-
1
-
-
32944466887
-
Ecological and evolutionary forces shaping microbial diversity in the human intestine
-
DOI 10.1016/j.cell.2006.02.017, PII S0092867406001929
-
Ley RE, Peterson DA, Gordon JI (2006) Ecological and evolutionary forces shaping microbial diversity in the human intestine. Cell 124:837-848. (Pubitemid 43261456)
-
(2006)
Cell
, vol.124
, Issue.4
, pp. 837-848
-
-
Ley, R.E.1
Peterson, D.A.2
Gordon, J.I.3
-
2
-
-
35348961403
-
An ecological and evolutionary perspective on humang-microbe mutualism and disease
-
DOI 10.1038/nature06245, PII NATURE06245
-
Dethlefsen L, McFall-Ngai M, Relman DA (2007) An ecological and evolutionary perspective on human-microbe mutualism and disease. Nature 449:811-818. (Pubitemid 47598621)
-
(2007)
Nature
, vol.449
, Issue.7164
, pp. 811-818
-
-
Dethlefsen, L.1
McFall-Ngai, M.2
Relman, D.A.3
-
3
-
-
77950251400
-
A human gut microbial gene catalogue established by metagenomic sequencing
-
MetaHIT Consortium
-
Qin J, et al.; MetaHIT Consortium (2010) A human gut microbial gene catalogue established by metagenomic sequencing. Nature 464:59-65.
-
(2010)
Nature
, vol.464
, pp. 59-65
-
-
Qin, J.1
-
4
-
-
35348968286
-
The Human Microbiome Project
-
DOI 10.1038/nature06244, PII NATURE06244
-
Turnbaugh PJ, et al. (2007) The human microbiome project. Nature 449:804-810. (Pubitemid 47598620)
-
(2007)
Nature
, vol.449
, Issue.7164
, pp. 804-810
-
-
Turnbaugh, P.J.1
Ley, R.E.2
Hamady, M.3
Fraser-Liggett, C.M.4
Knight, R.5
Gordon, J.I.6
-
5
-
-
33845874101
-
An obesity-associated gut microbiome with increased capacity for energy harvest
-
DOI 10.1038/nature05414, PII NATURE05414
-
Turnbaugh PJ, et al. (2006) An obesity-associated gut microbiome with increased capacity for energy harvest. Nature 444:1027-1031. (Pubitemid 46018515)
-
(2006)
Nature
, vol.444
, Issue.7122
, pp. 1027-1031
-
-
Turnbaugh, P.J.1
Ley, R.E.2
Mahowald, M.A.3
Magrini, V.4
Mardis, E.R.5
Gordon, J.I.6
-
6
-
-
77950250064
-
Metabolic syndrome and altered gut microbiota in mice lacking Toll-like receptor 5
-
Vijay-Kumar M, et al. (2010) Metabolic syndrome and altered gut microbiota in mice lacking Toll-like receptor 5. Science 328:228-231.
-
(2010)
Science
, vol.328
, pp. 228-231
-
-
Vijay-Kumar, M.1
-
7
-
-
77951700268
-
Changes in the composition of the human fecal microbiome after bacteriotherapy for recurrent Clostridium difficile-associated diarrhea
-
Khoruts A, Dicksved J, Jansson JK, Sadowsky MJ (2010) Changes in the composition of the human fecal microbiome after bacteriotherapy for recurrent Clostridium difficile-associated diarrhea. J Clin Gastroenterol 44:354-360.
-
(2010)
J Clin Gastroenterol
, vol.44
, pp. 354-360
-
-
Khoruts, A.1
Dicksved, J.2
Jansson, J.K.3
Sadowsky, M.J.4
-
8
-
-
33744804299
-
Metagenomic analysis of the human distal gut microbiome
-
DOI 10.1126/science.1124234
-
Gill SR, et al. (2006) Metagenomic analysis of the human distal gut microbiome. Science 312:1355-1359. (Pubitemid 43839542)
-
(2006)
Science
, vol.312
, Issue.5778
, pp. 1355-1359
-
-
Gill, S.R.1
Pop, M.2
DeBoy, R.T.3
Eckburg, P.B.4
Turnbaugh, P.J.5
Samuel, B.S.6
Gordon, J.I.7
Relman, D.A.8
Fraser-Liggett, C.M.9
Nelson, K.E.10
-
9
-
-
52049092682
-
Worlds within worlds: Evolution of the vertebrate gut microbiota
-
Ley RE, Lozupone CA, Hamady M, Knight R, Gordon JI (2008) Worlds within worlds: Evolution of the vertebrate gut microbiota. Nat Rev Microbiol 6:776-788.
-
(2008)
Nat Rev Microbiol
, vol.6
, pp. 776-788
-
-
Ley, R.E.1
Lozupone, C.A.2
Hamady, M.3
Knight, R.4
Gordon, J.I.5
-
10
-
-
58749112734
-
A core gut microbiome in obese and lean twins
-
Turnbaugh PJ, et al. (2009) A core gut microbiome in obese and lean twins. Nature 457:480-484.
-
(2009)
Nature
, vol.457
, pp. 480-484
-
-
Turnbaugh, P.J.1
-
11
-
-
70449713952
-
The NIH Human Microbiome Project
-
NIH HMP Working Group
-
Peterson J, et al.; NIH HMP Working Group (2009) The NIH Human Microbiome Project. Genome Res 19:2317-2323.
-
(2009)
Genome Res
, vol.19
, pp. 2317-2323
-
-
Peterson, J.1
-
12
-
-
70350125099
-
Human gut microbiome adopts an alternative state following small bowel transplantation
-
Hartman AL, et al. (2009) Human gut microbiome adopts an alternative state following small bowel transplantation. Proc Natl Acad Sci USA 106:17187-17192.
-
(2009)
Proc Natl Acad Sci USA
, vol.106
, pp. 17187-17192
-
-
Hartman, A.L.1
-
13
-
-
20244376755
-
Comparative metagenomics of microbial communities
-
DOI 10.1126/science.1107851
-
Tringe SG, et al. (2005) Comparative metagenomics of microbial communities. Science 308:554-557. (Pubitemid 40570586)
-
(2005)
Science
, vol.308
, Issue.5721
, pp. 554-557
-
-
Tringe, S.G.1
Von Mering, C.2
Kobayashi, A.3
Salamov, A.A.4
Chen, K.5
Chang, H.W.6
Podar, M.7
Short, J.M.8
Mathur, E.J.9
Detter, J.C.10
Bork, P.11
Hugenholtz, P.12
Rubin, E.M.13
-
14
-
-
66249145772
-
Statistical methods for detecting differentially abundant features in clinical metagenomic samples
-
White JR, Nagarajan N, Pop M (2009) Statistical methods for detecting differentially abundant features in clinical metagenomic samples. PLOS Comput Biol 5:e1000352.
-
(2009)
PLOS Comput Biol
, vol.5
-
-
White, J.R.1
Nagarajan, N.2
Pop, M.3
-
15
-
-
38449088143
-
Comparative metagenomics revealed commonly enriched gene sets in human gut microbiomes
-
Kurokawa K, et al. (2007) Comparative metagenomics revealed commonly enriched gene sets in human gut microbiomes. DNA Res 14:169-181.
-
(2007)
DNA Res
, vol.14
, pp. 169-181
-
-
Kurokawa, K.1
-
16
-
-
0034646538
-
Infectious history
-
Lederberg J (2000) Infectious history. Science 288:287-293.
-
(2000)
Science
, vol.288
, pp. 287-293
-
-
Lederberg, J.1
-
18
-
-
49649089054
-
Molecular eco-systems biology: Towards an understanding of community function
-
Raes J, Bork P (2008) Molecular eco-systems biology: Towards an understanding of community function. Nat Rev Microbiol 6:693-699.
-
(2008)
Nat Rev Microbiol
, vol.6
, pp. 693-699
-
-
Raes, J.1
Bork, P.2
-
20
-
-
77949495880
-
Predicting metabolic engineering knockout strategies for chemical production: Accounting for competing pathways
-
Tepper N, Shlomi T (2010) Predicting metabolic engineering knockout strategies for chemical production: Accounting for competing pathways. Bioinformatics 26: 536-543.
-
(2010)
Bioinformatics
, vol.26
, pp. 536-543
-
-
Tepper, N.1
Shlomi, T.2
-
21
-
-
78649677586
-
Environments that induce synthetic microbial ecosystems
-
Klitgord N, Segrè D (2010) Environments that induce synthetic microbial ecosystems. PLOS Comput Biol 6:e1001002.
-
(2010)
PLOS Comput Biol
, vol.6
-
-
Klitgord, N.1
Segrè, D.2
-
22
-
-
33644874819
-
From genomics to chemical genomics: New developments in KEGG
-
Kanehisa M, et al. (2006) From genomics to chemical genomics: New developments in KEGG. Nucleic Acids Res 34(Database issue):D354-D357.
-
(2006)
Nucleic Acids Res
, vol.34
, Issue.DATABASE ISSUE
-
-
Kanehisa, M.1
-
23
-
-
0034609791
-
The large-scale organization of metabolic networks
-
Jeong H, Tombor B, Albert R, Oltvai ZN, Barabási AL (2000) The large-scale organization of metabolic networks. Nature 407:651-654.
-
(2000)
Nature
, vol.407
, pp. 651-654
-
-
Jeong, H.1
Tombor, B.2
Albert, R.3
Oltvai, Z.N.4
Barabási, A.L.5
-
24
-
-
0037079050
-
Metabolic network structure determines key aspects of functionality and regulation
-
DOI 10.1038/nature01166
-
Stelling J, Klamt S, Bettenbrock K, Schuster S, Gilles ED (2002) Metabolic network structure determines key aspects of functionality and regulation. Nature 420: 190-193. (Pubitemid 35340124)
-
(2002)
Nature
, vol.420
, Issue.6912
, pp. 190-193
-
-
Stelling, J.1
Klamt, S.2
Bettenbrock, K.3
Schuster, S.4
Gilles, E.D.5
-
26
-
-
14644396645
-
Functional cartography of complex metabolic networks
-
DOI 10.1038/nature03288
-
Guimerà R, Nunes Amaral LA (2005) Functional cartography of complex metabolic networks. Nature 433:895-900. (Pubitemid 40314902)
-
(2005)
Nature
, vol.433
, Issue.7028
, pp. 895-900
-
-
Guimera, R.1
Amaral, L.A.N.2
-
27
-
-
44349157798
-
The evolution of modularity in bacterial metabolic networks
-
DOI 10.1073/pnas.0712149105
-
Kreimer A, Borenstein E, Gophna U, Ruppin E (2008) The evolution of modularity in bacterial metabolic networks. Proc Natl Acad Sci USA 105:6976-6981. (Pubitemid 351754515)
-
(2008)
Proceedings of the National Academy of Sciences of the United States of America
, vol.105
, Issue.19
, pp. 6976-6981
-
-
Kreimer, A.1
Borenstein, E.2
Gophna, U.3
Ruppin, E.4
-
28
-
-
24044504447
-
Functional essentiality from topology features in metabolic networks: A case study in yeast
-
DOI 10.1016/j.febslet.2005.07.033, PII S0014579305008811
-
Palumbo MC, Colosimo A, Giuliani A, Farina L (2005) Functional essentiality from topology features in metabolic networks: A case study in yeast. FEBS Lett 579: 4642-4646. (Pubitemid 41218640)
-
(2005)
FEBS Letters
, vol.579
, Issue.21
, pp. 4642-4646
-
-
Palumbo, M.C.1
Colosimo, A.2
Giuliani, A.3
Farina, L.4
-
29
-
-
77649227213
-
Decoupling Environment-Dependent and Independent Genetic Robustness across Bacterial Species
-
Freilich S, et al. (2010) Decoupling Environment-Dependent and Independent Genetic Robustness across Bacterial Species. PLOS Comput Biol 6:e1000690.
-
(2010)
PLOS Comput Biol
, vol.6
-
-
Freilich, S.1
-
30
-
-
33645211903
-
The effect of oxygen on biochemical networks and the evolution of complex life
-
Raymond J, Segrè D (2006) The effect of oxygen on biochemical networks and the evolution of complex life. Science 311:1764-1767.
-
(2006)
Science
, vol.311
, pp. 1764-1767
-
-
Raymond, J.1
Segrè, D.2
-
31
-
-
55749087868
-
Large-scale reconstruction and phylogenetic analysis of metabolic environments
-
Borenstein E, Kupiec M, Feldman MW, Ruppin E (2008) Large-scale reconstruction and phylogenetic analysis of metabolic environments. Proc Natl Acad Sci USA 105: 14482-14487.
-
(2008)
Proc Natl Acad Sci USA
, vol.105
, pp. 14482-14487
-
-
Borenstein, E.1
Kupiec, M.2
Feldman, M.W.3
Ruppin, E.4
-
32
-
-
59649085782
-
Topological signatures of species interactions in metabolic networks
-
Borenstein E, Feldman MW (2009) Topological signatures of species interactions in metabolic networks. J Comput Biol 16:191-200.
-
(2009)
J Comput Biol
, vol.16
, pp. 191-200
-
-
Borenstein, E.1
Feldman, M.W.2
-
33
-
-
25644458211
-
The subsystems approach to genome annotation and its use in the project to annotate 1000 genomes
-
DOI 10.1093/nar/gki866
-
Overbeek R, et al. (2005) The subsystems approach to genome annotation and its use in the project to annotate 1000 genomes. Nucleic Acids Res 33:5691-5702. (Pubitemid 41548835)
-
(2005)
Nucleic Acids Research
, vol.33
, Issue.17
, pp. 5691-5702
-
-
Overbeek, R.1
Begley, T.2
Butler, R.M.3
Choudhuri, J.V.4
Chuang, H.-Y.5
Cohoon, M.6
De Crecy-Lagard, V.7
Diaz, N.8
Disz, T.9
Edwards, R.10
Fonstein, M.11
Frank, E.D.12
Gerdes, S.13
Glass, E.M.14
Goesmann, A.15
Hanson, A.16
Iwata-Reuyl, D.17
Jensen, R.18
Jamshidi, N.19
Krause, L.20
Kubal, M.21
Larsen, N.22
Linke, B.23
McHardy, A.C.24
Meyer, F.25
Neuweger, H.26
Olsen, G.27
Olson, R.28
Osterman, A.29
Portnoy, V.30
Pusch, G.D.31
Rodionov, D.A.32
Rul33
ckert, C.34
Steiner, J.35
Stevens, R.36
Thiele, I.37
Vassieva, O.38
Ye, Y.39
Zagnitko, O.40
Vonstein, V.41
more..
-
34
-
-
33747139057
-
The outcomes of pathway database computations depend on pathway ontology
-
DOI 10.1093/nar/gkl438
-
Green ML, Karp PD (2006) The outcomes of pathway database computations depend on pathway ontology. Nucleic Acids Res 34:3687-3697. (Pubitemid 44400418)
-
(2006)
Nucleic Acids Research
, vol.34
, Issue.13
, pp. 3687-3697
-
-
Green, M.L.1
Karp, P.D.2
-
35
-
-
67649470562
-
Metabolic-network-driven analysis of bacterial ecological strategies
-
Freilich S, et al. (2009) Metabolic-network-driven analysis of bacterial ecological strategies. Genome Biol 10:R61.
-
(2009)
Genome Biol
, vol.10
-
-
Freilich, S.1
-
36
-
-
65249149643
-
Characterizing a model human gut microbiota composed of members of its two dominant bacterial phyla
-
Mahowald MA, et al. (2009) Characterizing a model human gut microbiota composed of members of its two dominant bacterial phyla. Proc Natl Acad Sci USA 106: 5859-5864.
-
(2009)
Proc Natl Acad Sci USA
, vol.106
, pp. 5859-5864
-
-
Mahowald, M.A.1
-
37
-
-
77949471116
-
The PTS transporters of Lactobacillus gasseri ATCC 33323
-
Francl AL, Thongaram T, Miller MJ (2010) The PTS transporters of Lactobacillus gasseri ATCC 33323. BMC Microbiol 10:77.
-
(2010)
BMC Microbiol
, vol.10
, pp. 77
-
-
Francl, A.L.1
Thongaram, T.2
Miller, M.J.3
-
38
-
-
77950669604
-
The effect of diet on the human gut microbiome: A metagenomic analysis in humanized gnotobiotic mice
-
Turnbaugh PJ, et al. (2009) The effect of diet on the human gut microbiome: A metagenomic analysis in humanized gnotobiotic mice. Sci Transl Med 1:6ra14.
-
(2009)
Sci Transl Med
, vol.1
-
-
Turnbaugh, P.J.1
-
39
-
-
71049156699
-
Identification of novel serological biomarkers for inflammatory bowel disease using Escherichia coli proteome chip
-
Chen C-S, et al. (2009) Identification of novel serological biomarkers for inflammatory bowel disease using Escherichia coli proteome chip. Mol Cell Proteomics 8:1765-1776.
-
(2009)
Mol Cell Proteomics
, vol.8
, pp. 1765-1776
-
-
Chen, C.-S.1
-
40
-
-
9944233058
-
Nitric oxide in inflammatory bowel disease: A universal messenger in an unsolved puzzle
-
DOI 10.1111/j.1365-2567.2004.01984.x
-
Kolios G, Valatas V, Ward SG (2004) Nitric oxide in inflammatory bowel disease: A universal messenger in an unsolved puzzle. Immunology 113:427-437. (Pubitemid 39593361)
-
(2004)
Immunology
, vol.113
, Issue.4
, pp. 427-437
-
-
Kolios, G.1
Valatas, V.2
Ward, S.G.3
-
41
-
-
77954588212
-
Adaptative nitric oxide overproduction in perivascular adipose tissue during early diet-induced obesity
-
Gil-Ortega M, et al. (2010) Adaptative nitric oxide overproduction in perivascular adipose tissue during early diet-induced obesity. Endocrinology 151:3299-3306.
-
(2010)
Endocrinology
, vol.151
, pp. 3299-3306
-
-
Gil-Ortega, M.1
-
42
-
-
67650364193
-
Induced nitric oxide synthase as a major player in the oncogenic transformation of inflamed tissue
-
Yang G-Y, Taboada S, Liao J (2009) Induced nitric oxide synthase as a major player in the oncogenic transformation of inflamed tissue. Methods Mol Biol 512:119-156.
-
(2009)
Methods Mol Biol
, vol.512
, pp. 119-156
-
-
Yang, G.-Y.1
Taboada, S.2
Liao, J.3
-
43
-
-
78651587618
-
Structural correlations in bacterial metabolic networks
-
Bernhardsson S, Gerlee P, Lizana L (2011) Structural correlations in bacterial metabolic networks. BMC Evol Biol 11:20.
-
(2011)
BMC Evol Biol
, vol.11
, pp. 20
-
-
Bernhardsson, S.1
Gerlee, P.2
Lizana, L.3
-
44
-
-
28444475529
-
Adaptive evolution of bacterial metabolic networks by horizontal gene transfer
-
DOI 10.1038/ng1686, PII N1686
-
Pál C, Papp B, Lercher MJ (2005) Adaptive evolution of bacterial metabolic networks by horizontal gene transfer. Nat Genet 37:1372-1375. (Pubitemid 41722195)
-
(2005)
Nature Genetics
, vol.37
, Issue.12
, pp. 1372-1375
-
-
Pal, C.1
Papp, B.2
Lercher, M.J.3
-
45
-
-
37549018487
-
Environmental variability and modularity of bacterial metabolic networks
-
Parter M, Kashtan N, Alon U (2007) Environmental variability and modularity of bacterial metabolic networks. BMC Evol Biol 7:169.
-
(2007)
BMC Evol Biol
, vol.7
, pp. 169
-
-
Parter, M.1
Kashtan, N.2
Alon, U.3
-
46
-
-
77958490531
-
Postprandial remodeling of the gut microbiota in Burmese pythons
-
Costello EK, Gordon JI, Secor SM, Knight R (2010) Postprandial remodeling of the gut microbiota in Burmese pythons. ISME J 4:1375-1385.
-
(2010)
ISME J
, vol.4
, pp. 1375-1385
-
-
Costello, E.K.1
Gordon, J.I.2
Secor, S.M.3
Knight, R.4
-
47
-
-
33947276100
-
Metabolic modeling of a mutualistic microbial community
-
Stolyar S, et al. (2007) Metabolic modeling of a mutualistic microbial community. Mol Syst Biol 3:92.
-
(2007)
Mol Syst Biol
, vol.3
, pp. 92
-
-
Stolyar, S.1
-
48
-
-
77956415336
-
Emergent cooperation in microbial metabolism
-
Wintermute EH, Silver PA (2010) Emergent cooperation in microbial metabolism. Mol Syst Biol 6:407.
-
(2010)
Mol Syst Biol
, vol.6
, pp. 407
-
-
Wintermute, E.H.1
Silver, P.A.2
-
49
-
-
77954241658
-
The large-scale organization of the bacterial network of ecological co-occurrence interactions
-
Freilich S, et al. (2010) The large-scale organization of the bacterial network of ecological co-occurrence interactions. Nucleic Acids Res 38:3857-3868.
-
(2010)
Nucleic Acids Res
, vol.38
, pp. 3857-3868
-
-
Freilich, S.1
-
50
-
-
60849095134
-
Quantifying environmental adaptation of metabolic pathways in metagenomics
-
Gianoulis TA, et al. (2009) Quantifying environmental adaptation of metabolic pathways in metagenomics. Proc Natl Acad Sci USA 106:1374-1379.
-
(2009)
Proc Natl Acad Sci USA
, vol.106
, pp. 1374-1379
-
-
Gianoulis, T.A.1
-
51
-
-
53749085229
-
A consensus yeast metabolic network reconstruction obtained from a community approach to systems biology
-
Herrgård MJ, et al. (2008) A consensus yeast metabolic network reconstruction obtained from a community approach to systems biology. Nat Biotechnol 26:1155-1160.
-
(2008)
Nat Biotechnol
, vol.26
, pp. 1155-1160
-
-
Herrgård, M.J.1
-
52
-
-
77951122415
-
Reconstruction annotation jamborees: A community approach to systems biology
-
Thiele I, Palsson BØ (2010) Reconstruction annotation jamborees: A community approach to systems biology. Mol Syst Biol 6:361.
-
(2010)
Mol Syst Biol
, vol.6
, pp. 361
-
-
Thiele, I.1
Palsson, B.Ø.2
-
53
-
-
38349164409
-
Computing topological parameters of biological networks
-
Assenov Y, Ramírez F, Schelhorn S-E, Lengauer T, Albrecht M (2008) Computing topological parameters of biological networks. Bioinformatics 24:282-284.
-
(2008)
Bioinformatics
, vol.24
, pp. 282-284
-
-
Assenov, Y.1
Ramírez, F.2
Schelhorn, S.-E.3
Lengauer, T.4
Albrecht, M.5
-
54
-
-
33745012299
-
Modularity and community structure in networks
-
Newman MEJ (2006) Modularity and community structure in networks. Proc Natl Acad Sci USA 103:8577-8582.
-
(2006)
Proc Natl Acad Sci USA
, vol.103
, pp. 8577-8582
-
-
Newman, M.E.J.1
|