-
1
-
-
77956501842
-
Central carbon metabolism as a minimal biochemical walk between precursors for biomass and energy
-
Noor E, Eden E, Milo R, Alon U. 2010. Central carbon metabolism as a minimal biochemical walk between precursors for biomass and energy. Mol Cell 39:809-820. https://doi.org/10.1016/j.molcel.2010.08.031
-
(2010)
Mol Cell
, vol.39
, pp. 809-820
-
-
Noor, E.1
Eden, E.2
Milo, R.3
Alon, U.4
-
2
-
-
47549110972
-
Carbon catabolite repression in bacteria: many ways to make the most out of nutrients
-
Gorke B, Stulke J. 2008. Carbon catabolite repression in bacteria: many ways to make the most out of nutrients. Nat Rev Microbiol 6:613-624. https://doi.org/10.1038/nrmicro1932
-
(2008)
Nat Rev Microbiol
, vol.6
, pp. 613-624
-
-
Gorke, B.1
Stulke, J.2
-
3
-
-
0016787183
-
Effects of varying the carbon source limiting growth on yield and maintenance characteristics of Escherichia coli in continuous culture
-
Hempfling WP, Mainzer SE. 1975. Effects of varying the carbon source limiting growth on yield and maintenance characteristics of Escherichia coli in continuous culture. J Bacteriol 123:1076-1087
-
(1975)
J Bacteriol
, vol.123
, pp. 1076-1087
-
-
Hempfling, W.P.1
Mainzer, S.E.2
-
4
-
-
0031927611
-
Demand theory of gene regulation. II. Quantitative application to the lactose and maltose operons of Escherichia coli
-
Savageau MA. 1998. Demand theory of gene regulation. II. Quantitative application to the lactose and maltose operons of Escherichia coli. Genetics 149:1677-1691
-
(1998)
Genetics
, vol.149
, pp. 1677-1691
-
-
Savageau, M.A.1
-
5
-
-
0034922896
-
Fuel ethanol production from lignocellulose: a challenge for metabolic engineering and process integration
-
Zaldivar J, Nielsen J, Olsson L. 2001. Fuel ethanol production from lignocellulose: a challenge for metabolic engineering and process integration. Appl Microbiol Biotechnol 56:17-34. https://doi.org/10.1007/s002530100624
-
(2001)
Appl Microbiol Biotechnol
, vol.56
, pp. 17-34
-
-
Zaldivar, J.1
Nielsen, J.2
Olsson, L.3
-
6
-
-
84924021824
-
Shifting sugars and shifting paradigms
-
Siegal ML. 2015. Shifting sugars and shifting paradigms. PLoS Biol 13:e1002068. https://doi.org/10.1371/journal.pbio.1002068
-
(2015)
PLoS Biol
, vol.13
-
-
Siegal, M.L.1
-
7
-
-
84901049716
-
Bet-hedging during bacterial diauxic shift
-
Solopova A, van Gestel J, Weissing FJ, Bachmann H, Teusink B, Kok J, Kuipers OP. 2014. Bet-hedging during bacterial diauxic shift. Proc Natl Acad Sci U S A 111:7427-7432. https://doi.org/10.1073/pnas.1320063111
-
(2014)
Proc Natl Acad Sci U S A
, vol.111
, pp. 7427-7432
-
-
Solopova, A.1
van Gestel, J.2
Weissing, F.J.3
Bachmann, H.4
Teusink, B.5
Kok, J.6
Kuipers, O.P.7
-
8
-
-
84893765873
-
Different levels of catabolite repression optimize growth in stable and variable environments
-
New AM, Cerulus B, Govers SK, Perez-Samper G, Zhu B, Boogmans S, Xavier JB, Verstrepen KJ. 2014. Different levels of catabolite repression optimize growth in stable and variable environments. PLoS Biol 12: e1001764. https://doi.org/10.1371/journal.pbio.1001764
-
(2014)
PLoS Biol
, vol.12
-
-
New, A.M.1
Cerulus, B.2
Govers, S.K.3
Perez-Samper, G.4
Zhu, B.5
Boogmans, S.6
Xavier, J.B.7
Verstrepen, K.J.8
-
9
-
-
84879489028
-
Adaptive laboratory evolution-principles and applications for biotechnology
-
Dragosits M, Mattanovich D. 2013. Adaptive laboratory evolution-principles and applications for biotechnology. Microb Cell Fact 12:64. https://doi.org/10.1186/1475-2859-12-64
-
(2013)
Microb Cell Fact
, vol.12
, pp. 64
-
-
Dragosits, M.1
Mattanovich, D.2
-
10
-
-
0026454741
-
Evolutionary adaptation to temperature. I. Fitness responses of Escherichia coli to changes in its thermal environment
-
Bennett AF, Lenski RE, Mittler JE. 1992. Evolutionary adaptation to temperature. I. Fitness responses of Escherichia coli to changes in its thermal environment. Evolution 46:16-30
-
(1992)
Evolution
, vol.46
, pp. 16-30
-
-
Bennett, A.F.1
Lenski, R.E.2
Mittler, J.E.3
-
11
-
-
84885060803
-
Fluctuating temperature leads to evolution of thermal generalism and preadaptation to novel environments
-
Ketola T, Mikonranta L, Zhang J, Saarinen K, Ormala AM, Friman VP, Mappes J, Laakso J. 2013. Fluctuating temperature leads to evolution of thermal generalism and preadaptation to novel environments. Evolution 67:2936-2944. https://doi.org/10.1111/evo.12148
-
(2013)
Evolution
, vol.67
, pp. 2936-2944
-
-
Ketola, T.1
Mikonranta, L.2
Zhang, J.3
Saarinen, K.4
Ormala, A.M.5
Friman, V.P.6
Mappes, J.7
Laakso, J.8
-
12
-
-
34250871223
-
An experimental evolutionary study on adaptation to temporally fluctuating pH in Escherichia coli
-
Hughes BS, Cullum AJ, Bennett AF. 2007. An experimental evolutionary study on adaptation to temporally fluctuating pH in Escherichia coli. Physiol Biochem Zool 80:406-421. https://doi.org/10.1086/518353
-
(2007)
Physiol Biochem Zool
, vol.80
, pp. 406-421
-
-
Hughes, B.S.1
Cullum, A.J.2
Bennett, A.F.3
-
13
-
-
6444223584
-
Divergent adaptation of Escherichia coli to cyclic ultraviolet light exposures
-
Alcantara-Diaz D, Brena-Valle M, Serment-Guerrero J. 2004. Divergent adaptation of Escherichia coli to cyclic ultraviolet light exposures. Mutagenesis 19:349-354. https://doi.org/10.1093/mutage/geh039
-
(2004)
Mutagenesis
, vol.19
, pp. 349-354
-
-
Alcantara-Diaz, D.1
Brena-Valle, M.2
Serment-Guerrero, J.3
-
14
-
-
84929711184
-
Escherichia coli populations in unpredictably fluctuating environments evolve to face novel stresses through enhanced efflux activity
-
Karve SM, Daniel S, Chavhan YD, Anand A, Kharola SS, Dey S. 2015. Escherichia coli populations in unpredictably fluctuating environments evolve to face novel stresses through enhanced efflux activity. J Evol Biol 28:1131-1143. https://doi.org/10.1111/jeb.12640
-
(2015)
J Evol Biol
, vol.28
, pp. 1131-1143
-
-
Karve, S.M.1
Daniel, S.2
Chavhan, Y.D.3
Anand, A.4
Kharola, S.S.5
Dey, S.6
-
15
-
-
0036218182
-
The experimental evolution of specialists, generalists, and the maintenance of diversity
-
Kassen R. 2002. The experimental evolution of specialists, generalists, and the maintenance of diversity. J Evol Biol 15:173-190. https://doi.org/10.1046/j.1420-9101.2002.00377.x
-
(2002)
J Evol Biol
, vol.15
, pp. 173-190
-
-
Kassen, R.1
-
16
-
-
35048822821
-
Evolution of a single niche specialist in variable environments
-
Jasmin JN, Kassen R. 2007. Evolution of a single niche specialist in variable environments. Proc Biol Sci 274:2761-2767. https://doi.org/10 .1098/rspb.2007.0936
-
(2007)
Proc Biol Sci
, vol.274
, pp. 2761-2767
-
-
Jasmin, J.N.1
Kassen, R.2
-
17
-
-
78649977942
-
The repeatability of adaptive radiation during long-term experimental evolution of Escherichia coli in a multiple nutrient environment
-
Saxer G, Doebeli M, Travisano M. 2010. The repeatability of adaptive radiation during long-term experimental evolution of Escherichia coli in a multiple nutrient environment. PLoS One 5:e14184. https://doi.org/10 .1371/journal.pone.0014184
-
(2010)
PLoS One
, vol.5
-
-
Saxer, G.1
Doebeli, M.2
Travisano, M.3
-
18
-
-
1642388599
-
Experimental evidence for sympatric ecological diversification due to frequencydependent competition in Escherichia coli
-
Friesen ML, Saxer G, Travisano M, Doebeli M. 2004. Experimental evidence for sympatric ecological diversification due to frequencydependent competition in Escherichia coli. Evolution 58:245-260
-
(2004)
Evolution
, vol.58
, pp. 245-260
-
-
Friesen, M.L.1
Saxer, G.2
Travisano, M.3
Doebeli, M.4
-
19
-
-
67650376275
-
Adaptive prediction of environmental changes by microorganisms
-
Mitchell A, Romano GH, Groisman B, Yona A, Dekel E, Kupiec M, Dahan O, Pilpel Y. 2009. Adaptive prediction of environmental changes by microorganisms. Nature 460:220-224. https://doi.org/10.1038/nature08112
-
(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
Dahan, O.7
Pilpel, Y.8
-
20
-
-
77649133888
-
Experimental evolution with E. coli in diverse resource environments. I. Fluctuating environments promote divergence of replicate populations
-
Cooper TF, Lenski RE. 2010. Experimental evolution with E. coli in diverse resource environments. I. Fluctuating environments promote divergence of replicate populations. BMC Evol Biol 10:11. https://doi.org/10 .1186/1471-2148-10-11
-
(2010)
BMC Evol Biol
, vol.10
, pp. 11
-
-
Cooper, T.F.1
Lenski, R.E.2
-
21
-
-
84857467293
-
Adaptive evolution of the lactose utilization network in experimentally evolved populations of Escherichia coli
-
Quan S, Ray JC, Kwota Z, Duong T, Balazsi G, Cooper TF, Monds RD. 2012. Adaptive evolution of the lactose utilization network in experimentally evolved populations of Escherichia coli. PLoS Genet 8:e1002444. https://doi.org/10.1371/journal.pgen.1002444
-
(2012)
PLoS Genet
, vol.8
-
-
Quan, S.1
Ray, J.C.2
Kwota, Z.3
Duong, T.4
Balazsi, G.5
Cooper, T.F.6
Monds, R.D.7
-
22
-
-
85020555093
-
Adaptation of Escherichia coli to long-term serial passage in complex medium: evidence of parallel evolution
-
Kram KE, Geiger C, Ismail WM, Lee H, Tang H, Foster PL, Finkel SE. 2017. Adaptation of Escherichia coli to long-term serial passage in complex medium: evidence of parallel evolution. mSystems 2:e00192-16. https://doi.org/10.1128/mSystems.00192-16
-
(2017)
mSystems
, vol.2
-
-
Kram, K.E.1
Geiger, C.2
Ismail, W.M.3
Lee, H.4
Tang, H.5
Foster, P.L.6
Finkel, S.E.7
-
23
-
-
75349114758
-
Whole-genome resequencing of Escherichia coli K-12 MG1655 undergoing short-term laboratory evolution in lactate minimal medium reveals flexible selection of adaptive mutations
-
Conrad TM, Joyce AR, Applebee MK, Barrett CL, Xie B, Gao Y, Palsson BO. 2009. Whole-genome resequencing of Escherichia coli K-12 MG1655 undergoing short-term laboratory evolution in lactate minimal medium reveals flexible selection of adaptive mutations. Genome Biol 10:R118. https://doi.org/10.1186/gb-2009-10-10-r118
-
(2009)
Genome Biol
, vol.10
-
-
Conrad, T.M.1
Joyce, A.R.2
Applebee, M.K.3
Barrett, C.L.4
Xie, B.5
Gao, Y.6
Palsson, B.O.7
-
24
-
-
84907269737
-
Evolution of Escherichia coli to 42 degrees C and subsequent genetic engineering reveals adaptive mechanisms and novel mutations
-
Sandberg TE, Pedersen M, LaCroix RA, Ebrahim A, Bonde M, Herrgard MJ, Palsson BO, Sommer M, Feist AM. 2014. Evolution of Escherichia coli to 42 degrees C and subsequent genetic engineering reveals adaptive mechanisms and novel mutations. Mol Biol Evol 31:2647-2662. https://doi .org/10.1093/molbev/msu209
-
(2014)
Mol Biol Evol
, vol.31
, pp. 2647-2662
-
-
Sandberg, T.E.1
Pedersen, M.2
LaCroix, R.A.3
Ebrahim, A.4
Bonde, M.5
Herrgard, M.J.6
Palsson, B.O.7
Sommer, M.8
Feist, A.M.9
-
25
-
-
84917705874
-
Use of adaptive laboratory evolution to discover key mutations enabling rapid growth of Escherichia coli K-12 MG1655 on glucose minimal medium
-
LaCroix RA, Sandberg TE, O'Brien EJ, Utrilla J, Ebrahim A, Guzman GI, Szubin R, Palsson BO, Feist AM. 2015. Use of adaptive laboratory evolution to discover key mutations enabling rapid growth of Escherichia coli K-12 MG1655 on glucose minimal medium. Appl Environ Microbiol 81:17-30. https://doi.org/10.1128/AEM.02246-14
-
(2015)
Appl Environ Microbiol
, vol.81
, pp. 17-30
-
-
LaCroix, R.A.1
Sandberg, T.E.2
O'Brien, E.J.3
Utrilla, J.4
Ebrahim, A.5
Guzman, G.I.6
Szubin, R.7
Palsson, B.O.8
Feist, A.M.9
-
26
-
-
84928889593
-
Global metabolic network reorganization by adaptive mutations allows fast growth of Escherichia coli on glycerol
-
Cheng KK, Lee BS, Masuda T, Ito T, Ikeda K, Hirayama A, Deng L, Dong J, Shimizu K, Soga T, Tomita M, Palsson BO, Robert M. 2014. Global metabolic network reorganization by adaptive mutations allows fast growth of Escherichia coli on glycerol. Nat Commun 5:3233. https://doi .org/10.1038/ncomms4233
-
(2014)
Nat Commun
, vol.5
, pp. 3233
-
-
Cheng, K.K.1
Lee, B.S.2
Masuda, T.3
Ito, T.4
Ikeda, K.5
Hirayama, A.6
Deng, L.7
Dong, J.8
Shimizu, K.9
Soga, T.10
Tomita, M.11
Palsson, B.O.12
Robert, M.13
-
27
-
-
78650546051
-
RNA polymerase mutants found through adaptive evolution reprogram Escherichia coli for optimal growth in minimal media
-
Conrad TM, Frazier M, Joyce AR, Cho BK, Knight EM, Lewis NE, Landick R, Palsson BO. 2010. RNA polymerase mutants found through adaptive evolution reprogram Escherichia coli for optimal growth in minimal media. Proc Natl Acad Sci U S A 107:20500-20505. https://doi.org/10 .1073/pnas.0911253107
-
(2010)
Proc Natl Acad Sci U S A
, 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
Landick, R.7
Palsson, B.O.8
-
28
-
-
84967180536
-
Global rebalancing of cellular resources by pleiotropic point mutations illustrates a multi-scale mechanism of adaptive evolution
-
Utrilla J, O'Brien EJ, Chen K, McCloskey D, Cheung J, Wang H, Armenta-Medina D, Feist AM, Palsson BO. 2016. Global rebalancing of cellular resources by pleiotropic point mutations illustrates a multi-scale mechanism of adaptive evolution. Cell Syst 2:260-271. https://doi.org/10 .1016/j.cels.2016.04.003
-
(2016)
Cell Syst
, vol.2
, pp. 260-271
-
-
Utrilla, J.1
O'Brien, E.J.2
Chen, K.3
McCloskey, D.4
Cheung, J.5
Wang, H.6
Armenta-Medina, D.7
Feist, A.M.8
Palsson, B.O.9
-
29
-
-
84867182301
-
Resistance to environmental stress requires the RNA chaperones CspC and CspE
-
Shenhar Y, Biran D, Ron EZ. 2012. Resistance to environmental stress requires the RNA chaperones CspC and CspE. Environ Microbiol Rep 4:532-539. https://doi.org/10.1111/j.1758-2229.2012.00358.x
-
(2012)
Environ Microbiol Rep
, vol.4
, pp. 532-539
-
-
Shenhar, Y.1
Biran, D.2
Ron, E.Z.3
-
30
-
-
84947583295
-
Overflow metabolism in Escherichia coli results from efficient proteome allocation
-
Basan M, Hui S, Okano H, Zhang Z, Shen Y, Williamson JR, Hwa T. 2015. Overflow metabolism in Escherichia coli results from efficient proteome allocation. Nature 528:99-104. https://doi.org/10.1038/nature15765
-
(2015)
Nature
, vol.528
, pp. 99-104
-
-
Basan, M.1
Hui, S.2
Okano, H.3
Zhang, Z.4
Shen, Y.5
Williamson, J.R.6
Hwa, T.7
-
31
-
-
84940862296
-
Acetate exposure determines the diauxic behavior of Escherichia coli during the glucose-acetate transition
-
Enjalbert B, Cocaign-Bousquet M, Portais JC, Letisse F. 2015. Acetate exposure determines the diauxic behavior of Escherichia coli during the glucose-acetate transition. J Bacteriol 197:3173-3181. https://doi.org/10 .1128/JB.00128-15
-
(2015)
J Bacteriol
, vol.197
, pp. 3173-3181
-
-
Enjalbert, B.1
Cocaign-Bousquet, M.2
Portais, J.C.3
Letisse, F.4
-
32
-
-
15544371346
-
Gene regulation at the single-cell level
-
Rosenfeld N, Young JW, Alon U, Swain PS, Elowitz MB. 2005. Gene regulation at the single-cell level. Science 307:1962-1965. https://doi .org/10.1126/science.1106914
-
(2005)
Science
, vol.307
, pp. 1962-1965
-
-
Rosenfeld, N.1
Young, J.W.2
Alon, U.3
Swain, P.S.4
Elowitz, M.B.5
-
33
-
-
58549108388
-
Reconstruction of biochemical networks in microorganisms
-
Feist AM, Herrgard MJ, Thiele I, Reed JL, Palsson BO. 2009. Reconstruction of biochemical networks in microorganisms. Nat Rev Microbiol 7:129-143. https://doi.org/10.1038/nrmicro1949
-
(2009)
Nat Rev Microbiol
, vol.7
, pp. 129-143
-
-
Feist, A.M.1
Herrgard, M.J.2
Thiele, I.3
Reed, J.L.4
Palsson, B.O.5
-
34
-
-
77749320898
-
What is flux balance analysis?
-
Orth JD, Thiele I, Palsson BO. 2010. What is flux balance analysis? Nat Biotechnol 28:245-248. https://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
-
35
-
-
65549092780
-
Use of randomized sampling for analysis of metabolic networks
-
Schellenberger J, Palsson BO. 2009. Use of randomized sampling for analysis of metabolic networks. J Biol Chem 284:5457-5461. https://doi .org/10.1074/jbc.R800048200
-
(2009)
J Biol Chem
, vol.284
, pp. 5457-5461
-
-
Schellenberger, J.1
Palsson, B.O.2
-
36
-
-
84864843180
-
In silico method for modelling metabolism and gene product expression at genome scale
-
Lerman JA, Hyduke DR, Latif H, Portnoy VA, Lewis NE, Orth JD, Schrimpe-Rutledge AC, Smith RD, Adkins JN, Zengler K, Palsson BO. 2012. In silico method for modelling metabolism and gene product expression at genome scale. Nat Commun 3:929. https://doi.org/10.1038/ncomms1928
-
(2012)
Nat Commun
, vol.3
, pp. 929
-
-
Lerman, J.A.1
Hyduke, D.R.2
Latif, H.3
Portnoy, V.A.4
Lewis, N.E.5
Orth, J.D.6
Schrimpe-Rutledge, A.C.7
Smith, R.D.8
Adkins, J.N.9
Zengler, K.10
Palsson, B.O.11
-
37
-
-
84885367114
-
Genomescale models of metabolism and gene expression extend and refine growth phenotype prediction
-
O'Brien EJ, Lerman JA, Chang RL, Hyduke DR, Palsson BO. 2013. Genomescale models of metabolism and gene expression extend and refine growth phenotype prediction. Mol Syst Biol 9:693. https://doi.org/10 .1038/msb.2013.52
-
(2013)
Mol Syst Biol
, vol.9
, pp. 693
-
-
O'Brien, E.J.1
Lerman, J.A.2
Chang, R.L.3
Hyduke, D.R.4
Palsson, B.O.5
-
38
-
-
79959256040
-
Repression of xylose-specific enzymes by ethanol in Scheffersomyces (Pichia) stipitis and utility of repitching xylose-grown populations to eliminate diauxic lag
-
Slininger PJ, Thompson SR, Weber S, Liu ZL, Moon J. 2011. Repression of xylose-specific enzymes by ethanol in Scheffersomyces (Pichia) stipitis and utility of repitching xylose-grown populations to eliminate diauxic lag. Biotechnol Bioeng 108:1801-1815. https://doi.org/10.1002/bit .23119
-
(2011)
Biotechnol Bioeng
, vol.108
, pp. 1801-1815
-
-
Slininger, P.J.1
Thompson, S.R.2
Weber, S.3
Liu, Z.L.4
Moon, J.5
-
39
-
-
85008192136
-
Increased production of L-serine in Escherichia coli through adaptive laboratory evolution
-
Mundhada H, Seoane JM, Schneider K, Koza A, Christensen HB, Klein T, Phaneuf PV, Herrgard M, Feist AM, Nielsen AT. 2017. Increased production of L-serine in Escherichia coli through adaptive laboratory evolution. Metab Eng 39:141-150. https://doi.org/10.1016/j.ymben.2016.11.008
-
(2017)
Metab Eng
, vol.39
, pp. 141-150
-
-
Mundhada, H.1
Seoane, J.M.2
Schneider, K.3
Koza, A.4
Christensen, H.B.5
Klein, T.6
Phaneuf, P.V.7
Herrgard, M.8
Feist, A.M.9
Nielsen, A.T.10
-
40
-
-
84861969435
-
Simultaneous utilization of glucose, xylose and arabinose in the presence of acetate by a consortium of Escherichia coli strains
-
Xia T, Eiteman MA, Altman E. 2012. Simultaneous utilization of glucose, xylose and arabinose in the presence of acetate by a consortium of Escherichia coli strains. Microb Cell Fact 11:77. https://doi.org/10.1186/1475-2859-11-77
-
(2012)
Microb Cell Fact
, vol.11
, pp. 77
-
-
Xia, T.1
Eiteman, M.A.2
Altman, E.3
-
41
-
-
85011072524
-
Dynamic substrate preferences predict metabolic properties of a simple microbial consortium
-
Erbilgin O, Bowen BP, Kosina SM, Jenkins S, Lau RK, Northen TR. 2017. Dynamic substrate preferences predict metabolic properties of a simple microbial consortium. BMC Bioinformatics 18:57. https://doi.org/10 .1186/s12859-017-1478-2
-
(2017)
BMC Bioinformatics
, vol.18
, pp. 57
-
-
Erbilgin, O.1
Bowen, B.P.2
Kosina, S.M.3
Jenkins, S.4
Lau, R.K.5
Northen, T.R.6
-
42
-
-
84954384044
-
Temporal variation in antibiotic environments slows down resistance evolution in pathogenic Pseudomonas aeruginosa
-
Roemhild R, Barbosa C, Beardmore RE, Jansen G, Schulenburg H. 2015. Temporal variation in antibiotic environments slows down resistance evolution in pathogenic Pseudomonas aeruginosa. Evol Appl 8:945-955. https://doi.org/10.1111/eva.12330
-
(2015)
Evol Appl
, vol.8
, pp. 945-955
-
-
Roemhild, R.1
Barbosa, C.2
Beardmore, R.E.3
Jansen, G.4
Schulenburg, H.5
-
43
-
-
84911470344
-
Targeting bacterial central metabolism for drug development
-
Murima P, McKinney JD, Pethe K. 2014. Targeting bacterial central metabolism for drug development. Chem Biol 21:1423-1432. https://doi .org/10.1016/j.chembiol.2014.08.020
-
(2014)
Chem Biol
, vol.21
, pp. 1423-1432
-
-
Murima, P.1
McKinney, J.D.2
Pethe, K.3
-
44
-
-
84962602150
-
Evolution of E. coli on [U-13C]glucose reveals a negligible isotopic influence on metabolism and physiology
-
Sandberg TE, Long CP, Gonzalez JE, Feist AM, Antoniewicz MR, Palsson BO. 2016. Evolution of E. coli on [U-13C]glucose reveals a negligible isotopic influence on metabolism and physiology. PLoS One 11: e0151130. https://doi.org/10.1371/journal.pone.0151130
-
(2016)
PLoS One
, vol.11
-
-
Sandberg, T.E.1
Long, C.P.2
Gonzalez, J.E.3
Feist, A.M.4
Antoniewicz, M.R.5
Palsson, B.O.6
-
45
-
-
84917686994
-
Identification of mutations in laboratory-evolved microbes from next-generation sequencing data using breseq
-
Deatherage DE, Barrick JE. 2014. Identification of mutations in laboratory-evolved microbes from next-generation sequencing data using breseq. Methods Mol Biol 1151:165-188. https://doi.org/10.1007/978-1-4939-0554-6_12
-
(2014)
Methods Mol Biol
, vol.1151
, pp. 165-188
-
-
Deatherage, D.E.1
Barrick, J.E.2
-
46
-
-
84859210032
-
Fast gapped-read alignment with Bowtie. 2
-
Langmead B, Salzberg SL. 2012. Fast gapped-read alignment with Bowtie. 2. Nat Methods 9:357-359. https://doi.org/10.1038/nmeth.1923
-
(2012)
Nat Methods
, vol.9
, pp. 357-359
-
-
Langmead, B.1
Salzberg, S.L.2
-
47
-
-
77952123055
-
Transcript assembly and quantification by RNA-Seq reveals unannotated transcripts and isoform switching during cell differentiation
-
Trapnell C, Williams BA, Pertea G, Mortazavi A, Kwan G, van Baren MJ, Salzberg SL, Wold BJ, Pachter L. 2010. Transcript assembly and quantification by RNA-Seq reveals unannotated transcripts and isoform switching during cell differentiation. Nat Biotechnol 28:511-515. https://doi .org/10.1038/nbt.1621
-
(2010)
Nat Biotechnol
, vol.28
, pp. 511-515
-
-
Trapnell, C.1
Williams, B.A.2
Pertea, G.3
Mortazavi, A.4
Kwan, G.5
van Baren, M.J.6
Salzberg, S.L.7
Wold, B.J.8
Pachter, L.9
-
48
-
-
84872198346
-
Differential analysis of gene regulation at transcript resolution with RNA-seq
-
Trapnell C, Hendrickson DG, Sauvageau M, Goff L, Rinn JL, Pachter L. 2013. Differential analysis of gene regulation at transcript resolution with RNA-seq. Nat Biotechnol 31:46-53. https://doi.org/10.1038/nbt .2450
-
(2013)
Nat Biotechnol
, vol.31
, pp. 46-53
-
-
Trapnell, C.1
Hendrickson, D.G.2
Sauvageau, M.3
Goff, L.4
Rinn, J.L.5
Pachter, L.6
-
49
-
-
80054069179
-
A comprehensive genome-scale reconstruction of Escherichia coli metabolism-2011
-
Orth JD, Conrad TM, Na J, Lerman JA, Nam H, Feist AM, Palsson BO. 2011. A comprehensive genome-scale reconstruction of Escherichia coli metabolism-2011. Mol Syst Biol 7:535. https://doi.org/10.1038/msb.2011.65
-
(2011)
Mol Syst Biol
, vol.7
, pp. 535
-
-
Orth, J.D.1
Conrad, T.M.2
Na, J.3
Lerman, J.A.4
Nam, H.5
Feist, A.M.6
Palsson, B.O.7
-
50
-
-
34347258175
-
Quantitative prediction of cellular metabolism with constraint-based models: the COBRA Toolbox
-
Becker SA, Feist AM, Mo ML, Hannum G, Palsson BO, Herrgard MJ. 2007. Quantitative prediction of cellular metabolism with constraint-based models: the COBRA Toolbox. Nat Protoc 2:727-738. https://doi.org/10 .1038/nprot.2007.99
-
(2007)
Nat Protoc
, vol.2
, pp. 727-738
-
-
Becker, S.A.1
Feist, A.M.2
Mo, M.L.3
Hannum, G.4
Palsson, B.O.5
Herrgard, M.J.6
-
51
-
-
84940751701
-
Escher: a web application for building, sharing, and embedding data-rich visualizations of biological pathways
-
King ZA, Drager A, Ebrahim A, Sonnenschein N, Lewis NE, Palsson BO. 2015. Escher: a web application for building, sharing, and embedding data-rich visualizations of biological pathways. PLoS Comput Biol 11: e1004321. https://doi.org/10.1371/journal.pcbi.1004321
-
(2015)
PLoS Comput Biol
, vol.11
-
-
King, Z.A.1
Drager, A.2
Ebrahim, A.3
Sonnenschein, N.4
Lewis, N.E.5
Palsson, B.O.6
-
52
-
-
85030725050
-
-
bioRxiv
-
Lloyd CJ, Ebrahim A, Yang L, King ZA, Catoiu E, O'Brien EJ, Liu JK, Palsson BO. 2017. COBRAme: a computational framework for building and manipulating models of metabolism and gene expression. bioRxiv https://doi.org/10.1101/106559
-
(2017)
COBRAme: a computational framework for building and manipulating models of metabolism and gene expression
-
-
Lloyd, C.J.1
Ebrahim, A.2
Yang, L.3
King, Z.A.4
Catoiu, E.5
O'Brien, E.J.6
Liu, J.K.7
Palsson, B.O.8
-
53
-
-
84995608089
-
solveME: fast and reliable solution of nonlinear ME models
-
Yang L, Ma D, Ebrahim A, Lloyd CJ, Saunders MA, Palsson BO. 2016. solveME: fast and reliable solution of nonlinear ME models. BMC Bioinformatics 17:391. https://doi.org/10.1186/s12859-016-1240-1
-
(2016)
BMC Bioinformatics
, vol.17
, pp. 391
-
-
Yang, L.1
Ma, D.2
Ebrahim, A.3
Lloyd, C.J.4
Saunders, M.A.5
Palsson, B.O.6
-
54
-
-
85010036575
-
Reliable and efficient solution of genome-scale models of metabolism and macromolecular expression
-
Ma D, Yang L, Fleming RM, Thiele I, Palsson BO, Saunders MA. 2017. Reliable and efficient solution of genome-scale models of metabolism and macromolecular expression. Sci Rep 7:40863. https://doi.org/10 .1038/srep40863
-
(2017)
Sci Rep
, vol.7
, pp. 40863
-
-
Ma, D.1
Yang, L.2
Fleming, R.M.3
Thiele, I.4
Palsson, B.O.5
Saunders, M.A.6
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