Advanced Search
Display options
Filter resources
Text Availability
Article type
Publication date
Species
Language
Sex
Age
Showing 1 to 12 of 295 entries
Sorted by: Best Match Show Resources per page
Metabolic flux balance analysis and the in silico analysis of Escherichia coli K-12 gene deletions

k-12

Edwards JS, Palsson BO.
GSID: SYOhVtZZY7wJ
JS Edwards, BO Palsson - BMC bioinformatics, 2000 - bmcbioinformatics.biomedcentral …

Genome sequencing and bioinformatics are producing detailed lists of the molecular components contained in many prokaryotic organisms. From this 'parts catalogue' of a microbial cell, in silico representations of integrated metabolic functions can be constructed and analyzed …

Cite
Edwards, J. S., & Palsson, B. O. (2000). Metabolic flux balance analysis and the in silico analysis of Escherichia coli K-12 gene deletions. BMC bioinformatics, 1(1), 1-10.
Edwards, Jeremy S., and Bernhard O. Palsson. "Metabolic flux balance analysis and the in silico analysis of Escherichia coli K-12 gene deletions." BMC bioinformatics 1.1 (2000): 1-10.
Copy Download .nbib Format: MLA
Escherichia coli K-12 undergoes adaptive evolution to achieve in silico predicted optimal growth

k-12

Edwards JS, Palsson BO.
GSID: nVsDZZLJhqcJ
RU Ibarra, JS Edwards, BO Palsson - Nature, 2002 - nature.com

… coli K-12 on several substrates (acetate, succinate, malate, glucose and glycerol). All … coli K-12 on malate was predicted a priori by using PPP. The results for growth with malate … coli K-12 MG1655 annotated genome sequence and...

Cite
Ibarra, R. U., Edwards, J. S., & Palsson, B. O. (2002). Escherichia coli K-12 undergoes adaptive evolution to achieve in silico predicted optimal growth. Nature, 420(6912), 186-189.
Ibarra, Rafael U., Jeremy S. Edwards, and Bernhard O. Palsson. "Escherichia coli K-12 undergoes adaptive evolution to achieve in silico predicted optimal growth." Nature 420.6912 (2002): 186-189.
Copy Download .nbib Format: MLA
Genome-wide reconstruction of OxyR and SoxRS transcriptional regulatory networks under oxidative stress in Escherichia coli K-12 MG1655

k-12

Seo SW, Kim D, Palsson BO.
GSID: QrpPjS9jwy8J
SW Seo, D Kim, R Szubin, BO Palsson - Cell Reports, 2015 - Elsevier

Three transcription factors (TFs), OxyR, SoxR, and SoxS, play a critical role in transcriptional regulation of the defense system for oxidative stress in bacteria. However, their full genome-wide regulatory potential is unknown. Here, we perform a genome-scale reconstruction of...

Cite
Seo, S. W., Kim, D., Szubin, R., & Palsson, B. O. (2015). Genome-wide reconstruction of OxyR and SoxRS transcriptional regulatory networks under oxidative stress in Escherichia coli K-12 MG1655. Cell Reports, 12(8), 1289-1299.
Seo, Sang Woo, et al. "Genome-wide reconstruction of OxyR and SoxRS transcriptional regulatory networks under oxidative stress in Escherichia coli K-12 MG1655." Cell Reports 12.8 (2015): 1289-1299.
Copy Download .nbib Format: MLA
Description and Interpretation of Adaptive Evolution of Escherichia coli K-12 MG1655 by Using a Genome-Scale In Silico Metabolic Model

k-12

Fong SS, Palsson BØ.
GSID: U5QGkTk9898J
SS Fong, JY Marciniak, BØ Palsson - Journal of bacteriology, 2003 - Am Soc Microbiol

… coli K-12 wild-type strain MG1655 was grown on 2 g of lactate per liter, we found that at 30C it operated in region 2 of the lactate PhPP (Fig. 2A and B), which is a region characterized by...

Cite
Fong, S. S., Marciniak, J. Y., & Palsson, B. Ø. (2003). Description and interpretation of adaptive evolution of Escherichia coli K-12 MG1655 by using a genome-scale in silico metabolic model. Journal of bacteriology, 185(21), 6400-6408.
Fong, Stephen S., Jennifer Y. Marciniak, and Bernhard Ø. Palsson. "Description and interpretation of adaptive evolution of Escherichia coli K-12 MG1655 by using a genome-scale in silico metabolic model." Journal of bacteriology 185.21 (2003): 6400-6408.
Copy Download .nbib Format: MLA
Adaptive Evolution of Escherichia coli K-12 MG1655 during Growth on a Nonnative Carbon Source, l-1,2-Propanediol

k-12

Lee DH, Palsson BØ.
GSID: FRPtvHCTUXIJ
DH Lee, BØ Palsson - Applied and environmental microbiology, 2010 - Am Soc Microbiol

… In this study, we evolved Escherichia coli K-12 MG1655 with a nonnative carbon source, L-1,2-propanediol (L-1,2-PDO), for 700 generations. We found that (i) experimental evolution of E. coli for 700 generations in 1,2-PDO-supplemented minimal medium resulted in …

Cite
Lee, D. H., & Palsson, B. Ø. (2010). Adaptive evolution of Escherichia coli K-12 MG1655 during growth on a Nonnative carbon source, L-1, 2-propanediol. Applied and environmental microbiology, 76(13), 4158-4168.
Lee, Dae-Hee, and Bernhard Ø. Palsson. "Adaptive evolution of Escherichia coli K-12 MG1655 during growth on a Nonnative carbon source, L-1, 2-propanediol." Applied and environmental microbiology 76.13 (2010): 4158-4168.
Copy Download .nbib Format: MLA
Effective intercellular communication distances are determined by the relative time constants for cyto/chemokine secretion and diffusion

science instructors

Palsson BO.
GSID: B5ctToukfA0J
K Francis, BO Palsson - Proceedings of the National …, 1997 - National Acad Sciences

A cell's ability to effectively communicate with a neighboring cell is essential for tissue function and ultimately for the organism to which it belongs. One important mode of …

Cite
Francis, K., & Palsson, B. O. (1997). Effective intercellular communication distances are determined by the relative time constants for cyto/chemokine secretion and diffusion. Proceedings of the National Academy of Sciences, 94(23), 12258-12262.
Francis, Karl, and Bernhard O. Palsson. "Effective intercellular communication distances are determined by the relative time constants for cyto/chemokine secretion and diffusion." Proceedings of the National Academy of Sciences 94.23 (1997): 12258-12262.
Copy Download .nbib Format: MLA
The developmental transcriptome of contrasting Arctic charr ( Salvelinus alpinus) morphs.

F1000Research

Gudbrandsson J, Ahi EP, Franzdottir SR, Kapralova KH, Kristjansson BK, Steinhaeuser SS, Maier VH, Johannesson IM, Snorrason SS, Jonsson ZO, Palsson A.
PMID: 27635217
F1000Res. 2015 Jun 01;4:136. doi: 10.12688/f1000research.6402.1. eCollection 2015.

Species and populations with parallel evolution of specific traits can help illuminate how predictable adaptations and divergence are at the molecular and developmental level. Following the last glacial period, dwarfism and specialized bottom feeding morphology evolved rapidly in several...

Cite
Gudbrandsson J, Ahi EP, Franzdottir SR, et al. The developmental transcriptome of contrasting Arctic charr ( Salvelinus alpinus) morphs. F1000Res. 2015;4:136doi: 10.12688/f1000research.6402.1.
Gudbrandsson, J., Ahi, E. P., Franzdottir, S. R., Kapralova, K. H., Kristjansson, B. K., Steinhaeuser, S. S., Maier, V. H., Johannesson, I. M., Snorrason, S. S., Jonsson, Z. O., & Palsson, A. (2015). The developmental transcriptome of contrasting Arctic charr ( Salvelinus alpinus) morphs. F1000Research, 4136. https://doi.org/10.12688/f1000research.6402.1
Gudbrandsson, Johannes, et al. "The developmental transcriptome of contrasting Arctic charr ( Salvelinus alpinus) morphs." F1000Research vol. 4 (2015): 136. doi: https://doi.org/10.12688/f1000research.6402.1
Gudbrandsson J, Ahi EP, Franzdottir SR, Kapralova KH, Kristjansson BK, Steinhaeuser SS, Maier VH, Johannesson IM, Snorrason SS, Jonsson ZO, Palsson A. The developmental transcriptome of contrasting Arctic charr ( Salvelinus alpinus) morphs. F1000Res. 2015 Jun 01;4:136. doi: 10.12688/f1000research.6402.1. eCollection 2015. PMID: 27635217; PMCID: PMC5007756.
Copy Download .nbib Format: NLM
Understanding the Causes and Implications of Endothelial Metabolic Variation in Cardiovascular Disease through Genome-Scale Metabolic Modeling.

Frontiers in cardiovascular medicine

McGarrity S, Halldórsson H, Palsson S, Johansson PI, Rolfsson Ó.
PMID: 27148541
Front Cardiovasc Med. 2016 Apr 18;3:10. doi: 10.3389/fcvm.2016.00010. eCollection 2016.

High-throughput biochemical profiling has led to a requirement for advanced data interpretation techniques capable of integrating the analysis of gene, protein, and metabolic profiles to shed light on genotype-phenotype relationships. Herein, we consider the current state of knowledge of...

Cite
McGarrity S, Halldórsson H, Palsson S, et al. Understanding the Causes and Implications of Endothelial Metabolic Variation in Cardiovascular Disease through Genome-Scale Metabolic Modeling. Front Cardiovasc Med. 2016;3:10doi: 10.3389/fcvm.2016.00010.
McGarrity, S., Halldórsson, H., Palsson, S., Johansson, P. I., & Rolfsson, �. �. (2016). Understanding the Causes and Implications of Endothelial Metabolic Variation in Cardiovascular Disease through Genome-Scale Metabolic Modeling. Frontiers in cardiovascular medicine, 310. https://doi.org/10.3389/fcvm.2016.00010
McGarrity, Sarah, et al. "Understanding the Causes and Implications of Endothelial Metabolic Variation in Cardiovascular Disease through Genome-Scale Metabolic Modeling." Frontiers in cardiovascular medicine vol. 3 (2016): 10. doi: https://doi.org/10.3389/fcvm.2016.00010
McGarrity S, Halldórsson H, Palsson S, Johansson PI, Rolfsson Ó. Understanding the Causes and Implications of Endothelial Metabolic Variation in Cardiovascular Disease through Genome-Scale Metabolic Modeling. Front Cardiovasc Med. 2016 Apr 18;3:10. doi: 10.3389/fcvm.2016.00010. eCollection 2016. PMID: 27148541; PMCID: PMC4834436.
Copy Download .nbib Format: NLM
Coarse graining from variationally enhanced sampling applied to the Ginzburg-Landau model.

Proceedings of the National Academy of Sciences of the United States of America

Invernizzi M, Valsson O, Parrinello M.
PMID: 28292890
Proc Natl Acad Sci U S A. 2017 Mar 28;114(13):3370-3374. doi: 10.1073/pnas.1618455114. Epub 2017 Mar 14.

A powerful way to deal with a complex system is to build a coarse-grained model capable of catching its main physical features, while being computationally affordable. Inevitably, such coarse-grained models introduce a set of phenomenological parameters, which are often...

Cite
Invernizzi M, Valsson O, Parrinello M. Coarse graining from variationally enhanced sampling applied to the Ginzburg-Landau model. Proc Natl Acad Sci U S A. 2017;114(13):3370-3374doi: 10.1073/pnas.1618455114.
Invernizzi, M., Valsson, O., & Parrinello, M. (2017). Coarse graining from variationally enhanced sampling applied to the Ginzburg-Landau model. Proceedings of the National Academy of Sciences of the United States of America, 114(13), 3370-3374. https://doi.org/10.1073/pnas.1618455114
Invernizzi, Michele, et al. "Coarse graining from variationally enhanced sampling applied to the Ginzburg-Landau model." Proceedings of the National Academy of Sciences of the United States of America vol. 114,13 (2017): 3370-3374. doi: https://doi.org/10.1073/pnas.1618455114
Invernizzi M, Valsson O, Parrinello M. Coarse graining from variationally enhanced sampling applied to the Ginzburg-Landau model. Proc Natl Acad Sci U S A. 2017 Mar 28;114(13):3370-3374. doi: 10.1073/pnas.1618455114. Epub 2017 Mar 14. PMID: 28292890; PMCID: PMC5380034.
Copy Download .nbib Format: NLM
Interactions of perfluoroalkyl substances with a phospholipid bilayer studied by neutron reflectometry.

Journal of colloid and interface science

Nouhi S, Ahrens L, Campos Pereira H, Hughes AV, Campana M, Gutfreund P, Palsson GK, Vorobiev A, Hellsing MS.
PMID: 29073553
J Colloid Interface Sci. 2018 Feb 01;511:474-481. doi: 10.1016/j.jcis.2017.09.102. Epub 2017 Sep 28.

The interactions between perfluoroalkyl substances (PFASs) and a phospholipid bilayer (1,2-dimyristoyl-sn-glycero-3-phosphocholine) were investigated at the molecular level using neutron reflectometry. Representative PFASs with different chain length and functional groups were selected in this study including: perfluorobutane sulfonate (PFBS), perfluorohexanoate...

Cite
Nouhi S, Ahrens L, Campos Pereira H, et al. Interactions of perfluoroalkyl substances with a phospholipid bilayer studied by neutron reflectometry. J Colloid Interface Sci. 2017;511:474-481doi: 10.1016/j.jcis.2017.09.102.
Nouhi, S., Ahrens, L., Campos Pereira, H., Hughes, A. V., Campana, M., Gutfreund, P., Palsson, G. K., Vorobiev, A., & Hellsing, M. S. (2018). Interactions of perfluoroalkyl substances with a phospholipid bilayer studied by neutron reflectometry. Journal of colloid and interface science, 511474-481. https://doi.org/10.1016/j.jcis.2017.09.102
Nouhi, Shirin, et al. "Interactions of perfluoroalkyl substances with a phospholipid bilayer studied by neutron reflectometry." Journal of colloid and interface science vol. 511 (2018): 474-481. doi: https://doi.org/10.1016/j.jcis.2017.09.102
Nouhi S, Ahrens L, Campos Pereira H, Hughes AV, Campana M, Gutfreund P, Palsson GK, Vorobiev A, Hellsing MS. Interactions of perfluoroalkyl substances with a phospholipid bilayer studied by neutron reflectometry. J Colloid Interface Sci. 2018 Feb 01;511:474-481. doi: 10.1016/j.jcis.2017.09.102. Epub 2017 Sep 28. PMID: 29073553.
Copy Download .nbib Format: NLM
Multi-radionuclide digital autoradiography of the intra-aortic atherosclerotic plaques using a monoclonal antibody targeting oxidized low-density lipoprotein.

American journal of nuclear medicine and molecular imaging

Orbom A, Jansson B, Schiopu A, Evans-Axelsson S, Nilsson J, Fredrikson GN, Strand SE.
PMID: 24753983
Am J Nucl Med Mol Imaging. 2014 Mar 20;4(2):172-80. eCollection 2014.

The aim of this study was to use multi-radionuclide autoradiography to compare the different distributions of three radiolabelled tracers in an atherosclerotic mouse model. This method, along with immunohistochemistry, was applied to investigate the intra-aortic distribution of 2-deoxy-2-[(18)F]fluoro-D-glucose ((18)F-FDG),...

Cite
Orbom A, Jansson B, Schiopu A, et al. Multi-radionuclide digital autoradiography of the intra-aortic atherosclerotic plaques using a monoclonal antibody targeting oxidized low-density lipoprotein. Am J Nucl Med Mol Imaging. 2014;4(2):172-80
Orbom, A., Jansson, B., Schiopu, A., Evans-Axelsson, S., Nilsson, J., Fredrikson, G. N., & Strand, S. E. (2014). Multi-radionuclide digital autoradiography of the intra-aortic atherosclerotic plaques using a monoclonal antibody targeting oxidized low-density lipoprotein. American journal of nuclear medicine and molecular imaging, 4(2), 172-80.
Orbom, Anders, et al. "Multi-radionuclide digital autoradiography of the intra-aortic atherosclerotic plaques using a monoclonal antibody targeting oxidized low-density lipoprotein." American journal of nuclear medicine and molecular imaging vol. 4,2 (2014): 172-80.
Orbom A, Jansson B, Schiopu A, Evans-Axelsson S, Nilsson J, Fredrikson GN, Strand SE. Multi-radionuclide digital autoradiography of the intra-aortic atherosclerotic plaques using a monoclonal antibody targeting oxidized low-density lipoprotein. Am J Nucl Med Mol Imaging. 2014 Mar 20;4(2):172-80. eCollection 2014. PMID: 24753983; PMCID: PMC3992210.
Copy Download .nbib Format: NLM
Thermodynamical Description of a Quasi-First-Order Phase Transition from the Well-Tempered Ensemble.

Journal of chemical theory and computation

Valsson O, Parrinello M.
PMID: 26592265
J Chem Theory Comput. 2013 Dec 10;9(12):5267-76. doi: 10.1021/ct400859f. Epub 2013 Nov 21.

We explore the performance of the well-tempered ensemble combined with parallel tempering (PT-WTE) in obtaining a thermodynamical description of a given molecular system. We carefully explain the theoretical procedure employed to extract all the relevant thermodynamical quantities from a...

Cite
Valsson O, Parrinello M. Thermodynamical Description of a Quasi-First-Order Phase Transition from the Well-Tempered Ensemble. J Chem Theory Comput. 2013;9(12):5267-76doi: 10.1021/ct400859f.
Valsson, O., & Parrinello, M. (2013). Thermodynamical Description of a Quasi-First-Order Phase Transition from the Well-Tempered Ensemble. Journal of chemical theory and computation, 9(12), 5267-76. https://doi.org/10.1021/ct400859f
Valsson, Omar, and Parrinello, Michele. "Thermodynamical Description of a Quasi-First-Order Phase Transition from the Well-Tempered Ensemble." Journal of chemical theory and computation vol. 9,12 (2013): 5267-76. doi: https://doi.org/10.1021/ct400859f
Valsson O, Parrinello M. Thermodynamical Description of a Quasi-First-Order Phase Transition from the Well-Tempered Ensemble. J Chem Theory Comput. 2013 Dec 10;9(12):5267-76. doi: 10.1021/ct400859f. Epub 2013 Nov 21. PMID: 26592265.
Copy Download .nbib Format: NLM
Showing 1 to 12 of 295 entries