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Characterising the Gene Regulatory Networks Governing Photosynthesis: From Basic Understanding to Targeted Engineering

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Publications

Benchmarking Orthogroup Inference Accuracy: Revisiting Orthobench

Author(s): David Emms Steven Kelly
Published in: Genome Biology and Evolution, 2020, ISSN 1759-6653
Publisher: Oxford University Press
DOI: 10.1093/gbe/evaa211

Conditional stomatal closure in a fern shares molecular features with flowering plant active stomatal responses

Author(s): Andrew Plackett David Emms Steven Kelly Alistair Hetherington Jane Langdale
Published in: Current Biology, 2021, ISSN 0960-9822
Publisher: Cell Press
DOI: 10.1016/j.cub.2021.08.008

Rubisco Adaptation Is More Limited by Phylogenetic Constraint Than by Catalytic Trade-off

Author(s): Jacques W Bouvier, David M Emms, Timothy Rhodes, Jai S Bolton, Amelia Brasnett, Alice Eddershaw, Jochem R Nielsen, Anastasia Unitt, Spencer M Whitney, Steven Kelly
Published in: Molecular Biology and Evolution, 2021, ISSN 0737-4038
Publisher: Oxford University Press
DOI: 10.1093/molbev/msab079

SHOOT: phylogenetic gene search and ortholog inference

Author(s): David Emms, Steven Kelly
Published in: Genome Biology, 2022, ISSN 1465-6906
Publisher: BioMed Central
DOI: 10.1186/s13059-022-02652-8

NO GAMETOPHORES 2 Is a Novel Regulator of the 2D to 3D Growth Transition in the Moss Physcomitrella patens

Author(s): Laura Moody Steven Kelly Roxaana Clayton Zoe Weeks David Emms Jane A.Langdale
Published in: Current Biology, 2021, ISSN 0960-9822
Publisher: Cell Press
DOI: 10.1016/j.cub.2020.10.077

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

Author(s): Rona Costello, David M Emms, Steven Kelly
Published in: Molecular Biology and Evolution, 37/4, 2019, Page(s) 969-981, ISSN 0737-4038
Publisher: Oxford University Press
DOI: 10.1093/molbev/msz275

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

Author(s): Basel Abu-Jamous, Steven Kelly
Published in: Genome Biology, 19/1, 2018, ISSN 1474-7596
Publisher: BioMed Central
DOI: 10.1186/s13059-018-1536-8

The economics of organellar gene loss and endosymbiotic gene transfer

Author(s): Steven Kelly
Published in: Genome Biology, 5, 2021, ISSN 1474-760X
Publisher: BioMed Central
DOI: 10.1101/2020.10.01.322487

Installation of C4 photosynthetic pathway enzymes in rice using a single construct.

Author(s): Maria Ermakova; Stéphanie Arrivault; Rita Giuliani; Florence R. Danila; Hugo Alonso-Cantabrana; Hugo Alonso-Cantabrana; Daniela Vlad; Hirofumi Ishihara; Regina Feil; Manuela Guenther; Gian Luca Borghi; Sarah Covshoff; Martha Ludwig; Asaph B. Cousins; Jane A. Langdale; Steven L. Kelly; John E. Lunn; Mark Stitt; Susanne von Caemmerer; Robert T. Furbank
Published in: Plant Biotechnology Journal, 32, 2021, ISSN 1467-7644
Publisher: Blackwell Publishing Inc.
DOI: 10.1111/pbi.13487

The Quest for Orthologs benchmark service and consensus calls in 2020

Author(s): Altenhoff, Adrian M; Garrayo-Ventas, Javier; Cosentino, Salvatore; Emms, David; Glover, Natasha M; Hernández-Plaza, Ana; Nevers, Yannis; Sundesha, Vicky; Szklarczyk, Damian; Fernández, José M; Codó, Laia; for Orthologs Consortium, the Quest; Gelpi, Josep Ll; Huerta-Cepas, Jaime; Iwasaki, Wataru; Kelly, Steven; Lecompte, Odile; Muffato, Matthieu; Martin, Maria J; Capella-Gutierrez, Salvador;
Published in: Nucleic Acids Research, 48 (W1), 29, 2020, ISSN 0305-1048
Publisher: Oxford University Press
DOI: 10.3929/ethz-b-000425390

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

Author(s): Alexander J. Hetherington; Alexander J. Hetherington; David M. Emms; Steven L. Kelly; Liam Dolan; Liam Dolan
Published in: Scientific Reports, Vol 10, Iss 1, Pp 1-10 (2020), 30, 2020, ISSN 2045-2322
Publisher: Nature Publishing Group
DOI: 10.1101/2019.12.16.878298

The Quest for Orthologs benchmark service and consensus calls in 2020

Author(s): Adrian M Altenhoff, Javier Garrayo-Ventas, Salvatore Cosentino, David Emms, Natasha M Glover, Ana Hernández-Plaza, Yannis Nevers, Vicky Sundesha, Damian Szklarczyk, José M Fernández, Laia Codó, the Quest for Orthologs Consortium, Josep Ll Gelpi, Jaime Huerta-Cepas, Wataru Iwasaki, Steven Kelly, Odile Lecompte, Matthieu Muffato, Maria J Martin, Salvador Capella-Gutierrez, Paul D Thomas, Erik
Published in: Nucleic Acids Research, 48/W1, 2020, Page(s) W538-W545, ISSN 0305-1048
Publisher: Oxford University Press
DOI: 10.1093/nar/gkaa308

Codon choice directs constitutive mRNA levels in trypanosomes

Author(s): de Freitas Nascimento, Janaina; Kelly, Steven; Sunter, Jack; Carrington, Mark
Published in: eLife, 2, 2018, ISSN 2050-084X
Publisher: eLife Sciences Publications
DOI: 10.17863/CAM.23265

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

Author(s): Michael P. Dunne, Steven Kelly
Published in: BMC Genomics, 19/1, 2018, ISSN 1471-2164
Publisher: BioMed Central
DOI: 10.1186/s12864-018-4704-z

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

Author(s): Emily A. Seward, Steven Kelly
Published in: Genome Biology, 19/1, 2018, ISSN 1474-760X
Publisher: Springer Nature
DOI: 10.1186/s13059-018-1480-7

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

Author(s): Friederike Grosse-Holz, Steven Kelly, Svenja Blaskowski, Farnusch Kaschani, Markus Kaiser, Renier A.L. van der Hoorn
Published in: Plant Biotechnology Journal, 16/5, 2018, Page(s) 1068-1084, ISSN 1467-7644
Publisher: Blackwell Publishing Inc.
DOI: 10.1111/pbi.12852

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

Author(s): Steven Kelly
Published in: Molecular Biology and Evolution, 35/7, 2018, Page(s) 1616-1625, ISSN 0737-4038
Publisher: Oxford University Press
DOI: 10.1093/molbev/msy043

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

Author(s): Steven Kelly, Alasdair Ivens, G. Adam Mott, Ellis O’Neill, David Emms, Olivia Macleod, Paul Voorheis, Kevin Tyler, Matthew Clark, Jacqueline Matthews, Keith Matthews, Mark Carrington
Published in: Genome Biology and Evolution, 9/8, 2017, Page(s) 2093-2109, ISSN 1759-6653
Publisher: Oxford University Press
DOI: 10.1093/gbe/evx152

STRIDE: Species Tree Root Inference from Gene Duplication Events.

Author(s): Emms, DM; Kelly, S
Published in: Molecular Biology and Evolution, 5, 2017, ISSN 1537-1719
Publisher: Oxford University Press
DOI: 10.1101/140020

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

Author(s): Florence R Danila, William Paul Quick, Rosemary G White, Steven Kelly, Susanne von Caemmerer, Robert T Furbank
Published in: Journal of Experimental Botany, 69/5, 2018, Page(s) 1135-1145, ISSN 0022-0957
Publisher: Oxford University Press
DOI: 10.1093/jxb/erx456

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

Author(s): Bruno Catarino, Alexander J. Hetherington, David M. Emms, Steven Kelly, Liam Dolan
Published in: Molecular Biology and Evolution, 33/11, 2016, Page(s) 2815-2819, ISSN 0737-4038
Publisher: Oxford University Press
DOI: 10.1093/molbev/msw155

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

Author(s): Suvi Honkanen, Victor A.S. Jones, Giulia Morieri, Clement Champion, Alexander J. Hetherington, Steve Kelly, Hélène Proust, Denis Saint-Marcoux, Helen Prescott, Liam Dolan
Published in: Current Biology, 26/23, 2016, Page(s) 3238-3244, ISSN 0960-9822
Publisher: Cell Press
DOI: 10.1016/j.cub.2016.09.062

Dietary nitrogen alters codon bias and genome composition in parasitic microorganisms

Author(s): Emily A. Seward, Steven Kelly
Published in: Genome Biology, 17/1, 2016, ISSN 1474-760X
Publisher: BioMed Central
DOI: 10.1186/s13059-016-1087-9

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

Author(s): C. A. Brackley, D. Michieletto, F. Mouvet, J. Johnson, S. Kelly, P. R. Cook, D. Marenduzzo
Published in: Nucleus, 7/5, 2016, Page(s) 453-461, ISSN 1949-1034
Publisher: Landes Bioscience
DOI: 10.1080/19491034.2016.1239684

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

Author(s): David M. Emms, Sarah Covshoff, Julian M. Hibberd, Steven Kelly
Published in: Molecular Biology and Evolution, 33/7, 2016, Page(s) 1796-1806, ISSN 0737-4038
Publisher: Oxford University Press
DOI: 10.1093/molbev/msw057

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

Author(s): Richard Smith-Unna, Chris Boursnell, Rob Patro, Julian M. Hibberd, Steven Kelly
Published in: Genome Research, 26/8, 2016, Page(s) 1134-1144, ISSN 1088-9051
Publisher: Cold Spring Harbor Laboratory Press
DOI: 10.1101/gr.196469.115

Engineering biosynthesis of high-value compounds in photosynthetic organisms

Author(s): Ellis C. O’Neill, Steven Kelly
Published in: Critical Reviews in Biotechnology, 2016, Page(s) 1-24, ISSN 0738-8551
Publisher: Taylor & Francis
DOI: 10.1080/07388551.2016.1237467

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

Author(s): Michael P. Dunne, Steven Kelly
Published in: BMC Genomics, 18/1, 2017, ISSN 1471-2164
Publisher: BioMed Central
DOI: 10.1186/s12864-017-3771-x

OrthoFinder: phylogenetic orthology inference for comparative genomics

Author(s): David M. Emms, Steven Kelly
Published in: Genome Biology, 20/1, 2019, ISSN 1474-7596
Publisher: BioMed Central
DOI: 10.1186/s13059-019-1832-y

Subdivision of Light Signaling Networks Contributes to Partitioning of C 4 Photosynthesis

Author(s): Ross-W. Hendron, Steven Kelly
Published in: Plant Physiology, 182/3, 2020, Page(s) 1297-1309, ISSN 0032-0889
Publisher: American Society of Plant Biologists
DOI: 10.1104/pp.19.01053

Transcriptome, proteome and draft genome of Euglena gracilis

Author(s): ThankGod E. Ebenezer, Martin Zoltner, Alana Burrell, Anna Nenarokova, Anna M. G. Novák Vanclová, Binod Prasad, Petr Soukal, Carlos Santana-Molina, Ellis O’Neill, Nerissa N. Nankissoor, Nithya Vadakedath, Viktor Daiker, Samson Obado, Sara Silva-Pereira, Andrew P. Jackson, Damien P. Devos, Julius Lukeš, Michael Lebert, Sue Vaughan, Vladimίr Hampl, Mark Carrington, Michael L. Ginger, Joel B. Da
Published in: BMC Biology, 17/1, 2019, ISSN 1741-7007
Publisher: BioMed Central
DOI: 10.1186/s12915-019-0626-8

Codon choice directs constitutive mRNA levels in trypanosomes.

Author(s): Janaina de Freitas Nascimento; Steven Kelly; Jack Sunter; Mark Carrington
Published in: eLife, 19, 2018, ISSN 2050-084X
Publisher: eLife Sciences Publications
DOI: 10.7554/elife.32467

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

Author(s): Peng Wang; Ross-William Hendron; Steven L. Kelly
Published in: New Phytologist, 20, 2017, ISSN 0028-646X
Publisher: Blackwell Publishing Inc.
DOI: 10.1111/nph.14682

Multiple Metabolic Innovations and Losses Are Associated with Major Transitions in Land Plant Evolution

Author(s): Naomi Cannell, David M. Emms, Alexander J. Hetherington, John MacKay, Steven Kelly, Liam Dolan, Lee J. Sweetlove
Published in: Current Biology, 30/10, 2020, Page(s) 1783-1800.e11, ISSN 0960-9822
Publisher: Cell Press
DOI: 10.1016/j.cub.2020.02.086