John Reid
From SysbioGroup
Contents |
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
