Matthew A. Oberhardt, Ph.D. - Publications

2010 University of Virginia, Charlottesville, VA 
Computational Systems Biology

17 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
2016 Auslander N, Wagner A, Oberhardt M, Ruppin E. Data-Driven Metabolic Pathway Compositions Enhance Cancer Survival Prediction. Plos Computational Biology. 12: e1005125. PMID 27673682 DOI: 10.1371/Journal.Pcbi.1005125  0.366
2016 Shaked I, Oberhardt MA, Atias N, Sharan R, Ruppin E. Metabolic Network Prediction of Drug Side Effects. Cell Systems. 2: 209-13. PMID 27135366 DOI: 10.1016/J.Cels.2016.03.001  0.373
2016 Oberhardt MA, Zarecki R, Reshef L, Xia F, Duran-Frigola M, Schreiber R, Henry CS, Ben-Tal N, Dwyer DJ, Gophna U, Ruppin E. Systems-Wide Prediction of Enzyme Promiscuity Reveals a New Underground Alternative Route for Pyridoxal 5'-Phosphate Production in E. coli. Plos Computational Biology. 12: e1004705. PMID 26821166 DOI: 10.1371/Journal.Pcbi.1004705  0.385
2014 Oberhardt MA, Gianchandani EP. Genome-scale modeling and human disease: an overview. Frontiers in Physiology. 5: 527. PMID 25667572 DOI: 10.3389/Fphys.2014.00527  0.711
2014 Eilam O, Zarecki R, Oberhardt M, Ursell LK, Kupiec M, Knight R, Gophna U, Ruppin E. Glycan degradation (GlyDeR) analysis predicts mammalian gut microbiota abundance and host diet-specific adaptations. Mbio. 5. PMID 25118239 DOI: 10.1128/Mbio.01526-14  0.353
2014 Zarecki R, Oberhardt MA, Reshef L, Gophna U, Ruppin E. A novel nutritional predictor links microbial fastidiousness with lowered ubiquity, growth rate, and cooperativeness. Plos Computational Biology. 10: e1003726. PMID 25033033 DOI: 10.1371/Journal.Pcbi.1003726  0.394
2014 Zarecki R, Oberhardt MA, Yizhak K, Wagner A, Shtifman Segal E, Freilich S, Henry CS, Gophna U, Ruppin E. Maximal sum of metabolic exchange fluxes outperforms biomass yield as a predictor of growth rate of microorganisms. Plos One. 9: e98372. PMID 24866123 DOI: 10.1371/Journal.Pone.0098372  0.38
2013 Oberhardt MA, Yizhak K, Ruppin E. Metabolically re-modeling the drug pipeline. Current Opinion in Pharmacology. 13: 778-85. PMID 23731523 DOI: 10.1016/J.Coph.2013.05.006  0.334
2011 Oberhardt MA, Pucha?ka J, Martins dos Santos VA, Papin JA. Reconciliation of genome-scale metabolic reconstructions for comparative systems analysis. Plos Computational Biology. 7: e1001116. PMID 21483480 DOI: 10.1371/Journal.Pcbi.1001116  0.641
2011 Benedict KF, Mac Gabhann F, Amanfu RK, Chavali AK, Gianchandani EP, Glaw LS, Oberhardt MA, Thorne BC, Yang JH, Papin JA, Peirce SM, Saucerman JJ, Skalak TC. Systems analysis of small signaling modules relevant to eight human diseases. Annals of Biomedical Engineering. 39: 621-35. PMID 21132372 DOI: 10.1007/S10439-010-0208-Y  0.613
2010 Oberhardt MA, Goldberg JB, Hogardt M, Papin JA. Metabolic network analysis of Pseudomonas aeruginosa during chronic cystic fibrosis lung infection. Journal of Bacteriology. 192: 5534-48. PMID 20709898 DOI: 10.1128/Jb.00900-10  0.62
2009 Oberhardt MA, Palsson BØ, Papin JA. Applications of genome-scale metabolic reconstructions. Molecular Systems Biology. 5: 320. PMID 19888215 DOI: 10.1038/Msb.2009.77  0.669
2009 Oberhardt MA, Chavali AK, Papin JA. Flux balance analysis: interrogating genome-scale metabolic networks. Methods in Molecular Biology (Clifton, N.J.). 500: 61-80. PMID 19399432 DOI: 10.1007/978-1-59745-525-1_3  0.72
2008 Pucha?ka J, Oberhardt MA, Godinho M, Bielecka A, Regenhardt D, Timmis KN, Papin JA, Martins dos Santos VA. Genome-scale reconstruction and analysis of the Pseudomonas putida KT2440 metabolic network facilitates applications in biotechnology. Plos Computational Biology. 4: e1000210. PMID 18974823 DOI: 10.1371/Journal.Pcbi.1000210  0.663
2008 Gianchandani EP, Oberhardt MA, Burgard AP, Maranas CD, Papin JA. Predicting biological system objectives de novo from internal state measurements. Bmc Bioinformatics. 9: 43. PMID 18218092 DOI: 10.1186/1471-2105-9-43  0.716
2008 Oberhardt MA, Pucha?ka J, Fryer KE, Martins dos Santos VA, Papin JA. Genome-scale metabolic network analysis of the opportunistic pathogen Pseudomonas aeruginosa PAO1. Journal of Bacteriology. 190: 2790-803. PMID 18192387 DOI: 10.1128/Jb.01583-07  0.665
2007 Robertson SH, Smith CK, Langhans AL, McLinden SE, Oberhardt MA, Jakab KR, Dzamba B, DeSimone DW, Papin JA, Peirce SM. Multiscale computational analysis of Xenopus laevis morphogenesis reveals key insights of systems-level behavior. Bmc Systems Biology. 1: 46. PMID 17953751 DOI: 10.1186/1752-0509-1-46  0.556
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