-
1
-
-
79951493627
-
On the future of genomic data
-
Kahn SD (2011) On the future of genomic data. Science 331:728-729.
-
(2011)
Science
, vol.331
, pp. 728-729
-
-
Kahn, S.D.1
-
2
-
-
79952802463
-
Riding the wave of biological data
-
Gross M (2011) Riding the wave of biological data. Curr Biol 21:R204-R206.
-
(2011)
Curr Biol
, vol.21
, pp. R204-R206
-
-
Gross, M.1
-
3
-
-
72849144434
-
Sequencing technologies-the next generation
-
Metzker ML (2010) Sequencing technologies-The next generation. Nat Rev Genet 11:31-46.
-
(2010)
Nat Rev Genet
, vol.11
, pp. 31-46
-
-
Metzker, M.L.1
-
4
-
-
84906861310
-
High-throughput discovery metabolomics
-
Fuhrer T, Zamboni N (2015) High-throughput discovery metabolomics. Curr Opin Biotechnol 31:73-78.
-
(2015)
Curr Opin Biotechnol
, vol.31
, pp. 73-78
-
-
Fuhrer, T.1
Zamboni, N.2
-
5
-
-
84904279616
-
High-throughput proteomics
-
Zhang Z, Wu S, Stenoien DL, Paša-Toli-c L (2014) High-throughput proteomics. Annu Rev Anal Chem (Palo Alto, Calif) 7:427-454.
-
(2014)
Annu Rev Anal Chem (Palo Alto, Calif
, vol.7
, pp. 427-454
-
-
Zhang, Z.1
Wu, S.2
Stenoien, D.L.3
Paša-Tolic, L.4
-
6
-
-
84876576325
-
Computational solutions for omics data
-
Berger B, Peng J, Singh M (2013) Computational solutions for omics data. Nat Rev Genet 14:333-346.
-
(2013)
Nat Rev Genet
, vol.14
, pp. 333-346
-
-
Berger, B.1
Peng, J.2
Singh, M.3
-
7
-
-
0014991329
-
Regulation of isocitrate dehydrogenase activity in Escherichia coli on adaptation to acetate
-
Holms WH, Bennett PM (1971) Regulation of isocitrate dehydrogenase activity in Escherichia coli on adaptation to acetate. J Gen Microbiol 65:57-68.
-
(1971)
J Gen Microbiol
, vol.65
, pp. 57-68
-
-
Holms, W.H.1
Bennett, P.M.2
-
8
-
-
47649125318
-
Tuning gene expression to changing environments: From rapid responses to evolutionary adaptation
-
López-Maury L, Marguerat S, Bähler J (2008) Tuning gene expression to changing environments: From rapid responses to evolutionary adaptation. Nat Rev Genet 9:583-593.
-
(2008)
Nat Rev Genet
, vol.9
, pp. 583-593
-
-
López-Maury, L.1
Marguerat, S.2
Bähler, J.3
-
9
-
-
84921369209
-
Post-translational modifications as key regulators of bacterial metabolic fluxes
-
Pisithkul T, Patel NM, Amador-Noguez D (2015) Post-translational modifications as key regulators of bacterial metabolic fluxes. Curr Opin Microbiol 24:29-37.
-
(2015)
Curr Opin Microbiol
, vol.24
, pp. 29-37
-
-
Pisithkul, T.1
Patel, N.M.2
Amador-Noguez, D.3
-
10
-
-
84892876508
-
Beyond gene expression: The impact of protein post-translational modifications in bacteria
-
Cain JA, Solis N, Cordwell SJ (2014) Beyond gene expression: The impact of protein post-translational modifications in bacteria. J Proteomics 97:265-286.
-
(2014)
J Proteomics
, vol.97
, pp. 265-286
-
-
Cain, J.A.1
Solis, N.2
Cordwell, S.J.3
-
11
-
-
84880426255
-
Acetyl-phosphate is a critical determinant of lysine acetylation in e. Coli
-
Weinert BT, et al. (2013) Acetyl-phosphate is a critical determinant of lysine acetylation in E. Coli. Mol Cell 51:265-272.
-
(2013)
Mol Cell
, vol.51
, pp. 265-272
-
-
Weinert, B.T.1
-
12
-
-
84905378213
-
Stoichiometry of site-specific lysine acetylation in an entire proteome
-
Baeza J, et al. (2014) Stoichiometry of site-specific lysine acetylation in an entire proteome. J Biol Chem 289:21326-21338.
-
(2014)
J Biol Chem
, vol.289
, pp. 21326-21338
-
-
Baeza, J.1
-
14
-
-
84879536162
-
The Escherichia coli phosphotyrosine proteome relates to core pathways and virulence
-
Hansen A-M, et al. (2013) The Escherichia coli phosphotyrosine proteome relates to core pathways and virulence. PLoS Pathog 9:e1003403.
-
(2013)
PLoS Pathog
, vol.9
, pp. e1003403
-
-
Hansen, A.-M.1
-
15
-
-
84930642844
-
Posttranslational regulation of microbial metabolism
-
Kochanowski K, Sauer U, Noor E (2015) Posttranslational regulation of microbial metabolism. Curr Opin Microbiol 27:10-17.
-
(2015)
Curr Opin Microbiol
, vol.27
, pp. 10-17
-
-
Kochanowski, K.1
Sauer, U.2
Noor, E.3
-
16
-
-
84930947811
-
Global dynamics of Escherichia coli phosphoproteome in central carbon metabolism under changing culture conditions
-
Lim S, Marcellin E, Jacob S, Nielsen LK (2015) Global dynamics of Escherichia coli phosphoproteome in central carbon metabolism under changing culture conditions. J Proteomics 126:24-33.
-
(2015)
J Proteomics
, vol.126
, pp. 24-33
-
-
Lim, S.1
Marcellin, E.2
Jacob, S.3
Nielsen, L.K.4
-
18
-
-
84892788440
-
Constraint-based models predict metabolic and associated cellular functions
-
Bordbar A, Monk JM, King ZA, Palsson BO (2014) Constraint-based models predict metabolic and associated cellular functions. Nat Rev Genet 15:107-120.
-
(2014)
Nat Rev Genet
, vol.15
, pp. 107-120
-
-
Bordbar, A.1
Monk, J.M.2
King, Z.A.3
Palsson, B.O.4
-
19
-
-
84858439602
-
Constraining the metabolic genotypephenotype relationship using a phylogeny of in silico methods
-
Lewis NE, Nagarajan H, Palsson BO (2012) Constraining the metabolic genotypephenotype relationship using a phylogeny of in silico methods. Nat Rev Microbiol 10:291-305.
-
(2012)
Nat Rev Microbiol
, vol.10
, pp. 291-305
-
-
Lewis, N.E.1
Nagarajan, H.2
Palsson, B.O.3
-
20
-
-
39749166860
-
Phosphoproteome analysis of e. Coli reveals evolutionary conservation of bacterial ser/thr/tyr phosphorylation
-
Macek B, et al. (2008) Phosphoproteome analysis of E. Coli reveals evolutionary conservation of bacterial Ser/Thr/Tyr phosphorylation. Mol Cell Proteomics 7:299-307.
-
(2008)
Mol Cell Proteomics
, vol.7
, pp. 299-307
-
-
Macek, B.1
-
21
-
-
61649089277
-
Lysine acetylation is a highly abundant and evolutionarily conserved modification in Escherichia coli
-
Zhang J, et al. (2009) Lysine acetylation is a highly abundant and evolutionarily conserved modification in Escherichia coli. Mol Cell Proteomics 8:215-225.
-
(2009)
Mol Cell Proteomics
, vol.8
, pp. 215-225
-
-
Zhang, J.1
-
22
-
-
56649114286
-
The diversity of lysine-acetylated proteins in Escherichia coli
-
Yu BJ, Kim JA, Moon JH, Ryu SE, Pan J-G (2008) The diversity of lysine-acetylated proteins in Escherichia coli. J Microbiol Biotechnol 18:1529-1536.
-
(2008)
J Microbiol Biotechnol
, vol.18
, pp. 1529-1536
-
-
Yu, B.J.1
Kim, J.A.2
Moon, J.H.3
Ryu, S.E.4
Pan, J.-G.5
-
23
-
-
78650516004
-
Identification of lysine succinylation as a new post-translational modification
-
Zhang Z, et al. (2011) Identification of lysine succinylation as a new post-translational modification. Nat Chem Biol 7:58-63.
-
(2011)
Nat Chem Biol
, vol.7
, pp. 58-63
-
-
Zhang, Z.1
-
25
-
-
68949161807
-
Programming cells by multiplex genome engineering and accelerated evolution
-
Wang HH, et al. (2009) Programming cells by multiplex genome engineering and accelerated evolution. Nature 460:894-898.
-
(2009)
Nature
, vol.460
, pp. 894-898
-
-
Wang, H.H.1
-
27
-
-
85006855427
-
RNA structural determinants of optimal codons revealed by mage-seq
-
Kelsic ED, et al. (2016) RNA structural determinants of optimal codons revealed by MAGE-seq. Cell Syst 3:563-571.e6.
-
(2016)
Cell Syst
, vol.3
, pp. 563
-
-
Kelsic, E.D.1
-
28
-
-
46749145356
-
Geeqbox: A matlab toolbox for generalized estimating equations and quasi-least squares
-
Shults J, Ratcliffe SJ (2008) GEEQBOX: A MATLAB toolbox for generalized estimating equations and quasi-least squares. J Stat Softw 25:1-14.
-
(2008)
J Stat Softw
, vol.25
, pp. 1-14
-
-
Shults, J.1
Ratcliffe, S.J.2
-
29
-
-
80052961459
-
Twisted schiff base intermediates and substrate locale revise transaldolase mechanism
-
Lehwess-Litzmann A, et al. (2011) Twisted Schiff base intermediates and substrate locale revise transaldolase mechanism. Nat Chem Biol 7:678-684.
-
(2011)
Nat Chem Biol
, vol.7
, pp. 678-684
-
-
Lehwess-Litzmann, A.1
-
30
-
-
85039922037
-
Ancient regulatory role of lysine acetylation in central metabolism
-
Nakayasu ES, et al. (2017) Ancient regulatory role of lysine acetylation in central metabolism. MBio 8:e01894-17.
-
(2017)
MBio
, vol.8
, pp. e01894-e01917
-
-
Nakayasu, E.S.1
-
31
-
-
85049696396
-
Encoding human serine phosphopeptides in bacteria for proteome-wide identification of phosphorylation-dependent interactions
-
Barber KW, et al. (2018) Encoding human serine phosphopeptides in bacteria for proteome-wide identification of phosphorylation-dependent interactions. Nat Biotechnol 36:638-644.
-
(2018)
Nat Biotechnol
, vol.36
, pp. 638-644
-
-
Barber, K.W.1
-
32
-
-
13444262374
-
Ecocyc: A comprehensive database resource for Escherichia coli
-
Keseler IM, et al. (2005) EcoCyc: A comprehensive database resource for Escherichia coli. Nucleic Acids Res 33:D334-D337.
-
(2005)
Nucleic Acids Res
, vol.33
, pp. D334-D337
-
-
Keseler, I.M.1
-
33
-
-
79551662521
-
Quantitative prediction of cellular metabolism with constraint-based models: The cobra toolbox v2.0
-
Schellenberger J, et al. (2011) Quantitative prediction of cellular metabolism with constraint-based models: The COBRA Toolbox v2.0. Nat Protoc 6:1290-1307.
-
(2011)
Nat Protoc
, vol.6
, pp. 1290-1307
-
-
Schellenberger, J.1
-
35
-
-
65549092780
-
Use of randomized sampling for analysis of metabolic networks
-
Schellenberger J, Palsson BOø (2009) Use of randomized sampling for analysis of metabolic networks. J Biol Chem 284:5457-5461.
-
(2009)
J Biol Chem
, vol.284
, pp. 5457-5461
-
-
Schellenberger, J.1
Palsson, B.Oø.2
-
36
-
-
84861963767
-
Genome-scale promoter engineering by coselection mage
-
Wang HH, et al. (2012) Genome-scale promoter engineering by coselection MAGE. Nat Methods 9:591-593.
-
(2012)
Nat Methods
, vol.9
, pp. 591-593
-
-
Wang, H.H.1
-
37
-
-
33644753023
-
Amber force-field parameters for phosphorylated amino acids in different protonation states: Phosphoserine, phosphothreonine, phosphotyrosine, and phosphohistidine
-
Homeyer N, Horn AHC, Lanig H, Sticht H (2006) AMBER force-field parameters for phosphorylated amino acids in different protonation states: Phosphoserine, phosphothreonine, phosphotyrosine, and phosphohistidine. J Mol Model 12:281-289.
-
(2006)
J Mol Model
, vol.12
, pp. 281-289
-
-
Homeyer, N.1
Ahc, H.2
Lanig, H.3
Sticht, H.4
-
38
-
-
84884192184
-
Routine microsecond molecular dynamics simulations with amber on GPUs. 2. Explicit solvent particle mesh ewald
-
Salomon-Ferrer R, Götz AW, Poole D, Le Grand S, Walker RC (2013) Routine microsecond molecular dynamics simulations with AMBER on GPUs. 2. Explicit solvent particle mesh Ewald. J Chem Theory Comput 9:3878-3888.
-
(2013)
J Chem Theory Comput
, vol.9
, pp. 3878-3888
-
-
Salomon-Ferrer, R.1
Götz, A.W.2
Poole, D.3
Le Grand, S.4
Walker, R.C.5
-
39
-
-
84904760980
-
-
Accessed July 8, 2015
-
Case DA, et al. (2014) Amber 14. Available at https://orbilu.uni.lu/handle/10993/16614. Accessed July 8, 2015.
-
(2014)
Amber 14
-
-
Case, D.A.1
-
40
-
-
0001398008
-
How well does a restrained electrostatic potential (resp model perform in calculating conformational energies of organic and biological molecules?
-
Wang J, Cieplak P, Kollman PA (2000) How well does a restrained electrostatic potential (RESP) model perform in calculating conformational energies of organic and biological molecules? J Comput Chem 21:1049-1074.
-
(2000)
J Comput Chem
, vol.21
, pp. 1049-1074
-
-
Wang, J.1
Cieplak, P.2
Kollman, P.A.3
-
41
-
-
33748518255
-
Comparison of multiple amber force fields and development of improved protein backbone parameters
-
Hornak V, et al. (2006) Comparison of multiple Amber force fields and development of improved protein backbone parameters. Proteins 65:712-725.
-
(2006)
Proteins
, vol.65
, pp. 712-725
-
-
Hornak, V.1
-
42
-
-
84866924952
-
Steinernema glaseri surface enolase: Molecular cloning, biological characterization, and role in host immune suppression
-
Liu H, et al. (2012) Steinernema glaseri surface enolase: Molecular cloning, biological characterization, and role in host immune suppression. Mol Biochem Parasitol 185: 89-98.
-
(2012)
Mol Biochem Parasitol
, vol.185
, pp. 89-98
-
-
Liu, H.1
-
43
-
-
58149316581
-
The crystal structure and identification of nqm1/ygr043c, a transaldolase from saccharomyces cerevisiae
-
Huang H, et al. (2008) The crystal structure and identification of NQM1/YGR043C, a transaldolase from Saccharomyces cerevisiae. Proteins 73:1076-1081.
-
(2008)
Proteins
, vol.73
, pp. 1076-1081
-
-
Huang, H.1
-
44
-
-
0344189008
-
[180] serine transhydroxymethylase (rabbit?liver
-
Schirch LV (1971) [180] Serine transhydroxymethylase (rabbit?liver). Methods Enzymol 17:335-340.
-
(1971)
Methods Enzymol
, vol.17
, pp. 335-340
-
-
Schirch, L.V.1
|