James Foadi

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James is a mathematical and computational physicist with 20 years experience in the development of methods for X-ray crystallography.

He is currently a member of the Membrane Protein Laboratory and collaborates closely with I24 staff for the development of novel algorithms to manage multiple crystals.

Email: james.foadi@diamond.ac.uk
Tel: +44 (0) 1235 778790

Key Research Area

Key Research Areas

  • Development of algorithmic methods for crystallography.
  • Statistics applied to crystallography.
  • The R platform for statistical computing and programming. 
  1. Research Expertise
  2. Collaborations
  3. Publications
  4. Biography
Research Expertise -

Current Research Interests

The development of statistical and mathematical algorithms for processing data in protein crystallography is a fundamental area of research in structural biology. All the existing computer programs used in the field are based on statistics and mathematics which have been implemented in algorithms and, ultimately, computer software. All these programs have been designed to help researchers in structural biology to process data they have collected with a specific technique and to turn these data in a 3D structure of the biological molecule of interest.

My specific research niche has been in the development of processing methods for data from multiple crystals. If a good-quality crystal is available, this is normally used to collect a complete data set. Quite often, though, individual crystals are rapidly damaged by the intensely energetic x-ray beams, and stop providing data before a full collection has been reached. In such cases data from different crystals can be collated in a statistical sensible way to provide a complete data set. In collaboration with Gwyndaf Evans I have written BLEND, a computer program for data handling and processing of data from multiple crystals. The program is available from within the CCP4 suite of programs for crystallography.

I am very interested in applying statistics to structural biology. I develop methods and programs using the very powerful and popular R platform for statistical computing. In collaboration with David Waterman I have created the first R package for crystallography, calle "cRy".

As a member of the Membrane Protein Laboratory, I support users both in data collection and data processing. I also interact with beamline scientists and Diamond staff in general both from a scientific point of view and in providing support for users activities.
 

Collaborations - +

Collaborations

  1. CCP4 core group This group is based at the Research Complex at Harwell and maintains the large CCP4 platform for macromolecular crystallography. I interact routinely with all core members for issues related to working programs and especially for the installation and maintenance of my program BLEND.
  2. Istituto di Cristallografia - IC (Italy) This is a large institute part of the Italian national research council (CNR). Researchers at IC provide both experimental and computational technologies to deal with several typologies of crystallographic data. I collaborate with Drs R. Caliandro, D, Belviso and D. Siliqi on various techniques and algorithms for protein crystallography, and in the delucidation of the structure of the photosynthetic Reaction Centre with specific antennas connected.
  3. Dr David Waterman - CCP4 / DIALS Development of a package for crystallography, cRy, within the R platform for statistical computing. 
Publications - +

Publications

  • 2013 J. Foadi – "Introduction to R for CCP4 users" – in CCP4 Newsletter on Protein Crystallography, number 49, Summer 2013, 33­44 2013 J. Foadi, P. Aller, Y. Alguel, A. Cameron, D. Axford, R. Owen, W. Armour, D. Waterman, S. Iwata and G. Evans – "Clustering procedures for the optimal selection of data sets from multiple crystals in macromolecular crystallography" – Acta Cryst. D, 69, 1617­1632
  • 2012 D. Axford, R. L. Owen, J. Aishima, J. Foadi, A. W. Morgan, J. I. Robinson, J. E. Nettleship, R. I. Owens, I. Moraes, E. E. Fry, J. M. Grimes, K. Harlos, A. Kotecha, J. Ren, G. Sutton, T. S. Walter, D. I. Stuart and G. Evans – "In situ macromolecular crystallography using microbeams" – Acta Cryst. D, 68, 592­600
  • 2011 J. Foadi and G. Evans ­ "On the allowed values for the triclinic unit cell angles" ­ Acta Cryst. A, 67, 93­95 2008 J. Foadi and G. Evans ­ "Elucidations on the reciprocal lattice and the Ewald sphere" ­ Eur. J. Phys., 29, 1059­1068

 

Biography - +

Biography

James is a mathematical and computational physicist with 20 years experience in the development of methods for X-ray crystallography. He is currently a member of the Membrane Protein Laboratory and collaborates closely with I24 staff for the development of novel algorithms to manage multiple crystals.