
Dillon, M.20
Caporaso, J.G.21
Dorrestein, P.C.22
Knight, R.23
more..
-
51
-
-
85070972872
-
RedBiom: A rapid sample discovery and feature characterization system
-
McDonald D, Kaehler B, Gonzalez A, DeReus J, Ackermann G, Marotz C, Huttley G, Knight R. 2019. redbiom: a rapid sample discovery and feature characterization system. mSystems 4:e00215-19. https://doi.org/10.1128/mSystems.00215-19.
-
(2019)
mSystems
, vol.4
, pp. e00215-e00219
-
-
McDonald, D.1
Kaehler, B.2
Gonzalez, A.3
DeReus, J.4
Ackermann, G.5
Marotz, C.6
Huttley, G.7
Knight, R.8
-
52
-
-
85020080492
-
Deblur rapidly resolves single-nucleotide community sequence patterns
-
Amir A, McDonald D, Navas-Molina JA, Kopylova E, Morton JT, Zech Xu Z, Kightley EP, Thompson LR, Hyde ER, Gonzalez A, Knight R. 2017. Deblur rapidly resolves single-nucleotide community sequence patterns. mSystems 2:e00191-16. https://doi.org/10.1128/mSystems.00191-16.
-
(2017)
mSystems
, vol.2
, pp. e00191-e00216
-
-
Amir, A.1
McDonald, D.2
Navas-Molina, J.A.3
Kopylova, E.4
Morton, J.T.5
Zech Xu, Z.6
Kightley, E.P.7
Thompson, L.R.8
Hyde, E.R.9
Gonzalez, A.10
Knight, R.11
-
53
-
-
85032968165
-
Correcting for microbial blooms in fecal samples during room-temperature shipping
-
Amir A, McDonald D, Navas-Molina JA, Debelius J, Morton JT, Hyde E, Robbins-Pianka A, Knight R. 2017. Correcting for microbial blooms in fecal samples during room-temperature shipping. mSystems 2:e00199 -16. https://doi.org/10.1128/mSystems.00199-16.
-
(2017)
mSystems
, vol.2
, pp. e00199-e00216
-
-
Amir, A.1
McDonald, D.2
Navas-Molina, J.A.3
Debelius, J.4
Morton, J.T.5
Hyde, E.6
Robbins-Pianka, A.7
Knight, R.8
-
54
-
-
84857122937
-
An improved Greengenes taxonomy with explicit ranks for ecological and evolutionary analyses of bacteria and archaea
-
McDonald D, Price MN, Goodrich J, Nawrocki EP, Desantis TZ, Probst A, Andersen GL, Knight R, Hugenholtz P. 2012. An improved Greengenes taxonomy with explicit ranks for ecological and evolutionary analyses of bacteria and archaea. ISME J 6:610–618. https://doi.org/10.1038/ismej.2011.139.
-
(2012)
ISME J
, vol.6
, pp. 610-618
-
-
McDonald, D.1
Price, M.N.2
Goodrich, J.3
Nawrocki, E.P.4
Desantis, T.Z.5
Probst, A.6
Andersen, G.L.7
Knight, R.8
Hugenholtz, P.9
-
55
-
-
85069676260
-
Reproducible, interactive, scalable and extensible microbiome data science using QIIME 2
-
Bolyen E, Rideout JR, Dillon MR, Bokulich NA, Abnet CC, Al-Ghalith GA, Alexander H, Alm EJ, Arumugam M, Asnicar F, Bai Y, Bisanz JE, Bittinger K, Brejnrod A, Brislawn CJ, Brown CT, Callahan BJ, Caraballo-Rodríguez AM, Chase J, Cope EK, Da Silva R, Diener C, Dorrestein PC, Douglas GM, Durall DM, Duvallet C, Edwardson CF, Ernst M, Estaki M, Fouquier J, Gauglitz JM, Gibbons SM, Gibson DL, Gonzalez A, Gorlick K, Guo J, Hillmann B, Holmes S, Holste H, Huttenhower C, Huttley GA, Janssen S, Jarmusch AK, Jiang L, Kaehler BD, Kang KB, Keefe CR, Keim P, Kelley ST, Knights D, Koester I, Kosciolek T, Kreps J, Langille MGI, Lee J, Ley R, Liu YX, Loftfield E, Lozupone C, Maher M, Marotz C, Martin BD, McDonald D, McIver LJ, Melnik AV, Metcalf JL, Morgan SC, Morton JT, Naimey AT, Navas-Molina JA, Nothias LF, Orchanian SB, Pearson T, Peoples SL, Petras D, Preuss ML, Pruesse E, Rasmussen LB, Rivers A, Robeson MS, Rosenthal P, Segata N, Shaffer M, Shiffer A, Sinha R, Song SJ, Spear JR, Swafford AD, Thompson LR, Torres PJ, Trinh P, Tripathi A, Turnbaugh PJ, Ul-Hasan S, van der Hooft JJJ, Vargas F, Vázquez-Baeza Y, Vogtmann E, von Hippel M, Walters W, Wan Y, Wang M, Warren J, Weber KC, Williamson CHD, Willis AD, Xu ZZ, Zaneveld JR, Zhang Y, Zhu Q, Knight R, Caporaso JG. 2019. Reproducible, interactive, scalable and extensible microbiome data science using QIIME 2. Nat Biotechnol 37:852– 857. https://doi.org/10.1038/ s41587-019-0209-9.
-
(2019)
Nat Biotechnol
, vol.37
, pp. 852-857
-
-
Bolyen, E.1
Rideout, J.R.2
Dillon, M.R.3
Bokulich, N.A.4
Abnet, C.C.5
Al-Ghalith, G.A.6
Alexander, H.7
Alm, E.J.8
Arumugam, M.9
Asnicar, F.10
Bai, Y.11
Bisanz, J.E.12
Bittinger, K.13
Brejnrod, A.14
Brislawn, C.J.15
Brown, C.T.16
Callahan, B.J.17
Caraballo-Rodríguez, A.M.18
Chase, J.19
Cope, E.K.20
da Silva, R.21
Diener, C.22
Dorrestein, P.C.23
Douglas, G.M.24
Durall, D.M.25
Duvallet, C.26
Edwardson, C.F.27
Ernst, M.28
Estaki, M.29
Fouquier, J.30
Gauglitz, J.M.31
Gibbons, S.M.32
Gibson, D.L.33
Gonzalez, A.34
Gorlick, K.35
Guo, J.36
Hillmann, B.37
Holmes, S.38
Holste, H.39
Huttenhower, C.40
Huttley, G.A.41
Janssen, S.42
Jarmusch, A.K.43
Jiang, L.44
Kaehler, B.D.45
Kang, K.B.46
Keefe, C.R.47
Keim, P.48
Kelley, S.T.49
Knights, D.50
Koester, I.51
Kosciolek, T.52
Kreps, J.53
Langille, M.G.I.54
Lee, J.55
Ley, R.56
Liu, Y.X.57
Loftfield, E.58
Lozupone, C.59
Maher, M.60
Marotz, C.61
Martin, B.D.62
McDonald, D.63
McIver, L.J.64
Melnik, A.V.65
Metcalf, J.L.66
Morgan, S.C.67
Morton, J.T.68
Naimey, A.T.69
Navas-Molina, J.A.70
Nothias, L.F.71
Orchanian, S.B.72
Pearson, T.73
Peoples, S.L.74
Petras, D.75
Preuss, M.L.76
Pruesse, E.77
Rasmussen, L.B.78
Rivers, A.79
Robeson, M.S.80
Rosenthal, P.81
Segata, N.82
Shaffer, M.83
Shiffer, A.84
Sinha, R.85
Song, S.J.86
Spear, J.R.87
Swafford, A.D.88
Thompson, L.R.89
Torres, P.J.90
Trinh, P.91
Tripathi, A.92
Turnbaugh, P.J.93
Ul-Hasan, S.94
van der Hooft, J.J.J.95
Vargas, F.96
Vázquez-Baeza, Y.97
Vogtmann, E.98
von Hippel, M.99
Walters, W.100
Wan, Y.101
Wang, M.102
Warren, J.103
Weber, K.C.104
Williamson, C.H.D.105
Willis, A.D.106
Xu, Z.Z.107
Zaneveld, J.R.108
Zhang, Y.109
Zhu, Q.110
Knight, R.111
Caporaso, J.G.112
more..
-
56
-
-
85015975393
-
Normalization and microbial differential abundance strategies depend upon data characteristics
-
Weiss S, Xu ZZ, Peddada S, Amir A, Bittinger K, Gonzalez A, Lozupone C, Zaneveld JR, Vázquez-Baeza Y, Birmingham A, Hyde ER, Knight R. 2017. Normalization and microbial differential abundance strategies depend upon data characteristics. Microbiome 5:27. https://doi.org/10.1186/ s40168-017-0237-y.
-
(2017)
Microbiome
, vol.5
, pp. 27
-
-
Weiss, S.1
Xu, Z.Z.2
Peddada, S.3
Amir, A.4
Bittinger, K.5
Gonzalez, A.6
Lozupone, C.7
Zaneveld, J.R.8
Vázquez-Baeza, Y.9
Birmingham, A.10
Hyde, E.R.11
Knight, R.12
-
57
-
-
84864010118
-
SEPP: SATé-enabled phylogenetic placement
-
Mirarab S, Nguyen N, Warnow T. 2012. SEPP: SATé-enabled phylogenetic placement. Pac Symp Biocomput 2012:247–258. https://doi.org/10.1142/ 9789814366496_0024.
-
(2012)
Pac Symp Biocomput
, vol.2012
, pp. 247-258
-
-
Mirarab, S.1
Nguyen, N.2
Warnow, T.3
-
58
-
-
85046907278
-
Phylogenetic placement of exact amplicon sequences improves associations with clinical information
-
Janssen S, McDonald D, Gonzalez A, Navas-Molina JA, Jiang L, Xu ZZ, Winker K, Kado DM, Orwoll E, Manary M, Mirarab S, Knight R. 2018. Phylogenetic placement of exact amplicon sequences improves associations with clinical information. mSystems 3:e00021-18. https://doi.org/10.1128/mSystems.00021-18.
-
(2018)
mSystems
, vol.3
, pp. e00021-e00118
-
-
Janssen, S.1
McDonald, D.2
Gonzalez, A.3
Navas-Molina, J.A.4
Jiang, L.5
Xu, Z.Z.6
Winker, K.7
Kado, D.M.8
Orwoll, E.9
Manary, M.10
Mirarab, S.11
Knight, R.12
-
59
-
-
29144464937
-
UniFrac: A new phylogenetic method for comparing microbial communities
-
Lozupone C, Knight R. 2005. UniFrac: a new phylogenetic method for comparing microbial communities. Appl Environ Microbiol 71: 8228–8235. https://doi.org/10.1128/AEM.71.12.8228-8235.2005.
-
(2005)
Appl Environ Microbiol
, vol.71
, pp. 8228-8235
-
-
Lozupone, C.1
Knight, R.2
-
61
-
-
0001884644
-
Individual comparisons by ranking methods
-
Wilcoxon F. 1945. Individual comparisons by ranking methods. Biom Bull 1(6):80 – 83. https://doi.org/10.2307/3001968.
-
(1945)
Biom Bull
, vol.1
, Issue.6
, pp. 80-83
-
-
Wilcoxon, F.1
-
62
-
-
85063635731
-
Sirius 4: A rapid tool for turning tandem mass spectra into metabolite structure information
-
Dührkop K, Fleischauer M, Ludwig M, Aksenov AA, Melnik AV, Meusel M, Dorrestein PC, Rousu J, Böcker S. 2019. SIRIUS 4: a rapid tool for turning tandem mass spectra into metabolite structure information. Nat Methods 16:299–302. https://doi.org/10.1038/s41592-019-0344-8.
-
(2019)
Nat Methods
, vol.16
, pp. 299-302
-
-
Dührkop, K.1
Fleischauer, M.2
Ludwig, M.3
Aksenov, A.A.4
Melnik, A.V.5
Meusel, M.6
Dorrestein, P.C.7
Rousu, J.8
Böcker, S.9
-
63
-
-
77954772536
-
MzMine 2: Modular framework for processing, visualizing, and analyzing mass spectrometry-based molecular profile data
-
Pluskal T, Castillo S, Villar-Briones A, Orešič M. 2010. MZmine 2: modular framework for processing, visualizing, and analyzing mass spectrometry-based molecular profile data. BMC Bioinformatics 11:395. https://doi.org/10.1186/1471-2105-11-395.
-
(2010)
BMC Bioinformatics
, vol.11
, pp. 395
-
-
Pluskal, T.1
Castillo, S.2
Villar-Briones, A.3
Orešič, M.4
-
64
-
-
84979865433
-
MetaboAnalyst 3.0—making metabolomics more meaningful
-
Xia J, Sinelnikov IV, Han B, Wishart DS. 2015. MetaboAnalyst 3.0—making metabolomics more meaningful. Nucleic Acids Res 43: W251–W257. https://doi.org/10.1093/nar/gkv380.
-
(2015)
Nucleic Acids Res
, vol.43
, pp. W251-W257
-
-
Xia, J.1
Sinelnikov, I.V.2
Han, B.3
Wishart, D.S.4
-
65
-
-
85047556074
-
MetaboAnalyst 4.0: Towards more transparent and integrative metabolomics analysis
-
Chong J, Soufan O, Li C, Caraus I, Li S, Bourque G, Wishart DS, Xia J. 2018. MetaboAnalyst 4.0: towards more transparent and integrative metabolomics analysis. Nucleic Acids Res 46(W1):W486 –W494. https://doi.org/10.1093/nar/gky310.
-
(2018)
Nucleic Acids Res
, vol.46
, Issue.W1
, pp. W486-W494
-
-
Chong, J.1
Soufan, O.2
Li, C.3
Caraus, I.4
Li, S.5
Bourque, G.6
Wishart, D.S.7
Xia, J.8
-
66
-
-
84981297901
-
Sharing and community curation of mass spectrometry data with Global Natural Products Social Molecular Networking
-
Wang M, Carver JJ, Phelan VV, Sanchez LM, Garg N, Peng Y, Nguyen DD, Watrous J, Kapono CA, Luzzatto-Knaan T, Porto C, Bouslimani A, Melnik AV, Meehan MJ, Liu WT, Crüsemann M, Boudreau PD, Esquenazi E, Sandoval-Calderón M, Kersten RD, Pace LA, Quinn RA, Duncan KR, Hsu CC, Floros DJ, Gavilan RG, Kleigrewe K, Northen T, Dutton RJ, Parrot D, Carlson EE, Aigle B, Michelsen CF, Jelsbak L, Sohlenkamp C, Pevzner P, Edlund A, McLean J, Piel J, Murphy BT, Gerwick L, Liaw CC, Yang YL, Humpf HU, Maansson M, Keyzers RA, Sims AC, Johnson AR, Sidebottom AM, Sedio BE, Klitgaard A, Larson CB, Boya CAP, Torres-Mendoza D, Gonzalez DJ, Silva DB, Marques LM, Demarque DP, Pociute E, O’Neill EC, Briand E, Helfrich EJN, Granatosky EA, Glukhov E, Ryffel F, Houson H, Mohimani H, Kharbush JJ, Zeng Y, Vorholt JA, Kurita KL, Charusanti P, McPhail KL, Nielsen KF, Vuong L, Elfeki M, Traxler MF, Engene N, Koyama N, Vining OB, Baric R, Silva RR, Mascuch SJ, Tomasi S, Jenkins S, Macherla V, Hoffman T, Agarwal V, Williams PG, Dai J, Neupane R, Gurr J, Rodríguez AMC, Lamsa A, Zhang C, Dorrestein K, Duggan BM, Almaliti J, Allard PM, Phapale P, Nothias LF, Alexandrov T, Litaudon M, Wolfender JL, Kyle JE, Metz TO, Peryea T, Nguyen DT, VanLeer D, Shinn P, Jadhav A, Müller R, Waters KM, Shi W, Liu X, Zhang L, Knight R, Jensen PR, Palsson B, Pogliano K, Linington RG, Gutiérrez M, Lopes NP, Gerwick WH, Moore BS, Dorrestein PC, Bandeira N. 2016. Sharing and community curation of mass spectrometry data with Global Natural Products Social Molecular Networking. Nat Biotechnol 34:828 – 837. https://doi.org/10.1038/nbt.3597.
-
(2016)
Nat Biotechnol
, vol.34
, pp. 828-837
-
-
Wang, M.1
Carver, J.J.2
Phelan, V.V.3
Sanchez, L.M.4
Garg, N.5
Peng, Y.6
Nguyen, D.D.7
Watrous, J.8
Kapono, C.A.9
Luzzatto-Knaan, T.10
Porto, C.11
Bouslimani, A.12
Melnik, A.V.13
Meehan, M.J.14
Liu, W.T.15
Crüsemann, M.16
Boudreau, P.D.17
Esquenazi, E.18
Sandoval-Calderón, M.19
Kersten, R.D.20
Pace, L.A.21
Quinn, R.A.22
Duncan, K.R.23
Hsu, C.C.24
Floros, D.J.25
Gavilan, R.G.26
Kleigrewe, K.27
Northen, T.28
Dutton, R.J.29
Parrot, D.30
Carlson, E.E.31
Aigle, B.32
Michelsen, C.F.33
Jelsbak, L.34
Sohlenkamp, C.35
Pevzner, P.36
Edlund, A.37
McLean, J.38
Piel, J.39
Murphy, B.T.40
Gerwick, L.41
Liaw, C.C.42
Yang, Y.L.43
Humpf, H.U.44
Maansson, M.45
Keyzers, R.A.46
Sims, A.C.47
Johnson, A.R.48
Sidebottom, A.M.49
Sedio, B.E.50
Klitgaard, A.51
Larson, C.B.52
Boya, C.A.P.53
Torres-Mendoza, D.54
Gonzalez, D.J.55
Silva, D.B.56
Marques, L.M.57
Demarque, D.P.58
Pociute, E.59
O’Neill, E.C.60
Briand, E.61
Helfrich, E.J.N.62
Granatosky, E.A.63
Glukhov, E.64
Ryffel, F.65
Houson, H.66
Mohimani, H.67
Kharbush, J.J.68
Zeng, Y.69
Vorholt, J.A.70
Kurita, K.L.71
Charusanti, P.72
McPhail, K.L.73
Nielsen, K.F.74
Vuong, L.75
Elfeki, M.76
Traxler, M.F.77
Engene, N.78
Koyama, N.79
Vining, O.B.80
Baric, R.81
Silva, R.R.82
Mascuch, S.J.83
Tomasi, S.84
Jenkins, S.85
Macherla, V.86
Hoffman, T.87
Agarwal, V.88
Williams, P.G.89
Dai, J.90
Neupane, R.91
Gurr, J.92
Rodríguez, A.M.C.93
Lamsa, A.94
Zhang, C.95
Dorrestein, K.96
Duggan, B.M.97
Almaliti, J.98
Allard, P.M.99
more..
-
67
-
-
34748888866
-
Proposed minimum reporting standards for chemical analysis. Chemical Analysis Working Group (CAWG) Metabolomics Standards Initiative (MSI)
-
Sumner LW, Amberg A, Barrett D, Beale MH, Beger R, Daykin CA, Fan TWM, Fiehn O, Goodacre R, Griffin JL, Hankemeier T, Hardy N, Harnly J, Higashi R, Kopka J, Lane AN, Lindon JC, Marriott P, Nicholls AW, Reily MD, Thaden JJ, Viant MR. 2007. Proposed minimum reporting standards for chemical analysis. Chemical Analysis Working Group (CAWG) Metabolomics Standards Initiative (MSI). Metabolomics 3:211–221. https://doi.org/10.1007/s11306-007-0082-2.
-
(2007)
Metabolomics
, vol.3
, pp. 211-221
-
-
Sumner, L.W.1
Amberg, A.2
Barrett, D.3
Beale, M.H.4
Beger, R.5
Daykin, C.A.6
Fan, T.W.M.7
Fiehn, O.8
Goodacre, R.9
Griffin, J.L.10
Hankemeier, T.11
Hardy, N.12
Harnly, J.13
Higashi, R.14
Kopka, J.15
Lane, A.N.16
Lindon, J.C.17
Marriott, P.18
Nicholls, A.W.19
Reily, M.D.20
Thaden, J.J.21
Viant, M.R.22
more..
-
68
-
-
85079058385
-
-
bioRxiv https://www.biorxiv.org/content/10.1101/812404v1
-
Nothias LF, Petras D, Schmid R, Dührkop K, Rainer J, Sarvepalli A, Protsyuk I, Ernst M, Tsugawa H, Fleischauer M, Aicheler F, Aksenov A, Alka O, Allard PM, Barsch A, Cachet X, Caraballo M, Silva RRD, Dang T, Garg N, Gauglitz JM, Gurevich A, Isaac G, Jarmusch AK, Kameník Z, Kang KB, Kessler N, Koester I, Korf A, Gouellec AL, Ludwig M, Christian MH, McCall LI, McSayles J, Meyer SW, Mohimani H, Morsy M, Moyne O, Neumann S, Neuweger H, Nguyen NH, Nothias-Esposito M, Paolini J, Phelan VV, Pluskal T, Quinn RA, Rogers S, Shrestha B, Tripathi A, van der Hooft JJJ, Vargas F, Weldon KC, Witting M, Yang H, Zhang Z, Zubeil F, Kohlbacher O, Böcker S, Alexandrov T, Bandeira N, Wang M, Dorrestein PC. 2019. Feature-based molecular networking in the GNPS analysis environment. bioRxiv https://doi.org/10.1101/812404 https://www.biorxiv.org/content/10.1101/812404v1.
-
(2019)
Feature-Based Molecular Networking in the GNPS Analysis Environment
-
-
Nothias, L.F.1
Petras, D.2
Schmid, R.3
Dührkop, K.4
Rainer, J.5
Sarvepalli, A.6
Protsyuk, I.7
Ernst, M.8
Tsugawa, H.9
Fleischauer, M.10
Aicheler, F.11
Aksenov, A.12
Alka, O.13
Allard, P.M.14
Barsch, A.15
Cachet, X.16
Caraballo, M.17
Silva, R.R.D.18
Dang, T.19
Garg, N.20
Gauglitz, J.M.21
Gurevich, A.22
Isaac, G.23
Jarmusch, A.K.24
Kameník, Z.25
Kang, K.B.26
Kessler, N.27
Koester, I.28
Korf, A.29
Gouellec, A.L.30
Ludwig, M.31
Christian, M.H.32
McCall, L.I.33
McSayles, J.34
Meyer, S.W.35
Mohimani, H.36
Morsy, M.37
Moyne, O.38
Neumann, S.39
Neuweger, H.40
Nguyen, N.H.41
Nothias-Esposito, M.42
Paolini, J.43
Phelan, V.V.44
Pluskal, T.45
Quinn, R.A.46
Rogers, S.47
Shrestha, B.48
Tripathi, A.49
van der Hooft, J.J.J.50
Vargas, F.51
Weldon, K.C.52
Witting, M.53
Yang, H.54
Zhang, Z.55
Zubeil, F.56
Kohlbacher, O.57
Böcker, S.58
Alexandrov, T.59
Bandeira, N.60
Wang, M.61
Dorrestein, P.C.62
more..
-
69
-
-
80054913451
-
FlasH: Fast length adjustment of short reads to improve genome assemblies
-
Magoč T, Salzberg SL. 2011. FLASH: fast length adjustment of short reads to improve genome assemblies. Bioinformatics 27:2957–2963. https://doi.org/10.1093/bioinformatics/btr507.
-
(2011)
Bioinformatics
, vol.27
, pp. 2957-2963
-
-
Magoč, T.1
Salzberg, S.L.2
-
70
-
-
85056718799
-
Evaluating the information content of shallow shotgun metagenomics
-
Hillmann B, Al-Ghalith GA, Shields-Cutler RR, Zhu Q, Gohl DM, Beckman KB, Knight R, Knights D. 2018. Evaluating the information content of shallow shotgun metagenomics. mSystems 3:e00069-18. https://doi.org/10.1128/mSystems.00069-18.
-
(2018)
mSystems
, vol.3
, pp. e00069-e00118
-
-
Hillmann, B.1
Al-Ghalith, G.A.2
Shields-Cutler, R.R.3
Zhu, Q.4
Gohl, D.M.5
Beckman, K.B.6
Knight, R.7
Knights, D.8
-
71
-
-
84859210032
-
Fast gapped-read alignment with Bowtie 2
-
Langmead B, Salzberg SL. 2012. Fast gapped-read alignment with Bowtie 2. Nat Methods 9:357–359. https://doi.org/10.1038/nmeth.1923.
-
(2012)
Nat Methods
, vol.9
, pp. 357-359
-
-
Langmead, B.1
Salzberg, S.L.2
-
72
-
-
84976871272
-
Reference sequence (RefSeq) database at NCBI: Current status, taxonomic expansion, and functional annotation
-
O’Leary NA, Wright MW, Brister JR, Ciufo S, Haddad D, McVeigh R, Rajput B, Robbertse B, Smith-White B, Ako-Adjei D, Astashyn A, Badretdin A, Bao Y, Blinkova O, Brover V, Chetvernin V, Choi J, Cox E, Ermolaeva O, Farrell CM, Goldfarb T, Gupta T, Haft D, Hatcher E, Hlavina W, Joardar VS, Kodali VK, Li W, Maglott D, Masterson P, McGarvey KM, Murphy MR, O’Neill K, Pujar S, Rangwala SH, Rausch D, Riddick LD, Schoch C, Shkeda A, Storz SS, Sun H, Thibaud-Nissen F, Tolstoy I, Tully RE, Vatsan AR, Wallin C, Webb D, Wu W, Landrum MJ, Kimchi A, Tatusova T, DiCuccio M, Kitts P, Murphy TD, Pruitt KD. 2016. Reference sequence (RefSeq) database at NCBI: current status, taxonomic expansion, and functional annotation. Nucleic Acids Res 44(D1):D733–D745. https://doi.org/10.1093/nar/gkv 1189.
-
(2016)
Nucleic Acids Res
, vol.44
, Issue.D1
, pp. D733-D745
-
-
O’Leary, N.A.1
Wright, M.W.2
Brister, J.R.3
Ciufo, S.4
Haddad, D.5
McVeigh, R.6
Rajput, B.7
Robbertse, B.8
Smith-White, B.9
Ako-Adjei, D.10
Astashyn, A.11
Badretdin, A.12
Bao, Y.13
Blinkova, O.14
Brover, V.15
Chetvernin, V.16
Choi, J.17
Cox, E.18
Ermolaeva, O.19
Farrell, C.M.20
Goldfarb, T.21
Gupta, T.22
Haft, D.23
Hatcher, E.24
Hlavina, W.25
Joardar, V.S.26
Kodali, V.K.27
Li, W.28
Maglott, D.29
Masterson, P.30
McGarvey, K.M.31
Murphy, M.R.32
O’Neill, K.33
Pujar, S.34
Rangwala, S.H.35
Rausch, D.36
Riddick, L.D.37
Schoch, C.38
Shkeda, A.39
Storz, S.S.40
Sun, H.41
Thibaud-Nissen, F.42
Tolstoy, I.43
Tully, R.E.44
Vatsan, A.R.45
Wallin, C.46
Webb, D.47
Wu, W.48
Landrum, M.J.49
Kimchi, A.50
Tatusova, T.51
DiCuccio, M.52
Kitts, P.53
Murphy, T.D.54
Pruitt, K.D.55
more..
-
73
-
-
84991526597
-
Emperor: A tool for visualizing high-throughput microbial community data
-
Vázquez-Baeza Y, Pirrung M, Gonzalez A, Knight R. 2013. EMPeror: a tool for visualizing high-throughput microbial community data. Gigascience 2:16. https://doi.org/10.1186/2047-217X-2-16.
-
(2013)
Gigascience
, vol.2
, pp. 16
-
-
Vázquez-Baeza, Y.1
Pirrung, M.2
Gonzalez, A.3
Knight, R.4
-
74
-
-
85075911011
-
Phylogenomics of 10,575 genomes reveals evolutionary proximity between domains Bacteria and Archaea
-
Zhu Q, Mai U, Pfeiffer W, Janssen S, Asnicar F, Sanders JG, Belda-Ferre P, Al-Ghalith GA, Kopylova E, McDonald D, Kosciolek T, Yin JB, Huang S, Salam N, Jiao JY, Wu Z, Xu ZZ, Cantrell K, Yang Y, Sayyari E, Rabiee M, Morton JT, Podell S, Knights D, Li WJ, Huttenhower C, Segata N, Smarr L, Mirarab S, Knight R. 2019. Phylogenomics of 10,575 genomes reveals evolutionary proximity between domains Bacteria and Archaea. Nat Commun 10:5477. https://doi.org/10.1038/s41467-019-13443-4.
-
(2019)
Nat Commun
, vol.10
, pp. 5477
-
-
Zhu, Q.1
Mai, U.2
Pfeiffer, W.3
Janssen, S.4
Asnicar, F.5
Sanders, J.G.6
Belda-Ferre, P.7
Al-Ghalith, G.A.8
Kopylova, E.9
McDonald, D.10
Kosciolek, T.11
Yin, J.B.12
Huang, S.13
Salam, N.14
Jiao, J.Y.15
Wu, Z.16
Xu, Z.Z.17
Cantrell, K.18
Yang, Y.19
Sayyari, E.20
Rabiee, M.21
Morton, J.T.22
Podell, S.23
Knights, D.24
Li, W.J.25
Huttenhower, C.26
Segata, N.27
Smarr, L.28
Mirarab, S.29
Knight, R.30
more..
|