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John Reid
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Community assessment to advance computational prediction of cancer drug combinations in a pharmacogenomic screen
MP Menden, D Wang, MJ Mason, B Szalai, KC Bulusu, Y Guan, T Yu, ...
Nature communications 10 (1), 2674, 2019
2902019
Pseudotime estimation: deconfounding single cell time series
JE Reid, L Wernisch
Bioinformatics 32 (19), 2973-2980, 2016
1412016
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), e99518, 2019
912019
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
612011
STEME: efficient EM to find motifs in large data sets
JE Reid, L Wernisch
Nucleic acids research 39 (18), e126-e126, 2011
592011
Clusternomics: Integrative context-dependent clustering for heterogeneous datasets
E Gabasova, J Reid, L Wernisch
PLoS computational biology 13 (10), e1005781, 2017
562017
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
472009
Integration of multiple epigenomic marks improves prediction of variant impact in saturation mutagenesis reporter assay
D Shigaki, O Adato, AN Adhikari, S Dong, A Hawkins‐Hooker, F Inoue, ...
Human mutation 40 (9), 1280-1291, 2019
452019
Variable structure motifs for transcription factor binding sites
JE Reid, KJ Evans, N Dyer, L Wernisch, S Ott
BMC genomics 11, 1-18, 2010
332010
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
212018
Misclassification risk and uncertainty quantification in deep classifiers
M Sensoy, M Saleki, S Julier, R Aydogan, J Reid
Proceedings of the IEEE/CVF winter conference on applications of computer …, 2021
202021
STEME: a robust, accurate motif finder for large data sets
JE Reid, L Wernisch
PloS one 9 (3), e90735, 2014
172014
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
152010
GPseudoRank: a permutation sampler for single cell orderings
ME Strauß, JE Reid, L Wernisch
Bioinformatics 35 (4), 611-618, 2019
122019
Grandmaster-level chess without search
A Ruoss, G Delétang, S Medapati, J Grau-Moya, LK Wenliang, E Catt, ...
arXiv preprint arXiv:2402.04494, 2024
92024
Reinforcement learning for information retrieval
A Kuhnle, M Aroca-Ouellette, A Basu, M Sensoy, J Reid, D Zhang
Proceedings of the 44th International ACM SIGIR Conference on Research and …, 2021
92021
GPseudoClust: deconvolution of shared pseudo-profiles at single-cell resolution
ME Strauss, PDW Kirk, JE Reid, L Wernisch
Bioinformatics 36 (5), 1484-1491, 2020
82020
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
82018
Nonparametric Bayesian inference of transcriptional branching and recombination identifies regulators of early human germ cell development
CA Penfold, A Sybirna, J Reid, Y Huang, L Wernisch, Z Ghahramani, ...
bioRxiv, 2017
7*2017
Transcriptional programs: modelling higher order structure in transcriptional control
JE Reid, S Ott, L Wernisch
BMC bioinformatics 10, 1-12, 2009
52009
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Articles 1–20