Journal Articles


  1. Pseudotime estimation: deconfounding single cell time series
    Reid, John E.; Wernisch, Lorenz;
    Bioinformatics 2016, , btw372.
  2. Conserved cis-regulatory modules control robustness in Msx1 expression at single cell resolution
    Vance, Keith W.; Woodcock, Dan J.; Reid, John E.; Bretschneider, Till; Ott, Sascha; Koentges, Georgy;
    Genome Biology and Evolution 2015, , evv179.
  3. STEME: A Robust, Accurate Motif Finder for Large Data Sets
    Reid, John E.; Wernisch, Lorenz;
    PLoS ONE 2014, 9, e90735.
  4. STEME: efficient EM to find motifs in large data sets
    Reid, J.E.; Wernisch, L.;
    Nucleic Acids Research 2011, 39, e126–e126.
  5. Nodal cis-regulatory elements reveal epiblast and primitive endoderm heterogeneity in the peri-implantation mouse embryo
    Granier, Céline; Gurchenkov, Vasily; Perea-Gomez, Aitana; Camus, Anne; Ott, Sascha; Papanayotou, Costis; Iranzo, Julian; Moreau, Anne; Reid, John; Koentges, Georgy; Sabéran-Djoneidi, Délara; Collignon, Jérôme;
    Developmental Biology 2011, 349, 350-362.
  6. An alignment-free model for comparison of regulatory sequences
    Koohy, H.; Dyer, N.P.; Reid, J.E.; Koentges, G.; Ott, S.;
    Bioinformatics 2010, 26, 2391.
  7. Variable structure motifs for transcription factor binding sites
    Reid, J.; Evans, K.; Dyer, N.; Wernisch, L.; Ott, S.;
    BMC Genomics 2010, 11, 30.
  8. Transcriptional programs: Modelling higher order structure in transcriptional control
    Reid, J.; Ott, S.; Wernisch, L.;
    BMC Bioinformatics 2009, 10, 218.
  9. Evolutionarily conserved regulatory motifs in the promoter of the Arabidopsis clock gene LATE ELONGATED HYPOCOTYL
    Spensley, M.; Kim, J.Y.; Picot, E.; Reid, J.; Ott, S.; Helliwell, C.; Carré, I.A.;
    The Plant Cell Online 2009, 21, 2606–2623.

Theses


  1. Probabilistic models of transcriptional regulation
    John Reid
    Supervisor : : Lorenz Wernisch
    Cambridge University, 2013.
  2. A comparison of various neural network architectures for learning context-dependent game strategies
    John Reid
    Supervisor : : Karl MacDorman
    Cambridge University, 1994.