Publications & Presentations

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

Data-Driven Reconstruction and Simulation of Transcriptional Regulatory Networks in the Htt Allelic Series. Michael Beste, Tun-Hsiang Yang, Jeanne Latourelle, Boris Hayete , Liliana Menalled , Dani Brunner , Vadim Alexandrov , Seung Kwak, David Howland, Jeff Aaronson , Iya Khalil, James Rosinski. CHDI Foundation, Inc.‘s 11th Annual HD Therapeutics Conference. Palm Springs, CA. 2016.

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. 2016. 10(1):6-18. PMID: 26685993

Investigation of Mechanisms of Response in Multiple Myeloma Via Bayesian Causal Inference: An Early Analysis of the CoMMpass Study Data. Fred Gruber, Boris Hayete, Jonathan Keats, Kyle McBride, Karl Runge, Mary DeRome, Sagar Lonial, Iya Khalil, Daniel Auclair. American Society of Hematology (ASH) 57th Annual Meeting & Exposition. Orlando, FL. 2015.

Treatment Patterns Among Schizophrenia Patients Receiving Paliperidone Palmitate or Atypical Oral Antipsychotics in Community Behavioral Health Organizations. Jeffrey P. Anderson, Kruti Joshi, Zeynep Icten, Veronica Alas. 28th Annual US Psychiatric and Mental Health Congress. San Diego, CA. 2015.

Predictors of Remission in Schizophrenia Patients Treated With Paliperidone Palmitate or Oral Antipsychotics in Community Behavioral Health Organizations. Zeynep Icten, Kruti Joshi, Jeff Anderson, Veronica Alas. 28th Annual US Psychiatric and Mental Health Congress. San Diego, CA. 2015.

Power of Reverse Engineering and Forward Simulation Platform for Driving Precision Medicine. Khalil I, Wasserman S. Pharmaceutical R&D Information Systems Management Executive Forum. Plainsboro Township, NJ. 2015.

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. PMID: 25180505

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.

HD causal modeling using network ensemble simulations of gene expression data. Jong-Min Lee, Kevin Correia, Douglas D. Barker, James F. Gusella,  Marcy E. MacDonald,Paul D. McDonagh, Jignesh R. Parikh, Iya G. Khalil, Keith Elliston, Seung Kwak. CHDI Foundation, Inc.‘s Annual HD Therapeutics Conference. Palm Springs, CA.

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.

Learning Models for Metabolic Syndrome from Medical Claims Data. Church B, Steinberg G. Strata Rx Conference. San Francisco, CA. 2012.

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. PMID: 21423713

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. PMID: 19931138

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. PMID: 19844582

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. PMID: 20948615

Achieving confidence in mechanism for drug discovery and development. Pitluk Z, Khalil I. Drug Discov Today. 2007. 12(21-22):924-30. PMID: 17993410

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. PMID: 17299420

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. PMID: 15763567

Systems biology for cancer. Khalil IG, Hill C. Curr Opin Oncol. 2005. 17(1):44-8. PMID: 15608512

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. PMID: 16204838

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. PMID: 15208190