John Reid
John Reid
Alan Turing Institute
Verified email at - Homepage
TitleCited byYear
Pseudotime estimation: deconfounding single cell time series
JE Reid, L Wernisch
Bioinformatics 32 (19), 2973-2980, 2016
STEME: efficient EM to find motifs in large data sets
JE Reid, L Wernisch
Nucleic acids research 39 (18), e126-e126, 2011
Evolutionarily conserved regulatory motifs in the promoter of the Arabidopsis clock gene LATE ELONGATED HYPOCOTYL
M Spensley, JY Kim, E Picot, J Reid, S Ott, C Helliwell, IA Carré
The Plant Cell 21 (9), 2606-2623, 2009
Nodal cis-regulatory elements reveal epiblast and primitive endoderm heterogeneity in the peri-implantation mouse embryo
C Granier, V Gurchenkov, A Perea-Gomez, A Camus, S Ott, ...
Developmental biology 349 (2), 350-362, 2011
Variable structure motifs for transcription factor binding sites
JE Reid, KJ Evans, N Dyer, L Wernisch, S Ott
BMC genomics 11 (1), 30, 2010
Clusternomics: Integrative context-dependent clustering for heterogeneous datasets
E Gabasova, J Reid, L Wernisch
PLoS computational biology 13 (10), e1005781, 2017
An alignment-free model for comparison of regulatory sequences
H Koohy, NP Dyer, JE Reid, G Koentges, S Ott
Bioinformatics 26 (19), 2391-2397, 2010
STEME: a robust, accurate motif finder for large data sets
JE Reid, L Wernisch
PloS one 9 (3), e90735, 2014
Metabolic regulation of pluripotency and germ cell fate through α‐ketoglutarate
J Tischler, WH Gruhn, J Reid, E Allgeyer, F Buettner, C Marr, F Theis, ...
The EMBO journal 38 (1), 2019
GPseudoRank: a permutation sampler for single cell orderings
ME Strauß, JE Reid, L Wernisch
Bioinformatics 35 (4), 611-618, 2018
Nonparametric Bayesian inference of transcriptional branching and recombination identifies regulators of early germ cell development
CA Penfold, A Sybirna, J Reid, Y Huang, L Wernisch, M Grant, ...
bioRxiv, 167684, 2018
Transcriptional programs: modelling higher order structure in transcriptional control
JE Reid, S Ott, L Wernisch
BMC bioinformatics 10 (1), 218, 2009
Integration of Multiple Epigenomic Marks Improves Prediction of Variant Impact in Saturation Mutagenesis Reporter Assay
D Shigaki, O Adato, AN Adhikar, S Dong, A Hawkins‐Hooker, F Inoue, ...
Human mutation, 2019
Branch-recombinant Gaussian processes for analysis of perturbations in biological time series
CA Penfold, A Sybirna, JE Reid, Y Huang, L Wernisch, Z Ghahramani, ...
Bioinformatics 34 (17), i1005-i1013, 2018
Projection layers improve deep learning models of regulatory DNA function
A Hawkins-Hooker, H Kenlay, JE Reid
F1000Research 8, 2019
Machine learning based classification of cells into chronological stages using single-cell transcriptomics
SP Singh, S Janjuha, S Chaudhuri, S Reinhardt, A Kränkel, S Dietz, ...
Scientific reports 8 (1), 17156, 2018
SCRAM: Spatially Coherent Randomized Attention Maps
DA Calian, P Roelants, J Cali, B Carr, K Dubba, JE Reid, D Zhang
arXiv preprint arXiv:1905.10308, 2019
GPseudoClust: deconvolution of shared pseudo-trajectories at single-cell resolution
M Strauss, PDW Kirk, JE Reid, L Wernisch
BioRxiv, 567115, 2019
GPseudoRank: MCMC for sampling from posterior distributions of pseudo-orderings using Gaussian processes
ME Strauss, JE Reid, L Wernisch
bioRxiv, 211417, 2017
Mutual information estimation for transcriptional regulatory network inference
J Ish-Horowicz, J Reid
bioRxiv, 132647, 2017
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