The DOI matches its Crossref record; 6 of the 6 references it cites were found in a registry or an index.
Insight into human alveolar macrophage and M. tuberculosis interactions via metabolic reconstructions
Open accessAbstract
Metabolic coupling of Mycobacterium tuberculosis to its host is foundational to its pathogenesis. Computational genome‐scale metabolic models have shown utility in integrating ‐omic as well as physiologic data for systemic, mechanistic analysis of metabolism. To date, integrative analysis of host–pathogen interactions using in silico mass‐balanced, genome‐scale models has not been performed. We, therefore, constructed a cell‐specific alveolar macrophage model, iAB‐AMØ‐1410, from the global human metabolic reconstruction, Recon 1. The model successfully predicted experimentally verified ATP and nitric oxide production rates in macrophages. This model was then integrated with an M. tuberculosis H37Rv model, iNJ661, to build an integrated host–pathogen genome‐scale reconstruction, iAB‐AMØ‐1410‐Mt‐661. The integrated host–pathogen network enables simulation of the metabolic changes during infection. The resulting reaction activity and gene essentiality targets of the integrated model represent an altered infectious state. High‐throughput data from infected macrophages were mapped onto the host–pathogen network and were able to describe three distinct pathological states. Integrated host–pathogen reconstructions thus form a foundation upon which understanding the biology and pathophysiology of infections can be developed.
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Quantitative prediction of cellular metabolism with constraint-based models: the COBRA Toolbox v2.0
Schellenberger, J., Que, R., Fleming, R. M. T., Thiele, I., Orth, J. D., Feist, A. M., Zielinski, D. C., Bordbar, A., Lewis, N. E., Rahmanian, S., et al. (2011) · Nature Protocols · doi:10.1038/nprot.2011.308 · Cited by 1,835
Self-citationTranscriptional Adaptation of Mycobacterium tuberculosis within Macrophages
Schnappinger, D., Ehrt, S., Voskuil, M. I., Liu, Y., Mangan, J. A., Monahan, I. M., Dolganov, G., Efron, B., Butcher, P. D., Nathan, C., et al. (2003) · The Journal of Experimental Medicine · doi:10.1084/jem.20030846 · Cited by 1,420
Tuberculosis — metabolism and respiration in the absence of growth
Boshoff, H. I. M., & Barry, C. E. (2005) · Nature Reviews Microbiology · doi:10.1038/nrmicro1065 · Cited by 448
Famili, I., Förster, J., Nielsen, J., & Palsson, B. O. (2003) · Proceedings of the National Academy of Sciences · doi:10.1073/pnas.2235812100 · Cited by 353
Self-citationNitrate Enhances the Survival of Mycobacterium tuberculosis during Inhibition of Respiration
Sohaskey, C. D. (2008) · Journal of Bacteriology · doi:10.1128/jb.01857-07 · Cited by 108
Sulfite Reduction in Mycobacteria
Pinto, R., Harrison, J. S., Hsu, T., Jacobs, W. R., & Leyh, T. S. (2007) · Journal of Bacteriology · doi:10.1128/jb.00487-07 · Cited by 46 · cited 1×
“In addition, our gene essentiality results are further validated by in vitro M. tb tests (Pinto et al, 2007) of the essentiality of sulfite reduction (sirA).”
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Network medicine: a network-based approach to human disease
Barabási, A.-L., Gulbahce, N., & Loscalzo, J. (2011) · Nature Reviews Genetics · doi:10.1038/nrg2918 · Cited by 5,034
Quantitative prediction of cellular metabolism with constraint-based models: the COBRA Toolbox v2.0
Schellenberger, J., Que, R., Fleming, R. M. T., Thiele, I., Orth, J. D., Feist, A. M., Zielinski, D. C., Bordbar, A., Lewis, N. E., Rahmanian, S., et al. (2011) · Nature Protocols · doi:10.1038/nprot.2011.308 · Cited by 1,835
Self-citationA community-driven global reconstruction of human metabolism
Thiele, I., Swainston, N., Fleming, R. M. T., Hoppe, A., Sahoo, S., Aurich, M. K., Haraldsdottir, H., Mo, M. L., Rolfsson, O., Stobbe, M. D., et al. (2013) · Nature Biotechnology · doi:10.1038/nbt.2488 · Cited by 1,019
Self-citationConstraining the metabolic genotype–phenotype relationship using a phylogeny of in silico methods
Lewis, N. E., Nagarajan, H., & Palsson, B. O. (2012) · Nature Reviews Microbiology · doi:10.1038/nrmicro2737 · Cited by 779
Self-citationRecon 2.2: from reconstruction to model of human metabolism
Swainston, N., Smallbone, K., Hefzi, H., Dobson, P. D., Brewer, J., Hanscho, M., Zielinski, D. C., Ang, K. S., Gardiner, N. J., Gutierrez, J. M., et al. (2016) · Metabolomics · doi:10.1007/s11306-016-1051-4 · Cited by 285
Self-citationNetwork Context and Selection in the Evolution to Enzyme Specificity
Nam, H., Lewis, N. E., Lerman, J. A., Lee, D.-H., Chang, R. L., Kim, D., & Palsson, B. O. (2012) · Science · doi:10.1126/science.1216861 · Cited by 277
Self-citationModeling metabolism of the human gut microbiome
Magnúsdóttir, S., & Thiele, I. (2018) · Current Opinion in Biotechnology · doi:10.1016/j.copbio.2017.12.005 · Cited by 127
Metabolic network modeling of microbial communities
Biggs, M. B., Medlock, G. L., Kolling, G. L., & Papin, J. A. (2015) · WIREs Systems Biology and Medicine · doi:10.1002/wsbm.1308 · Cited by 124
Using the reconstructed genome-scale human metabolic network to study physiology and pathology
Bordbar, A., & Palsson, B. O. (2012) · Journal of Internal Medicine · doi:10.1111/j.1365-2796.2011.02494.x · Cited by 115
Self-citationA systems biology approach to studying the role of microbes in human health
Thiele, I., Heinken, A., & Fleming, R. M. (2013) · Current Opinion in Biotechnology · doi:10.1016/j.copbio.2012.10.001 · Cited by 114
Genome-scale models in human metabologenomics
Mardinoglu, A., & Palsson, B. Ø. (2025) · Nature Reviews Genetics · doi:10.1038/s41576-024-00768-0 · Cited by 54
Self-citation
Metadata
- Authors
- Bordbar, A., Lewis, N. E., Schellenberger, J., Palsson, B. Ø., & Jamshidi, N.
- Venue
- Molecular Systems Biology
- Published
- 2010-01
- Volume
- 6
- Issue
- 1
- Pages
- 422-422
- ISSN
- 1744-4292 (ISSN-L)
- OpenAlex
- W1988136571
- Cited by
- 252
- References
- 6
- FWCI
- 8.15
- Type
- journal article
- Language
- en
- Open access
- gold
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