John (Jay) Ryan

Primary Responsibilities: Contribute to the development of software projects; Analyze, design, and co-manage software deployment strategies; Review and provide feedback and suggestions for coding practices; Write technical and administrative documentation; Lead technical project meetings with stakeholders and developers

Primary Responsibilities: Manage junior developers; Oversee and contribute to the development of software projects; Communicate and collaborate with clients; Participate in the management and operations of the company; Administrate on-premises and cloud servers

Deal Pack Web

• Worked alongside other developers to develop Deal Pack Web, a web application for Automotive Dealerships to manage and report inventory, customers, and financial transactions
• Co-maintained multiple Git repositories and performed deployments to staging and production environments
• Improved the process of estimating and delivered an accurate project timeline
• Facilitated communication between the development and product support teams to deliver consistent product features to production
• Designed, planned, and led development of a system that schedules and executes long-running operations asynchronously, and integrated that system with a .NET framework web application

Virtual Screening

• Parkin Activator Virtual Screening (as a service for Vincere Biosciences): Led a virtual screening of over 10 million compounds using AutoDock-GPU; collaborated with biologists, medicinal chemists, and computational chemists; developed and executed a complete custom virtual screening pipeline

Biological Simulation - Simulation Environment for Experimental Design (SEED)

• Worked alongside other developers to develop SEED, a patented cell simulation platform and native cross-platform graphical client for managing and viewing simulations
• Collaborated with Mayo Clinic to simulate and predict disease related changes, which they validated in mice
• Collaborated with Oxford to simulate and predict disease related changes in human iPSCs
• Led a team of two developers in porting the simulation software to CUDA to run on Nvidia GPUs
• Developed a web-based application to manage simulation data using the Vue.js framework
• Led a team of three developers to create a web Application Programming Interface (API) using the Express Node.js framework
• Led several teams of two to four developers for feature additions and project maintenance
• Maintained a large MySQL database for storing and reporting simulation and biological data

Analytics

• Collaboration with Southern Research Institute: Created network graphs of interaction data, ran statistical analyses, correlated interaction data with novel and public data, and produced data for publication
• Collaboration with Michigan State University: Created network graphs of publicly available and novel interaction data produced by MSU, and created visualizations to exemplify significance of novel data
• Contract for Vincere Biosciences: Used statistical analysis of interaction networks and text-mining of scientific publications to identify and prioritize potential targets for therapeutics

• Behrouz B, Merchant K, Ryan JW, Hardage B, Lee A. Using computer modeling to accelerate drug discovery for Parkinson’s disease: Insights from genetics and transcriptomics. Neuro4D. May 2019. Germany
• Lee AD, Hall JC, Ryan JW, Behrouz B. Converging pathways in genetic and sporadic Parkinson’s Disease: Using Unbiased Network Analysis to Connect the Dots. Society for Neuroscience, 2018. San Diego.
• Behrouz B, Ryan JW, Dodds DA, Vincent L, Lee AD. In Silico Simulation of LRRK2 Pathways: A Search for Druggable Targets. Society for Neuroscience, 2017. Washington, DC.
• Lee AD, Ikeda I, Dodds DA, Ryan JW, Behrouz B. Physical Dynamics Inside the Lysosome Link GBA Mutation to Parkinson’s Disease. Society for Neuroscience, 2017. Washington, DC.
• Ikeda IC, Behrouz B, Ryan JW, Sweeney TJ, Lee AD. Computer Simulation of GBA Related Pathways with Implications for Parkinson’s Disease. Society for Neuroscience, 2016. Washington, DC.
• Lee AD, Ryan JW, Widener AM, Dodds DA, Sweeney TJ, Behrouz B. Pathway Simulation Using SEED as a Method for Elucidating the Downstream Impacts of Lrrk2. International Conference on LRRK2, 2016. UK.
• Ryan JW, Widener AM, Ikeda IC, Sweeney TJ, Lee AD, Behrouz B. In silico simulation of Lrrk2 interactions in Parkinson’s Disease using SEED. Society for Neuroscience, 2016. San Diego.
• Behrouz B, Ryan JW, Morrison JJ, Green AM, Schappell L, Inman KS, Lee AD. A computational model of protein handling pathways in Parkinson's disease using SEED. Society for Neuroscience, 2015. Chicago.
• Lee AD, Ryan JW, Morrison JJ, Green AM, Schappell L, Inman KS, Behrouz B. SEED - A virtual test tube for Parkinson's disease research. Society for Neuroscience annual meeting, 2015. Chicago.
• Morrison JJ, Ryan JW, Green AM, Schappell L, Inman KS, Lee AD, Behrouz B. An In Silico Analysis of alpha-synuclein Interactions Using SEED. Society for Neuroscience, 2015. Chicago.
• Ryan JW, Morrison JJ, Green AM, Schappell L, Inman KS, Lee AD, Behrouz B. In Silico Visualization of the Endosomal Pathway in Parkinson’s disease using SEED. Society for Neuroscience annual meeting, 2015. Chicago.

• Boas, S., Fox, S., McMeekin, L., Ryan, J., Cook, L.M., Willicott, C., Simmons, M., Carlisle, S., Stephen, C.A., Zhang, S., Joyce, K., Rocha, E., Crossman, D., Becker, K., Hendrickson, C., Lefkowitz, E., Roberts, R., Volpicelli-Daley, L., Ma, J., Greenamyre, T., Caldwell, G., Caldwell, K., Lee, A., Gamble, K.L., Cowell, R.M. Utilization of cell-type-specific transcriptional profiles to guide prioritization of risk genes, pathways, and cell types in Parkinson Disease Studies. Npj Parkinsons Dis. Submitted for publication January, 2022.
• Fox, S.N., McMeekin, L.J., Savage, C.H., Boas, S.M., Simmons, M.S., Farmer, C.B., Ryan, J., Pereboeva, L., Becker, K., Auwerx, J., Sudarshan, S., Ma, J., Lee, A. Estrogen-related receptor gamma regulates mitochondrial and synaptic genes and modulates vulnerability to synucleinopathy. npj Parkinsons Dis. 8, 106 (2022). https://doi.org/10.1038/s41531-022-00369-w
• Soliman, A. S., Umstead, A., Grabinski, T., Kanaan, N. M., Lee, A., Ryan, J., Lamp, J., & Vega, I. E. (2021). EFhd2 brain interactome reveals its association with different cellular and molecular processes. Journal of Neurochemistry, 159, 992– 1007. https://doi.org/10.1111/jnc.15517

Discovery and Development of Parkin Activators as Therapies for Parkinson’s Disease.

As a service for Vincere Biosciences, perform virtual screening to identify activators of the protein parkin.

Discovery and Development of USP30 inhibitors as Disease-Modifying Therapy for Parkinson's disease.

As a service for Vincere Biosciences, perform analytics to identify disease indications.

In collaboration with University of Oxford, utilize the SEED simulation platform to simulate and verify the response of inducible pluripotent stem cells from patients with Parkinson’s disease.

Computer Simulation of Lrrk2 Interactions to Identify Therapeutic Targets for Parkinson's Disease In collaboration with Mayo Clinic, Utilize the SEED simulation platform from NeuroInitiative to model and simulation pathways related to Lrrk2 in search of novel therapeutic targets.