Transcriptional programs: Modelling higher order structure in transcriptional control. - John E. Reid; Sascha Ott; Lorenz Wernisch (BMC Bioinform., 2009)

An alignment-free model for comparison of regulatory sequences. - Hashem Koohy; Nigel P. Dyer; John E. Reid; Georgy Koentges; Sascha Ott (Bioinform., 2010)

Pseudotime estimation: deconfounding single cell time series. - John E. Reid; Lorenz Wernisch (Bioinform., 2016)

Clusternomics: Integrative context-dependent clustering for heterogeneous datasets. - Evelina Gabasova; John E. Reid; Lorenz Wernisch (PLoS Comput. Biol., 2017)

Branch-recombinant Gaussian processes for analysis of perturbations in biological time series. - Christopher A. Penfold; Anastasiya Sybirna; John E. Reid; Yun Huang; Lorenz Wernisch; Zoubin Ghahramani; Murray Grant; M. Azim Surani (Bioinform., 2018)

GPseudoRank: a permutation sampler for single cell orderings. - Magdalena E. Strauß; John E. Reid; Lorenz Wernisch (Bioinform., 2019)

SCRAM: Spatially Coherent Randomized Attention Maps. - Dan Andrei Calian; Peter Roelants; Jacques Calì; Ben Carr; Krishna Dubba; John E. Reid; Dell Zhang (CoRR, 2019)

Projection layers improve deep learning models of regulatory DNA function. - Alex Hawkins-Hooker; Henry Kenlay; John E. Reid (F1000Research, 2019)

GPseudoClust: deconvolution of shared pseudo-profiles at single-cell resolution. - Magdalena E. Strauß; Paul D. W. Kirk; John E. Reid; Lorenz Wernisch (Bioinform., 2020)