Resume

Professional experience

October 2011 - Present: Head of Discovery Informatics, e-Therapeutics plc, Oxford, UK

e-Therapeutics plc is a drug discovery and development company and a pioneer in network pharmacology, a distinctive new approach to the discovery of medicines. Network pharmacology involves the construction of in silico, network models of disease followed by application of network analysis to determine the set of proteins most critical in that disease. Molecules capable of targeting that set of proteins are then identified using techniques from chemoinformatics and chemical biology.

At e-Therapeutics I direct a diverse group of bioinformatics, chemoinformatics, network science and machine learning experts and software engineers responsible for the development of the next generation of the core discovery platform.

Development of the platform is focused on three key areas. The first area, disease network construction, is being addressed with techniques aimed at the integration of multiple sources of cellular interaction data combined with network sampling and selective filtering approaches. The second area, disease network analysis, is focused on mathematical techniques to assess the impact of specific protein target sets on network function as well as approaches to identify optimal target sets in terms of network impact. The third area, chemical biology, is using data integration combined with machine learning to improve assessment of a compoundís biological footprint.

In addition to directing platform development I also work closely with the discovery biology group on the development of systems level models of disease, their embodiment in protein interaction networks and the analysis of those networks to identify suitable interventions and drug candidates.

July 2007 - September 2011: Associate Director
July 2006 - July 2007: Sr. Architect and IT Manager
Jan. 2004 - July 2006: Sr. Architect, Bioinformatics, Five Prime Therapeutics, San Francisco, CA

Five Prime Therapeutics is a drug discovery and development company that has developed a novel discovery platform aimed at mining its library of secreted and extra-cellular proteins for medically relavent proteins and anti-bodies.

At Five Prime I was responsible for the direction, design and implementation of the core software system supporting Five Prime's discovery platform. The system performed integration, tracking, analysis and visualization of data from all pieces of the discovery platform including molecular biology, protein chemistry, bioinformatic analysis and in vitro and in vivo screening. Development of the system replaced a number of standalone, ad-hoc data management solutions tied together by manual processes with one integrated solution. The core architecture facilitated rapid development and system evolution, allowing data management to keep track with and help drive the development of new automation and screening technology.

In addition to directing the platform software development I was also involved in a number of bioinformatic projects. These projects included the development of biological network analysis techniques for both biomarker identification and mechanism of action studies, and large scale sequence analysis using cloud based parallel computing. In addition, I designed and developed a software system aimed at accelerating the hit to lead stage of the discovery process by providing a unified view of a potential lead protein's experimental profile via the integration of multiple internal and external data sources.

Jan. 2002 - Dec. 2003: Group Leader, Bioinformatics
Oct. 2000 - Dec. 2001: Research Scientist, Bioinformatics, Clontech, Palo Alto, CA

Clontech is a life science research tool manufacturer with a range of products primarily in the fields of cell biology, molecular biology, and protein technologies.

At Clontech I managed the software development team within the department of bioinformatics. During my time at Clontech I specified, designed and implemented an expansion of the bioinformatics application suite from a system supporting one product to a suite of ten applications supporting six product lines. In addition, a toolset used internally for the design of Clontech's gene chips, protein chips and disease profiling chips was also designed and developed.

Feb. 1993 - Oct. 2000: Fellow in Theoretical Neurobiology, The Neurosciences Institute, San Diego, CA

The Neurosciences Institute is a non-profit scientific research organization dedicated to learning about the brain. Under the leadership of Nobel Laureate Gerald M. Edelman, the Institute focuses its research on the principles underlying how we perceive and act upon the world, how we learn and remember, and how consciousness arises.

While at the Neurosciences Institute I conducted research aimed at elucidating the biological basis of higher brain function. Of particular interest was the influence of context on visual perception, and the cortical networks underlying such context dependence, which I addressed using both large-scale neural simulations and human brain imaging. In addition to my work on visual perception I was also actively involved in the development of The Institute's machine psychology laboratory which aimed to study the neural basis of behaviour by coupling robotic devices to simulated nervous systems.

Education

1992: Awarded Ph.D. in Computational Biology from The Department of Physiological Sciences, The University of Newcastle upon Tyne, UK

My thesis work was concerned with the mathematical analysis of artificial neural networks and, in particular, the comparison to traditional system approximation and modeling techniques such as Volterra series. One outcome of the research was a novel algorithm for the calculation of the Volterra kernels of unknown, non-linear dynamic systems. The developed algorithm has since found application in a number of diverse areas from the characterization of the dynamics of chemical reaction systems to modeling the dynamic interactions within the human brain.

1989: Awarded B.Eng. (1st class) in Electrical and Electronic Engineering from The University of Newcastle upon Tyne, UK

My undergraduate studies placed a final emphasis on microprocessor and computer engineering. The academic work was complemented by an industrial sponsorship from Marconi Radar Systems.

Publications

Journal Papers

Meeting papers and abstracts

Contact email: jonny at jonnywray dot com