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For: Oberhardt MA, Goldberg JB, Hogardt M, Papin JA. Metabolic network analysis of Pseudomonas aeruginosa during chronic cystic fibrosis lung infection. J Bacteriol 2010;192:5534-48. [PMID: 20709898 DOI: 10.1128/JB.00900-10] [Citation(s) in RCA: 81] [Impact Index Per Article: 5.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/15/2022]  Open
Number Cited by Other Article(s)
1
Upregulation of TLR4-Dependent ATP Production Is Critical for Glaesserella parasuis LPS-Mediated Inflammation. Cells 2023;12:cells12050751. [PMID: 36899887 PMCID: PMC10001010 DOI: 10.3390/cells12050751] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/01/2023] [Revised: 02/15/2023] [Accepted: 02/24/2023] [Indexed: 03/02/2023]  Open
2
Rajput A, Tsunemoto H, Sastry AV, Szubin R, Rychel K, Sugie J, Pogliano J, Palsson BO. Machine learning from Pseudomonas aeruginosa transcriptomes identifies independently modulated sets of genes associated with known transcriptional regulators. Nucleic Acids Res 2022;50:3658-3672. [PMID: 35357493 PMCID: PMC9023270 DOI: 10.1093/nar/gkac187] [Citation(s) in RCA: 18] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/12/2021] [Revised: 02/28/2022] [Accepted: 03/29/2022] [Indexed: 12/16/2022]  Open
3
Mohammad FK, Palukuri MV, Shivakumar S, Rengaswamy R, Sahoo S. A Computational Framework for Studying Gut-Brain Axis in Autism Spectrum Disorder. Front Physiol 2022;13:760753. [PMID: 35330929 PMCID: PMC8940246 DOI: 10.3389/fphys.2022.760753] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/18/2021] [Accepted: 01/17/2022] [Indexed: 12/28/2022]  Open
4
Medeiros Filho F, do Nascimento APB, Costa MDOCE, Merigueti TC, de Menezes MA, Nicolás MF, Dos Santos MT, Carvalho-Assef APD, da Silva FAB. A Systematic Strategy to Find Potential Therapeutic Targets for Pseudomonas aeruginosa Using Integrated Computational Models. Front Mol Biosci 2021;8:728129. [PMID: 34616771 PMCID: PMC8488468 DOI: 10.3389/fmolb.2021.728129] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/29/2021] [Accepted: 08/31/2021] [Indexed: 12/26/2022]  Open
5
Gil-Gil T, Ochoa-Sánchez LE, Baquero F, Martínez JL. Antibiotic resistance: Time of synthesis in a post-genomic age. Comput Struct Biotechnol J 2021;19:3110-3124. [PMID: 34141134 PMCID: PMC8181582 DOI: 10.1016/j.csbj.2021.05.034] [Citation(s) in RCA: 16] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/26/2021] [Revised: 05/13/2021] [Accepted: 05/20/2021] [Indexed: 12/20/2022]  Open
6
Lewis JE, Forshaw TE, Boothman DA, Furdui CM, Kemp ML. Personalized Genome-Scale Metabolic Models Identify Targets of Redox Metabolism in Radiation-Resistant Tumors. Cell Syst 2021;12:68-81.e11. [PMID: 33476554 PMCID: PMC7905848 DOI: 10.1016/j.cels.2020.12.001] [Citation(s) in RCA: 32] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/16/2020] [Revised: 08/04/2020] [Accepted: 12/16/2020] [Indexed: 12/14/2022]
7
McGill SL, Yung Y, Hunt KA, Henson MA, Hanley L, Carlson RP. Pseudomonas aeruginosa reverse diauxie is a multidimensional, optimized, resource utilization strategy. Sci Rep 2021;11:1457. [PMID: 33446818 PMCID: PMC7809481 DOI: 10.1038/s41598-020-80522-8] [Citation(s) in RCA: 24] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/03/2020] [Accepted: 12/17/2020] [Indexed: 12/19/2022]  Open
8
Zardini Buzatto A, Abdel Jabar M, Nizami I, Dasouki M, Li L, Abdel Rahman AM. Lipidome Alterations Induced by Cystic Fibrosis, CFTR Mutation, and Lung Function. J Proteome Res 2020;20:549-564. [PMID: 33089695 DOI: 10.1021/acs.jproteome.0c00556] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/15/2022]
9
Leonard-Duke J, Evans S, Hannan RT, Barker TH, Bates JHT, Bonham CA, Moore BB, Kirschner DE, Peirce SM. Multi-scale models of lung fibrosis. Matrix Biol 2020;91-92:35-50. [PMID: 32438056 DOI: 10.1016/j.matbio.2020.04.003] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/05/2020] [Revised: 03/13/2020] [Accepted: 04/15/2020] [Indexed: 02/08/2023]
10
Sundararaghavan A, Mukherjee A, Sahoo S, Suraishkumar GK. Mechanism of the oxidative stress‐mediated increase in lipid accumulation by the bacterium,R. opacusPD630: Experimental analysis and genome‐scale metabolic modeling. Biotechnol Bioeng 2020;117:1779-1788. [DOI: 10.1002/bit.27330] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/06/2019] [Revised: 02/22/2020] [Accepted: 03/09/2020] [Indexed: 12/13/2022]
11
Park H, McGill SL, Arnold AD, Carlson RP. Pseudomonad reverse carbon catabolite repression, interspecies metabolite exchange, and consortial division of labor. Cell Mol Life Sci 2020;77:395-413. [PMID: 31768608 PMCID: PMC7015805 DOI: 10.1007/s00018-019-03377-x] [Citation(s) in RCA: 27] [Impact Index Per Article: 5.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/04/2019] [Revised: 11/04/2019] [Accepted: 11/12/2019] [Indexed: 10/25/2022]
12
Cesur MF, Siraj B, Uddin R, Durmuş S, Çakır T. Network-Based Metabolism-Centered Screening of Potential Drug Targets in Klebsiella pneumoniae at Genome Scale. Front Cell Infect Microbiol 2020;9:447. [PMID: 31993376 PMCID: PMC6970976 DOI: 10.3389/fcimb.2019.00447] [Citation(s) in RCA: 26] [Impact Index Per Article: 5.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/19/2019] [Accepted: 12/12/2019] [Indexed: 01/28/2023]  Open
13
Merigueti TC, Carneiro MW, Carvalho-Assef APD, Silva-Jr FP, da Silva FAB. FindTargetsWEB: A User-Friendly Tool for Identification of Potential Therapeutic Targets in Metabolic Networks of Bacteria. Front Genet 2019;10:633. [PMID: 31333719 PMCID: PMC6620235 DOI: 10.3389/fgene.2019.00633] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/27/2019] [Accepted: 06/17/2019] [Indexed: 11/13/2022]  Open
14
Metabolic Modeling of Cystic Fibrosis Airway Communities Predicts Mechanisms of Pathogen Dominance. mSystems 2019;4:mSystems00026-19. [PMID: 31020043 PMCID: PMC6478966 DOI: 10.1128/msystems.00026-19] [Citation(s) in RCA: 25] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/14/2019] [Accepted: 03/29/2019] [Indexed: 01/08/2023]  Open
15
Wojciech J, Kamila M, Wojciech B. Investigation of the population dynamics within a Pseudomonas aeruginosa biofilm using a flow based biofilm model system and flow cytometric evaluation of cellular physiology. BIOFOULING 2018;34:835-850. [PMID: 30332894 DOI: 10.1080/08927014.2018.1508569] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/11/2018] [Revised: 07/16/2018] [Accepted: 07/25/2018] [Indexed: 06/08/2023]
16
Zhu Y, Czauderna T, Zhao J, Klapperstueck M, Maifiah MHM, Han ML, Lu J, Sommer B, Velkov T, Lithgow T, Song J, Schreiber F, Li J. Genome-scale metabolic modeling of responses to polymyxins in Pseudomonas aeruginosa. Gigascience 2018;7:4931736. [PMID: 29688451 PMCID: PMC6333913 DOI: 10.1093/gigascience/giy021] [Citation(s) in RCA: 37] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/17/2017] [Revised: 01/19/2018] [Accepted: 02/22/2018] [Indexed: 01/06/2023]  Open
17
Cesur MF, Abdik E, Güven-Gülhan Ü, Durmuş S, Çakır T. Computational Systems Biology of Metabolism in Infection. EXPERIENTIA SUPPLEMENTUM (2012) 2018;109:235-282. [PMID: 30535602 DOI: 10.1007/978-3-319-74932-7_6] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/09/2023]
18
Chua SL, Ding Y, Liu Y, Cai Z, Zhou J, Swarup S, Drautz-Moses DI, Schuster SC, Kjelleberg S, Givskov M, Yang L. Reactive oxygen species drive evolution of pro-biofilm variants in pathogens by modulating cyclic-di-GMP levels. Open Biol 2017;6:rsob.160162. [PMID: 27881736 PMCID: PMC5133437 DOI: 10.1098/rsob.160162] [Citation(s) in RCA: 55] [Impact Index Per Article: 6.9] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/02/2016] [Accepted: 10/23/2016] [Indexed: 12/14/2022]  Open
19
Wang X, Li W, Zhang Y, Feng Y, Zhao X, He Y, Zhang J, Chen L. Chronic obstructive pulmonary disease candidate gene prioritization based on metabolic networks and functional information. PLoS One 2017;12:e0184299. [PMID: 28873096 PMCID: PMC5584748 DOI: 10.1371/journal.pone.0184299] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/23/2017] [Accepted: 08/21/2017] [Indexed: 02/07/2023]  Open
20
Otero-Muras I, Banga JR. Automated Design Framework for Synthetic Biology Exploiting Pareto Optimality. ACS Synth Biol 2017;6:1180-1193. [PMID: 28350462 DOI: 10.1021/acssynbio.6b00306] [Citation(s) in RCA: 26] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/14/2022]
21
Carey MA, Papin JA, Guler JL. Novel Plasmodium falciparum metabolic network reconstruction identifies shifts associated with clinical antimalarial resistance. BMC Genomics 2017;18:543. [PMID: 28724354 PMCID: PMC5518114 DOI: 10.1186/s12864-017-3905-1] [Citation(s) in RCA: 31] [Impact Index Per Article: 3.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/23/2017] [Accepted: 06/27/2017] [Indexed: 02/06/2023]  Open
22
Robinson JL, Jaslove JM, Murawski AM, Fazen CH, Brynildsen MP. An integrated network analysis reveals that nitric oxide reductase prevents metabolic cycling of nitric oxide by Pseudomonas aeruginosa. Metab Eng 2017;41:67-81. [PMID: 28363762 DOI: 10.1016/j.ymben.2017.03.006] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/25/2016] [Revised: 12/21/2016] [Accepted: 03/27/2017] [Indexed: 01/08/2023]
23
Biggs MB, Papin JA. Managing uncertainty in metabolic network structure and improving predictions using EnsembleFBA. PLoS Comput Biol 2017;13:e1005413. [PMID: 28263984 PMCID: PMC5358886 DOI: 10.1371/journal.pcbi.1005413] [Citation(s) in RCA: 30] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/27/2016] [Revised: 03/20/2017] [Accepted: 02/15/2017] [Indexed: 11/19/2022]  Open
24
Jinawath N, Bunbanjerdsuk S, Chayanupatkul M, Ngamphaiboon N, Asavapanumas N, Svasti J, Charoensawan V. Bridging the gap between clinicians and systems biologists: from network biology to translational biomedical research. J Transl Med 2016;14:324. [PMID: 27876057 PMCID: PMC5120462 DOI: 10.1186/s12967-016-1078-3] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/23/2016] [Accepted: 11/08/2016] [Indexed: 01/22/2023]  Open
25
Metabolic flux analyses of Pseudomonas aeruginosa cystic fibrosis isolates. Metab Eng 2016;38:251-263. [PMID: 27637318 DOI: 10.1016/j.ymben.2016.09.002] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/22/2016] [Revised: 06/07/2016] [Accepted: 09/11/2016] [Indexed: 01/22/2023]
26
Maldonado RF, Sá-Correia I, Valvano MA. Lipopolysaccharide modification in Gram-negative bacteria during chronic infection. FEMS Microbiol Rev 2016;40:480-93. [PMID: 27075488 PMCID: PMC4931227 DOI: 10.1093/femsre/fuw007] [Citation(s) in RCA: 410] [Impact Index Per Article: 45.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Revised: 08/23/2015] [Accepted: 03/10/2016] [Indexed: 12/16/2022]  Open
27
Varga JJ, Barbier M, Mulet X, Bielecki P, Bartell JA, Owings JP, Martinez-Ramos I, Hittle LE, Davis MR, Damron FH, Liechti GW, Puchałka J, dos Santos VAPM, Ernst RK, Papin JA, Albertí S, Oliver A, Goldberg JB. Genotypic and phenotypic analyses of a Pseudomonas aeruginosa chronic bronchiectasis isolate reveal differences from cystic fibrosis and laboratory strains. BMC Genomics 2015;16:883. [PMID: 26519161 PMCID: PMC4628258 DOI: 10.1186/s12864-015-2069-0] [Citation(s) in RCA: 26] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/21/2015] [Accepted: 10/03/2015] [Indexed: 01/24/2023]  Open
28
Vital-Lopez FG, Reifman J, Wallqvist A. Biofilm Formation Mechanisms of Pseudomonas aeruginosa Predicted via Genome-Scale Kinetic Models of Bacterial Metabolism. PLoS Comput Biol 2015;11:e1004452. [PMID: 26431398 PMCID: PMC4592021 DOI: 10.1371/journal.pcbi.1004452] [Citation(s) in RCA: 43] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/13/2015] [Accepted: 07/14/2015] [Indexed: 12/28/2022]  Open
29
Kim M, Yi JS, Lakshmanan M, Lee DY, Kim BG. Transcriptomics-based strain optimization tool for designing secondary metabolite overproducing strains of Streptomyces coelicolor. Biotechnol Bioeng 2015;113:651-60. [PMID: 26369755 DOI: 10.1002/bit.25830] [Citation(s) in RCA: 33] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/11/2015] [Revised: 08/26/2015] [Accepted: 09/07/2015] [Indexed: 12/23/2022]
30
An Integrated Modeling and Experimental Approach to Study the Influence of Environmental Nutrients on Biofilm Formation of Pseudomonas aeruginosa. BIOMED RESEARCH INTERNATIONAL 2015;2015:506782. [PMID: 25954752 PMCID: PMC4411446 DOI: 10.1155/2015/506782] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 09/24/2014] [Accepted: 02/09/2015] [Indexed: 12/18/2022]
31
Bacterial Adaptation during Chronic Respiratory Infections. Pathogens 2015;4:66-89. [PMID: 25738646 PMCID: PMC4384073 DOI: 10.3390/pathogens4010066] [Citation(s) in RCA: 117] [Impact Index Per Article: 11.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/03/2014] [Revised: 02/15/2015] [Accepted: 02/25/2015] [Indexed: 01/22/2023]  Open
32
Shi C, Yin J, Liu Z, Wu JX, Zhao Q, Ren J, Yao N. A systematic simulation of the effect of salicylic acid on sphingolipid metabolism. FRONTIERS IN PLANT SCIENCE 2015;6:186. [PMID: 25859253 PMCID: PMC4373270 DOI: 10.3389/fpls.2015.00186] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/20/2014] [Accepted: 03/08/2015] [Indexed: 05/04/2023]
33
Hosseinkhan N, Zarrineh P, Masoudi-Nejad A. Analysis of Genome-scale Expression Network in Four Major Bacterial Residents of Cystic Fibrosis Lung. Curr Genomics 2014;15:408-18. [PMID: 25435803 PMCID: PMC4245700 DOI: 10.2174/1389202915666140818205444] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/21/2013] [Revised: 07/06/2014] [Accepted: 08/15/2014] [Indexed: 11/22/2022]  Open
34
Diez D, Agustí A, Wheelock CE. Network Analysis in the Investigation of Chronic Respiratory Diseases. From Basics to Application. Am J Respir Crit Care Med 2014;190:981-8. [DOI: 10.1164/rccm.201403-0421pp] [Citation(s) in RCA: 38] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/14/2022]  Open
35
Line L, Alhede M, Kolpen M, Kühl M, Ciofu O, Bjarnsholt T, Moser C, Toyofuku M, Nomura N, Høiby N, Jensen PØ. Physiological levels of nitrate support anoxic growth by denitrification of Pseudomonas aeruginosa at growth rates reported in cystic fibrosis lungs and sputum. Front Microbiol 2014;5:554. [PMID: 25386171 PMCID: PMC4208399 DOI: 10.3389/fmicb.2014.00554] [Citation(s) in RCA: 68] [Impact Index Per Article: 6.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/14/2014] [Accepted: 10/03/2014] [Indexed: 12/13/2022]  Open
36
Wu X, Chen L, Wang X. Network biomarkers, interaction networks and dynamical network biomarkers in respiratory diseases. Clin Transl Med 2014;3:16. [PMID: 24995123 PMCID: PMC4072888 DOI: 10.1186/2001-1326-3-16] [Citation(s) in RCA: 44] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/03/2014] [Accepted: 06/12/2014] [Indexed: 11/17/2022]  Open
37
Thiele I, Vlassis N, Fleming RMT. fastGapFill: efficient gap filling in metabolic networks. Bioinformatics 2014;30:2529-31. [PMID: 24812336 PMCID: PMC4147887 DOI: 10.1093/bioinformatics/btu321] [Citation(s) in RCA: 74] [Impact Index Per Article: 6.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/16/2022]  Open
38
Qin X. Chronic pulmonary pseudomonal infection in patients with cystic fibrosis: A model for early phase symbiotic evolution. Crit Rev Microbiol 2014;42:144-57. [PMID: 24766052 DOI: 10.3109/1040841x.2014.907235] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/31/2022]
39
Masoudi-Nejad A, Asgari Y. Metabolic cancer biology: structural-based analysis of cancer as a metabolic disease, new sights and opportunities for disease treatment. Semin Cancer Biol 2014;30:21-9. [PMID: 24495661 DOI: 10.1016/j.semcancer.2014.01.007] [Citation(s) in RCA: 31] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/21/2013] [Revised: 01/15/2014] [Accepted: 01/18/2014] [Indexed: 12/21/2022]
40
Madeira A, dos Santos SC, Santos PM, Coutinho CP, Tyrrell J, McClean S, Callaghan M, Sá-Correia I. Proteomic profiling of Burkholderia cenocepacia clonal isolates with different virulence potential retrieved from a cystic fibrosis patient during chronic lung infection. PLoS One 2013;8:e83065. [PMID: 24349432 PMCID: PMC3862766 DOI: 10.1371/journal.pone.0083065] [Citation(s) in RCA: 23] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/25/2013] [Accepted: 11/07/2013] [Indexed: 11/18/2022]  Open
41
Comparative metabolic systems analysis of pathogenic Burkholderia. J Bacteriol 2013;196:210-26. [PMID: 24163337 DOI: 10.1128/jb.00997-13] [Citation(s) in RCA: 35] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022]  Open
42
Novel multiscale modeling tool applied to Pseudomonas aeruginosa biofilm formation. PLoS One 2013;8:e78011. [PMID: 24147108 PMCID: PMC3798466 DOI: 10.1371/journal.pone.0078011] [Citation(s) in RCA: 52] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/01/2013] [Accepted: 09/12/2013] [Indexed: 01/05/2023]  Open
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Oberhardt MA, Yizhak K, Ruppin E. Metabolically re-modeling the drug pipeline. Curr Opin Pharmacol 2013;13:778-85. [DOI: 10.1016/j.coph.2013.05.006] [Citation(s) in RCA: 29] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/17/2013] [Revised: 05/04/2013] [Accepted: 05/06/2013] [Indexed: 02/07/2023]
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Schmidt BJ, Ebrahim A, Metz TO, Adkins JN, Palsson BØ, Hyduke DR. GIM3E: condition-specific models of cellular metabolism developed from metabolomics and expression data. ACTA ACUST UNITED AC 2013;29:2900-8. [PMID: 23975765 DOI: 10.1093/bioinformatics/btt493] [Citation(s) in RCA: 85] [Impact Index Per Article: 7.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/12/2022]
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Vital-Lopez FG, Wallqvist A, Reifman J. Bridging the gap between gene expression and metabolic phenotype via kinetic models. BMC SYSTEMS BIOLOGY 2013;7:63. [PMID: 23875723 PMCID: PMC3733621 DOI: 10.1186/1752-0509-7-63] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 09/27/2012] [Accepted: 06/27/2013] [Indexed: 01/22/2023]
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Manos J, Hu H, Rose BR, Wainwright CE, Zablotska IB, Cheney J, Turnbull L, Whitchurch CB, Grimwood K, Harmer C, Anuj SN, Harbour C. Virulence factor expression patterns in Pseudomonas aeruginosa strains from infants with cystic fibrosis. Eur J Clin Microbiol Infect Dis 2013;32:1583-92. [DOI: 10.1007/s10096-013-1916-7] [Citation(s) in RCA: 20] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/10/2013] [Accepted: 06/17/2013] [Indexed: 12/16/2022]
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Csermely P, Korcsmáros T, Kiss HJM, London G, Nussinov R. Structure and dynamics of molecular networks: a novel paradigm of drug discovery: a comprehensive review. Pharmacol Ther 2013;138:333-408. [PMID: 23384594 PMCID: PMC3647006 DOI: 10.1016/j.pharmthera.2013.01.016] [Citation(s) in RCA: 512] [Impact Index Per Article: 42.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/22/2013] [Accepted: 01/22/2013] [Indexed: 02/02/2023]
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Kim YM, Schmidt BJ, Kidwai AS, Jones MB, Deatherage Kaiser BL, Brewer HM, Mitchell HD, Palsson BO, McDermott JE, Heffron F, Smith RD, Peterson SN, Ansong C, Hyduke DR, Metz TO, Adkins JN. Salmonella modulates metabolism during growth under conditions that induce expression of virulence genes. MOLECULAR BIOSYSTEMS 2013;9:1522-34. [PMID: 23559334 PMCID: PMC3665296 DOI: 10.1039/c3mb25598k] [Citation(s) in RCA: 43] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/14/2022]
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Xu Z, Fang X, Wood TK, Huang ZJ. A systems-level approach for investigating Pseudomonas aeruginosa biofilm formation. PLoS One 2013;8:e57050. [PMID: 23451140 PMCID: PMC3579789 DOI: 10.1371/journal.pone.0057050] [Citation(s) in RCA: 27] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/16/2012] [Accepted: 01/16/2013] [Indexed: 12/14/2022]  Open
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Filiatrault MJ, Tombline G, Wagner VE, Van Alst N, Rumbaugh K, Sokol P, Schwingel J, Iglewski BH. Pseudomonas aeruginosa PA1006, which plays a role in molybdenum homeostasis, is required for nitrate utilization, biofilm formation, and virulence. PLoS One 2013;8:e55594. [PMID: 23409004 PMCID: PMC3568122 DOI: 10.1371/journal.pone.0055594] [Citation(s) in RCA: 29] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/08/2012] [Accepted: 12/27/2012] [Indexed: 12/31/2022]  Open
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