A more up-to-date list of publications may be found on my Google Scholar page.

Journal Articles


  1. Machine learning based classification of cells into chronological stages using single-cell transcriptomics
    Singh, Sumeet Pal; Janjuha, Sharan; Chaudhuri, Samata; Reinhardt, Susanne; Kränkel, Annekathrin; Dietz, Sevina; Eugster, Anne; Bilgin, Halil; Korkmaz, Selçuk; Zararsız, Gökmen; Ninov, Nikolay; Reid, John E.;
    Scientific Reports 2018, 8, 17156.
  2. Metabolic regulation of pluripotency and germ cell fate through α‐ketoglutarate
    Tischler, Julia; Gruhn, Wolfram H.; Reid, John; Allgeyer, Edward; Buettner, Florian; Marr, Carsten; Theis, Fabian; Simons, Ben D.; Wernisch, Lorenz; Surani, M. Azim;
    The EMBO Journal 2018, , e99518.
  3. GPseudoRank: a permutation sampler for single cell orderings
    Strauß, Magdalena E.; Reid, John E.; Wernisch, Lorenz;
    Bioinformatics 2018, , .
  4. Branch-recombinant Gaussian processes for analysis of perturbations in biological time series
    Penfold, Christopher A.; Sybirna, Anastasiya; Reid, John E.; Huang, Yun; Wernisch, Lorenz; Ghahramani, Zoubin; Grant, Murray; Surani, M. Azim;
    Bioinformatics 2018, 34, i1005-i1013.
  5. Clusternomics: Integrative context-dependent clustering for heterogeneous datasets
    Gabasova, Evelina; Reid, John; Wernisch, Lorenz;
    PLOS Computational Biology 2017, 13, e1005781.
  6. Pseudotime estimation: deconfounding single cell time series
    Reid, John E.; Wernisch, Lorenz;
    Bioinformatics 2016, , btw372.
  7. 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.
  8. STEME: A Robust, Accurate Motif Finder for Large Data Sets
    Reid, John E.; Wernisch, Lorenz;
    PLoS ONE 2014, 9, e90735.
  9. 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.
  10. STEME: efficient EM to find motifs in large data sets
    Reid, J.E.; Wernisch, L.;
    Nucleic Acids Research 2011, 39, e126–e126.
  11. 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.
  12. Variable structure motifs for transcription factor binding sites
    Reid, J.; Evans, K.; Dyer, N.; Wernisch, L.; Ott, S.;
    BMC Genomics 2010, 11, 30.
  13. Transcriptional programs: Modelling higher order structure in transcriptional control
    Reid, J.; Ott, S.; Wernisch, L.;
    BMC Bioinformatics 2009, 10, 218.
  14. 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.

Preprints


  1. Projection layers improve deep learning models of regulatory DNA function
    Hawkins-Hooker, Alex; Kenlay, Henry; Reid, John;
    bioRxiv 2018, , 412734.
  2. Nonparametric Bayesian inference of transcriptional branching and recombination identifies regulators of early human germ cell development
    Penfold, Christopher Andrew; Sybirna, Anastasiya; Reid, John; Huang, Yun; Wernisch, Lorenz; Ghahramani, Zoubin; Grant, Murray; Surani, M. Azim;
    bioRxiv 2017, , 167684.
  3. Mutual Information Estimation For Transcriptional Regulatory Network Inference
    Ish-Horowicz, Jonathan; Reid, John;
    bioRxiv 2017, , 132647.

Theses


  1. Probabilistic models of transcriptional regulation
    John Reid
    PhD, Cambridge University, 2013.
  2. A comparison of various neural network architectures for learning context-dependent game strategies
    John Reid
    Diploma in Computer Science, Cambridge University, 1994.