Publications & Presentations

Learn more about GNS’s products and solutions from our peer-reviewed publications, conference abstracts, and presentations:

Reverse Engineering and Evaluation of Prediction Models for Progression to Type 2 Diabetes: An Application of Machine Learning Using Electronic Health Records. Anderson JP, Parikh JR, Shenfeld DK, Ivanov V, Marks C, Church BW, Laramie JM, Mardekian J, Piper BA, Willke RJ, Rublee DA.  Journal of Diabetes Science and Technology. 2015. 10(1):6-18.

Novel Predictive Models for Metabolic Syndrome Risk- A “Big Data” Analytic Approach. Steinberg GB, Church BW, McCall CJ, Scott AB, Kalis BP. Am J Manag Care. 2014. 20(6):e221-e228.

Identification of Determinants of Progression to Type 2 Diabetes Using Electronic Health Records and Big Data Analytics. Anderson JP, Parikh JR, Shenfeld DK, Church BW, Laramie JM, Piper BA, Willke RJ, Mardekian J, Rublee DA. ISPOR 19th International Meeting. Montreal, Canada. 2014. PDB27.

A mathematical model of long-term outcomes in Parkinson’s disease. Hayete B, Laramie J, Bienkowska J, Eberly S, Khalil I, Lang A, Marek K, Oakes D, Shoulson I, Singleton A, Song T, Verma A, Wien M, Ravina B. 17th International Congress of Parkinson’s Disease and Movement Disorders. Sydney, Australia. 2013. LBA-19.

Data-driven computational modeling to identify biomarkers of response to lenvatinib (E7080) in melanoma.Kadowaki T, Funahashi Y, Matsui J, Pavan K, Sachdev P, O’Brien J, Xing H, McDonagh PD, Khalil I, Kurzrock R, Hong DS, Nemunaitis J. 104th Annual Meeting of the American Association for Cancer Research. Washington, DC. 2013. 4025.

Confirmation of peroxiredoxin II as a driver gene for doxorubicin sensitivity identified from drug-induced expression profiling of the NCI-60 cell lines using Reverse Engineering (REFS) network models. Monks A, Hose CD, Hayete B, Runge K, DeCaprio D, Teicher BA, Khalil I, McDonagh PD, Doroshow JH. 103rd Annual Meeting of the American Association for Cancer Research. Chicago, IL. 2012. 5663.

Reverse-engineered, forward-simulation of MEK-dependent molecular networks reveal novel regulators of cell cycle and cancer cell survival. Gendelman R, Xing H, Sarde P, Mirzoeva OK, Feiler H, Gray JW, McDonagh PD, Khalil I, Korn WM. 103rd Annual Meeting of the American Association for Cancer Research. Chicago, IL. 2012. 986.

Causal modeling using network ensemble simulations of genetic and gene expression data predicts genes involved in rheumatoid arthritis. Xing H, McDonagh PD, Bienkowska J, Cashorali T, Runge K, Miller RE, Decaprio D, Church B, Roubenoff R, Khalil IG, Carulli J. PLoS Comput Biol. 2011. 7(3):e1001105.

Quantification and analysis of combination drug synergy in high-throughput transcriptome studies. Gümüs ZH, Siso-Nadal F, Gjrezi A, McDonagh P, Khalil I, Giannakakou P, Weinstein H. IEEE International Conference on Bioinformatics and Bioengineering, 2010. pp. 238-243.

The potential of biologic network models in understanding the etiopathogenesis of ovarian cancer. Khalil I, Brewer MA, Neyarapally T, Runowicz CD. Gynecol Oncol. 2010. 116(2):282-5.

Cross-talk between signaling pathways can generate robust oscillations in calcium and cAMP. Siso-Nadal F, Fox JJ, Laporte SA, Hébert TE, Swain PS. PLoS One. 2009. 4(10):e7189.

Customized care 2020: how medical sequencing and network biology will enable personalized medicine.Boguski MS, Arnaout R, Hill C. F1000 Biol Rep. 2009. 1:73.

Achieving confidence in mechanism for drug discovery and development. Pitluk Z, Khalil I. Drug Discov Today. 2007. 12(21-22):924-30.

A systems biology dynamical model of mammalian G1 cell cycle progression. Haberichter T, Mädge B, Christopher RA, Yoshioka N, Dhiman A, Miller R, Gendelman R, Aksenov SV, Khalil IG, Dowdy SF. Mol Syst Biol. 2007. 3:84.

An integrated approach for inference and mechanistic modeling for advancing drug development. Aksenov SV, Church B, Dhiman A, Georgieva A, Sarangapani R, Helmlinger G, Khalil IG. FEBS Lett. 2005. 579(8):1878-83.

Systems biology for cancer. Khalil IG, Hill C. Curr Opin Oncol. 2005. 17(1):44-8.

The statistical mechanics of complex signaling networks: nerve growth factor signaling. Brown KS, Hill CC, Calero GA, Myers CR, Lee KH, Sethna JP, Cerione RA. Phys Biol. 2004. 1(3-4):184-95.

Data-driven computer simulation of human cancer cell. Christopher R, Dhiman A, Fox J, Gendelman R, Haberitcher T, Kagle D, Spizz G, Khalil IG, Hill C. Ann N Y Acad Sci. 2004. 1020:132-53.