Steve Kelly
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OrthoFinder: solving fundamental biases in whole genome comparisons dramatically improves orthogroup inference accuracy
DM Emms, S Kelly
Genome Biology 16 (1), 1-14, 2015
OrthoFinder: phylogenetic orthology inference for comparative genomics
DM Emms, S Kelly
Genome biology 20 (1), 1-14, 2019
TransRate: reference-free quality assessment of de novo transcriptome assemblies
R Smith-Unna, C Boursnell, R Patro, JM Hibberd, S Kelly
Genome research 26 (8), 1134-1144, 2016
Exon skipping is correlated with exon circularization
S Kelly, C Greenman, PR Cook, A Papantonis
Journal of molecular biology 427 (15), 2414-2417, 2015
Functional genomics in Trypanosoma brucei: a collection of vectors for the expression of tagged proteins from endogenous and ectopic gene loci
S Kelly, J Reed, S Kramer, L Ellis, H Webb, J Sunter, J Salje, N Marinsek, ...
Molecular and biochemical parasitology 154 (1), 103-109, 2007
Horizontal transfer of an adaptive chimeric photoreceptor from bryophytes to ferns
FW Li, JC Villarreal, S Kelly, CJ Rothfels, M Melkonian, E Frangedakis, ...
Proceedings of the National Academy of Sciences 111 (18), 6672-6677, 2014
Deep Evolutionary Comparison of Gene Expression Identifies Parallel Recruitment of Trans-Factors in Two Independent Origins of C4 Photosynthesis.
S Aubry, S Kelly, BM Kümpers, RD Smith-Unna, JM Hibberd
PLoS genetics 10 (6), e1004365, 2014
Simulated binding of transcription factors to active and inactive regions folds human chromosomes into loops, rosettes and topological domains
CA Brackley, J Johnson, S Kelly, PR Cook, D Marenduzzo
Nucleic Acids Research 44 (8), 3503-3512, 2016
STAG: species tree inference from all genes
D Emms, S Kelly
BioRxiv, 267914, 2018
A modular and optimized single marker system for generating Trypanosoma brucei cell lines expressing T7 RNA polymerase and the tetracycline repressor
SK Poon, L Peacock, W Gibson, K Gull, S Kelly
Open biology 2 (2), 110037, 2012
STRIDE: Species Tree Root Inference from Gene Duplication Events
DM Emms, S Kelly
Molecular Biology and Evolution, msx259, 2017
Genome‐wide transcript analysis of early maize leaf development reveals gene cohorts associated with the differentiation of C4 Kranz anatomy
P Wang, S Kelly, JP Fouracre, JA Langdale
The Plant Journal 75 (4), 656-670, 2013
Genome-wide analysis reveals extensive functional interaction between DNA replication initiation and transcription in the genome of Trypanosoma brucei
C Tiengwe, L Marcello, H Farr, N Dickens, S Kelly, M Swiderski, ...
Cell reports 2 (1), 185-197, 2012
Reconciling conflicting phylogenies in the origin of sweet potato and dispersal to Polynesia
P Muñoz-Rodríguez, T Carruthers, JRI Wood, BRM Williams, K Weitemier, ...
Current Biology 28 (8), 1246-1256. e12, 2018
Comparative life cycle transcriptomics revises Leishmania mexicana genome annotation and links a chromosome duplication with parasitism of vertebrates
M Fiebig, S Kelly, E Gluenz
PLoS pathogens 11 (10), e1005186, 2015
Archaeal phylogenomics provides evidence in support of a methanogenic origin of the Archaea and a thaumarchaeal origin for the eukaryotes
S Kelly, B Wickstead, K Gull
Proceedings of the Royal Society B: Biological Sciences 278 (1708), 1009-1018, 2011
The mechanism forming the cell surface of tip-growing rooting cells is conserved among land plants
S Honkanen, VAS Jones, G Morieri, C Champion, AJ Hetherington, ...
Current Biology 26 (23), 3238-3244, 2016
Phylogenetic trees do not reliably predict feature diversity
S Kelly, R Grenyer, RW Scotland
Diversity and Distributions 20 (5), 600-612, 2014
Shared origins of a key enzyme during the evolution of C4 and CAM metabolism
PA Christin, M Arakaki, CP Osborne, A Bräutigam, RF Sage, JM Hibberd, ...
Journal of experimental botany 65 (13), 3609-3621, 2014
Clust: automatic extraction of optimal co-expressed gene clusters from gene expression data
B Abu-Jamous, S Kelly
Genome biology 19 (1), 172, 2018
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