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Aarash Bordbar - Publications

Affiliations: 
2014 Bioengineering University of California, San Diego, La Jolla, CA 
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39 high-probability publications. We are testing a new system for linking publications to authors. You can help! If you notice any inaccuracies, please sign in and mark papers as correct or incorrect matches. If you identify any major omissions or other inaccuracies in the publication list, please let us know.

Year Citation  Score
2020 Nemkov T, Stefanoni D, Bordbar A, Issaian A, Palsson BO, Dumont LJ, Hay AM, Song A, Xia Y, Redzic JS, Eisenmesser EZ, Zimring JC, Kleinman S, Hansen KC, Busch M, et al. Blood donor exposome and impact of common drugs on red blood cell metabolism. Jci Insight. PMID 33351786 DOI: 10.1172/jci.insight.146175  0.427
2019 Heirendt L, Arreckx S, Pfau T, Mendoza SN, Richelle A, Heinken A, Haraldsdóttir HS, Wachowiak J, Keating SM, Vlasov V, Magnusdóttir S, Ng CY, Preciat G, Žagare A, Chan SHJ, ... ... Bordbar A, et al. Creation and analysis of biochemical constraint-based models using the COBRA Toolbox v.3.0. Nature Protocols. PMID 30787451 DOI: 10.1038/S41596-018-0098-2  0.801
2018 Yurkovich JT, Bordbar A, Sigurjónsson ÓE, Palsson BO. Systems biology as an emerging paradigm in transfusion medicine. Bmc Systems Biology. 12: 31. PMID 29514691 DOI: 10.1186/S12918-018-0558-X  0.738
2017 Yurkovich JT, Zielinski DC, Yang L, Paglia G, Rolfsson O, Sigurjónsson ÓE, Broddrick JT, Bordbar A, Wichuk K, Brynjólfsson S, Palsson S, Gudmundsson S, Palsson BO. Quantitative time-course metabolomics in human red blood cells reveal the temperature dependence of human metabolic networks. The Journal of Biological Chemistry. PMID 29030425 DOI: 10.1074/Jbc.M117.804914  0.796
2017 Rolfsson Ó, Johannsson F, Magnusdottir M, Paglia G, Sigurjonsson ÓE, Bordbar A, Palsson S, Brynjólfsson S, Guðmundsson S, Palsson B. Mannose and fructose metabolism in red blood cells during cold storage in SAGM. Transfusion. PMID 28833234 DOI: 10.1111/Trf.14266  0.543
2017 Bordbar A, Yurkovich JT, Paglia G, Rolfsson O, Sigurjónsson ÓE, Palsson BO. Elucidating dynamic metabolic physiology through network integration of quantitative time-course metabolomics. Scientific Reports. 7: 46249. PMID 28387366 DOI: 10.1038/Srep46249  0.779
2017 Rolfsson Ó, Sigurjonsson ÓE, Magnusdottir M, Johannsson F, Paglia G, Guðmundsson S, Bordbar A, Palsson S, Brynjólfsson S, Guðmundsson S, Palsson B. Metabolomics comparison of red cells stored in four additive solutions reveals differences in citrate anticoagulant permeability and metabolism. Vox Sanguinis. PMID 28370161 DOI: 10.1111/Vox.12506  0.546
2017 Zielinski DC, Jamshidi N, Corbett AJ, Bordbar A, Thomas A, Palsson BO. Systems biology analysis of drivers underlying hallmarks of cancer cell metabolism. Scientific Reports. 7: 41241. PMID 28120890 DOI: 10.1038/Srep41241  0.784
2016 Hefzi H, Ang KS, Hanscho M, Bordbar A, Ruckerbauer D, Lakshmanan M, Orellana CA, Baycin-Hizal D, Huang Y, Ley D, Martinez VS, Kyriakopoulos S, Jiménez NE, Zielinski DC, Quek LE, et al. A Consensus Genome-scale Reconstruction of Chinese Hamster Ovary Cell Metabolism. Cell Systems. 3: 434-443.e8. PMID 27883890 DOI: 10.1016/J.Cels.2016.10.020  0.817
2016 D'Alessandro A, Nemkov T, Yoshida T, Bordbar A, Palsson BO, Hansen KC. Citrate metabolism in red blood cells stored in additive solution-3. Transfusion. PMID 27813142 DOI: 10.1111/Trf.13892  0.572
2016 Ebrahim A, Brunk E, Tan J, O'Brien EJ, Kim D, Szubin R, Lerman JA, Lechner A, Sastry A, Bordbar A, Feist AM, Palsson BO. Multi-omic data integration enables discovery of hidden biological regularities. Nature Communications. 7: 13091. PMID 27782110 DOI: 10.1038/Ncomms13091  0.748
2016 Paglia G, D'Alessandro A, Rolfsson Ó, Sigurjónsson ÓE, Bordbar A, Palsson S, Nemkov T, Hansen KC, Gudmundsson S, Palsson BO. Biomarkers defining the metabolic age of red blood cells during cold storage. Blood. PMID 27554084 DOI: 10.1182/Blood-2016-06-721688  0.546
2016 Paglia G, Sigurjónsson ÓE, Bordbar A, Rolfsson Ó, Magnusdottir M, Palsson S, Wichuk K, Gudmundsson S, Palsson BO. Metabolic fate of adenine in red blood cells during storage in SAGM solution. Transfusion. PMID 27491795 DOI: 10.1111/Trf.13740  0.554
2016 Mih N, Brunk E, Bordbar A, Palsson BO. A Multi-scale Computational Platform to Mechanistically Assess the Effect of Genetic Variation on Drug Responses in Human Erythrocyte Metabolism. Plos Computational Biology. 12: e1005039. PMID 27467583 DOI: 10.1371/Journal.Pcbi.1005039  0.809
2016 Bordbar A, Johansson PI, Paglia G, Harrison SJ, Wichuk K, Magnusdottir M, Valgeirsdottir S, Gybel-Brask M, Ostrowski SR, Palsson S, Rolfsson O, Sigurjónsson OE, Hansen MB, Gudmundsson S, Palsson BO. Identified metabolic signature for assessing red blood cell unit quality is associated with endothelial damage markers and clinical outcomes. Transfusion. PMID 26749434 DOI: 10.1111/Trf.13460  0.421
2016 Yurkovich JT, Zielinski DC, Paglia G, Rolfsson O, Sigurjónsson OE, Bordbar A, Palsson B. Metabolic Analysis of Red Blood Cells Stored at High Temperature Blood. 128: 3848-3848. DOI: 10.1182/Blood.V128.22.3848.3848  0.457
2016 Bordbar A, Palsson BO. Unravelling why some people have drug side effects The Biochemist. 38: 31-34. DOI: 10.1042/bio03801031  0.355
2015 Bordbar A, McCloskey D, Zielinski DC, Sonnenschein N, Jamshidi N, Palsson BO. Personalized Whole-Cell Kinetic Models of Metabolism for Discovery in Genomics and Pharmacodynamics. Cell Systems. 1: 283-292. PMID 27136057 DOI: 10.1016/J.Cels.2015.10.003  0.795
2015 Ebrahim A, Almaas E, Bauer E, Bordbar A, Burgard AP, Chang RL, Dräger A, Famili I, Feist AM, Fleming RM, Fong SS, Hatzimanikatis V, Herrgård MJ, Holder A, Hucka M, et al. Do genome-scale models need exact solvers or clearer standards? Molecular Systems Biology. 11: 831. PMID 26467284 DOI: 10.15252/Msb.20156157  0.686
2015 Zielinski DC, Filipp FV, Bordbar A, Jensen K, Smith JW, Herrgard MJ, Mo ML, Palsson BO. Pharmacogenomic and clinical data link non-pharmacokinetic metabolic dysregulation to drug side effect pathogenesis. Nature Communications. 6: 7101. PMID 26055627 DOI: 10.1038/Ncomms8101  0.788
2015 Bordbar A, McCloskey D, Zielinski DC, Sonnenschein N, Jamshidi N, Palsson BO. Personalized Whole-Cell Kinetic Models of Metabolism for Discovery in Genomics and Pharmacodynamics Cell Systems. 1: 283-292. DOI: 10.1016/j.cels.2015.10.003  0.819
2014 Nam H, Campodonico M, Bordbar A, Hyduke DR, Kim S, Zielinski DC, Palsson BO. A systems approach to predict oncometabolites via context-specific genome-scale metabolic networks. Plos Computational Biology. 10: e1003837. PMID 25232952 DOI: 10.1371/Journal.Pcbi.1003837  0.713
2014 Bordbar A, Nagarajan H, Lewis NE, Latif H, Ebrahim A, Federowicz S, Schellenberger J, Palsson BO. Minimal metabolic pathway structure is consistent with associated biomolecular interactions. Molecular Systems Biology. 10: 737. PMID 24987116 DOI: 10.15252/Msb.20145243  0.765
2014 Thomas A, Rahmanian S, Bordbar A, Palsson BØ, Jamshidi N. Network reconstruction of platelet metabolism identifies metabolic signature for aspirin resistance. Scientific Reports. 4: 3925. PMID 24473230 DOI: 10.1038/Srep03925  0.719
2014 Bordbar A, Monk JM, King ZA, Palsson BO. Constraint-based models predict metabolic and associated cellular functions. Nature Reviews. Genetics. 15: 107-20. PMID 24430943 DOI: 10.1038/Nrg3643  0.751
2014 Bordbar A, Palsson BO. Moving toward genome-scale kinetic models: The mass action stoichiometric simulation approach Functional Coherence of Molecular Networks in Bioinformatics. 201-220. DOI: 10.1007/978-1-4614-0320-3_8  0.422
2013 Lewis NE, Liu X, Li Y, Nagarajan H, Yerganian G, O'Brien E, Bordbar A, Roth AM, Rosenbloom J, Bian C, Xie M, Chen W, Li N, Baycin-Hizal D, Latif H, et al. Genomic landscapes of Chinese hamster ovary cell lines as revealed by the Cricetulus griseus draft genome. Nature Biotechnology. 31: 759-65. PMID 23873082 DOI: 10.1038/Nbt.2624  0.747
2013 Jamshidi N, Bordbar A, Palsson B. Modeling Mycobacterium tuberculosis H37Rv in silico Systems Biology of Tuberculosis. 1-19. DOI: 10.1007/978-1-4614-4966-9_1  0.584
2012 Thiele I, Fleming RM, Que R, Bordbar A, Diep D, Palsson BO. Multiscale modeling of metabolism and macromolecular synthesis in E. coli and its application to the evolution of codon usage. Plos One. 7: e45635. PMID 23029152 DOI: 10.1371/Journal.Pone.0045635  0.703
2012 Bordbar A, Mo ML, Nakayasu ES, Schrimpe-Rutledge AC, Kim YM, Metz TO, Jones MB, Frank BC, Smith RD, Peterson SN, Hyduke DR, Adkins JN, Palsson BO. Model-driven multi-omic data analysis elucidates metabolic immunomodulators of macrophage activation. Molecular Systems Biology. 8: 558. PMID 22735334 DOI: 10.1038/Msb.2012.21  0.796
2012 Bordbar A, Palsson BO. Using the reconstructed genome-scale human metabolic network to study physiology and pathology. Journal of Internal Medicine. 271: 131-41. PMID 22142339 DOI: 10.1111/J.1365-2796.2011.02494.X  0.614
2011 Bordbar A, Feist AM, Usaite-Black R, Woodcock J, Palsson BO, Famili I. A multi-tissue type genome-scale metabolic network for analysis of whole-body systems physiology. Bmc Systems Biology. 5: 180. PMID 22041191 DOI: 10.1186/1752-0509-5-180  0.821
2011 Schellenberger J, Que R, Fleming RM, Thiele I, Orth JD, Feist AM, Zielinski DC, Bordbar A, Lewis NE, Rahmanian S, Kang J, Hyduke DR, Palsson BØ. Quantitative prediction of cellular metabolism with constraint-based models: the COBRA Toolbox v2.0. Nature Protocols. 6: 1290-307. PMID 21886097 DOI: 10.1038/Nprot.2011.308  0.791
2011 Bordbar A, Jamshidi N, Palsson BO. iAB-RBC-283: A proteomically derived knowledge-base of erythrocyte metabolism that can be used to simulate its physiological and patho-physiological states. Bmc Systems Biology. 5: 110. PMID 21749716 DOI: 10.1186/1752-0509-5-110  0.748
2011 Hyduke D, Schellenberger J, Que R, Fleming R, Thiele I, Orth J, Feist A, Zielinski D, Bordbar A, Lewis N, Rahmanian S, Kang J, Palsson B. COBRA Toolbox 2.0 Protocol Exchange. DOI: 10.1038/Protex.2011.234  0.723
2011 Thiele I, Fleming RMT, Que R, Bordbar A, Palsson BO. A Systems Biology Approach to the Evolution of Codon Use Pattern Nature Precedings. DOI: 10.1038/Npre.2011.6312.1  0.604
2010 Lewis NE, Schramm G, Bordbar A, Schellenberger J, Andersen MP, Cheng JK, Patel N, Yee A, Lewis RA, Eils R, König R, Palsson BØ. Large-scale in silico modeling of metabolic interactions between cell types in the human brain. Nature Biotechnology. 28: 1279-85. PMID 21102456 DOI: 10.1038/Nbt.1711  0.817
2010 Bordbar A, Lewis NE, Schellenberger J, Palsson BØ, Jamshidi N. Insight into human alveolar macrophage and M. tuberculosis interactions via metabolic reconstructions. Molecular Systems Biology. 6: 422. PMID 20959820 DOI: 10.1038/Msb.2010.68  0.812
2010 Thiele I, Fleming RM, Bordbar A, Schellenberger J, Palsson BØ. Functional characterization of alternate optimal solutions of Escherichia coli's transcriptional and translational machinery. Biophysical Journal. 98: 2072-81. PMID 20483314 DOI: 10.1016/J.Bpj.2010.01.060  0.777
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