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Multi-omics integration accurately predicts cellular state in unexplored conditions for Escherichia coli.

Nature communications

Kim M, Rai N, Zorraquino V, Tagkopoulos I.
PMID: 27713404
Nat Commun. 2016 Oct 07;7:13090. doi: 10.1038/ncomms13090.

A significant obstacle in training predictive cell models is the lack of integrated data sources. We develop semi-supervised normalization pipelines and perform experimental characterization (growth, transcriptional, proteome) to create Ecomics, a consistent, quality-controlled multi-omics compendium for Escherichia coli with...

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Kim M, Rai N, Zorraquino V, et al. Multi-omics integration accurately predicts cellular state in unexplored conditions for Escherichia coli. Nat Commun. 2016;7:13090doi: 10.1038/ncomms13090.
Kim, M., Rai, N., Zorraquino, V., & Tagkopoulos, I. (2016). Multi-omics integration accurately predicts cellular state in unexplored conditions for Escherichia coli. Nature communications, 713090. https://doi.org/10.1038/ncomms13090
Kim, Minseung, et al. "Multi-omics integration accurately predicts cellular state in unexplored conditions for Escherichia coli." Nature communications vol. 7 (2016): 13090. doi: https://doi.org/10.1038/ncomms13090
Kim M, Rai N, Zorraquino V, Tagkopoulos I. Multi-omics integration accurately predicts cellular state in unexplored conditions for Escherichia coli. Nat Commun. 2016 Oct 07;7:13090. doi: 10.1038/ncomms13090. PMID: 27713404; PMCID: PMC5059772.
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[Dependence of bacteria length on the growth phase of a bacterial culture].

Doklady Akademii nauk

Medvinskiĭ AB, Shakhbazian VIu, Krest'eva IB, Tsyganov MA, Kuz'min SV, Ivanitskiĭ GR.
PMID: 1490186
Dokl Akad Nauk. 1992;326(1):194-7.

No abstract available.

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Medvinskiĭ AB, Shakhbazian VIu, Krest'eva IB, et al. Zavisimost' dliny bakterii ot fazy rosta bakterial'noĭ kul'tury. [Dependence of bacteria length on the growth phase of a bacterial culture]. Dokl Akad Nauk. 1992;326(1):194-7
Medvinskiĭ, A. B., Shakhbazian, V. I. u., Krest'eva, I. B., Tsyganov, M. A., Kuz'min, S. V., & Ivanitskiĭ, G. R. (1992). Zavisimost' dliny bakterii ot fazy rosta bakterial'noĭ kul'tury. [Dependence of bacteria length on the growth phase of a bacterial culture]. Doklady Akademii nauk, 326(1), 194-7.
Medvinskiĭ, A B, et al. "Zavisimost' dliny bakterii ot fazy rosta bakterial'noĭ kul'tury." [Dependence of bacteria length on the growth phase of a bacterial culture]. Doklady Akademii nauk vol. 326,1 (1992): 194-7.
Medvinskiĭ AB, Shakhbazian VIu, Krest'eva IB, Tsyganov MA, Kuz'min SV, Ivanitskiĭ GR. Zavisimost' dliny bakterii ot fazy rosta bakterial'noĭ kul'tury. [Dependence of bacteria length on the growth phase of a bacterial culture]. Dokl Akad Nauk. 1992;326(1):194-7. Russian. PMID: 1490186.
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[Viability of Escherichia coli cultures].

Mikrobiologiia

Marchenkova TV, Gurevich IuL.
PMID: 796631
Mikrobiologiia. 1976 Nov-Dec;45(6):1100-2.

In the logarithmic phase of batch cultures of E. coli B and MRE-600, a high percentage (upto 80%) of the cells did not grow. Viability of the cells was estimated by inoculation on plates, in agar drops, and on...

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Marchenkova TV, Gurevich IuL. Zhiznesposobnost' kul'tury kishechnoĭ palochki [Viability of Escherichia coli cultures]. Mikrobiologiia. 1976;45(6):1100-2
Marchenkova, T. V., & Gurevich, I. u. L. (1976). Zhiznesposobnost' kul'tury kishechnoĭ palochki [Viability of Escherichia coli cultures]. Mikrobiologiia, 45(6), 1100-2.
Marchenkova, T V, and Gurevich, Iu L. "Zhiznesposobnost' kul'tury kishechnoĭ palochki" [Viability of Escherichia coli cultures]. Mikrobiologiia vol. 45,6 (1976): 1100-2.
Marchenkova TV, Gurevich IuL. Zhiznesposobnost' kul'tury kishechnoĭ palochki [Viability of Escherichia coli cultures]. Mikrobiologiia. 1976 Nov-Dec;45(6):1100-2. Russian. PMID: 796631.
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Control of Escherichia coli growth rate through cell density.

Microbiological research

Carbonell X, Corchero JL, Cubarsí R, Vila P, Villaverde A.
PMID: 12501989
Microbiol Res. 2002;157(4):257-65. doi: 10.1078/0944-5013-00167.

The transition from the exponential to the stationary phase of Escherichia coli cultures has been investigated regarding nutrient availability. This analysis strongly suggests that the declining of the cell division rate is not caused by mere nutrient limitation but...

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Carbonell X, Corchero JL, Cubarsí R, et al. Control of Escherichia coli growth rate through cell density. Microbiol Res. 2002;157(4):257-65doi: 10.1078/0944-5013-00167.
Carbonell, X., Corchero, J. L., Cubarsí, R., Vila, P., & Villaverde, A. (2002). Control of Escherichia coli growth rate through cell density. Microbiological research, 157(4), 257-65. https://doi.org/10.1078/0944-5013-00167
Carbonell, Xavier, et al. "Control of Escherichia coli growth rate through cell density." Microbiological research vol. 157,4 (2002): 257-65. doi: https://doi.org/10.1078/0944-5013-00167
Carbonell X, Corchero JL, Cubarsí R, Vila P, Villaverde A. Control of Escherichia coli growth rate through cell density. Microbiol Res. 2002;157(4):257-65. doi: 10.1078/0944-5013-00167. PMID: 12501989.
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Robust growth of Escherichia coli.

Current biology : CB

Wang P, Robert L, Pelletier J, Dang WL, Taddei F, Wright A, Jun S.
PMID: 20537537
Curr Biol. 2010 Jun 22;20(12):1099-103. doi: 10.1016/j.cub.2010.04.045. Epub 2010 May 27.

The quantitative study of the cell growth has led to many fundamental insights in our understanding of a wide range of subjects, from the cell cycle to senescence. Of particular importance is the growth rate, whose constancy represents a...

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Wang P, Robert L, Pelletier J, et al. Robust growth of Escherichia coli. Curr Biol. 2010;20(12):1099-103doi: 10.1016/j.cub.2010.04.045.
Wang, P., Robert, L., Pelletier, J., Dang, W. L., Taddei, F., Wright, A., & Jun, S. (2010). Robust growth of Escherichia coli. Current biology : CB, 20(12), 1099-103. https://doi.org/10.1016/j.cub.2010.04.045
Wang, Ping, et al. "Robust growth of Escherichia coli." Current biology : CB vol. 20,12 (2010): 1099-103. doi: https://doi.org/10.1016/j.cub.2010.04.045
Wang P, Robert L, Pelletier J, Dang WL, Taddei F, Wright A, Jun S. Robust growth of Escherichia coli. Curr Biol. 2010 Jun 22;20(12):1099-103. doi: 10.1016/j.cub.2010.04.045. Epub 2010 May 27. PMID: 20537537; PMCID: PMC2902570.
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Density-Dependent Recycling Promotes the Long-Term Survival of Bacterial Populations during Periods of Starvation.

mBio

Takano S, Pawlowska BJ, Gudelj I, Yomo T, Tsuru S.
PMID: 28174316
mBio. 2017 Feb 07;8(1). doi: 10.1128/mBio.02336-16.

The amount of natural resources in the Earth's environment is in flux, which can trigger catastrophic collapses of ecosystems. How populations survive under nutrient-poor conditions is a central question in ecology. Curiously, some bacteria persist for a long time...

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Takano S, Pawlowska BJ, Gudelj I, et al. Density-Dependent Recycling Promotes the Long-Term Survival of Bacterial Populations during Periods of Starvation. mBio. 2017;8(1)doi: 10.1128/mBio.02336-16.
Takano, S., Pawlowska, B. J., Gudelj, I., Yomo, T., & Tsuru, S. (2017). Density-Dependent Recycling Promotes the Long-Term Survival of Bacterial Populations during Periods of Starvation. mBio, 8(1), . https://doi.org/10.1128/mBio.02336-16
Takano, Sotaro, et al. "Density-Dependent Recycling Promotes the Long-Term Survival of Bacterial Populations during Periods of Starvation." mBio vol. 8,1 (2017). doi: https://doi.org/10.1128/mBio.02336-16
Takano S, Pawlowska BJ, Gudelj I, Yomo T, Tsuru S. Density-Dependent Recycling Promotes the Long-Term Survival of Bacterial Populations during Periods of Starvation. mBio. 2017 Feb 07;8(1). doi: 10.1128/mBio.02336-16. PMID: 28174316; PMCID: PMC5296608.
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Relationship of Escherichia coli density to growth rate and cell age.

Journal of bacteriology

Martínez-Salas E, Martín JA, Vicente M.
PMID: 7016845
J Bacteriol. 1981 Jul;147(1):97-100. doi: 10.1128/jb.147.1.97-100.1981.
Free PMC Article

The cell densities of Escherichia coli strains B/rA, BrF, and K-12 (OV-2) were measured at several growth rates and found to be very near 1.105 g/ml in all cases. Ninety percent of the cells of any exponentially growing population...

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Martínez-Salas E, Martín JA, Vicente M. Relationship of Escherichia coli density to growth rate and cell age. J Bacteriol. 1981;147(1):97-100doi: 10.1128/jb.147.1.97-100.1981.
Martínez-Salas, E., Martín, J. A., & Vicente, M. (1981). Relationship of Escherichia coli density to growth rate and cell age. Journal of bacteriology, 147(1), 97-100. https://doi.org/10.1128/jb.147.1.97-100.1981
Martínez-Salas, E, et al. "Relationship of Escherichia coli density to growth rate and cell age." Journal of bacteriology vol. 147,1 (1981): 97-100. doi: https://doi.org/10.1128/jb.147.1.97-100.1981
Martínez-Salas E, Martín JA, Vicente M. Relationship of Escherichia coli density to growth rate and cell age. J Bacteriol. 1981 Jul;147(1):97-100. doi: 10.1128/jb.147.1.97-100.1981. PMID: 7016845; PMCID: PMC216012.
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A simple and rapid method for isolating mutator strains in Escherichia coli B. & K-12.

Indian journal of experimental biology

Singh A, Chopra VL.
PMID: 3914450
Indian J Exp Biol. 1985 Oct;23(10):604-5.

No abstract available.

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Singh A, Chopra VL. A simple and rapid method for isolating mutator strains in Escherichia coli B. & K-12. Indian J Exp Biol. 1985;23(10):604-5
Singh, A., & Chopra, V. L. (1985). A simple and rapid method for isolating mutator strains in Escherichia coli B. & K-12. Indian journal of experimental biology, 23(10), 604-5.
Singh, A, and Chopra, V L. "A simple and rapid method for isolating mutator strains in Escherichia coli B. & K-12." Indian journal of experimental biology vol. 23,10 (1985): 604-5.
Singh A, Chopra VL. A simple and rapid method for isolating mutator strains in Escherichia coli B. & K-12. Indian J Exp Biol. 1985 Oct;23(10):604-5. PMID: 3914450.
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Constancy of growth on simple and complex media.

Journal of bacteriology

Wang CH, Koch AL.
PMID: 363700
J Bacteriol. 1978 Dec;136(3):969-75. doi: 10.1128/jb.136.3.969-975.1978.
Free PMC Article

An apparatus has been developed in which bacterial growth can be measured very precisely over short intervals of time. Its precision is presented and used to assess the constancy of growth in batch culture. Under certain conditions, i.e., Luria...

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Wang CH, Koch AL. Constancy of growth on simple and complex media. J Bacteriol. 1978;136(3):969-75doi: 10.1128/jb.136.3.969-975.1978.
Wang, C. H., & Koch, A. L. (1978). Constancy of growth on simple and complex media. Journal of bacteriology, 136(3), 969-75. https://doi.org/10.1128/jb.136.3.969-975.1978
Wang, C H, and Koch, A L. "Constancy of growth on simple and complex media." Journal of bacteriology vol. 136,3 (1978): 969-75. doi: https://doi.org/10.1128/jb.136.3.969-975.1978
Wang CH, Koch AL. Constancy of growth on simple and complex media. J Bacteriol. 1978 Dec;136(3):969-75. doi: 10.1128/jb.136.3.969-975.1978. PMID: 363700; PMCID: PMC218532.
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[Oscillation in the number of bacteria during starvation].

Biofizika

Vakhitov TIa.
PMID: 10439867
Biofizika. 1999 May-Jun;44(3):503-4.

Factors stimulating the increase in the numbers of Escherichia coli bacteria and accelerating their death were studied. It was shown that oscillations in the numbers of viable bacteria are due to periodic changes in the activity of these two...

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Vakhitov TIa. Kolebanie chislennosti bakteriĭ v protsesse golodaniia. [Oscillation in the number of bacteria during starvation]. Biofizika. 1999;44(3):503-4
Vakhitov, T. I. a. (1999). Kolebanie chislennosti bakteriĭ v protsesse golodaniia. [Oscillation in the number of bacteria during starvation]. Biofizika, 44(3), 503-4.
Vakhitov, T Ia. "Kolebanie chislennosti bakteriĭ v protsesse golodaniia." [Oscillation in the number of bacteria during starvation]. Biofizika vol. 44,3 (1999): 503-4.
Vakhitov TIa. Kolebanie chislennosti bakteriĭ v protsesse golodaniia. [Oscillation in the number of bacteria during starvation]. Biofizika. 1999 May-Jun;44(3):503-4. Russian. PMID: 10439867.
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Colony architectonics and heterogeneity of Escherichia coli populations.

Doklady biophysics : proceedings of the Academy of Sciences of the USSR, Biophysics section

Kravchenko VV, Medvinskii AB, Aslanidi KB, Ivanitskii GR.
PMID: 11029027
Dokl Biophys. 2000 Jan-Jun;370:1-3.

No abstract available.

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Kravchenko VV, Medvinskii AB, Aslanidi KB, et al. Colony architectonics and heterogeneity of Escherichia coli populations. Dokl Biophys. 2000;370:1-3
Kravchenko, V. V., Medvinskii, A. B., Aslanidi, K. B., & Ivanitskii, G. R. (2000). Colony architectonics and heterogeneity of Escherichia coli populations. Doklady biophysics : proceedings of the Academy of Sciences of the USSR, Biophysics section, 3701-3.
Kravchenko, V V, et al. "Colony architectonics and heterogeneity of Escherichia coli populations." Doklady biophysics : proceedings of the Academy of Sciences of the USSR, Biophysics section vol. 370 (2000): 1-3.
Kravchenko VV, Medvinskii AB, Aslanidi KB, Ivanitskii GR. Colony architectonics and heterogeneity of Escherichia coli populations. Dokl Biophys. 2000 Jan-Jun;370:1-3. PMID: 11029027.
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Hypercomplexity.

Acta biotheoretica

Norris V, Cabin A, Zemirline A.
PMID: 16583272
Acta Biotheor. 2005;53(4):313-30. doi: 10.1007/s10441-005-4882-3.

What is biological complexity? How many sorts exist? Are there levels of complexity? How are they related to one another? How is complexity related to the emergence of new phenotypes? To try to get to grips with these questions,...

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Norris V, Cabin A, Zemirline A. Hypercomplexity. Acta Biotheor. 2005;53(4):313-30doi: 10.1007/s10441-005-4882-3.
Norris, V., Cabin, A., & Zemirline, A. (2005). Hypercomplexity. Acta biotheoretica, 53(4), 313-30. https://doi.org/10.1007/s10441-005-4882-3
Norris, Vic, et al. "Hypercomplexity." Acta biotheoretica vol. 53,4 (2005): 313-30. doi: https://doi.org/10.1007/s10441-005-4882-3
Norris V, Cabin A, Zemirline A. Hypercomplexity. Acta Biotheor. 2005;53(4):313-30. doi: 10.1007/s10441-005-4882-3. PMID: 16583272.
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Showing 1 to 12 of 18 entries