Dr Steve Kelly: List of publications

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Gene Duplication Accelerates the Pace of Protein Gain and Loss from Plant Organelles.

Subdivision of Light Signaling Networks Contributes to Partitioning of C4 Photosynthesis.

Metabolic quirks and the colourful history of the Euglena gracilis secondary plastid.

Gene expression data support the hypothesis that Isoetes rootlets are true roots and not modified leaves

OrthoFinder: phylogenetic orthology inference for comparative genomics.

A taxonomic monograph of Ipomoea integrated across phylogenetic scales.

Neofunctionalisation of basic helix-loop-helix proteins occurred when embryophytes colonised the land.

Transcriptome, proteome and draft genome of Euglena gracilis.

The molecular evolution of C4 photosynthesis: opportunities for understanding and improving the world's most productive plants.

OrthoFinder: phylogenetic orthology inference for comparative genomics

Subdivision of light signalling networks contributes to cellular partitioning of C4 photosynthesis in maize

Chromatin clues to the trypanosome parasite's uniform coat.

Clust: automatic extraction of optimal co-expressed gene clusters from gene expression data.

The continuing evolution of publishing in the biological sciences.

Selection-driven cost-efficiency optimization of transcripts modulates gene evolutionary rate in bacteria.

The Amount of Nitrogen Used for Photosynthesis Modulates Molecular Evolution in Plants.

Somatic hybridization provides segregating populations for the identification of causative mutations in sterile mutants of the moss Physcomitrella patens.

OMGene: mutual improvement of gene models through optimisation of evolutionary conservation.

Reconciling conflicting phylogenies in the origin of sweet potato and dispersal to Polynesia

Multiplex fluorescent, activity-based protein profiling identifies active α-glycosidases and other hydrolases in plants.

Codon choice directs constitutive mRNA levels in trypanosomes.

Genetic Regulation of the 2D to 3D Growth Transition in the Moss Physcomitrella patens.

Simultaneous Clustering of Multiple Heterogeneous Gene Expression Datasets

Multiple mechanisms for enhanced plasmodesmata density in disparate subtypes of C4 grasses.

STRIDE: Species Tree Root Inference from Gene Duplication Events.

The Mechanism Forming the Cell Surface of Tip-Growing Rooting Cells Is Conserved among Land Plants.

The transcriptome, extracellular proteome and active secretome of agroinfiltrated Nicotiana benthamiana uncover a large, diverse protease repertoire.

Transcriptional control of photosynthetic capacity: conservation and divergence from Arabidopsis to rice.

Genome sequencing reveals metabolic and cellular interdependence in an amoeba-kinetoplastid symbiosis.

Engineering biosynthesis of high-value compounds in photosynthetic organisms.

An Alternative Strategy for Trypanosome Survival in the Mammalian Bloodstream Revealed through Genome and Transcriptome Analysis of the Ubiquitous Bovine Parasite Trypanosoma (Megatrypanum) theileri.

Candidate regulators of Early Leaf Development in Maize Perturb Hormone Signalling and Secondary Cell Wall Formation When Constitutively Expressed in Rice.

OrthoFiller: utilising data from multiple species to improve the completeness of genome annotations.

Functional PTB phosphate transporters are present in streptophyte algae and early diverging land plants.

Evolution of the endomembrane systems of trypanosomatids - conservation and specialisation.

Characterization of RBP9 and RBP10, two developmentally regulated RNA-binding proteins in Trypanosoma brucei.

Transcriptome Sequence of the Bloodstream Form of Trypanoplasma borreli, a Hematozoic Parasite of Fish Transmitted by Leeches.

Description of Phytomonas oxycareni n. sp. from the Salivary Glands of Oxycarenus lavaterae.

Genome Sequence of Phytomonas françai, a Cassava (Manihot esculenta) Latex Parasite.

OrthoFiller: utilising data from multiple species to improve the completeness of genome annotations

Euglena gracilis Genome and Transcriptome: Organelles, Nuclear Genome Assembly Strategies and Initial Features.

The Mechanism Forming the Cell Surface of Tip-Growing Rooting Cells Is Conserved among Land Plants.

Dietary nitrogen alters codon bias and genome composition in parasitic microorganisms.

The Stepwise Increase in the Number of Transcription Factor Families in the Precambrian Predated the Diversification of Plants On Land.

Simulating topological domains in human chromosomes with a fitting-free model.

TransRate: reference-free quality assessment of de novo transcriptome assemblies.

Independent and Parallel Evolution of New Genes by Gene Duplication in Two Origins of C4 Photosynthesis Provides New Insight into the Mechanism of Phloem Loading in C4 Species.

Simulated binding of transcription factors to active and inactive regions folds human chromosomes into loops, rosettes and topological domains.

Combined Chlorophyll Fluorescence and Transcriptomic Analysis Identifies the P3/P4 Transition as a Key Stage in Rice Leaf Photosynthetic Development.

C4 Photosynthesis in the Rice Paddy: Insights from the Noxious Weed Echinochloa glabrescens.

Genome of Leptomonas pyrrhocoris: a high-quality reference for monoxenous trypanosomatids and new insights into evolution of Leishmania

RSL Class I Genes Controlled the Development of Epidermal Structures in the Common Ancestor of Land Plants.

Comparative Life Cycle Transcriptomics Revises Leishmania mexicana Genome Annotation and Links a Chromosome Duplication with Parasitism of Vertebrates.

Two forward genetic screens for vein density mutants in sorghum converge on a cytochrome P450 gene in the brassinosteroid pathway.

An Ancestral Role for CONSTITUTIVE TRIPLE RESPONSE1 Proteins in Both Ethylene and Abscisic Acid Signaling.

OrthoFinder: solving fundamental biases in whole genome comparisons dramatically improves orthogroup inference accuracy.

Exon Skipping Is Correlated with Exon Circularization

Exon Skipping Is Correlated with Exon Circularization.

RNA-Seq based phylogeny recapitulates previous phylogeny of the genus Flaveria (Asteraceae) with some modifications Evolutionary developmental biology and morphology

RNA-Seq based phylogeny recapitulates previous phylogeny of the genus Flaveria (Asteraceae) with some modifications.

Splicing of many human genes involves sites embedded within introns.

Phytomonas: trypanosomatids adapted to plant environments.

SLaP mapper: a webserver for identifying and quantifying spliced-leader addition and polyadenylation site usage in kinetoplastid genomes.

The impact of widespread regulatory neofunctionalization on homeolog gene evolution following whole-genome duplication in maize.

Touching from a distance: Evolution of interplay between the nuclear pore complex, nuclear basket, and the mitotic spindle.

Shared origins of a key enzyme during the evolution of C4 and CAM metabolism.

Deep evolutionary comparison of gene expression identifies parallel recruitment of trans-factors in two independent origins of C4 photosynthesis.

Horizontal transfer of an adaptive chimeric photoreceptor from bryophytes to ferns.

Nuclear pore complex evolution: a trypanosome Mlp analogue functions in chromosomal segregation but lacks transcriptional barrier activity.

A draft genome for the African crocodilian trypanosome Trypanosoma grayi.

Phylogenetic trees do not reliably predict feature diversity

Genome-wide transcript analysis of early maize leaf development reveals gene cohorts associated with the differentiation of C4 Kranz anatomy.

Genome-wide transcript analysis of early maize leaf development reveals gene cohorts associated with the differentiation of C4 Kranz anatomy

Adaptin evolution in kinetoplastids and emergence of the variant surface glycoprotein coat in African trypanosomatids

DendroBLAST: Approximate Phylogenetic Trees in the Absence of Multiple Sequence Alignments

Evolution of GOLDEN2-LIKE gene function in C(3) and C (4) plants.

Differential Localization of the Two T. brucei Poly(A) Binding Proteins to the Nucleus and RNP Granules Suggests Binding to Distinct mRNA Pools

Evolution of GOLDEN2-LIKE gene function in C3 and C4 plants

Nitric oxide generated by the rice blast fungus Magnaporthe oryzae drives plant infection.

Genome-wide analysis reveals extensive functional interaction between DNA replication initiation and transcription in the genome of Trypanosoma brucei.

MergeAlign: improving multiple sequence alignment performance by dynamic reconstruction of consensus multiple sequence alignments.

Genome organization is a major component of gene expression control in response to stress and during the cell division cycle in trypanosomes.

A modular and optimized single marker system for generating Trypanosoma brucei cell lines expressing T7 RNA polymerase and the tetracycline repressor.

A modular and optimized single marker system for generating Trypanosoma brucei cell lines expressing T7 RNA polymerase and the tetracycline repressor

Ab initio identification of novel regulatory elements in the genome of Trypanosoma brucei by Bayesian inference on sequence segmentation

Archaeal phylogenomics provides evidence in support of a methanogenic origin of the Archaea and a thaumarchaeal origin for the eukaryotes.

Archaeal phylogenomics provides evidence in support of a methanogenic origin of the Archaea and a thaumarchaeal origin for the eukaryotes

Identification of a crenarchaeal orthologue of Elf1: implications for chromatin and transcription in Archaea.

Functional genomics in Trypanosoma brucei: a collection of vectors for the expression of tagged proteins from endogenous and ectopic gene loci.

Diversification of function by different isoforms of conventionally shared RNA polymerase subunits

Diversification of function by different isoforms of conventionally shared RNA polymerase subunits.

Characterization and differential nuclear localization of Nopp140 and a novel Nopp140-like protein in trypanosomes.

An in silico analysis of trypanosornatid RNA polymerases: insights into their unusual transcription

Benchmarking Orthogroup Inference Accuracy: Revisiting Orthobench

NO GAMETOPHORES 2 is a novel regulator of the 2D to 3D growth transition in the moss Physcomitrium patens