Professional

Jacob Feala, PhD

Current position:
Sanford|Burnham Medical Research Institute
Paternostro Lab
Postdoctoral Associate
Sept. 2008 – current

Research

I work on computational approaches to optimize drug combinations in cancer. One approach I use is to build in-silico models of cellular networks, for example genome-scale metabolic networks in cancer and non-cancer cells, in order to predict which sets of compounds selectively inhibit biological functions in cancer with minimal impact on normal tissues. The other approach is to design and implement iterative search algorithms to optimize drug-dose inputs when provided a phenotype output. These search algorithms can be run using an iterative high-throughput screen in order to optimize some phenotype such as cell viability in response to a combination of compounds.

Publications

Research Papers:

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

Broderick KE, Feala J, McCulloch A, Paternostro G, Sharma VS, Pilz RB, Boss GR (2006) The nitric oxide scavenger cobinamide profoundly improves survival in a Drosophila melanogaster model of bacterial sepsis. Faseb J 20: 1865-1873.

Broderick KE, Balasubramanian M, Chan A, Potluri P, Feala J, Belke DD, McCulloch A, Sharma VS, Pilz RB, Bigby TD, Boss GR (2007) The cobalamin precursor cobinamide detoxifies nitroprusside-generated cyanide. Exp Biol Med (Maywood) 232(6): 789-98

Feala JD, Coquin L, McCulloch AD, Paternostro G (2007) Flexibility in energy metabolism supports hypoxia tolerance in Drosophila flight muscle: metabolomic and computational systems analysis. Mol Syst Biol 3: 99 Nature MSB

Feala JD, Omens JH, Paternostro G, McCulloch AD (2008) Discovering regulators of the Drosophila cardiac hypoxia response using automated phenotyping technology. Ann NY Acad Sci 1123:169-77 PubMed Wiley

Calzolari D, Bruschi S, Coquin L, Schofield J, Feala JD, Reed JC, McCulloch AD, Paternostro G. (2008) Search algorithms as a framework for the optimization of drug combinations. PLoS Comp. Biol. 4(12):e1000249 PLoS CB

[First and second authors contributed equally]
Coquin L, Feala JD, McCulloch AD, Paternostro G. (2008) Metabolomic and flux-balance analysis of age-related decline of hypoxia tolerance in Drosophila muscle tissue. Mol Syst Biol. 4:233 Nature MSB

Feala JD, Coquin L, McCulloch AD, Paternostro G, Zhou D, Haddad GG (2009) Metabolism as means for hypoxia adaptation: metabolic profiling and flux balance analysis. BMC Syst Biol. 3(1):91 PubMed BioMed Central

Reviews:

Feala JD, Coquin L, Paternostro G, McCulloch AD (2007) Integrating metabolomics and phenomics with systems models of cardiac hypoxia. Prog Biophys Mol Biol. 96(1-3):209-25 PubMed ScienceDirect

Feala J.D., Cortes J., Duxbury P.M., Piermarocchi C., McCulloch A.D., Paternostro G.: Systems approaches and algorithms for discovery of combinatorial therapies. Wiley Interdisciplinary Reviews Systems Biology and Medicine DOI: 10.1002/wsbm.51, 2009 WIREs arXiv:0903.0662v1 [q-bio.QM] ArXiv

Platform presentations

Feala JD, McCulloch AD, Paternostro G (2008) Systems model of the ATP-generating metabolic network in Drosophila flight muscle. 49th Annual Drosophila Research Conference, San Diego, CA .ppt

Feala JD, McCulloch AD, Paternostro G (2007) Systems analysis of cardiac hypoxia in Drosophila: phenotypes, metabolomics, and modeling. BMES Annual Meeting, Hollywood, CA .ppt

Feala JD, Coquin L, McCulloch AD, Paternostro G (2006) Flexibility in energy metabolism supports hypoxia tolerance in Drosophila flight muscle: metabolomic and computational systems analysis. RECOMB Satellite Conf on Sys Bio and Comp Proteomics, La Jolla, CA .ppt video