Curriculum vitae

Sally B. Prime
BSc, PhD
Postal address:
Sunnybrook
37, North Hinksey Village
Oxford OX2 0NA
United Kingdom

Phone: +44 (0)1865 247403
http://www.maproom.co.uk
Suceava 2001

Extensive experience in Bioinformatics, scientific instrumentation, statistical data analysis, signal and image processing, and computer science. Skilled in leading multiple projects and multi-disciplinary research teams. An experienced software engineer with a PhD in theoretical chemistry. Has developed complex software in support of leading-edge medical and bioinformatics technologies.

EDUCATION

1977Queen Elizabeth College, London University
 PhD Theoretical Chemistry
 "Perturbation Theory Methods in the Calculation of Electronic Excitation Energies in Atoms and Molecules"
1974Queen Elizabeth College, London University
 BSc Chemistry, 1st Class
1971A levels - Chemistry, Pure Mathematics, Applied Mathematics
 

EMPLOYMENT SUMMARY

1995 - 2001Director of Bioinformatics, Oxford GlycoSciences
1989 - 1995Software Section Leader, Oxford GlycoSystems
1987 - 1989Senior Software Engineer, Expert Systems International
1982 - 1987Senior Software Engineer, Oxford Research Systems
1981 - 1982Visiting Lecturer in Theoretical Chemistry, University of London
1977 - 1981Lecturer in Physical Chemistry, Kenyatta University, Kenya
 

EMPLOYMENT HISTORY

1995 - 2001 Director of Bioinformatics, Oxford GlycoSciences (UK) Ltd

In 1995, OGS embarked on the development the world's first large scale automated Proteomics factory, using electrophoresis of 2D gels and mass spectrometry to identify proteins of biological and pharmaceutical significance. I was appointed Director of Bioinformatics and my responsibilities included:

  • The architecture and management of the software infrastructure in support of these new processes, including the Laboratory Information Management System, imaging and mass spectrometry data capture and analysis, and development of statistical and visualisation methods for end-user interrogation of the integrated data.
  • Development of alliances with key academic groups and specialised software contractors, and management of collaborative development and research projects, including:
  • Specialised LIMS system for Proteomics, with the bioinformatics consultancy firm, Pangea Systems
  • Customisation of the Melanie image analysis software, with Ron Appel, University of Geneva
  • Development of improved image analysis algorithms, with Roland Wilson, University of Warwick
  • Integration of Sequest software by Jimmy Eng and John Yates for tandem spectrum interpretation, with Ruedi Aebersold, University of Washington
  • Isotopic peak deconvolution in MALDI spectra, with John Skilling, MaxEnt Solutions
  • Integration of Mowse mass-matching software, with Darryl Pappin, ICRF

OGS now has extensive and fully operational facilities in Oxfordshire supported by this system.

By 2001, I was directing a team of 12, comprising software developers, data analysts and bioinformaticians. Responsibilities of the team included:

  • Development, delivery and support of novel Proteomics databases and data mining applications for major pharmaceutical company customers and internal target discovery research
  • Development of image processing software in support of in-house Proteomics operations
  • Improved Bayesian scoring statistics to increase sensitivity of protein mass spectral interpretation
  • Bioinformatics research for new product development

1989 - 1995 Software Section Leader, Oxford GlycoSystems

On joining OGS, I developed instrumentation and software for the analysis of carbohydrates, becoming head of the software team of 3 in 1991. My own main projects were:

  • Design and implementation of a real-time embedded operating system for custom-built 68000-based instrument controllers, used by OGS for all its instrument products.
  • Calibration of LC systems for size and charge separation of carbohydrates, and structural interpretation of the elution times of chromatographic peaks
  • Design of a feedback optimising system to determine the most efficient experimental strategy in parallel and sequential sequencing reactions.
  • Design and implementation of carbohydrate sequencing analysis software application (EVE) which coupled the biological modelling of in-vivo glycoprotein synthesis with the modelling of rules for exo-glycosidase specificity to deduce the sequence of carbohydrates analysed with the OGS RAAM Glycosequencer instruments.

1987 - 1989 Senior Software Engineer, Expert Systems International

  • Support and development of an assembler implementation of the Prolog language running under DOS, and a C implementation under UNIX
  • Management of a network of workstations
  • Development of a graphical debugging system for the Prolog language

1982 - 1987 Senior Software Engineer, NMR Imaging Development Group, Oxford Research Systems

  • Implemented all aspects of computer control, data acquisition, Fourier analysis, data processing, graphical display and user interface for the world's first high field Magnetic Resonance Imaging instruments.
  • Worked closely with electronics engineers and NMR scientists to design interfaces and protocols for instrument control and data analysis.
  • Designed and implemented a 3D image display and processing system.
In 1984, the company was acquired by Bruker, and I worked on the original designs for their Biospec and MedSpec range of imaging spectrometers.

1981 - 1982 Visiting Lecturer in Theoretical Chemistry, University of London

1977 - 1981 Lecturer in Physical Chemistry, Kenyatta University, Kenya

PUBLICATIONS

S Prime, M A Robb, 'Unlinked Cluster Corrections to Coupled Electron Pair Theories' Chem. Phys. Letts. 35,86 (1975)
S Prime, M A Robb, 'Many Body Perturbation Methods in a Discrete Orbital Basis: Application to CH4 and Ne' Theoret. Chim. Acta 42,181 (1976)
S Prime, M A Robb, 'Ionization Potentials of CH4 and H2O Computed using Quasi-Degenerate Many Body Perturbation Theory' Chem. Phys. Letts. 47,527 (1977)
M A Robb, D Hegarty, S Prime, 'Many Body Perturbation Methods for the Calculation of Excited States' 'Excited States in Quantum Chemistry' ed. C A Nicolaides and D Beck, Plenum NY (1978)
S Prime, C Rees and M A Robb, 'Size Consistency in Multi-Reference Double Excitation CI Calculations' Mol Phys. 44,173 (1981)
I Cresshull, R Gordon, P Martin, R Ordidge, S Prime, W Timms, 'A Multi-Purpose NMR research System for Imaging and In Vivo Spectroscopy' 'Society of Magnetic Resonance in Medicine 2nd Annual Meeting' (1983)
G K Radda, P Styles, P Bore, G Galloway, R Ordidge, R Gordon, W Timms, S Prime, 'The Investigation of Structure and Metabolism by In Vivo NMR' 'Cerebral Blood Flow and Metabolism Measurement' Eds Hartmann/Hoyer, Springer-Verlag (1985)
F Van der Vyver, R Ordidge, S Prime, 'Proton Chemical Shift Imaging In Vitro and In Vivo Studies at 1.89 Tesla' 'Recent Developments in Medical Nuclear Magnetic Resonance' Antwerp (1985)
R Parekh, S Prime, 'Sequencing of oligosaccharides' US Patent number 5427744. (1995)
G Guile, P Rudd, D Wing, S Prime, R Dwek, 'A Rapid High Resolution High-Performance Liquid Chromatographic Method for Separating Glycan Mixtures and Analyzing Oligosacccharide Profiles' Analytical Biochemistry 240,210-226 (1996)
S Prime, J Dearnley, A Ventom, R Parekh, C Edge 'Oligosaccharide sequencing based on exo- and endoglycosidase digestion and liquid chromatographic analysis of the products' Journal of Chromatography A, 720, 263-274 (1996)
R Parekh, S Prime, 'Sequencing Loop Apparatus' US Patent number 5667984. (1997)
R Parekh, S Prime, R Townsend, N Wedd, 'A Method for De Novo Peptide Sequence Determination' Patent application number 08/877605 (1997)
S Prime, T Merry, 'Exoglycosidase Sequencing of N-linked Glycans by the Reagent Analysis Method (RAAM)' 'Glycoanalysis Protocols' Ed. Hounsell (1998)
R Parekh, R Amess, R Bruce, S Prime, A Platt, 'Computer Assisted Methods and Apparatus for Identification and Characterization of Biomolecules in a Biological Sample' US Patent number 6064754 (2000)
R Parekh, R Amess, R Bruce, S Prime, A Platt, 'Computer-assisted isolation and characterization of proteins' US Patent number 6,278,794 (2001)