-
1
-
-
20544444045
-
Diversity of the human intestinal microbial flora
-
Eckburg PB, Bik EM, Bernstein CN, Purdom E, Dethlefsen L, Sargent M, Gill SR, Nelson KE, Relman DA. 2005. Diversity of the human intestinal microbial flora. Science 308:1635-1638. http://dx.doi.org/10 .1126/science.1110591.
-
(2005)
Science
, vol.308
, pp. 1635-1638
-
-
Eckburg, P.B.1
Bik, E.M.2
Bernstein, C.N.3
Purdom, E.4
Dethlefsen, L.5
Sargent, M.6
Gill, S.R.7
Nelson, K.E.8
Relman, D.A.9
-
2
-
-
77950251400
-
A human gut microbial gene catalogue established by metagenomic sequencing
-
Qin J, Li R, Raes J, Arumugam M, Burgdorf KS, Manichanh C, Nielsen T, Pons N, Levenez F, Yamada T, Mende DR, Li J, Xu J, Li S, Li D, Cao J, Wang B, Liang H, Zheng H, Xie Y, Tap J, Lepage P, Bertalan M, Batto JM, Hansen T, Le Paslier D, Linneberg A, Nielsen HB, Pelletier E, Renault P, Sicheritz-Ponten T, Turner K, Zhu H, Yu C, Li S, Jian M, Zhou Y, Li Y, Zhang X, Li S, Qin N, Yang H, Wang J, Brunak S, Dore J, Guarner F, Kristiansen K, Pedersen O, Parkhill J, Weissenbach J, Meta HITC, Bork P, Ehrlich SD, Wang J. 2010. A human gut microbial gene catalogue established by metagenomic sequencing. Nature 464:59- 65. http://dx.doi.org/10.1038/nature08821.
-
(2010)
Nature
, vol.464
-
-
Qin, J.1
Li, R.2
Raes, J.3
Arumugam, M.4
Burgdorf, K.S.5
Manichanh, C.6
Nielsen, T.7
Pons, N.8
Levenez, F.9
Yamada, T.10
Mende, D.R.11
Li, J.12
Xu, J.13
Li, S.14
Li, D.15
Cao, J.16
Wang, B.17
Liang, H.18
Zheng, H.19
Xie, Y.20
Tap, J.21
Lepage, P.22
Bertalan, M.23
Batto, J.M.24
Hansen, T.25
Le Paslier, D.26
Linneberg, A.27
Nielsen, H.B.28
Pelletier, E.29
Renault, P.30
Sicheritz-Ponten, T.31
Turner, K.32
Zhu, H.33
Yu, C.34
Li, S.35
Jian, M.36
Zhou, Y.37
Li, Y.38
Zhang, X.39
Li, S.40
Qin, N.41
Yang, H.42
Wang, J.43
Brunak, S.44
Dore, J.45
Guarner, F.46
Kristiansen, K.47
Pedersen, O.48
Parkhill, J.49
Weissenbach, J.50
Meta, H.I.T.C.51
Bork, P.52
Ehrlich, S.D.53
Wang, J.54
more..
-
3
-
-
70449713952
-
The NIH Human Microbiome Project
-
NIH HMP Working Group, Peterson J, Garges S, Giovanni M, McInnes P, Wang L, Schloss JA, Bonazzi V, McEwen JE, Wetterstrand KA, Deal C, Baker CC, Di Francesco V, Howcroft TK, Karp RW, Lunsford RD, Wellington CR, Belachew T, Wright M, Giblin C, David H, Mills M, Salomon R, Mullins C, Akolkar B, Begg L, Davis C, Grandison L, Humble M, Khalsa J, Little AR, Peavy H, Pontzer C, Portnoy M, Sayre MH, Starke-Reed P, Zakhari S, Read J, Watson B, Guyer M. 2009. The NIH Human Microbiome Project. Genome Res. 19:2317-2323. http://dx .doi.org/10.1101/gr.096651.109.
-
(2009)
Genome Res.
, vol.19
, pp. 2317-2323
-
-
Peterson, J.1
Garges, S.2
Giovanni, M.3
McInnes, P.4
Wang, L.5
Schloss, J.A.6
Bonazzi, V.7
McEwen, J.E.8
Wetterstrand, K.A.9
Deal, C.10
Baker, C.C.11
Di Francesco, V.12
Howcroft, T.K.13
Karp, R.W.14
Lunsford, R.D.15
Wellington, C.R.16
Belachew, T.17
Wright, M.18
Giblin, C.19
David, H.20
Mills, M.21
Salomon, R.22
Mullins, C.23
Akolkar, B.24
Begg, L.25
Davis, C.26
Grandison, L.27
Humble, M.28
Khalsa, J.29
Little, A.R.30
Peavy, H.31
Pontzer, C.32
Portnoy, M.33
Sayre, M.H.34
Starke-Reed, P.35
Zakhari, S.36
Read, J.37
Watson, B.38
Guyer, M.39
more..
-
4
-
-
78751580602
-
Dominant and diet-responsive groups of bacteria within the human colonic microbiota
-
Walker AW, Ince J, Duncan SH, Webster LM, Holtrop G, Ze XL, 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. http://dx.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.L.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
-
5
-
-
84881559009
-
Faecalibacterium prausnitzii and human intestinal health
-
Miquel S, Martin R, Rossi O, Bermudez-Humaran L, Chatel J, Sokol H, Thomas M, Wells J, Langella P. 2013. Faecalibacterium prausnitzii and human intestinal health. Curr. Opin. Microbiol. 16:255-261. http://dx .doi.org/10.1016/j.mib.2013.06.003.
-
(2013)
Curr. Opin. Microbiol.
, vol.16
, pp. 255-261
-
-
Miquel, S.1
Martin, R.2
Rossi, O.3
Bermudez-Humaran, L.4
Chatel, J.5
Sokol, H.6
Thomas, M.7
Wells, J.8
Langella, P.9
-
6
-
-
84867074831
-
A metagenomewide association study of gut microbiota in type 2 diabetes
-
Qin J, Li Y, Cai Z, Li S, Zhu J, Zhang F, Liang S, Zhang W, Guan Y, Shen D, Peng Y, Zhang D, Jie Z, Wu W, Qin Y, Xue W, Li J, Han L, Lu D, Wu P, Dai Y, Sun X, Li Z, Tang A, Zhong S, Li X, Chen W, Xu R, Wang M, Feng Q, Gong M, Yu J, Zhang Y, Zhang M, Hansen T, Sanchez G, Raes J, Falony G, Okuda S, Almeida M, LeChatelier E, Renault P, Pons N, Batto JM, Zhang Z, Chen H, Yang R, Zheng W, Li S, Yang H, Wang J, Ehrlich SD, Nielsen R, Pedersen O, Kristiansen K, Wang J. 2012. A metagenomewide association study of gut microbiota in type 2 diabetes. Nature 490:55- 60. http://dx.doi.org/10.1038/nature11450.
-
(2012)
Nature
, vol.490
-
-
Qin, J.1
Li, Y.2
Cai, Z.3
Li, S.4
Zhu, J.5
Zhang, F.6
Liang, S.7
Zhang, W.8
Guan, Y.9
Shen, D.10
Peng, Y.11
Zhang, D.12
Jie, Z.13
Wu, W.14
Qin, Y.15
Xue, W.16
Li, J.17
Han, L.18
Lu, D.19
Wu, P.20
Dai, Y.21
Sun, X.22
Li, Z.23
Tang, A.24
Zhong, S.25
Li, X.26
Chen, W.27
Xu, R.28
Wang, M.29
Feng, Q.30
Gong, M.31
Yu, J.32
Zhang, Y.33
Zhang, M.34
Hansen, T.35
Sanchez, G.36
Raes, J.37
Falony, G.38
Okuda, S.39
Almeida, M.40
LeChatelier, E.41
Renault, P.42
Pons, N.43
Batto, J.M.44
Zhang, Z.45
Chen, H.46
Yang, R.47
Zheng, W.48
Li, S.49
Yang, H.50
Wang, J.51
Ehrlich, S.D.52
Nielsen, R.53
Pedersen, O.54
Kristiansen, K.55
Wang, J.56
more..
-
7
-
-
84878709716
-
Gut metagenome in European women with normal, impaired and diabetic glucose control
-
Karlsson FH, Tremaroli V, Nookaew I, Bergstrom G, Behre CJ, Fagerberg B, Nielsen J, Backhed F. 2013. Gut metagenome in European women with normal, impaired and diabetic glucose control. Nature 498: 99-103. http://dx.doi.org/10.1038/nature12198.
-
(2013)
Nature
, vol.498
, pp. 99-103
-
-
Karlsson, F.H.1
Tremaroli, V.2
Nookaew, I.3
Bergstrom, G.4
Behre, C.J.5
Fagerberg, B.6
Nielsen, J.7
Backhed, F.8
-
8
-
-
84866168894
-
Functional interactions between the gut microbiota and host metabolism
-
Tremaroli V, Backhed F. 2012. Functional interactions between the gut microbiota and host metabolism. Nature 489:242-249. http://dx.doi.org /10.1038/nature11552.
-
(2012)
Nature
, vol.489
, pp. 242-249
-
-
Tremaroli, V.1
Backhed, F.2
-
9
-
-
55949124035
-
Faecalibacterium prausnitzii is an anti-inflammatory commensal bacterium identified by gut microbiota analysis of Crohn disease patients
-
Sokol H, Pigneur B, Watterlot L, Lakhdari O, Bermudez-Humaran LG, Gratadoux JJ, Blugeon S, Bridonneau C, Furet JP, Corthier G, Grangette C, Vasquez N, Pochart P, Trugnan G, Thomas G, Blottiere HM, Dore J, Marteau P, Seksik P, Langella P. 2008. Faecalibacterium prausnitzii is an anti-inflammatory commensal bacterium identified by gut microbiota analysis of Crohn disease patients. Proc. Natl. Acad. Sci. U. S. A. 105:16731-16736. http://dx.doi.org/10.1073/pnas.0804812105.
-
(2008)
Proc. Natl. Acad. Sci. U. S. A.
, vol.105
, pp. 16731-16736
-
-
Sokol, H.1
Pigneur, B.2
Watterlot, L.3
Lakhdari, O.4
Bermudez-Humaran, L.G.5
Gratadoux, J.J.6
Blugeon, S.7
Bridonneau, C.8
Furet, J.P.9
Corthier, G.10
Grangette, C.11
Vasquez, N.12
Pochart, P.13
Trugnan, G.14
Thomas, G.15
Blottiere, H.M.16
Dore, J.17
Marteau, P.18
Seksik, P.19
Langella, P.20
more..
-
10
-
-
63849241608
-
Diversity, metabolism and microbial ecology of butyrate-producing bacteria from the human large intestine
-
Louis P, Flint HJ. 2009. Diversity, metabolism and microbial ecology of butyrate-producing bacteria from the human large intestine. FEMS Microbiol. Lett. 294:1- 8. http://dx.doi.org/10.1111/j.1574-6968.2009 .01514.x.
-
(2009)
FEMS Microbiol. Lett.
, vol.294
-
-
Louis, P.1
Flint, H.J.2
-
11
-
-
0036866628
-
Growth requirements and fermentation products of Fusobacterium prausnitzii, and a proposal to reclassify it as Faecalibacterium prausnitzii gen
-
Duncan SH, Hold GL, Harmsen HJ, Stewart CS, Flint HJ. 2002. Growth requirements and fermentation products of Fusobacterium prausnitzii, and a proposal to reclassify it as Faecalibacterium prausnitzii gen. nov., comb. nov. Int. J. Syst. Evol. Microbiol. 52:2141-2146. http://dx.doi.org /10.1099/ijs.0.02241-0.
-
(2002)
nov., comb. nov. Int. J. Syst. Evol. Microbiol.
, vol.52
, pp. 2141-2146
-
-
Duncan, S.H.1
Hold, G.L.2
Harmsen, H.J.3
Stewart, C.S.4
Flint, H.J.5
-
12
-
-
84899422808
-
Ecology and metabolism of the beneficial intestinal commensal bacterium
-
Miquel S, Martin R, Bridonneau C, Robert V, Sokol H, Bermudez- Humaran LG, Thomas M, Langella P. 2014. Ecology and metabolism of the beneficial intestinal commensal bacterium. Gut Microbes 5:146-151. http://dx.doi.org/10.4161/gmic.27651.
-
(2014)
Gut Microbes
, vol.5
, pp. 146-151
-
-
Miquel, S.1
Martin, R.2
Bridonneau, C.3
Robert, V.4
Sokol, H.5
Bermudez-Humaran, L.G.6
Thomas, M.7
Langella, P.8
-
13
-
-
84855717953
-
Cultured representatives of two major phylogroups of human colonic Faecalibacterium prausnitzii can utilize pectin, uronic acids, and host-derived substrates for growth
-
Lopez-Siles M, Khan TM, Duncan SH, Harmsen HJ, Garcia-Gil LJ, Flint HJ. 2012. Cultured representatives of two major phylogroups of human colonic Faecalibacterium prausnitzii can utilize pectin, uronic acids, and host-derived substrates for growth. Appl. Environ. Microbiol. 78:420-428. http://dx.doi.org/10.1128/AEM.06858-11.
-
(2012)
Appl. Environ. Microbiol.
, vol.78
, pp. 420-428
-
-
Lopez-Siles, M.1
Khan, T.M.2
Duncan, S.H.3
Harmsen, H.J.4
Garcia-Gil, L.J.5
Flint, H.J.6
-
14
-
-
63849164050
-
Effect of inulin on the human gut microbiota: stimulation of Bifidobacterium adolescentis and Faecalibacterium prausnitzii
-
Ramirez-Farias C, Slezak K, Fuller Z, Duncan A, Holtrop G, Louis P. 2009. Effect of inulin on the human gut microbiota: stimulation of Bifidobacterium adolescentis and Faecalibacterium prausnitzii. Br. J. Nutr. 101:541-550. http://dx.doi.org/10.1017/S0007114508019880.
-
(2009)
Br. J. Nutr.
, vol.101
, pp. 541-550
-
-
Ramirez-Farias, C.1
Slezak, K.2
Fuller, Z.3
Duncan, A.4
Holtrop, G.5
Louis, P.6
-
15
-
-
84864795465
-
Recent advances in reconstruction and applications of genome-scale metabolic models
-
Kim TY, Sohn SB, Kim YB, Kim WJ, Lee SY. 2012. Recent advances in reconstruction and applications of genome-scale metabolic models. Curr. Opin. Biotechnol. 23:617-623. http://dx.doi.org/10.1016/j.copbio.2011 .10.007.
-
(2012)
Curr. Opin. Biotechnol.
, vol.23
, pp. 617-623
-
-
Kim, T.Y.1
Sohn, S.B.2
Kim, Y.B.3
Kim, W.J.4
Lee, S.Y.5
-
16
-
-
84872272279
-
A systems biology approach to studying the role of microbes in human health
-
Thiele I, Heinken A, Fleming RM. 2013. A systems biology approach to studying the role of microbes in human health. Curr. Opin. Biotechnol. 24:4-12. http://dx.doi.org/10.1016/j.copbio.2012.10.001.
-
(2013)
Curr. Opin. Biotechnol.
, vol.24
, pp. 4-12
-
-
Thiele, I.1
Heinken, A.2
Fleming, R.M.3
-
17
-
-
33144470047
-
Characterization of metabolism in the Fe(III)-reducing organism Geobacter sulfurreducens by constraint- based modeling
-
Mahadevan R, Bond DR, Butler JE, Esteve-Nunez A, Coppi MV, Palsson BO, Schilling CH, Lovley DR. 2006. Characterization of metabolism in the Fe(III)-reducing organism Geobacter sulfurreducens by constraint- based modeling. Appl. Environ. Microbiol. 72:1558-1568. http: //dx.doi.org/10.1128/AEM.72.2.1558-1568.2006.
-
(2006)
Appl. Environ. Microbiol.
, vol.72
, pp. 1558-1568
-
-
Mahadevan, R.1
Bond, D.R.2
Butler, J.E.3
Esteve-Nunez, A.4
Coppi, M.V.5
Palsson, B.O.6
Schilling, C.H.7
Lovley, D.R.8
-
18
-
-
80051537012
-
Metabolic network reconstruction of Chlamydomonas offers insight into lightdriven algal metabolism
-
Chang RL, Ghamsari L, Manichaikul A, Hom EF, Balaji S, Fu W, Shen Y, Hao T, Palsson BO, Salehi-Ashtiani K, Papin JA. 2011. Metabolic network reconstruction of Chlamydomonas offers insight into lightdriven algal metabolism. Mol. Syst. Biol. 7:518. http://dx.doi.org/10.1038 /msb.2011.52.
-
(2011)
Mol. Syst. Biol.
, vol.7
, pp. 518
-
-
Chang, R.L.1
Ghamsari, L.2
Manichaikul, A.3
Hom, E.F.4
Balaji, S.5
Fu, W.6
Shen, Y.7
Hao, T.8
Palsson, B.O.9
Salehi-Ashtiani, K.10
Papin, J.A.11
-
19
-
-
84876590179
-
Dissecting the energy metabolism in Mycoplasma pneumoniae through genome-scale metabolic modeling
-
Wodke JA, Puchalka J, Lluch-Senar M, Marcos J, Yus E, Godinho M, Gutierrez-Gallego R, dos Santos VA, Serrano L, Klipp E, Maier T. 2013. Dissecting the energy metabolism in Mycoplasma pneumoniae through genome-scale metabolic modeling. Mol. Syst. Biol. 9:653. http://dx.doi .org/10.1038/msb.2013.6.
-
(2013)
Mol. Syst. Biol.
, vol.9
, pp. 653
-
-
Wodke, J.A.1
Puchalka, J.2
Lluch-Senar, M.3
Marcos, J.4
Yus, E.5
Godinho, M.6
Gutierrez-Gallego, R.7
dos Santos, V.A.8
Serrano, L.9
Klipp, E.10
Maier, T.11
-
20
-
-
23944440242
-
Modeling Lactococcus lactis using a genome-scale flux model
-
Oliveira AP, Nielsen J, Forster J. 2005. Modeling Lactococcus lactis using a genome-scale flux model. BMC Microbiol. 5:39. http://dx.doi.org/10 .1186/1471-2180-5-39.
-
(2005)
BMC Microbiol.
, vol.5
, pp. 39
-
-
Oliveira, A.P.1
Nielsen, J.2
Forster, J.3
-
21
-
-
41149169317
-
Systems analysis of metabolism in the pathogenic trypanosomatid Leishmania major
-
Chavali AK, Whittemore JD, Eddy JA, Williams KT, Papin JA. 2008. Systems analysis of metabolism in the pathogenic trypanosomatid Leishmania major. Mol. Syst. Biol. 4:177. http://dx.doi.org/10.1038/msb.2008 .15.
-
(2008)
Mol. Syst. Biol.
, vol.4
, pp. 177
-
-
Chavali, A.K.1
Whittemore, J.D.2
Eddy, J.A.3
Williams, K.T.4
Papin, J.A.5
-
22
-
-
34447636258
-
Modeling Neisseria meningitidis metabolism: from genome to metabolic fluxes
-
Baart GJ, Zomer B, de Haan A, van der Pol LA, Beuvery EC, Tramper J, Martens DE. 2007. Modeling Neisseria meningitidis metabolism: from genome to metabolic fluxes. Genome Biol. 8:R136. http://dx.doi.org/10 .1186/gb-2007-8-7-r136.
-
(2007)
Genome Biol.
, vol.8
-
-
Baart, G.J.1
Zomer, B.2
de Haan, A.3
van der Pol, L.A.4
Beuvery, E.C.5
Tramper, J.6
Martens, D.E.7
-
23
-
-
75149129569
-
A protocol for generating a high-quality genome-scale metabolic reconstruction
-
Thiele I, Palsson BO. 2010. A protocol for generating a high-quality genome-scale metabolic reconstruction. Nat. Protoc. 5:93-121. http://dx .doi.org/10.1038/nprot.2009.203.
-
(2010)
Nat. Protoc.
, vol.5
, pp. 93-121
-
-
Thiele, I.1
Palsson, B.O.2
-
24
-
-
84861898310
-
IMG: the Integrated Microbial Genomes database and comparative analysis system
-
Markowitz VM, Chen IM, Palaniappan K, Chu K, Szeto E, Grechkin Y, Ratner A, Jacob B, Huang J, Williams P, Huntemann M, Anderson I, Mavromatis K, Ivanova NN, Kyrpides NC. 2012. IMG: the Integrated Microbial Genomes database and comparative analysis system. Nucleic Acids Res. 40:D115-D122. http://dx.doi.org/10.1093/nar/gkr1044.
-
(2012)
Nucleic Acids Res.
, vol.40
-
-
Markowitz, V.M.1
Chen, I.M.2
Palaniappan, K.3
Chu, K.4
Szeto, E.5
Grechkin, Y.6
Ratner, A.7
Jacob, B.8
Huang, J.9
Williams, P.10
Huntemann, M.11
Anderson, I.12
Mavromatis, K.13
Ivanova, N.N.14
Kyrpides, N.C.15
-
25
-
-
40549120596
-
The RAST Server: rapid annotations using subsystems technology
-
Aziz RK, Bartels D, Best AA, DeJongh M, Disz T, Edwards RA, Formsma K, Gerdes S, Glass EM, Kubal M, Meyer F, Olsen GJ, Olson R, Osterman AL, Overbeek RA, McNeil LK, Paarmann D, Paczian T, Parrello B, Pusch GD, Reich C, Stevens R, Vassieva O, Vonstein V, Wilke A, Zagnitko O. 2008. The RAST Server: rapid annotations using subsystems technology. BMC Genomics 9:75. http://dx.doi.org/10.1186 /1471-2164-9-75.
-
(2008)
BMC Genomics
, vol.9
, pp. 75
-
-
Aziz, R.K.1
Bartels, D.2
Best, A.A.3
DeJongh, M.4
Disz, T.5
Edwards, R.A.6
Formsma, K.7
Gerdes, S.8
Glass, E.M.9
Kubal, M.10
Meyer, F.11
Olsen, G.J.12
Olson, R.13
Osterman, A.L.14
Overbeek, R.A.15
McNeil, L.K.16
Paarmann, D.17
Paczian, T.18
Parrello, B.19
Pusch, G.D.20
Reich, C.21
Stevens, R.22
Vassieva, O.23
Vonstein, V.24
Wilke, A.25
Zagnitko, O.26
more..
-
26
-
-
77956696072
-
High-throughput generation, optimization and analysis of genomescale metabolic models
-
Henry CS, DeJongh M, Best AA, Frybarger PM, Linsay B, Stevens RL. 2010. High-throughput generation, optimization and analysis of genomescale metabolic models. Nat. Biotechnol. 28:977-982. http://dx.doi.org/10 .1038/nbt.1672.
-
(2010)
Nat. Biotechnol.
, vol.28
, pp. 977-982
-
-
Henry, C.S.1
DeJongh, M.2
Best, A.A.3
Frybarger, P.M.4
Linsay, B.5
Stevens, R.L.6
-
27
-
-
79551662521
-
Quantitative prediction of cellular metabolism with constraint-based models: the COBRA Toolbox v2.0
-
Schellenberger J, Que R, Fleming RM, Thiele I, Orth JD, Feist AM, Zielinski DC, Bordbar A, Lewis NE, Rahmanian S, Kang J, Hyduke DR, Palsson BO. 2011. Quantitative prediction of cellular metabolism with constraint-based models: the COBRA Toolbox v2.0. Nat. Protoc. 6:1290- 1307. http://dx.doi.org/10.1038/nprot.2011.308.
-
(2011)
Nat. Protoc.
, vol.6
-
-
Schellenberger, J.1
Que, R.2
Fleming, R.M.3
Thiele, I.4
Orth, J.D.5
Feist, A.M.6
Zielinski, D.C.7
Bordbar, A.8
Lewis, N.E.9
Rahmanian, S.10
Kang, J.11
Hyduke, D.R.12
Palsson, B.O.13
-
28
-
-
84871588520
-
Systems-level characterization of a host-microbe metabolic symbiosis in the mammalian gut
-
Heinken A, Sahoo S, Fleming RM, Thiele I. 2013. Systems-level characterization of a host-microbe metabolic symbiosis in the mammalian gut. Gut Microbes 4:28-40. http://dx.doi.org/10.4161/gmic.22370.
-
(2013)
Gut Microbes
, vol.4
, pp. 28-40
-
-
Heinken, A.1
Sahoo, S.2
Fleming, R.M.3
Thiele, I.4
-
29
-
-
77951612556
-
BiGG: a Biochemical Genetic and Genomic knowledgebase of large scale metabolic reconstructions
-
Schellenberger J, Park JO, Conrad TM, Palsson BO. 2010. BiGG: a Biochemical Genetic and Genomic knowledgebase of large scale metabolic reconstructions. BMC Bioinformatics 11:213. http://dx.doi.org/10.1186 /1471-2105-11-213.
-
(2010)
BMC Bioinformatics
, vol.11
, pp. 213
-
-
Schellenberger, J.1
Park, J.O.2
Conrad, T.M.3
Palsson, B.O.4
-
30
-
-
34548219522
-
Comparative genomic reconstruction of transcriptional regulatory networks in bacteria
-
Rodionov DA. 2007. Comparative genomic reconstruction of transcriptional regulatory networks in bacteria. Chem. Rev. 107:3467-3497. http: //dx.doi.org/10.1021/cr068309+.
-
(2007)
Chem. Rev.
, vol.107
, pp. 3467-3497
-
-
Rodionov, D.A.1
-
31
-
-
77954254495
-
Reg- Predict: an integrated system for regulon inference in prokaryotes by comparative genomics approach
-
Novichkov PS, Rodionov DA, Stavrovskaya ED, Novichkova ES, Kazakov AE, Gelfand MS, Arkin AP, Mironov AA, Dubchak I. 2010. Reg- Predict: an integrated system for regulon inference in prokaryotes by comparative genomics approach. Nucleic Acids Res. 38:W299-W307. http: //dx.doi.org/10.1093/nar/gkq531.
-
(2010)
Nucleic Acids Res.
, vol.38
-
-
Novichkov, P.S.1
Rodionov, D.A.2
Stavrovskaya, E.D.3
Novichkova, E.S.4
Kazakov, A.E.5
Gelfand, M.S.6
Arkin, A.P.7
Mironov, A.A.8
Dubchak, I.9
-
32
-
-
75549086541
-
RegPrecise: a database of curated genomic inferences of transcriptional regulatory interactions in prokaryotes
-
Novichkov PS, Laikova ON, Novichkova ES, Gelfand MS, Arkin AP, Dubchak I, Rodionov DA. 2010. RegPrecise: a database of curated genomic inferences of transcriptional regulatory interactions in prokaryotes. Nucleic Acids Res. 38:D111-D118. http://dx.doi.org/10.1093 /nar/gkp894.
-
(2010)
Nucleic Acids Res.
, vol.38
-
-
Novichkov, P.S.1
Laikova, O.N.2
Novichkova, E.S.3
Gelfand, M.S.4
Arkin, A.P.5
Dubchak, I.6
Rodionov, D.A.7
-
33
-
-
23144463910
-
RibEx: a web server for locating riboswitches and other conserved bacterial regulatory elements
-
Abreu-Goodger C, Merino E. 2005. RibEx: a web server for locating riboswitches and other conserved bacterial regulatory elements. Nucleic Acids Res. 33:W690-692. http://dx.doi.org/10.1093/nar/gki445.
-
(2005)
Nucleic Acids Res.
, vol.33
-
-
Abreu-Goodger, C.1
Merino, E.2
-
34
-
-
65649126379
-
Connecting extracellular metabolomic measurements to intracellular flux states in yeast.BMCSyst
-
Mo ML, Palsson BO, Herrgard MJ. 2009. Connecting extracellular metabolomic measurements to intracellular flux states in yeast.BMCSyst. Biol. 3:37. http://dx.doi.org/10.1186/1752-0509-3-37.
-
(2009)
Biol.
, vol.3
, pp. 37
-
-
Mo, M.L.1
Palsson, B.O.2
Herrgard, M.J.3
-
35
-
-
0037021804
-
Characterizing the metabolic phenotype: a phenotype phase plane analysis
-
Edwards JS, Ramakrishna R, Palsson BO. 2002. Characterizing the metabolic phenotype: a phenotype phase plane analysis. Biotechnol. Bioeng. 77:27-36. http://dx.doi.org/10.1002/bit.10047.
-
(2002)
Biotechnol. Bioeng.
, vol.77
, pp. 27-36
-
-
Edwards, J.S.1
Ramakrishna, R.2
Palsson, B.O.3
-
36
-
-
0035031148
-
Fusobacterium prausnitzii and related species represent a dominant group within the human fecal flora
-
Suau A, Rochet V, Sghir A, Gramet G, Brewaeys S, Sutren M, Rigottier-Gois L, Dore J. 2001. Fusobacterium prausnitzii and related species represent a dominant group within the human fecal flora. Syst. Appl. Microbiol. 24:139-145. http://dx.doi.org/10.1078/0723-2020-00015.
-
(2001)
Syst. Appl. Microbiol.
, vol.24
, pp. 139-145
-
-
Suau, A.1
Rochet, V.2
Sghir, A.3
Gramet, G.4
Brewaeys, S.5
Sutren, M.6
Rigottier-Gois, L.7
Dore, J.8
-
37
-
-
77956914321
-
Association between Faecalibacterium prausnitzii and dietary fibre in colonic fermentation in healthy human subjects
-
Benus RFJ, van der Werf TS, Welling GW, Judd PA, Taylor MA, Harmsen HJM, Whelan K. 2010. Association between Faecalibacterium prausnitzii and dietary fibre in colonic fermentation in healthy human subjects. Br. J. Nutr. 104:693-700. http://dx.doi.org/10.1017/S000711 4510001030.
-
(2010)
Br. J. Nutr.
, vol.104
, pp. 693-700
-
-
Benus, R.F.J.1
van der Werf, T.S.2
Welling, G.W.3
Judd, P.A.4
Taylor, M.A.5
Harmsen, H.J.M.6
Whelan, K.7
-
38
-
-
84856231790
-
Monitoring metabolites consumption and secretion in cultured cells using ultra-performance liquid chromatography quadrupole-time of flight mass spectrometry (UPLC-Q-ToF-MS)
-
Paglia G, Hrafnsdottir S, Magnusdottir M, Fleming RM, Thorlacius S, Palsson BO, Thiele I. 2012. Monitoring metabolites consumption and secretion in cultured cells using ultra-performance liquid chromatography quadrupole-time of flight mass spectrometry (UPLC-Q-ToF-MS). Anal. Bioanal. Chem. 402:1183-1198. http://dx.doi.org/10.1007/s00216 -011-5556-4.
-
(2012)
Anal. Bioanal. Chem.
, vol.402
, pp. 1183-1198
-
-
Paglia, G.1
Hrafnsdottir, S.2
Magnusdottir, M.3
Fleming, R.M.4
Thorlacius, S.5
Palsson, B.O.6
Thiele, I.7
-
39
-
-
84863989287
-
The gut anaerobe Faecalibacterium prausnitzii uses an extracellular electron shuttle to grow at oxic-anoxic interphases
-
Khan MT, Duncan SH, Stams AJ, van Dijl JM, Flint HJ, Harmsen HJ. 2012. The gut anaerobe Faecalibacterium prausnitzii uses an extracellular electron shuttle to grow at oxic-anoxic interphases. ISME J. 6:1578-1585. http://dx.doi.org/10.1038/ismej.2012.5.
-
(2012)
ISME J.
, vol.6
, pp. 1578-1585
-
-
Khan, M.T.1
Duncan, S.H.2
Stams, A.J.3
van Dijl, J.M.4
Flint, H.J.5
Harmsen, H.J.6
-
40
-
-
77955437093
-
A eubacterial riboswitch class that senses the coenzyme tetrahydrofolate
-
Ames TD, Rodionov DA, Weinberg Z, Breaker RR. 2010. A eubacterial riboswitch class that senses the coenzyme tetrahydrofolate. Chem. Biol. 17:681-685. http://dx.doi.org/10.1016/j.chembiol.2010.05.020.
-
(2010)
Chem. Biol.
, vol.17
, pp. 681-685
-
-
Ames, T.D.1
Rodionov, D.A.2
Weinberg, Z.3
Breaker, R.R.4
-
41
-
-
84875055328
-
Major phenylpropanoid-derived metabolites in the human gut can arise from microbial fermentation of protein
-
Russell WR, Duncan SH, Scobbie L, Duncan G, Cantlay L, Calder AG, Anderson SE, Flint HJ. 2013. Major phenylpropanoid-derived metabolites in the human gut can arise from microbial fermentation of protein. Mol. Nutr. Food Res. 57:523-535. http://dx.doi.org/10.1002/mnfr .201200594.
-
(2013)
Mol. Nutr. Food Res.
, vol.57
, pp. 523-535
-
-
Russell, W.R.1
Duncan, S.H.2
Scobbie, L.3
Duncan, G.4
Cantlay, L.5
Calder, A.G.6
Anderson, S.E.7
Flint, H.J.8
-
42
-
-
58149490653
-
A novel class of modular transporters for vitamins in prokaryotes
-
Rodionov DA, Hebbeln P, Eudes A, ter Beek J, Rodionova IA, Erkens GB, Slotboom DJ, Gelfand MS, Osterman AL, Hanson AD, Eitinger T. 2009. A novel class of modular transporters for vitamins in prokaryotes. J. Bacteriol. 191:42-51. http://dx.doi.org/10.1128/JB.01208-08.
-
(2009)
J. Bacteriol.
, vol.191
, pp. 42-51
-
-
Rodionov, D.A.1
Hebbeln, P.2
Eudes, A.3
ter Beek, J.4
Rodionova, I.A.5
Erkens, G.B.6
Slotboom, D.J.7
Gelfand, M.S.8
Osterman, A.L.9
Hanson, A.D.10
Eitinger, T.11
-
43
-
-
84906067601
-
Novel physiological and metabolic insights into the beneficial gut microbe Faecalibacterium prausnitzii-from carbohydrates to current
-
University Medical Center Groningen, University of Groningen, Groningen, The Netherlands
-
Khan MT. 2013. Novel physiological and metabolic insights into the beneficial gut microbe Faecalibacterium prausnitzii-from carbohydrates to current. University Medical Center Groningen, University of Groningen, Groningen, The Netherlands
-
(2013)
-
-
Khan, M.T.1
-
44
-
-
0037470975
-
A genomic view of the human-Bacteroides thetaiotaomicron symbiosis
-
Xu J, Bjursell MK, Himrod J, Deng S, Carmichael LK, Chiang HC, Hooper LV, Gordon JI. 2003. A genomic view of the human-Bacteroides thetaiotaomicron symbiosis. Science 299:2074-2076. http://dx.doi.org /10.1126/science.1080029.
-
(2003)
Science
, vol.299
, pp. 2074-2076
-
-
Xu, J.1
Bjursell, M.K.2
Himrod, J.3
Deng, S.4
Carmichael, L.K.5
Chiang, H.C.6
Hooper, L.V.7
Gordon, J.I.8
-
45
-
-
13244273427
-
Characterization of the RokA and HexA broad-substrate-specificity hexokinases from Bacteroides fragilis and their role in hexose and N-acetylglucosamine utilization
-
Brigham CJ, Malamy MH. 2005. Characterization of the RokA and HexA broad-substrate-specificity hexokinases from Bacteroides fragilis and their role in hexose and N-acetylglucosamine utilization. J. Bacteriol. 187: 890-901. http://dx.doi.org/10.1128/JB.187.3.890-901.2005.
-
(2005)
J. Bacteriol.
, vol.187
, pp. 890-901
-
-
Brigham, C.J.1
Malamy, M.H.2
-
46
-
-
77749320898
-
What is flux balance analysis?
-
Orth JD, Thiele I, Palsson BO. 2010. What is flux balance analysis? Nat. Biotechnol. 28:245-248. http://dx.doi.org/10.1038/nbt.1614.
-
(2010)
Nat. Biotechnol.
, vol.28
, pp. 245-248
-
-
Orth, J.D.1
Thiele, I.2
Palsson, B.O.3
-
47
-
-
84884686907
-
Semi-automated curation of metabolic models via flux balance analysis: a case study with Mycoplasma gallisepticum
-
Bautista EJ, Zinski J, Szczepanek SM, Johnson EL, Tulman ER, Ching WM, Geary SJ, Srivastava R. 2013. Semi-automated curation of metabolic models via flux balance analysis: a case study with Mycoplasma gallisepticum. Plos Comput. Biol. 9:e1003208. http://dx.doi.org/10.1371 /journal.pcbi.1003208.
-
(2013)
Plos Comput. Biol.
, vol.9
-
-
Bautista, E.J.1
Zinski, J.2
Szczepanek, S.M.3
Johnson, E.L.4
Tulman, E.R.5
Ching, W.M.6
Geary, S.J.7
Srivastava, R.8
-
48
-
-
84880783396
-
Reconstruction and validation of a genome-scale metabolic model for the filamentous fungus Neurospora crassa using FARM
-
Dreyfuss JM, Zucker JD, Hood HM, Ocasio LR, Sachs MS, Galagan JE. 2013. Reconstruction and validation of a genome-scale metabolic model for the filamentous fungus Neurospora crassa using FARM. PLoS Comput. Biol. 9:e1003126. http://dx.doi.org/10.1371/journal .pcbi.1003126.
-
(2013)
PLoS Comput. Biol.
, vol.9
-
-
Dreyfuss, J.M.1
Zucker, J.D.2
Hood, H.M.3
Ocasio, L.R.4
Sachs, M.S.5
Galagan, J.E.6
-
49
-
-
2342648924
-
Integrating high-throughput and computational data elucidates bacterial networks
-
Covert MW, Knight EM, Reed JL, Herrgard MJ, Palsson BO. 2004. Integrating high-throughput and computational data elucidates bacterial networks. Nature 429:92-96. http://dx.doi.org/10.1038/nature02456.
-
(2004)
Nature
, vol.429
, pp. 92-96
-
-
Covert, M.W.1
Knight, E.M.2
Reed, J.L.3
Herrgard, M.J.4
Palsson, B.O.5
-
50
-
-
84864258618
-
A whole-cell computational model predicts phenotype from genotype
-
Karr JR, Sanghvi JC, Macklin DN, Gutschow MV, Jacobs JM, Bolival B, Jr, Assad-Garcia N, Glass JI, Covert MW. 2012. A whole-cell computational model predicts phenotype from genotype. Cell 150:389-401. http: //dx.doi.org/10.1016/j.cell.2012.05.044.
-
(2012)
Cell
, vol.150
, pp. 389-401
-
-
Karr, J.R.1
Sanghvi, J.C.2
Macklin, D.N.3
Gutschow, M.V.4
Jacobs, J.M.5
Bolival Jr., B.6
Assad-Garcia, N.7
Glass, J.I.8
Covert, M.W.9
-
51
-
-
84866975246
-
Multiscale modeling of metabolism and macromolecular synthesis in E. coli and its application to the evolution of codon usage.
-
Thiele I, Fleming RM, Que R, Bordbar A, Diep D, Palsson BO. 2012. Multiscale modeling of metabolism and macromolecular synthesis in E. coli and its application to the evolution of codon usage. PLoS One 7:e45635. http://dx.doi.org/10.1371/journal.pone.0045635.
-
(2012)
PLoS One
, vol.7
-
-
Thiele, I.1
Fleming, R.M.2
Que, R.3
Bordbar, A.4
Diep, D.5
Palsson, B.O.6
-
52
-
-
77952774546
-
Functional characterization of alternate optimal solutions of Escherichia coli's transcriptional and translational machinery
-
Thiele I, Fleming RM, Bordbar A, Schellenberger J, Palsson BO. 2010. Functional characterization of alternate optimal solutions of Escherichia coli's transcriptional and translational machinery. Biophys. J. 98:2072- 2081. http://dx.doi.org/10.1016/j.bpj.2010.01.060.
-
(2010)
Biophys. J.
, vol.98
-
-
Thiele, I.1
Fleming, R.M.2
Bordbar, A.3
Schellenberger, J.4
Palsson, B.O.5
-
53
-
-
84880860962
-
Robust flux balance analysis of multiscale biochemical reaction networks
-
Sun Y, Fleming RM, Thiele I, Saunders MA. 2013. Robust flux balance analysis of multiscale biochemical reaction networks. BMC Bioinformatics 14:240. http://dx.doi.org/10.1186/1471-2105-14-240.
-
(2013)
BMC Bioinformatics
, vol.14
, pp. 240
-
-
Sun, Y.1
Fleming, R.M.2
Thiele, I.3
Saunders, M.A.4
-
54
-
-
84866283114
-
How can Faecalibacterium prausnitzii employ riboflavin for extracellular electron transfer?
-
Khan MT, Browne WR, van Dijl JM, Harmsen HJ. 2012. How can Faecalibacterium prausnitzii employ riboflavin for extracellular electron transfer? Antioxid. Redox Signal. 17:1433-1440. http://dx.doi.org/10 .1089/ars.2012.4701.
-
(2012)
Antioxid. Redox Signal.
, vol.17
, pp. 1433-1440
-
-
Khan, M.T.1
Browne, W.R.2
van Dijl, J.M.3
Harmsen, H.J.4
-
55
-
-
67449122992
-
Insights into the evolution of sialic acid catabolism among bacteria
-
Almagro-Moreno S, Boyd EF. 2009. Insights into the evolution of sialic acid catabolism among bacteria. BMC Evol. Biol. 9:118. http://dx.doi.org /10.1186/1471-2148-9-118.
-
(2009)
BMC Evol. Biol.
, vol.9
, pp. 118
-
-
Almagro-Moreno, S.1
Boyd, E.F.2
-
56
-
-
84897947195
-
Genome-scale metabolic reconstructions of Bifidobacterium adolescentis L2-32 and Faecalibacterium prausnitzii A2-165 and their interaction
-
El-Semman IE, Karlsson FH, Shoaie S, Nookaew I, Soliman TH, Nielsen J. 2014. Genome-scale metabolic reconstructions of Bifidobacterium adolescentis L2-32 and Faecalibacterium prausnitzii A2-165 and their interaction. BMC Syst. Biol. 8:41. http://dx.doi.org/10.1186/1752 -0509-8-41.
-
(2014)
BMC Syst. Biol.
, vol.8
, pp. 41
-
-
El-Semman, I.E.1
Karlsson, F.H.2
Shoaie, S.3
Nookaew, I.4
Soliman, T.H.5
Nielsen, J.6
-
57
-
-
79956157487
-
Prospects for systems biology and modeling of the gut microbiome
-
Karlsson FH, Nookaew I, Petranovic D, Nielsen J. 2011. Prospects for systems biology and modeling of the gut microbiome. Trends Biotechnol. 29:251-258. http://dx.doi.org/10.1016/j.tibtech.2011.01.009.
-
(2011)
Trends Biotechnol.
, vol.29
, pp. 251-258
-
-
Karlsson, F.H.1
Nookaew, I.2
Petranovic, D.3
Nielsen, J.4
-
58
-
-
34249284197
-
Use of axenic animals in studying the adaptation of mammals to their commensal intestinal microbiota
-
Smith K, McCoy KD, Macpherson AJ. 2007. Use of axenic animals in studying the adaptation of mammals to their commensal intestinal microbiota. Semin. Immunol. 19:59-69. http://dx.doi.org/10.1016/j .smim.2006.10.002.
-
(2007)
Semin. Immunol.
, vol.19
, pp. 59-69
-
-
Smith, K.1
McCoy, K.D.2
Macpherson, A.J.3
-
59
-
-
65249149643
-
Characterizing a model human gut microbiota composed of members of its two dominant bacterial phyla
-
Mahowald MA, Rey FE, Seedorf H, Turnbaugh PJ, Fulton RS, Wollam A, Shah N, Wang C, Magrini V, Wilson RK, Cantarel BL, Coutinho PM, Henrissat B, Crock LW, Russell A, Verberkmoes NC, Hettich RL, Gordon JI. 2009. Characterizing a model human gut microbiota composed of members of its two dominant bacterial phyla. Proc. Natl. Acad. Sci. U. S. A. 106:5859 -5864. http://dx.doi.org/10 .1073/pnas.0901529106.
-
(2009)
Proc. Natl. Acad. Sci. U. S. A.
, vol.106
, pp. 5859-5864
-
-
Mahowald, M.A.1
Rey, F.E.2
Seedorf, H.3
Turnbaugh, P.J.4
Fulton, R.S.5
Wollam, A.6
Shah, N.7
Wang, C.8
Magrini, V.9
Wilson, R.K.10
Cantarel, B.L.11
Coutinho, P.M.12
Henrissat, B.13
Crock, L.W.14
Russell, A.15
Verberkmoes, N.C.16
Hettich, R.L.17
Gordon, J.I.18
-
60
-
-
84877913270
-
Bacteroides thetaiotaomicron and Faecali- bacterium prausnitzii influence the production of mucus glycans and the development of goblet cells in the colonic epithelium of a gnotobiotic model rodent
-
Wrzosek L, Miquel S, Noordine ML, Bouet S, Chevalier-Curt MJ, Robert V, Philippe C, Bridonneau C, Cherbuy C, Robbe-Masselot C, Langella P, Thomas M. 2013. Bacteroides thetaiotaomicron and Faecali- bacterium prausnitzii influence the production of mucus glycans and the development of goblet cells in the colonic epithelium of a gnotobiotic model rodent. BMC Biol. 11:61. http://dx.doi.org/10.1186/1741-7007-11 -61.
-
(2013)
BMC Biol.
, vol.11
, pp. 61
-
-
Wrzosek, L.1
Miquel, S.2
Noordine, M.L.3
Bouet, S.4
Chevalier-Curt, M.J.5
Robert, V.6
Philippe, C.7
Bridonneau, C.8
Cherbuy, C.9
Robbe-Masselot, C.10
Langella, P.11
Thomas, M.12
-
61
-
-
84877356167
-
Some are more equal than others: the role of "keystone" species in the degradation of recalcitrant substrates
-
Ze X, Le Mougen F, Duncan SH, Louis P, Flint HJ. 2013. Some are more equal than others: the role of "keystone" species in the degradation of recalcitrant substrates. Gut Microbes 4:236-240. http://dx.doi.org/10 .4161/gmic.23998.
-
(2013)
Gut Microbes
, vol.4
, pp. 236-240
-
-
Ze, X.1
Le Mougen, F.2
Duncan, S.H.3
Louis, P.4
Flint, H.J.5
-
62
-
-
68249110221
-
The role of pH in determining the species composition of the human colonic microbiota
-
Duncan SH, Louis P, Thomson JM, Flint HJ. 2009. The role of pH in determining the species composition of the human colonic microbiota. Environ. Microbiol. 11:2112-2122. http://dx.doi.org/10.1111/j.1462 -2920.2009.01931.x.
-
(2009)
Environ. Microbiol.
, vol.11
, pp. 2112-2122
-
-
Duncan, S.H.1
Louis, P.2
Thomson, J.M.3
Flint, H.J.4
|