-
1
-
-
84863322344
-
Contextualizing context for synthetic biology - Identifying causes of failure of synthetic biological systems
-
S. Cardinale, and A.P. Arkin Contextualizing context for synthetic biology - Identifying causes of failure of synthetic biological systems Biotechnol. J. 7 2012 856 866
-
(2012)
Biotechnol. J.
, vol.7
, pp. 856-866
-
-
Cardinale, S.1
Arkin, A.P.2
-
2
-
-
84890217908
-
A wise consistency: Engineering biology for conformity, reliability, predictability
-
A.P. Arkin A wise consistency: Engineering biology for conformity, reliability, predictability Curr. Opin. Chem. Biol. 17 2013 893 901
-
(2013)
Curr. Opin. Chem. Biol.
, vol.17
, pp. 893-901
-
-
Arkin, A.P.1
-
4
-
-
70349797209
-
Chemotaxis: How bacteria use memory
-
N. Vladimirov, and V. Sourjik Chemotaxis: How bacteria use memory Biol. Chem. 390 2009 1097 1104
-
(2009)
Biol. Chem.
, vol.390
, pp. 1097-1104
-
-
Vladimirov, N.1
Sourjik, V.2
-
5
-
-
84870337135
-
Synergistic dual positive feedback loops established by molecular sequestration generate robust bimodal response
-
O.S. Venturelli, H. El-Samad, and R.M. Murray Synergistic dual positive feedback loops established by molecular sequestration generate robust bimodal response Proc. Natl. Acad. Sci. 2012 10.1073/pnas.1211902109
-
(2012)
Proc. Natl. Acad. Sci.
-
-
Venturelli, O.S.1
El-Samad, H.2
Murray, R.M.3
-
6
-
-
33845257870
-
Variability and memory of protein levels in human cells
-
A. Sigal, R. Milo, A. Cohen, N. Geva-Zatorsky, Y. Klein, Y. Liron, and et al. Variability and memory of protein levels in human cells Nature 444 2006 643 646
-
(2006)
Nature
, vol.444
, pp. 643-646
-
-
Sigal, A.1
Milo, R.2
Cohen, A.3
Geva-Zatorsky, N.4
Klein, Y.5
Liron, Y.6
-
7
-
-
23144432213
-
Optimality and evolutionary tuning of the expression level of a protein
-
E. Dekel, and U. Alon Optimality and evolutionary tuning of the expression level of a protein Nature 436 2005 588 592
-
(2005)
Nature
, vol.436
, pp. 588-592
-
-
Dekel, E.1
Alon, U.2
-
8
-
-
77955023666
-
BiP binding to the ER-stress sensor Ire1 tunes the homeostatic behavior of the unfolded protein response
-
D. Pincus, M.W. Chevalier, T. Aragon, E. van Anken, S.E. Vidal, H. El-Samad, and et al. BiP binding to the ER-stress sensor Ire1 tunes the homeostatic behavior of the unfolded protein response PLoS Biol. 8 2010 e1000415
-
(2010)
PLoS Biol.
, vol.8
-
-
Pincus, D.1
Chevalier, M.W.2
Aragon, T.3
Van Anken, E.4
Vidal, S.E.5
El-Samad, H.6
-
10
-
-
0031879114
-
Stochastic kinetic analysis of developmental pathway bifurcation in phage lambda-infected Escherichia coli cells
-
A. Arkin, J. Ross, and H.H. McAdams Stochastic kinetic analysis of developmental pathway bifurcation in phage lambda-infected Escherichia coli cells Genetics 149 1998 1633 1648
-
(1998)
Genetics
, vol.149
, pp. 1633-1648
-
-
Arkin, A.1
Ross, J.2
McAdams, H.H.3
-
11
-
-
84922231672
-
Population diversification in a yeast metabolic program promotes anticipation of environmental shifts
-
O.S. Venturelli, I. Zuleta, R.M. Murray, and H. El-Samad Population diversification in a yeast metabolic program promotes anticipation of environmental shifts PLoS Biol. 109 2015 E3324 E3333
-
(2015)
PLoS Biol.
, vol.109
, pp. E3324-E3333
-
-
Venturelli, O.S.1
Zuleta, I.2
Murray, R.M.3
El-Samad, H.4
-
12
-
-
0032080769
-
Differential temperature modulation by H-NS of the fimB and fimE recombinase genes which control the orientation of the type 1 fimbrial phase switch
-
P.B. Olsen, M. a Schembri, D.L. Gally, and P. Klemm Differential temperature modulation by H-NS of the fimB and fimE recombinase genes which control the orientation of the type 1 fimbrial phase switch FEMS Microbiol. Lett. 162 1998 17 23
-
(1998)
FEMS Microbiol. Lett.
, vol.162
, pp. 17-23
-
-
Olsen, P.B.1
Schembri, M.A.2
Gally, D.L.3
Klemm, P.4
-
13
-
-
23844557132
-
Phenotypic switching in Candida glabrata accompanied by changes in expression of genes with deduced functions in copper detoxification and stress
-
T. Srikantha, R. Zhao, K. Daniels, J. Radke, and D.R. Soll Phenotypic switching in Candida glabrata accompanied by changes in expression of genes with deduced functions in copper detoxification and stress Eukaryot. Cell 4 2005 1434 1445
-
(2005)
Eukaryot. Cell
, vol.4
, pp. 1434-1445
-
-
Srikantha, T.1
Zhao, R.2
Daniels, K.3
Radke, J.4
Soll, D.R.5
-
14
-
-
57649130757
-
Negative feedback that improves information transmission in yeast signalling
-
R.C. Yu, C.G. Pesce, A. Colman-Lerner, L. Lok, D. Pincus, E. Serra, and et al. Negative feedback that improves information transmission in yeast signalling Nature 456 2008 755 761
-
(2008)
Nature
, vol.456
, pp. 755-761
-
-
Yu, R.C.1
Pesce, C.G.2
Colman-Lerner, A.3
Lok, L.4
Pincus, D.5
Serra, E.6
-
15
-
-
84889582936
-
Msn2 coordinates a stoichiometric gene expression program
-
J. Stewart-Ornstein, C. Nelson, J. Derisi, J.S. Weissman, and H. El-Samad Msn2 coordinates a stoichiometric gene expression program Curr. Biol. 23 2013 2336 2345
-
(2013)
Curr. Biol.
, vol.23
, pp. 2336-2345
-
-
Stewart-Ornstein, J.1
Nelson, C.2
Derisi, J.3
Weissman, J.S.4
El-Samad, H.5
-
16
-
-
56949098506
-
Molecular titration and ultrasensitivity in regulatory networks
-
N.E. Buchler, and M. Louis Molecular titration and ultrasensitivity in regulatory networks J. Mol. Biol. 384 2008 1106 1119
-
(2008)
J. Mol. Biol.
, vol.384
, pp. 1106-1119
-
-
Buchler, N.E.1
Louis, M.2
-
17
-
-
45549085296
-
Predictive behavior within microbial genetic networks
-
I. Tagkopoulos, Y.-C. Liu, and S. Tavazoie Predictive behavior within microbial genetic networks Science 320 2008 1313 1317
-
(2008)
Science
, vol.320
, pp. 1313-1317
-
-
Tagkopoulos, I.1
Liu, Y.-C.2
Tavazoie, S.3
-
18
-
-
34848928442
-
Genes induced late in infection increase fitness of Vibrio cholerae after release into the environment
-
S. Schild, R. Tamayo, E.J. Nelson, F. Qadri, S.B. Calderwood, and A. Camilli Genes induced late in infection increase fitness of Vibrio cholerae after release into the environment Cell Host Microbe 2 2007 264 277
-
(2007)
Cell Host Microbe
, vol.2
, pp. 264-277
-
-
Schild, S.1
Tamayo, R.2
Nelson, E.J.3
Qadri, F.4
Calderwood, S.B.5
Camilli, A.6
-
19
-
-
67650376275
-
Adaptive prediction of environmental changes by microorganisms
-
A. Mitchell, G.H. Romano, B. Groisman, A. Yona, E. Dekel, M. Kupiec, and et al. Adaptive prediction of environmental changes by microorganisms Nature 460 2009 220 224
-
(2009)
Nature
, vol.460
, pp. 220-224
-
-
Mitchell, A.1
Romano, G.H.2
Groisman, B.3
Yona, A.4
Dekel, E.5
Kupiec, M.6
-
20
-
-
84873599343
-
Yeast adapts to a changing stressful environment by evolving cross-protection and anticipatory gene regulation
-
R. Dhar, R. Sägesser, C. Weikert, and A. Wagner Yeast adapts to a changing stressful environment by evolving cross-protection and anticipatory gene regulation Mol. Biol. Evol. 30 2013 573 588
-
(2013)
Mol. Biol. Evol.
, vol.30
, pp. 573-588
-
-
Dhar, R.1
Sägesser, R.2
Weikert, C.3
Wagner, A.4
-
21
-
-
84902769481
-
Programming a Pavlovian-like conditioning circuit in Escherichia coli
-
H. Zhang, M. Lin, H. Shi, W. Ji, L. Huang, X. Zhang, and et al. Programming a Pavlovian-like conditioning circuit in Escherichia coli Nat. Commun. 5 2014 3102
-
(2014)
Nat. Commun.
, vol.5
, pp. 3102
-
-
Zhang, H.1
Lin, M.2
Shi, H.3
Ji, W.4
Huang, L.5
Zhang, X.6
-
22
-
-
66749179869
-
The importance of being persistent: Heterogeneity of bacterial populations under antibiotic stress
-
O. Gefen, and N.Q. Balaban The importance of being persistent: Heterogeneity of bacterial populations under antibiotic stress FEMS Microbiol. Rev. 33 2009 704 717
-
(2009)
FEMS Microbiol. Rev.
, vol.33
, pp. 704-717
-
-
Gefen, O.1
Balaban, N.Q.2
-
23
-
-
76349122940
-
Linking environmental heterogeneity and reproductive success at single-cell resolution
-
M.N.P. Remus-Emsermann, and J.H.J. Leveau Linking environmental heterogeneity and reproductive success at single-cell resolution ISME J. 4 2010 215 222
-
(2010)
ISME J.
, vol.4
, pp. 215-222
-
-
Remus-Emsermann, M.N.P.1
Leveau, J.H.J.2
-
24
-
-
18844368812
-
Bacterial persistence: A model of survival in changing environments
-
E. Kussell, R. Kishony, N.Q. Balaban, and S. Leibler Bacterial persistence: A model of survival in changing environments Genetics 169 2005 1807 1814
-
(2005)
Genetics
, vol.169
, pp. 1807-1814
-
-
Kussell, E.1
Kishony, R.2
Balaban, N.Q.3
Leibler, S.4
-
25
-
-
14744282987
-
Diversity in times of adversity: Probabilistic strategies in microbial survival games
-
D.M. Wolf, V.V. Vazirani, and A.P. Arkin Diversity in times of adversity: Probabilistic strategies in microbial survival games J. Theor. Biol. 234 2005 227 253
-
(2005)
J. Theor. Biol.
, vol.234
, pp. 227-253
-
-
Wolf, D.M.1
Vazirani, V.V.2
Arkin, A.P.3
-
26
-
-
4644343922
-
Bacterial persistence as a phenotypic switch
-
N.Q. Balaban, J. Merrin, R. Chait, L. Kowalik, and S. Leibler Bacterial persistence as a phenotypic switch Science 305 2004 1622 1625
-
(2004)
Science
, vol.305
, pp. 1622-1625
-
-
Balaban, N.Q.1
Merrin, J.2
Chait, R.3
Kowalik, L.4
Leibler, S.5
-
27
-
-
25444489027
-
Phenotypic diversity, population growth, and information in fluctuating environments
-
E. Kussell, and S. Leibler Phenotypic diversity, population growth, and information in fluctuating environments Science 309 2005 2075 2078
-
(2005)
Science
, vol.309
, pp. 2075-2078
-
-
Kussell, E.1
Leibler, S.2
-
30
-
-
50049132233
-
Self-destructive cooperation mediated by phenotypic noise
-
M. Ackermann, B. Stecher, N.E. Freed, P. Songhet, W.-D. Hardt, and M. Doebeli Self-destructive cooperation mediated by phenotypic noise Nature 454 2008 987 990
-
(2008)
Nature
, vol.454
, pp. 987-990
-
-
Ackermann, M.1
Stecher, B.2
Freed, N.E.3
Songhet, P.4
Hardt, W.-D.5
Doebeli, M.6
-
31
-
-
70349234324
-
Cell death in Streptococcus mutans biofilms: A link between CSP and extracellular DNA
-
J.A. Perry, D.G. Cvitkovitch, and C.M. Lévesque Cell death in Streptococcus mutans biofilms: A link between CSP and extracellular DNA FEMS Microbiol. Lett. 299 2009 261 266
-
(2009)
FEMS Microbiol. Lett.
, vol.299
, pp. 261-266
-
-
Perry, J.A.1
Cvitkovitch, D.G.2
Lévesque, C.M.3
-
32
-
-
84869234725
-
Localized cell death focuses mechanical forces during 3D patterning in a biofilm
-
M. Asally, M. Kittisopikul, P. Rué, Y. Du, Z. Hu, T. Çaʇatay, and et al. Localized cell death focuses mechanical forces during 3D patterning in a biofilm Proc. Natl. Acad. Sci. USA 109 2012 18891 18896
-
(2012)
Proc. Natl. Acad. Sci. USA
, vol.109
, pp. 18891-18896
-
-
Asally, M.1
Kittisopikul, M.2
Rué, P.3
Du, Y.4
Hu, Z.5
Çaʇatay, T.6
-
33
-
-
0029661332
-
Complex adaptations and the evolution of evolvability
-
G.P. Wagner, and L. Altenberg Complex adaptations and the evolution of evolvability Evolution 50 1996 967 976
-
(1996)
Evolution
, vol.50
, pp. 967-976
-
-
Wagner, G.P.1
Altenberg, L.2
-
34
-
-
84905492667
-
Massive diversification in aging colonies of Escherichia coli
-
C. Saint-Ruf, M. Garfa-Traoré, V. Collin, C. Cordier, C. Franceschi, and I. Matic Massive diversification in aging colonies of Escherichia coli J. Bacteriol. 196 2014 3059 3073
-
(2014)
J. Bacteriol.
, vol.196
, pp. 3059-3073
-
-
Saint-Ruf, C.1
Garfa-Traoré, M.2
Collin, V.3
Cordier, C.4
Franceschi, C.5
Matic, I.6
-
35
-
-
0030620273
-
Evolution of high mutation rates in experimental populations of E. coli
-
P.D. Sniegowski, P.J. Gerrish, and R.E. Lenski Evolution of high mutation rates in experimental populations of E. coli Nature 387 1997 703 705
-
(1997)
Nature
, vol.387
, pp. 703-705
-
-
Sniegowski, P.D.1
Gerrish, P.J.2
Lenski, R.E.3
-
36
-
-
33845648557
-
Bacterial contingency loci: The role of simple sequence DNA repeats in bacterial adaptation
-
R. Moxon, C.D. Bayliss, and D. Hood Bacterial contingency loci: The role of simple sequence DNA repeats in bacterial adaptation Annu. Rev. Genet. 40 2006 307 333
-
(2006)
Annu. Rev. Genet.
, vol.40
, pp. 307-333
-
-
Moxon, R.1
Bayliss, C.D.2
Hood, D.3
-
37
-
-
79551513941
-
Standing genetic variation in contingency loci drives the rapid adaptation of Campylobacter jejuni to a novel host
-
J.P. Jerome, J.A. Bell, A.E. Plovanich-Jones, J.E. Barrick, C.T. Brown, and L.S. Mansfield Standing genetic variation in contingency loci drives the rapid adaptation of Campylobacter jejuni to a novel host PLoS One 2011 10.1371/journal.pone.0016399
-
(2011)
PLoS One
-
-
Jerome, J.P.1
Bell, J.A.2
Plovanich-Jones, A.E.3
Barrick, J.E.4
Brown, C.T.5
Mansfield, L.S.6
-
38
-
-
84874633779
-
Broad conditions favor the evolution of phase-variable loci
-
M.E. Palmer, M. Lipsitch, E.R. Moxon, and C.D. Bayliss Broad conditions favor the evolution of phase-variable loci MBio 4 2013 e00430-12
-
(2013)
MBio
, vol.4
, pp. e00430-e00512
-
-
Palmer, M.E.1
Lipsitch, M.2
Moxon, E.R.3
Bayliss, C.D.4
-
39
-
-
0345687900
-
Slipped-strand mispairing can function as a phase variation mechanism in Escherichia coli
-
J. Torres-Cruz, and M.W. van der Woude Slipped-strand mispairing can function as a phase variation mechanism in Escherichia coli J. Bacteriol. 185 2003 6990 6994
-
(2003)
J. Bacteriol.
, vol.185
, pp. 6990-6994
-
-
Torres-Cruz, J.1
Van Der Woude, M.W.2
-
40
-
-
66349113764
-
Unstable tandem repeats in promoters confer transcriptional evolvability
-
M.D. Vinces, M. Legendre, M. Caldara, M. Hagihara, and K.J. Verstrepen Unstable tandem repeats in promoters confer transcriptional evolvability Science 324 2009 1213 1216
-
(2009)
Science
, vol.324
, pp. 1213-1216
-
-
Vinces, M.D.1
Legendre, M.2
Caldara, M.3
Hagihara, M.4
Verstrepen, K.J.5
-
41
-
-
84859323535
-
Evolutionary pressures on simple sequence repeats in prokaryotic coding regions
-
W.-H. Lin, and E. Kussell Evolutionary pressures on simple sequence repeats in prokaryotic coding regions Nucleic Acids Res. 40 2012 2399 2413
-
(2012)
Nucleic Acids Res.
, vol.40
, pp. 2399-2413
-
-
Lin, W.-H.1
Kussell, E.2
-
42
-
-
84867631962
-
Fine-tuning gene networks using simple sequence repeats
-
R.G. Egbert, and E. Klavins Fine-tuning gene networks using simple sequence repeats Proc. Natl. Acad. Sci. USA 109 2012 16817 16822
-
(2012)
Proc. Natl. Acad. Sci. USA
, vol.109
, pp. 16817-16822
-
-
Egbert, R.G.1
Klavins, E.2
-
43
-
-
84886022252
-
Programming adaptive control to evolve increased metabolite production
-
H.H. Chou, and J.D. Keasling Programming adaptive control to evolve increased metabolite production Nat. Commun. 4 2013 2595
-
(2013)
Nat. Commun.
, vol.4
, pp. 2595
-
-
Chou, H.H.1
Keasling, J.D.2
-
44
-
-
84877280637
-
Harnessing mutagenic homologous recombination for targeted mutagenesis in vivo by TaGTEAM
-
S.P. Finney-Manchester, and N. Maheshri Harnessing mutagenic homologous recombination for targeted mutagenesis in vivo by TaGTEAM Nucleic Acids Res. 41 2013 e99
-
(2013)
Nucleic Acids Res.
, vol.41
, pp. e99
-
-
Finney-Manchester, S.P.1
Maheshri, N.2
-
45
-
-
84894055645
-
An orthogonal DNA replication system in yeast
-
A. Ravikumar, A. Arrieta, and C.C. Liu An orthogonal DNA replication system in yeast Nat. Chem. Biol. 10 2014 175 177
-
(2014)
Nat. Chem. Biol.
, vol.10
, pp. 175-177
-
-
Ravikumar, A.1
Arrieta, A.2
Liu, C.C.3
-
46
-
-
84918571678
-
Accurate information transmission through dynamic biochemical signaling networks
-
J. Selimkhanov, B. Taylor, J. Yao, A. Pilko, J. Albeck, A. Hoffmann, and et al. Accurate information transmission through dynamic biochemical signaling networks Science 346 2014 1370 1373
-
(2014)
Science
, vol.346
, pp. 1370-1373
-
-
Selimkhanov, J.1
Taylor, B.2
Yao, J.3
Pilko, A.4
Albeck, J.5
Hoffmann, A.6
-
47
-
-
84910594404
-
Genomically encoded analog memory with precise in vivo DNA writing in living cell populations
-
F. Farzadfard, and T.K. Lu Genomically encoded analog memory with precise in vivo DNA writing in living cell populations Science 2014 10.1126/science.1256272
-
(2014)
Science
-
-
Farzadfard, F.1
Lu, T.K.2
-
48
-
-
83255165732
-
In silico feedback for in vivo regulation of a gene expression circuit
-
A. Milias-Argeitis, S. Summers, J. Stewart-Ornstein, I. Zuleta, D. Pincus, H. El-Samad, and et al. In silico feedback for in vivo regulation of a gene expression circuit Nat. Biotechnol. 29 2011 1114 1116
-
(2011)
Nat. Biotechnol.
, vol.29
, pp. 1114-1116
-
-
Milias-Argeitis, A.1
Summers, S.2
Stewart-Ornstein, J.3
Zuleta, I.4
Pincus, D.5
El-Samad, H.6
-
49
-
-
84876566095
-
Indirect and suboptimal control of gene expression is widespread in bacteria
-
M.N. Price, A.M. Deutschbauer, J.M. Skerker, K.M. Wetmore, T. Ruths, J.S. Mar, and et al. Indirect and suboptimal control of gene expression is widespread in bacteria Mol. Syst. Biol. 9 2013 660
-
(2013)
Mol. Syst. Biol.
, vol.9
, pp. 660
-
-
Price, M.N.1
Deutschbauer, A.M.2
Skerker, J.M.3
Wetmore, K.M.4
Ruths, T.5
Mar, J.S.6
-
50
-
-
84861663597
-
Evolutionary trade-offs, Pareto optimality, and the geometry of phenotype space
-
O. Shoval, H. Sheftel, G. Shinar, Y. Hart, O. Ramote, A. Mayo, and et al. Evolutionary trade-offs, Pareto optimality, and the geometry of phenotype space Science 336 2012 1157 1160
-
(2012)
Science
, vol.336
, pp. 1157-1160
-
-
Shoval, O.1
Sheftel, H.2
Shinar, G.3
Hart, Y.4
Ramote, O.5
Mayo, A.6
-
51
-
-
49249112719
-
The shape of an ecological trade-off varies with environment
-
C.M. Jessup, and B.J.M. Bohannan The shape of an ecological trade-off varies with environment Ecol. Lett. 11 2008 947 959
-
(2008)
Ecol. Lett.
, vol.11
, pp. 947-959
-
-
Jessup, C.M.1
Bohannan, B.J.M.2
-
52
-
-
84884669749
-
A design-constraint trade-off underpins the diversity in ecologically important traits in species Escherichia coli
-
K. Phan, and T. Ferenci A design-constraint trade-off underpins the diversity in ecologically important traits in species Escherichia coli ISME J. 7 2013 2034 2043
-
(2013)
ISME J.
, vol.7
, pp. 2034-2043
-
-
Phan, K.1
Ferenci, T.2
-
53
-
-
79955806186
-
Engineering microbial biofuel tolerance and export using efflux pumps
-
M.J. Dunlop, Z.Y. Dossani, H.L. Szmidt, H.C. Chu, T.S. Lee, J.D. Keasling, and et al. Engineering microbial biofuel tolerance and export using efflux pumps Mol. Syst. Biol. 7 2011 487
-
(2011)
Mol. Syst. Biol.
, vol.7
, pp. 487
-
-
Dunlop, M.J.1
Dossani, Z.Y.2
Szmidt, H.L.3
Chu, H.C.4
Lee, T.S.5
Keasling, J.D.6
-
54
-
-
84875857527
-
Synthetic feedback loop model for increasing microbial biofuel production using a biosensor
-
M.E. Harrison, and M.J. Dunlop Synthetic feedback loop model for increasing microbial biofuel production using a biosensor Front. Microbiol. 3 2012 1 9
-
(2012)
Front. Microbiol.
, vol.3
, pp. 1-9
-
-
Harrison, M.E.1
Dunlop, M.J.2
-
55
-
-
33847309176
-
Balancing a heterologous mevalonate pathway for improved isoprenoid production in Escherichia coli
-
D.J. Pitera, C.J. Paddon, J.D. Newman, and J.D. Keasling Balancing a heterologous mevalonate pathway for improved isoprenoid production in Escherichia coli Metab. Eng. 9 2007 193 207
-
(2007)
Metab. Eng.
, vol.9
, pp. 193-207
-
-
Pitera, D.J.1
Paddon, C.J.2
Newman, J.D.3
Keasling, J.D.4
-
57
-
-
84869102255
-
A dynamic metabolite valve for the control of central carbon metabolism
-
K.V. Solomon, T.M. Sanders, and K.L.J. Prather A dynamic metabolite valve for the control of central carbon metabolism Metab. Eng. 14 2012 661 671
-
(2012)
Metab. Eng.
, vol.14
, pp. 661-671
-
-
Solomon, K.V.1
Sanders, T.M.2
Prather, K.L.J.3
-
58
-
-
84899628032
-
Metabolic flux redirection from a central metabolic pathway toward a synthetic pathway using a metabolic toggle switch
-
Y. Soma, K. Tsuruno, M. Wada, A. Yokota, and T. Hanai Metabolic flux redirection from a central metabolic pathway toward a synthetic pathway using a metabolic toggle switch Metab. Eng. 23 2014 175 184
-
(2014)
Metab. Eng.
, vol.23
, pp. 175-184
-
-
Soma, Y.1
Tsuruno, K.2
Wada, M.3
Yokota, A.4
Hanai, T.5
-
59
-
-
84887422015
-
Engineering dynamic pathway regulation using stress-response promoters
-
R.H. Dahl, F. Zhang, J. Alonso-Gutierrez, E. Baidoo, T.S. Batth, A.M. Redding-Johanson, and et al. Engineering dynamic pathway regulation using stress-response promoters Nat. Biotechnol. 31 2013 1039 1046
-
(2013)
Nat. Biotechnol.
, vol.31
, pp. 1039-1046
-
-
Dahl, R.H.1
Zhang, F.2
Alonso-Gutierrez, J.3
Baidoo, E.4
Batth, T.S.5
Redding-Johanson, A.M.6
-
60
-
-
13444302680
-
Promoters in the environment: Transcriptional regulation in its natural context
-
I. Cases, and V. de Lorenzo Promoters in the environment: Transcriptional regulation in its natural context Nat. Rev. Microbiol. 3 2005 105 118
-
(2005)
Nat. Rev. Microbiol.
, vol.3
, pp. 105-118
-
-
Cases, I.1
De Lorenzo, V.2
-
61
-
-
84905668376
-
Improving fatty acids production by engineering dynamic pathway regulation and metabolic control
-
P. Xu, L. Li, F. Zhang, G. Stephanopoulos, and M. Koffas Improving fatty acids production by engineering dynamic pathway regulation and metabolic control Proc. Natl. Acad. Sci. USA 111 2014 1 6
-
(2014)
Proc. Natl. Acad. Sci. USA
, vol.111
, pp. 1-6
-
-
Xu, P.1
Li, L.2
Zhang, F.3
Stephanopoulos, G.4
Koffas, M.5
-
62
-
-
84941242926
-
Synthetic biosensors for precise gene control and real-time monitoring of metabolites
-
J.K. Rogers, C.D. Guzman, N.D. Taylor, S. Raman, K. Anderson, and G.M. Church Synthetic biosensors for precise gene control and real-time monitoring of metabolites Nucleic Acids Res. 2015 10.1093/nar/gkv616
-
(2015)
Nucleic Acids Res.
-
-
Rogers, J.K.1
Guzman, C.D.2
Taylor, N.D.3
Raman, S.4
Anderson, K.5
Church, G.M.6
-
63
-
-
84920992414
-
Engineering complex synthetic transcriptional programs with CRISPR RNA scaffolds
-
J.G. Zalatan, M.E. Lee, R. Almeida, L.a. Gilbert, E.H. Whitehead, and M. La Russa Engineering complex synthetic transcriptional programs with CRISPR RNA scaffolds Cell 160 2014 339 350
-
(2014)
Cell
, vol.160
, pp. 339-350
-
-
Zalatan, J.G.1
Lee, M.E.2
Almeida, R.3
Gilbert, L.A.4
Whitehead, E.H.5
La Russa, M.6
-
64
-
-
0000640710
-
Modulation of chemical composition and other parameters of the cell by growth rate
-
ASM Press Washington DC
-
H. Bremer, and P. Dennis Modulation of chemical composition and other parameters of the cell by growth rate Escherichia coli and Salmonella typhimurium 1996 ASM Press Washington DC
-
(1996)
Escherichia Coli and Salmonella Typhimurium
-
-
Bremer, H.1
Dennis, P.2
-
65
-
-
84880772006
-
Effects of genetic variation on the E. coli host-circuit interface
-
S. Cardinale, M.P. Joachimiak, and A.P. Arkin Effects of genetic variation on the E. coli host-circuit interface Cell Rep. 4 2013 231 237
-
(2013)
Cell Rep.
, vol.4
, pp. 231-237
-
-
Cardinale, S.1
Joachimiak, M.P.2
Arkin, A.P.3
-
67
-
-
84930336873
-
Engineered ribosomal RNA operon copy-number variants of E. coli reveal the evolutionary trade-offs shaping rRNA operon number
-
Z. Gyorfy, G. Draskovits, V. Vernyik, F.F. Blattner, T. Gaal, and G. Posfai Engineered ribosomal RNA operon copy-number variants of E. coli reveal the evolutionary trade-offs shaping rRNA operon number Nucleic Acids Res. 43 2015 1783 1794
-
(2015)
Nucleic Acids Res.
, vol.43
, pp. 1783-1794
-
-
Gyorfy, Z.1
Draskovits, G.2
Vernyik, V.3
Blattner, F.F.4
Gaal, T.5
Posfai, G.6
-
68
-
-
84897463052
-
Modular composition of gene transcription networks
-
A. Gyorgy, and D. Del Vecchio Modular composition of gene transcription networks PLoS Comput. Biol. 2014 10.1371/journal.pcbi.1003486
-
(2014)
PLoS Comput. Biol.
-
-
Gyorgy, A.1
Del Vecchio, D.2
-
69
-
-
78650546051
-
RNA polymerase mutants found through adaptive evolution reprogram Escherichia coli for optimal growth in minimal media
-
T.M. Conrad, M. Frazier, A.R. Joyce, B.-K. Cho, E.M. Knight, N.E. Lewis, and et al. RNA polymerase mutants found through adaptive evolution reprogram Escherichia coli for optimal growth in minimal media Proc. Natl. Acad. Sci. USA 107 2010 20500 20505
-
(2010)
Proc. Natl. Acad. Sci. USA
, vol.107
, pp. 20500-20505
-
-
Conrad, T.M.1
Frazier, M.2
Joyce, A.R.3
Cho, B.-K.4
Knight, E.M.5
Lewis, N.E.6
-
70
-
-
84924370996
-
Mechanistic links between cellular trade-offs, gene expression, and growth
-
A.Y. Weiße, D.a. Oyarzún, V. Danos, and P.S. Swain Mechanistic links between cellular trade-offs, gene expression, and growth Proc. Natl. Acad. Sci. USA 2015 10.1073/pnas.1416533112
-
(2015)
Proc. Natl. Acad. Sci. USA
-
-
Weiße, A.Y.1
Oyarzún, D.A.2
Danos, V.3
Swain, P.S.4
-
71
-
-
84864258618
-
A whole-cell computational model predicts phenotype from genotype
-
J.R. Karr, J.C. Sanghvi, D.N. MacKlin, M.V. Gutschow, J.M. Jacobs, B. Bolival, and et al. A whole-cell computational model predicts phenotype from genotype Cell 150 2012 389 401
-
(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, B.6
-
72
-
-
8544232750
-
Growth versus maintenance: A trade-off dictated by RNA polymerase availability and sigma factor competition?
-
T. Nyström Growth versus maintenance: A trade-off dictated by RNA polymerase availability and sigma factor competition? Mol. Microbiol. 54 2004 855 862
-
(2004)
Mol. Microbiol.
, vol.54
, pp. 855-862
-
-
Nyström, T.1
-
73
-
-
84883792620
-
The form of a trade-off determines the response to competition
-
R. Maharjan, S. Nilsson, J. Sung, K. Haynes, R.E. Beardmore, L.D. Hurst, and et al. The form of a trade-off determines the response to competition Ecol. Lett. 16 2013 1267 1276
-
(2013)
Ecol. Lett.
, vol.16
, pp. 1267-1276
-
-
Maharjan, R.1
Nilsson, S.2
Sung, J.3
Haynes, K.4
Beardmore, R.E.5
Hurst, L.D.6
-
74
-
-
68249138705
-
Increased RNA polymerase availability directs resources towards growth at the expense of maintenance
-
B. Gummesson, L.U. Magnusson, M. Lovmar, K. Kvint, O. Persson, M. Ballesteros, and et al. Increased RNA polymerase availability directs resources towards growth at the expense of maintenance EMBO J. 28 2009 2209 2219
-
(2009)
EMBO J.
, vol.28
, pp. 2209-2219
-
-
Gummesson, B.1
Magnusson, L.U.2
Lovmar, M.3
Kvint, K.4
Persson, O.5
Ballesteros, M.6
-
75
-
-
84905376865
-
A resource allocator for transcription based on a highly fragmented T7 RNA polymerase
-
T.H. Segall-Shapiro, A.J. Meyer, A.D. Ellington, E.D. Sontag, and C.a. Voigt A resource allocator for transcription based on a highly fragmented T7 RNA polymerase Mol. Syst. Biol. 10 2014 742
-
(2014)
Mol. Syst. Biol.
, vol.10
, pp. 742
-
-
Segall-Shapiro, T.H.1
Meyer, A.J.2
Ellington, A.D.3
Sontag, E.D.4
Voigt, C.A.5
-
76
-
-
84873877553
-
Shared control of gene expression in bacteria by transcription factors and global physiology of the cell
-
S. Berthoumieux, H. de Jong, G. Baptist, C. Pinel, C. Ranquet, D. Ropers, and et al. Shared control of gene expression in bacteria by transcription factors and global physiology of the cell Mol. Syst. Biol. 9 2013 634
-
(2013)
Mol. Syst. Biol.
, vol.9
, pp. 634
-
-
Berthoumieux, S.1
De Jong, H.2
Baptist, G.3
Pinel, C.4
Ranquet, C.5
Ropers, D.6
-
77
-
-
84928927536
-
Quantifying cellular capacity identifies gene expression designs with reduced burden
-
F. Ceroni, R. Algar, G.-B. Stan, and T. Ellis Quantifying cellular capacity identifies gene expression designs with reduced burden Nat. Methods 2015 10.1038/nmeth.3339
-
(2015)
Nat. Methods
-
-
Ceroni, F.1
Algar, R.2
Stan, G.-B.3
Ellis, T.4
-
78
-
-
80052456127
-
Multi-input RNAi-based logic circuit for identification of specific cancer cells
-
A. Bird, J. Gurdon, T. Chen, J.K. Zhu, G. Lukinavicius, V. Masevicius, and et al. Multi-input RNAi-based logic circuit for identification of specific cancer cells Science 333 2011 1307 1312
-
(2011)
Science
, vol.333
, pp. 1307-1312
-
-
Bird, A.1
Gurdon, J.2
Chen, T.3
Zhu, J.K.4
Lukinavicius, G.5
Masevicius, V.6
-
79
-
-
34547916832
-
Environmental signal integration by a modular and gate
-
J.C. Anderson, C. a Voigt, and A.P. Arkin Environmental signal integration by a modular AND gate Mol. Syst. Biol. 3 2007 133
-
(2007)
Mol. Syst. Biol.
, vol.3
, pp. 133
-
-
Anderson, J.C.1
Voigt, C.A.2
Arkin, A.P.3
-
80
-
-
84868619337
-
Genetic programs constructed from layered logic gates in single cells
-
T.S. Moon, C. Lou, A. Tamsir, B.C. Stanton, and C.a. Voigt Genetic programs constructed from layered logic gates in single cells Nature 491 2012 249 253
-
(2012)
Nature
, vol.491
, pp. 249-253
-
-
Moon, T.S.1
Lou, C.2
Tamsir, A.3
Stanton, B.C.4
Voigt, C.A.5
-
81
-
-
84889685663
-
The centrality of RNA for engineering gene expression
-
J. Chappell, M.K. Takahashi, S. Meyer, D. Loughrey, K.E. Watters, and J. Lucks The centrality of RNA for engineering gene expression Biotechnol. J. 8 2013 1379 1395
-
(2013)
Biotechnol. J.
, vol.8
, pp. 1379-1395
-
-
Chappell, J.1
Takahashi, M.K.2
Meyer, S.3
Loughrey, D.4
Watters, K.E.5
Lucks, J.6
-
82
-
-
84934985382
-
A renaissance in RNA synthetic biology: New mechanisms, applications and tools for the future
-
J. Chappell, K.E. Watters, M.K. Takahashi, and J.B. Lucks A renaissance in RNA synthetic biology: New mechanisms, applications and tools for the future Curr. Opin. Chem. Biol. 28 2015 47 56
-
(2015)
Curr. Opin. Chem. Biol.
, vol.28
, pp. 47-56
-
-
Chappell, J.1
Watters, K.E.2
Takahashi, M.K.3
Lucks, J.B.4
-
85
-
-
42149139936
-
Transient heterogeneity in extracellular protease production by Bacillus subtilis
-
J.-W. Veening, O. a Igoshin, R.T. Eijlander, R. Nijland, L.W. Hamoen, and O.P. Kuipers Transient heterogeneity in extracellular protease production by Bacillus subtilis Mol. Syst. Biol. 4 2008 184
-
(2008)
Mol. Syst. Biol.
, vol.4
, pp. 184
-
-
Veening, J.-W.1
Igoshin, O.A.2
Eijlander, R.T.3
Nijland, R.4
Hamoen, L.W.5
Kuipers, O.P.6
-
86
-
-
2142854105
-
Single-copy green fluorescent protein gene fusions allow accurate measurement of Salmonella gene expression in vitro and during infection of mammalian cells
-
I. Hautefort, I. Hautefort, M.J. Proenca, M. Jose, and J.C.D. Hinton Single-copy green fluorescent protein gene fusions allow accurate measurement of Salmonella gene expression in vitro and during infection of mammalian cells Appl. Environ. Microbiol. 69 2003 7480 7491
-
(2003)
Appl. Environ. Microbiol.
, vol.69
, pp. 7480-7491
-
-
Hautefort, I.1
Hautefort, I.2
Proenca, M.J.3
Jose, M.4
Hinton, J.C.D.5
-
87
-
-
84878703583
-
Measuring carbon and N2 fixation in field populations of colonial and free-living unicellular cyanobacteria using nanometer-scale secondary ion mass spectrometry
-
R.A. Foster, S. Sztejrenszus, and M.M. Kuypers Measuring carbon and N2 fixation in field populations of colonial and free-living unicellular cyanobacteria using nanometer-scale secondary ion mass spectrometry J. Physiol. 49 2013 502 516
-
(2013)
J. Physiol.
, vol.49
, pp. 502-516
-
-
Foster, R.A.1
Sztejrenszus, S.2
Kuypers, M.M.3
-
88
-
-
84883326386
-
Design and characterization of synthetic fungal-bacterial consortia for direct production of isobutanol from cellulosic biomass
-
J.J. Minty, M.E. Singer, S. a Scholz, C.-H. Bae, J.-H. Ahn, C.E. Foster, and et al. Design and characterization of synthetic fungal-bacterial consortia for direct production of isobutanol from cellulosic biomass Proc. Natl. Acad. Sci. USA 110 2013 14592 14597
-
(2013)
Proc. Natl. Acad. Sci. USA
, vol.110
, pp. 14592-14597
-
-
Minty, J.J.1
Singer, M.E.2
Scholz, S.A.3
Bae, C.-H.4
Ahn, J.-H.5
Foster, C.E.6
-
89
-
-
70149113922
-
Synthesis of methyl halides from biomass using engineered microbes
-
T.S. Bayer, D.M. Widmaier, K. Temme, E.A. Mirsky, D.V. Santi, and C.A. Voigt Synthesis of methyl halides from biomass using engineered microbes J. Am. Chem. Soc. 131 2009 6508 6515
-
(2009)
J. Am. Chem. Soc.
, vol.131
, pp. 6508-6515
-
-
Bayer, T.S.1
Widmaier, D.M.2
Temme, K.3
Mirsky, E.A.4
Santi, D.V.5
Voigt, C.A.6
-
90
-
-
84926646130
-
Distributing a metabolic pathway among a microbial consortium enhances production of natural products
-
K. Zhou, K. Qiao, S. Edgar, and G. Stephanopoulos Distributing a metabolic pathway among a microbial consortium enhances production of natural products Nat. Biotechnol. 33 2015 377 383
-
(2015)
Nat. Biotechnol.
, vol.33
, pp. 377-383
-
-
Zhou, K.1
Qiao, K.2
Edgar, S.3
Stephanopoulos, G.4
-
91
-
-
84936803078
-
Engineering Escherichia coli coculture systems for the production of biochemical products
-
H. Zhang, B. Pereira, Z. Li, and G. Stephanopoulos Engineering Escherichia coli coculture systems for the production of biochemical products Proc. Natl. Acad. Sci. USA 112 2015 8266 8271
-
(2015)
Proc. Natl. Acad. Sci. USA
, vol.112
, pp. 8266-8271
-
-
Zhang, H.1
Pereira, B.2
Li, Z.3
Stephanopoulos, G.4
-
92
-
-
84897734212
-
Creating biological nanomaterials using synthetic biology
-
M.K. Rice, and W.C. Ruder Creating biological nanomaterials using synthetic biology Sci. Technol. Adv. Mater. 15 2014 014401
-
(2014)
Sci. Technol. Adv. Mater.
, vol.15
, pp. 014401
-
-
Rice, M.K.1
Ruder, W.C.2
-
93
-
-
17844374314
-
A synthetic multicellular system for programmed pattern formation
-
S. Basu, Y. Gerchman, and C.H. Collins A synthetic multicellular system for programmed pattern formation Nature 434 2005 1130 1134
-
(2005)
Nature
, vol.434
, pp. 1130-1134
-
-
Basu, S.1
Gerchman, Y.2
Collins, C.H.3
-
94
-
-
78651397316
-
Robust multicellular computing using genetically encoded NOR gates and chemical "wires"
-
A. Tamsir, J.J. Tabor, and C. a Voigt Robust multicellular computing using genetically encoded NOR gates and chemical "wires" Nature 469 2011 212 215
-
(2011)
Nature
, vol.469
, pp. 212-215
-
-
Tamsir, A.1
Tabor, J.J.2
Voigt, C.A.3
-
95
-
-
84875883112
-
Fundamentals of microbial community resistance and resilience
-
A. Shade, H. Peter, S.D. Allison, D.L. Baho, M. Berga, H. Bürgmann, and et al. Fundamentals of microbial community resistance and resilience Front. Microbiol. 3 2012 1 19
-
(2012)
Front. Microbiol.
, vol.3
, pp. 1-19
-
-
Shade, A.1
Peter, H.2
Allison, S.D.3
Baho, D.L.4
Berga, M.5
Bürgmann, H.6
-
96
-
-
0030871461
-
Energetics of syntrophic cooperation in methanogenic degradation
-
B. Schink Energetics of syntrophic cooperation in methanogenic degradation Microbiol. Mol. Biol. Rev. 61 1997 262 280
-
(1997)
Microbiol. Mol. Biol. Rev.
, vol.61
, pp. 262-280
-
-
Schink, B.1
-
97
-
-
0036419049
-
Effects of resource supplies on the structure and function of microbial communities.
-
V.H. Smith Effects of resource supplies on the structure and function of microbial communities. Anton. Leeuw. Int. J. Gen. Mol. Microbiol. 81 2002 99 106
-
(2002)
Anton. Leeuw. Int. J. Gen. Mol. Microbiol.
, vol.81
, pp. 99-106
-
-
Smith, V.H.1
-
98
-
-
84867405105
-
Competition, not cooperation, dominates interactions among culturable microbial species
-
K.R. Foster, and T. Bell Competition, not cooperation, dominates interactions among culturable microbial species Curr. Biol. 22 2012 1845 1850
-
(2012)
Curr. Biol.
, vol.22
, pp. 1845-1850
-
-
Foster, K.R.1
Bell, T.2
-
99
-
-
77956460746
-
Analysis of a thermophilic lignocellulose degrading microbial consortium and multi-species lignocellulolytic enzyme system
-
S. Wongwilaiwalin, U. Rattanachomsri, T. Laothanachareon, L. Eurwilaichitr, Y. Igarashi, and V. Champreda Analysis of a thermophilic lignocellulose degrading microbial consortium and multi-species lignocellulolytic enzyme system Enzym. Microb. Technol. 47 2010 283 290
-
(2010)
Enzym. Microb. Technol.
, vol.47
, pp. 283-290
-
-
Wongwilaiwalin, S.1
Rattanachomsri, U.2
Laothanachareon, T.3
Eurwilaichitr, L.4
Igarashi, Y.5
Champreda, V.6
-
100
-
-
51349112344
-
Network relationships of bacteria in a stable mixed culture
-
S. Kato, S. Haruta, Z.J. Cui, M. Ishii, and Y. Igarashi Network relationships of bacteria in a stable mixed culture Microb. Ecol. 56 2008 403 411
-
(2008)
Microb. Ecol.
, vol.56
, pp. 403-411
-
-
Kato, S.1
Haruta, S.2
Cui, Z.J.3
Ishii, M.4
Igarashi, Y.5
-
101
-
-
84937865855
-
Characterization of the facultative anaerobe Caldibacillus debilis GB1 and its use in a designed aerotolerant, cellulose degrading, co-culture with Clostridium thermocellum
-
S. Wushke, D. Levin, N. Cicek, and R. Sparling Characterization of the facultative anaerobe Caldibacillus debilis GB1 and its use in a designed aerotolerant, cellulose degrading, co-culture with Clostridium thermocellum Appl. Environ. Microbiol. 2015 10.1128/AEM.00735-15
-
(2015)
Appl. Environ. Microbiol.
-
-
Wushke, S.1
Levin, D.2
Cicek, N.3
Sparling, R.4
-
102
-
-
84860511582
-
The Black Queen Hypothesis: Evolution of dependencies through adaptive gene loss
-
J.J. Morris, R.E. Lenski, and E.R. Zinser The Black Queen Hypothesis: Evolution of dependencies through adaptive gene loss MBio 3 2012 1 7
-
(2012)
MBio
, vol.3
, pp. 1-7
-
-
Morris, J.J.1
Lenski, R.E.2
Zinser, E.R.3
-
103
-
-
84892708007
-
Ecological modeling from time-series inference: Insight into dynamics and stability of intestinal microbiota
-
R.R. Stein, V. Bucci, N.C. Toussaint, C.G. Buffie, G. Rätsch, E.G. Pamer, and et al. Ecological modeling from time-series inference: Insight into dynamics and stability of intestinal microbiota PLoS Comput. Biol. 2013 10.1371/journal.pcbi.1003388
-
(2013)
PLoS Comput. Biol.
-
-
Stein, R.R.1
Bucci, V.2
Toussaint, N.C.3
Buffie, C.G.4
Rätsch, G.5
Pamer, E.G.6
-
104
-
-
33947276100
-
Metabolic modeling of a mutualistic microbial community
-
S. Stolyar, S. Van Dien, K.L. Hillesland, N. Pinel, T.J. Lie, and J. a Leigh Metabolic modeling of a mutualistic microbial community Mol. Syst. Biol. 3 2007 92
-
(2007)
Mol. Syst. Biol.
, vol.3
, pp. 92
-
-
Stolyar, S.1
Van Dien, S.2
Hillesland, K.L.3
Pinel, N.4
Lie, T.J.5
Leigh, J.A.6
-
106
-
-
20744435030
-
Models of cooperation based on the Prisoner's Dilemma and the Snowdrift game
-
M. Doebeli, and C. Hauert Models of cooperation based on the Prisoner's Dilemma and the Snowdrift game Ecol. Lett. 8 2005 748 766
-
(2005)
Ecol. Lett.
, vol.8
, pp. 748-766
-
-
Doebeli, M.1
Hauert, C.2
-
107
-
-
71449096836
-
Strategies for cellular decision-making
-
T.J. Perkins, and P.S. Swain Strategies for cellular decision-making Mol. Syst. Biol. 5 2009 326
-
(2009)
Mol. Syst. Biol.
, vol.5
, pp. 326
-
-
Perkins, T.J.1
Swain, P.S.2
-
108
-
-
84925600482
-
Manipulation of the quorum sensing signal AI-2 affects the antibiotic-treated gut microbiota
-
J.A. Thompson, R.A. Oliveira, A. Djukovic, C. Ubeda, and K.B. Xavier Manipulation of the quorum sensing signal AI-2 affects the antibiotic-treated gut microbiota Cell Rep. 10 2015 1861 1871
-
(2015)
Cell Rep.
, vol.10
, pp. 1861-1871
-
-
Thompson, J.A.1
Oliveira, R.A.2
Djukovic, A.3
Ubeda, C.4
Xavier, K.B.5
-
109
-
-
84930153477
-
Programmable probiotics for detection of cancer in urine
-
T. Danino, A. Prindle, G.A. Kwong, M. Skalak, H. Li, and K. Allen Programmable probiotics for detection of cancer in urine Sci. Transl. Med. 7 2015 289ra84
-
(2015)
Sci. Transl. Med.
, vol.7
, pp. 289ra84
-
-
Danino, T.1
Prindle, A.2
Kwong, G.A.3
Skalak, M.4
Li, H.5
Allen, K.6
-
110
-
-
84893370250
-
Identifying gut microbe-host phenotype relationships using combinatorial communities in gnotobiotic mice
-
J.J. Faith, P.P. Ahern, V.K. Ridaura, J. Cheng, and J.I. Gordon Identifying gut microbe-host phenotype relationships using combinatorial communities in gnotobiotic mice Sci. Transl. Med. 6 2014 220ra11
-
(2014)
Sci. Transl. Med.
, vol.6
, pp. 220ra11
-
-
Faith, J.J.1
Ahern, P.P.2
Ridaura, V.K.3
Cheng, J.4
Gordon, J.I.5
-
111
-
-
79959855078
-
Predicting a human gut microbiota's response to diet in gnotobiotic mice
-
J.J. Faith, N.P. McNulty, F.E. Rey, and J.I. Gordon Predicting a human gut microbiota's response to diet in gnotobiotic mice Science 333 2011 101 104
-
(2011)
Science
, vol.333
, pp. 101-104
-
-
Faith, J.J.1
McNulty, N.P.2
Rey, F.E.3
Gordon, J.I.4
-
112
-
-
78649677586
-
Environments that induce synthetic microbial ecosystems
-
N. Klitgord, and D. Segre Environments that induce synthetic microbial ecosystems PLoS Comput. Biol. 6 2010 e1001002
-
(2010)
PLoS Comput. Biol.
, vol.6
-
-
Klitgord, N.1
Segre, D.2
-
113
-
-
84879744885
-
The long-term stability of the human gut microbiota
-
J.J. Faith, J.L. Guruge, M. Charbonneau, S. Subramanian, H. Seedorf, A.L. Goodman, and et al. The long-term stability of the human gut microbiota Science 2013 10.1126/science.1237439
-
(2013)
Science
-
-
Faith, J.J.1
Guruge, J.L.2
Charbonneau, M.3
Subramanian, S.4
Seedorf, H.5
Goodman, A.L.6
-
114
-
-
77956415336
-
Emergent cooperation in microbial metabolism
-
E.H. Wintermute, and P.a. Silver Emergent cooperation in microbial metabolism Mol. Syst. Biol. 6 2010 407
-
(2010)
Mol. Syst. Biol.
, vol.6
, pp. 407
-
-
Wintermute, E.H.1
Silver, P.A.2
-
116
-
-
33846936445
-
Synthetic cooperation in engineered yeast populations
-
W. Shou, S. Ram, and J.M.G. Vilar Synthetic cooperation in engineered yeast populations Proc. Natl. Acad. Sci. USA 104 2007 1877 1882
-
(2007)
Proc. Natl. Acad. Sci. USA
, vol.104
, pp. 1877-1882
-
-
Shou, W.1
Ram, S.2
Vilar, J.M.G.3
-
117
-
-
84899480571
-
Fitness and stability of obligate cross-feeding interactions that emerge upon gene loss in bacteria
-
S. Pande, H. Merker, K. Bohl, M. Reichelt, S. Schuster, L.F. de Figueiredo, and et al. Fitness and stability of obligate cross-feeding interactions that emerge upon gene loss in bacteria ISME J. 8 2014 953 962
-
(2014)
ISME J.
, vol.8
, pp. 953-962
-
-
Pande, S.1
Merker, H.2
Bohl, K.3
Reichelt, M.4
Schuster, S.5
De Figueiredo, L.F.6
-
118
-
-
0030427959
-
Tests of ecological mechanisms promoting the stable coexistence of two bacterial genotypes
-
E.P. Turner, V. Souza, and R.E. Lenski Tests of ecological mechanisms promoting the stable coexistence of two bacterial genotypes Ecology 1996 10.2307/2678832
-
(1996)
Ecology
-
-
Turner, E.P.1
Souza, V.2
Lenski, R.E.3
-
119
-
-
0343999422
-
Do "higher order interactions" in competition systems really exist?
-
Mark J. Pomerantz Do "higher order interactions" in competition systems really exist? Amer. Natur. 117 2015 583 591
-
(2015)
Amer. Natur.
, vol.117
, pp. 583-591
-
-
Pomerantz, M.J.1
-
121
-
-
57449090900
-
Defined spatial structure stabilizes a synthetic multispecies bacterial community
-
H.J. Kim, J.Q. Boedicker, J.W. Choi, and R.F. Ismagilov Defined spatial structure stabilizes a synthetic multispecies bacterial community Proc. Natl. Acad. Sci. USA 105 2008 18188 18193
-
(2008)
Proc. Natl. Acad. Sci. USA
, vol.105
, pp. 18188-18193
-
-
Kim, H.J.1
Boedicker, J.Q.2
Choi, J.W.3
Ismagilov, R.F.4
-
122
-
-
84925144072
-
Selection on soil microbiomes reveals reproducible impacts on plant function
-
K. Panke-buisse, A.C. Poole, J.K. Goodrich, R.E. Ley, and J. Kao-kniffin Selection on soil microbiomes reveals reproducible impacts on plant function ISME J. 9 2014 980 989
-
(2014)
ISME J.
, vol.9
, pp. 980-989
-
-
Panke-Buisse, K.1
Poole, A.C.2
Goodrich, J.K.3
Ley, R.E.4
Kao-Kniffin, J.5
-
123
-
-
84907342218
-
Clustering in community structure across replicate ecosystems following a long-term bacterial evolution experiment
-
H. Celiker, and J. Gore Clustering in community structure across replicate ecosystems following a long-term bacterial evolution experiment Nat. Commun. 5 2014 4643
-
(2014)
Nat. Commun.
, vol.5
, pp. 4643
-
-
Celiker, H.1
Gore, J.2
-
124
-
-
84861865655
-
Rewritable digital data storage in live cells via engineered control of recombination directionality
-
J. Bonnet, P. Subsoontorn, and D. Endy Rewritable digital data storage in live cells via engineered control of recombination directionality Proc. Natl. Acad. Sci. 109 2012 8884 8889
-
(2012)
Proc. Natl. Acad. Sci.
, vol.109
, pp. 8884-8889
-
-
Bonnet, J.1
Subsoontorn, P.2
Endy, D.3
-
125
-
-
84875230351
-
Synthetic circuits integrating logic and memory in living cells
-
P. Siuti, J. Yazbek, and T.K. Lu Synthetic circuits integrating logic and memory in living cells Nat. Biotechnol. 31 2013 448 452
-
(2013)
Nat. Biotechnol.
, vol.31
, pp. 448-452
-
-
Siuti, P.1
Yazbek, J.2
Lu, T.K.3
-
126
-
-
50949122967
-
Design and construction of a double inversion recombination switch for heritable sequential genetic memory
-
T.S. Ham, S.K. Lee, J.D. Keasling, and A.P. Arkin Design and construction of a double inversion recombination switch for heritable sequential genetic memory PLoS One 3 2008 1 9
-
(2008)
PLoS One
, vol.3
, pp. 1-9
-
-
Ham, T.S.1
Lee, S.K.2
Keasling, J.D.3
Arkin, A.P.4
-
127
-
-
0023650506
-
Shufflon: Multi-inversion of four contiguous DNA segments of plasmid R64 creates seven different open reading frames
-
T. Komano, A. Kubo, and T. Nisioka Shufflon: Multi-inversion of four contiguous DNA segments of plasmid R64 creates seven different open reading frames Nucleic Acids Res. 15 1987 1165 1172
-
(1987)
Nucleic Acids Res.
, vol.15
, pp. 1165-1172
-
-
Komano, T.1
Kubo, A.2
Nisioka, T.3
-
128
-
-
0025016820
-
Site-specific DNA recombination system Min of plasmid p15B: A cluster of overlapping invertible DNA segments
-
H. Sandmeier, S. Iida, J. Meyer, R. Hiestand-Nauer, and W. Arber Site-specific DNA recombination system Min of plasmid p15B: A cluster of overlapping invertible DNA segments Proc. Natl. Acad. Sci. USA 87 1990 1109 1113
-
(1990)
Proc. Natl. Acad. Sci. USA
, vol.87
, pp. 1109-1113
-
-
Sandmeier, H.1
Iida, S.2
Meyer, J.3
Hiestand-Nauer, R.4
Arber, W.5
-
129
-
-
0031028714
-
Nested DNA inversion as a paradigm of programmed gene rearrangement
-
J. Dworkin, and M.J. Blaser Nested DNA inversion as a paradigm of programmed gene rearrangement Proc. Natl. Acad. Sci. USA 94 1997 985 990
-
(1997)
Proc. Natl. Acad. Sci. USA
, vol.94
, pp. 985-990
-
-
Dworkin, J.1
Blaser, M.J.2
-
130
-
-
33646565046
-
A tightly regulated inducible expression system utilizing the fim inversion recombination switch
-
T.S. Ham, S.K. Lee, J.D. Keasling, and A.P. Arkin A tightly regulated inducible expression system utilizing the fim inversion recombination switch Biotechnol. Bioeng. 94 2006 1 4
-
(2006)
Biotechnol. Bioeng.
, vol.94
, pp. 1-4
-
-
Ham, T.S.1
Lee, S.K.2
Keasling, J.D.3
Arkin, A.P.4
-
131
-
-
79251595456
-
Construction of a genetic multiplexer to toggle between chemosensory pathways in Escherichia coli
-
T.S. Moon, E.J. Clarke, E.S. Groban, A. Tamsir, R.M. Clark, M. Eames, and et al. Construction of a genetic multiplexer to toggle between chemosensory pathways in Escherichia coli J. Mol. Biol. 406 2011 215 227
-
(2011)
J. Mol. Biol.
, vol.406
, pp. 215-227
-
-
Moon, T.S.1
Clarke, E.J.2
Groban, E.S.3
Tamsir, A.4
Clark, R.M.5
Eames, M.6
-
132
-
-
84925225805
-
Permanent genetic memory with > 1-byte capacity
-
L. Yang, A.A.K. Nielsen, J. Fernandez-Rodriguez, C.J. McClune, M.T. Laub, T.K. Lu, and et al. Permanent genetic memory with > 1-byte capacity Nat. Methods 11 2014 1261 1266
-
(2014)
Nat. Methods
, vol.11
, pp. 1261-1266
-
-
Yang, L.1
Nielsen, A.A.K.2
Fernandez-Rodriguez, J.3
McClune, C.J.4
Laub, M.T.5
Lu, T.K.6
-
133
-
-
84897482912
-
Programmable bacteria detect and record an environmental signal in the mammalian gut
-
J.W. Kotula, S.J. Kerns, L. a Shaket, L. Siraj, J.J. Collins, J.C. Way, and et al. Programmable bacteria detect and record an environmental signal in the mammalian gut Proc. Natl. Acad. Sci. USA 111 2014 4838 4843
-
(2014)
Proc. Natl. Acad. Sci. USA
, vol.111
, pp. 4838-4843
-
-
Kotula, J.W.1
Kerns, S.J.2
Shaket, L.A.3
Siraj, L.4
Collins, J.J.5
Way, J.C.6
-
134
-
-
84938323503
-
Programming a human commensal bacterium, Bacteroides thetaiotaomicron, to sense and respond to stimuli in the murine gut microbiota
-
M. Mimee, A.C. Tucker, C.A. Voigt, and T.K. Lu Programming a human commensal bacterium, Bacteroides thetaiotaomicron, to sense and respond to stimuli in the murine gut microbiota Cell Syst. 2015 10.1016/j.cels.2015.06.001
-
(2015)
Cell Syst.
-
-
Mimee, M.1
Tucker, A.C.2
Voigt, C.A.3
Lu, T.K.4
-
135
-
-
84872415347
-
Characterization of plasmid burden and copy number in Saccharomyces cerevisiae for optimization of metabolic engineering applications
-
A.S. Karim, K.A. Curran, and H.S. Alper Characterization of plasmid burden and copy number in Saccharomyces cerevisiae for optimization of metabolic engineering applications FEMS Yeast Res. 13 2013 107 116
-
(2013)
FEMS Yeast Res.
, vol.13
, pp. 107-116
-
-
Karim, A.S.1
Curran, K.A.2
Alper, H.S.3
-
136
-
-
84882626590
-
Designing and engineering evolutionary robust genetic circuits
-
S. Sleight, B. Bartley, J. Lieviant, and H. Sauro Designing and engineering evolutionary robust genetic circuits J. Biol. Eng. 4 2010 12
-
(2010)
J. Biol. Eng.
, vol.4
, pp. 12
-
-
Sleight, S.1
Bartley, B.2
Lieviant, J.3
Sauro, H.4
-
137
-
-
84939805158
-
Predicting the genetic stability of engineered DNA sequences with the EFM calculator
-
B.R. Jack, S.P. Leonard, D.M. Mishler, B.A. Renda, D. Leon, G.A. Suárez, and et al. Predicting the genetic stability of engineered DNA sequences with the EFM calculator ACS Synth. Biol. 2015 10.1021/acssynbio.5b00068
-
(2015)
ACS Synth. Biol.
-
-
Jack, B.R.1
Leonard, S.P.2
Mishler, D.M.3
Renda, B.A.4
Leon, D.5
Suárez, G.A.6
-
138
-
-
33646722147
-
Emergent properties of reduced-genome Escherichia coli
-
G. Pósfai, G. Plunkett, T. Fehér, D. Frisch, G.M. Keil, K. Umenhoffer, and et al. Emergent properties of reduced-genome Escherichia coli Science 312 2006 1044 1046
-
(2006)
Science
, vol.312
, pp. 1044-1046
-
-
Pósfai, G.1
Plunkett, G.2
Fehér, T.3
Frisch, D.4
Keil, G.M.5
Umenhoffer, K.6
-
139
-
-
56049102602
-
Superpositioning of deletions promotes growth of Escherichia coli with a reduced genome
-
H. Mizoguchi, Y. Sawano, J. Kato, and H. Mori Superpositioning of deletions promotes growth of Escherichia coli with a reduced genome DNA Res. 15 2008 277 284
-
(2008)
DNA Res.
, vol.15
, pp. 277-284
-
-
Mizoguchi, H.1
Sawano, Y.2
Kato, J.3
Mori, H.4
-
140
-
-
68449103617
-
Stabilized gene duplication enables long-term selection-free heterologous pathway expression
-
K.E.J. Tyo, P.K. Ajikumar, and G. Stephanopoulos Stabilized gene duplication enables long-term selection-free heterologous pathway expression Nat. Biotechnol. 27 2009 760 765
-
(2009)
Nat. Biotechnol.
, vol.27
, pp. 760-765
-
-
Tyo, K.E.J.1
Ajikumar, P.K.2
Stephanopoulos, G.3
-
141
-
-
84884645140
-
One-step cloning and chromosomal integration of DNA
-
F. St-Pierre, L. Cui, D.G. Priest, D. Endy, I.B. Dodd, and K.E. Shearwin One-step cloning and chromosomal integration of DNA ACS Synth. Biol. 2 2013 537 541
-
(2013)
ACS Synth. Biol.
, vol.2
, pp. 537-541
-
-
St-Pierre, F.1
Cui, L.2
Priest, D.G.3
Endy, D.4
Dodd, I.B.5
Shearwin, K.E.6
-
142
-
-
84884926579
-
Implementation of stable and complex biological systems through recombinase-assisted genome engineering
-
C.N.S. Santos, D.D. Regitsky, and Y. Yoshikuni Implementation of stable and complex biological systems through recombinase-assisted genome engineering Nat. Commun. 4 2013 2503
-
(2013)
Nat. Commun.
, vol.4
, pp. 2503
-
-
Santos, C.N.S.1
Regitsky, D.D.2
Yoshikuni, Y.3
-
145
-
-
84930197469
-
Targeted DNA degradation using a CRISPR device stably carried in the host genome
-
B.J. Caliando, and C.A. Voigt Targeted DNA degradation using a CRISPR device stably carried in the host genome Nat. Commun. 6 2015 6989
-
(2015)
Nat. Commun.
, vol.6
, pp. 6989
-
-
Caliando, B.J.1
Voigt, C.A.2
-
146
-
-
84922664743
-
Multilayered genetic safeguards limit growth of microorganisms to defined environments
-
R.R. Gallagher, J.R. Patel, A.L. Interiano, A.J. Rovner, and F.J. Isaacs Multilayered genetic safeguards limit growth of microorganisms to defined environments Nucleic Acids Res. 43 2015 1945 1954
-
(2015)
Nucleic Acids Res.
, vol.43
, pp. 1945-1954
-
-
Gallagher, R.R.1
Patel, J.R.2
Interiano, A.L.3
Rovner, A.J.4
Isaacs, F.J.5
-
147
-
-
84952801889
-
Synthetic auxotrophs with ligand-dependent essential genes for a BL21(DE3) biosafety strain
-
G. Lopez, and J.C. Anderson Synthetic auxotrophs with ligand-dependent essential genes for a BL21(DE3) biosafety strain ACS Synth. Biol. 2015 10.1021/acssynbio.5b00085
-
(2015)
ACS Synth. Biol.
-
-
Lopez, G.1
Anderson, J.C.2
-
148
-
-
84885791219
-
Genomically recoded organisms expand biological functions
-
M.J. Lajoie, A.J. Rovner, D.B. Goodman, H.-R. Aerni, A.D. Haimovich, G. Kuznetsov, and et al. Genomically recoded organisms expand biological functions Science 342 2013 357 360
-
(2013)
Science
, vol.342
, pp. 357-360
-
-
Lajoie, M.J.1
Rovner, A.J.2
Goodman, D.B.3
Aerni, H.-R.4
Haimovich, A.D.5
Kuznetsov, G.6
-
149
-
-
84922595374
-
Recoded organisms engineered to depend on synthetic amino acids
-
A.J. Rovner, A.D. Haimovich, S.R. Katz, Z. Li, M.W. Grome, B.M. Gassaway, and et al. Recoded organisms engineered to depend on synthetic amino acids Nature 518 2015 89 93
-
(2015)
Nature
, vol.518
, pp. 89-93
-
-
Rovner, A.J.1
Haimovich, A.D.2
Katz, S.R.3
Li, Z.4
Grome, M.W.5
Gassaway, B.M.6
-
150
-
-
84923112573
-
Biocontainment of genetically modified organisms by synthetic protein design
-
D.J. Mandell, M.J. Lajoie, M.T. Mee, R. Takeuchi, G. Kuznetsov, J.E. Norville, and et al. Biocontainment of genetically modified organisms by synthetic protein design Nature 518 2015 55 60
-
(2015)
Nature
, vol.518
, pp. 55-60
-
-
Mandell, D.J.1
Lajoie, M.J.2
Mee, M.T.3
Takeuchi, R.4
Kuznetsov, G.5
Norville, J.E.6
-
151
-
-
84897581176
-
Total synthesis of a functional designer eukaryotic chromosome
-
N. Annaluru, H. Muller, L.A. Mitchell, S. Ramalingam, G. Stracquadanio, S.M. Richardson, and et al. Total synthesis of a functional designer eukaryotic chromosome Science 344 2014 55 58
-
(2014)
Science
, vol.344
, pp. 55-58
-
-
Annaluru, N.1
Muller, H.2
Mitchell, L.A.3
Ramalingam, S.4
Stracquadanio, G.5
Richardson, S.M.6
-
152
-
-
84869451704
-
Genetic circuit performance under conditions relevant for industrial bioreactors
-
F. Moser, N.J. Broers, S. Hartmans, A. Tamsir, R. Kerkman, and J.a. Roubos Genetic circuit performance under conditions relevant for industrial bioreactors ACS Synth. Biol. 1 2012 555 564
-
(2012)
ACS Synth. Biol.
, vol.1
, pp. 555-564
-
-
Moser, F.1
Broers, N.J.2
Hartmans, S.3
Tamsir, A.4
Kerkman, R.5
Roubos, J.A.6
-
153
-
-
84862207235
-
Human gut-on-a-chip inhabited by microbial flora that experiences intestinal peristalsis-like motions and flow
-
H.J. Kim, D. Huh, G. Hamilton, and D.E. Ingber Human gut-on-a-chip inhabited by microbial flora that experiences intestinal peristalsis-like motions and flow Lab Chip 12 2012 2165
-
(2012)
Lab Chip
, vol.12
, pp. 2165
-
-
Kim, H.J.1
Huh, D.2
Hamilton, G.3
Ingber, D.E.4
|