John Reid

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Contact

Please feel free to contact me. I work at the Medical Research Council's Biostatistics Unit:

MRC Biostatistics Unit,
Institute of Public Health,
University Forvie Site,
Robinson Way,
Cambridge.
CB2 0SR
United Kingdom
Phone Number: +44 (0)1223 330366
Fax number: +44 (0)1223 330365
Email address: firstname.lastname@mrc-bsu.cam.ac.uk


Projects

Transcription factor binding site prediction
Gapped PSSMs
Transcriptional programs
Probabilistic motif search with suffix trees
Mixtures of beta distributions


Software

Python inference package : a package implementing inference techniques I have used in my research. It includes an implementation of Gaussian processes.
Boolean network inference in Python : inference of Boolean networks under constraints.
STEME : a fast motif finder based on MEME but implemented using suffix trees.
Python interval package : computations on intervals, sets of intervals and maps from intervals to values. Based on the boost.icl library.
Python cookbook package : a miscellany of python code, some collected from elsewhere, some written myself.


Publications

Nucleic Acids Res. 2011 Jul 23. [Epub ahead of print]
STEME: efficient EM to find motifs in large data sets.
Reid JE, Wernisch L
PubMed
Dev Biol. 2011 Jan 15;349(2):350-62. Epub 2010 Nov 1.
Nodal cis-regulatory elements reveal epiblast and primitive endoderm heterogeneity in the peri-implantation mouse embryo.
Granier C, Gurchenkov V, Perea-Gomez A, Camus A, Ott S, Papanayotou C, Iranzo J, Moreau A, Reid J, Koentges G, Sabéran-Djoneidi D, Collignon J.
PubMed
An alignment-free model for comparison of regulatory sequences. 
Bioinformatics. 2010 Oct 1;26(19):2391-7. Epub 2010 Aug 9.
Koohy H, Dyer NP, Reid JE, Koentges G, Ott S.
PubMed
Variable structure motifs for transcription factor binding sites.
BMC Genomics. 2010 Jan 14;11:30.
Reid JE, Evans KJ, Dyer N, Wernisch L, Ott S.
PubMed
Evolutionarily conserved regulatory motifs in the promoter of the Arabidopsis clock gene LATE ELONGATED HYPOCOTYL.
Plant Cell. 2009 Sep;21(9):2606-23. Epub 2009 Sep 29.
Spensley M, Kim JY, Picot E, Reid J, Ott S, Helliwell C, Carré IA.
PubMed
Transcriptional programs: modelling higher order structure in transcriptional control.
BMC Bioinformatics. 2009 Jul 16;10:218.
Reid JE, Ott S, Wernisch L.
PubMed


CV

2008- Member of Lorenz Wernisch's group, MRC Biostatistics Unit, Cambridge, UK
2005-2007 Member of Lorenz Wernisch's group, Dept. of Crystallography, Birkbeck College, London, UK
2005 Research assistant with Georgy Koentges' lab, Wolfson Institute, UCL
1994-2005 Various software development and consultancy roles mainly in financial sector, London, New York, Tokyo, Singapore
1993-1994 Diploma Computer Science, Cambridge, UK
1990-1993 B.A. Maths Hons, Cambridge, UK

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