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Selected Publications

Lee SH, Cunha D, Piermarocchi C, Paternostro G, Pinkerton A, Ladriere L, Marchetti P, Eizirik DL, Cnop M, Levine F., High-Throughput Screening and Bioinformatic Analysis to Ascertain Compounds that Prevent Saturated Fatty Acid-Induced β-Cell Apoptosis, Biochemical Pharmacology, Available online 15 May 2017, ISSN 0006-2952, (2017). PMID: 28522407

Szedlak A, Smith N, Liu L, Paternostro G, Piermarocchi C., Evolutionary and Topological Properties of Genes and Community Structures in Human Gene Regulatory Networks. PLoS Comput. Biol. 12(6):e1005009 (2016). PMID: 27359334

Ong, E., Szedlak, A., Kang, Y., Smith, P., Smith, N., McBride, M., Finlay, D., Vuori, K., Mason, J., Ball, E.D., Piermarocchi, C., and Paternostro, G. A scalable method for molecular network reconstruction identifies properties of targets and mutations in acute myeloid leukemia. arXiv:1407.6959, Journal of Computational Biology 22 266 (2015). PMID: 25844667

Kang Y, Tierney M, Ong E, Zhang L, Piermarocchi C, Sacco A, Paternostro G., Combinations of Kinase Inhibitors Protecting Myoblasts against Hypoxia., PLoS One. 2015 Jun 4;10(6):e0126718. doi: 10.1371/journal.pone.0126718 (2015). PMID: 26042811

Tran, T., Ong, E., Hodges, A., Paternostro, G., and Piermarocchi, C. Prediction of kinase inhibitor response using activity profiling, in vitro screening, and elastic net regression. BMC Systems Biology 8:74 (2014). PMID: 24961498

Szedlak A, Paternostro G, Piermarocchi C. Control of Asymmetric Hopfield Networks and Application to Cancer Attractors. PLoS One 9:e105842 (2014). PMID: 25170874

Kang Y, Tiziani S, Park G, Kaul M, Paternostro G. Cellular protection using Flt3 and PI3Kalpha inhibitors demonstrates multiple mechanisms of oxidative glutamate toxicity Nature Communications, 5:3672 (2014). PMC4128233

Kang Y, Hodges A, Ong E, Roberts W, Piermarocchi C, and Paternostro G. Identification of Drug Combinations Containing Imatinib for Treatment of BCR-ABL+ Leukemias. PLoS One 9:e102221 (2014). PMC4100887

Kang Y., Tran T., Zhang L., Ball E.D., Piermarocchi C., Paternostro G. Personalized Drug Combinations for the Treatment of Acute Myeloid Leukemia (AML) Patients. Blood 124:3616; ASH abstract (2014).

Tiziani S, Kang Y, Harjanto R, Axelrod J, Piermarocchi C, Roberts W, Paternostro G Metabolomics of the tumor microenvironment in pediatric acute lymphoblastic leukemia PLoS ONE 8:e82859 (2013). PMC3862732

Feala J. D., Cortes J., Duxbury P.M., McCulloch A.D, Piermarocchi C., Paternostro G.: Statistical Properties and Robustness of Biological Controller-Target Networks. PLoS ONE 7(1): e29374. doi:10.1371/journal.pone.0029374 2012

Tiziani S., Kang Y., Choi J. S., Roberts W., Paternostro G.: Metabolomic high-content nuclear magnetic resonance-based drug screening of a library of kinase inhibitors Nature Communications, 2 : 545 doi:10.1038/ncomms1562 2011

Feala J. D., Cortes J., Duxbury P.M., Piermarocchi C., McCulloch A.D., Paternostro G.: Systems approaches and algorithms for discovery of combinatorial therapies WIREs Syst Biol Med, 2:181-193 2010

Feala JD, Coquin L, Zhou D, Haddad GG, Paternostro G, McCulloch AD.: Metabolism as means for hypoxia adaptation: metabolic profiling and flux balance analysis. BMC Syst Biol. 2009 Sep 9;3:91 BMC Systems Biology

Calzolari D., Bruschi S., Coquin L., Schofield J., Feala J. D., Reed J.C., McCulloch A.D., Paternostro G.: Search algorithms as a framework for the optimization of drug combinations. PLoS Comp Biol 4(12):1-14, 2008 PLoS CB

Coquin L., Feala J. D., McCulloch A.D., Paternostro G.: Metabolomic and flux-balance analysis of age-related decline of hypoxia tolerance in Drosophila muscle tissue. Molecular Systems Biology, 4:233:1-13, 2008 Nature MSB

Bruschi S. Calzolari D., Coquin L., Paternostro G.: HORA suite: A database and software for human metabolomics. Metabolomics, 4:90-93, 2008 Springer

Calzolari D., Paternostro G. , Harrington Jr. P. L., Piermarocchi, C., Duxbury P. M. Selective control of the apoptosis signaling network in heterogeneous cell populations. PlosOne, Jun 20:2:e547, 2007 Plos

Feala J. D., Coquin L., McCulloch A.D., Paternostro G.: Flexibility in energy metabolism supports hypoxia tolerance in Drosophila flight muscle: metabolomic and computational systems analysis. Molecular Systems Biology, 3:99 :1-7, 2007 Nature MSB

Ferrarini, L., Bertelli, L., Feala, J., McCulloch, A.D., Paternostro, G.: A more efficient search strategy for aging genes based on connectivity. Bioinformatics, 21:338-348, 2005. PubMed Oxford Journals

Paternostro, G., Vignola, C., Bartsch, D-U., Omens, J.H., McCulloch, A.D., Reed, J.C.: Age-associated cardiac dysfunction in Drosophila melangaster. Circ Res, 88:1053-1058, 2001 PubMed Circ Res

Reed, J., Paternostro, G.: Post-mitochondrial regulation of apoptosis during heart failure. Proc Natl Acad Sci, USA, 96:7614-7616, 1999 PubMed PNAS

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