Publications by authors named "David Emms"

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Annotating the genome at single-nucleotide resolution with DNA foundation models.
Bernardo P de Almeida, Hugo Dalla-Torre, Guillaume Richard, Christopher Blum, Lorenz Hexemer, David M Emms

Nat Methods· November 2025

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Rubisco is evolving for improved catalytic efficiency and CO assimilation in plants.
Jacques W Bouvier, David M Emms, Steven Kelly

Proc Natl Acad Sci U S A· March 2024

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GENESPACE tracks regions of interest and gene copy number variation across multiple genomes.
John T Lovell, Avinash Sreedasyam, M Eric Schranz, Melissa Wilson, Joseph W Carlson, David Emms

Elife· September 2022

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The Quest for Orthologs orthology benchmark service in 2022.
Yannis Nevers, Tamsin E M Jones, Dushyanth Jyothi, Bethan Yates, Meritxell Ferret, David M Emms

Nucleic Acids Res· July 2022

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SHOOT: phylogenetic gene search and ortholog inference.
David Mark Emms, Steven Kelly

Genome Biol· March 2022

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Conditional stomatal closure in a fern shares molecular features with flowering plant active stomatal responses.
Andrew R G Plackett, David M Emms, Steven Kelly, Alistair M Hetherington, Jane A Langdale

Curr Biol· October 2021

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Rubisco Adaptation Is More Limited by Phylogenetic Constraint Than by Catalytic Trade-off.
Jacques W Bouvier, David M Emms, Timothy Rhodes, Jai S Bolton, Amelia Brasnett

Mol Biol Evol· June 2021

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NO GAMETOPHORES 2 Is a Novel Regulator of the 2D to 3D Growth Transition in the Moss Physcomitrella patens.
Laura A Moody, Steven Kelly, Roxaana Clayton, Zoe Weeks, David M Emms

Curr Biol· February 2021

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Benchmarking Orthogroup Inference Accuracy: Revisiting Orthobench.
David M Emms, Steven Kelly

Genome Biol Evol· December 2020

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Gene expression data support the hypothesis that Isoetes rootlets are true roots and not modified leaves.
Alexander J Hetherington, David M Emms, Steven Kelly, Liam Dolan

Sci Rep· December 2020

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The Quest for Orthologs benchmark service and consensus calls in 2020.
Adrian M Altenhoff, Javier Garrayo-Ventas, Salvatore Cosentino, David Emms, Natasha M Glover

Nucleic Acids Res· July 2020

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Multiple Metabolic Innovations and Losses Are Associated with Major Transitions in Land Plant Evolution.
Naomi Cannell, David M Emms, Alexander J Hetherington, John MacKay, Steven Kelly

Curr Biol· May 2020

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Gene Duplication Accelerates the Pace of Protein Gain and Loss from Plant Organelles.
Rona Costello, David M Emms, Steven Kelly

Mol Biol Evol· April 2020

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Agricultural Selection of Wheat Has Been Shaped by Plant-Microbe Interactions.
Andrzej Tkacz, Francesco Pini, Thomas R Turner, Eloïne Bestion, James Simmonds, David M Emms

Front Microbiol· February 2020

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OrthoFinder: phylogenetic orthology inference for comparative genomics.
David M Emms, Steven Kelly

Genome Biol· November 2019

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STRIDE: Species Tree Root Inference from Gene Duplication Events.
David M Emms, Steven Kelly

Mol Biol Evol· December 2017

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An Alternative Strategy for Trypanosome Survival in the Mammalian Bloodstream Revealed through Genome and Transcriptome Analysis of the Ubiquitous Bovine Parasite Trypanosoma (Megatrypanum) theileri.
Steven Kelly, Alasdair Ivens, G Adam Mott, Ellis O'Neill, David Emms

Genome Biol Evol· August 2017

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The Stepwise Increase in the Number of Transcription Factor Families in the Precambrian Predated the Diversification of Plants On Land.
Bruno Catarino, Alexander J Hetherington, David M Emms, Steven Kelly, Liam Dolan

Mol Biol Evol· November 2016

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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.
David M Emms, Sarah Covshoff, Julian M Hibberd, Steven Kelly

Mol Biol Evol· July 2016

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OrthoFinder: solving fundamental biases in whole genome comparisons dramatically improves orthogroup inference accuracy.
David M Emms, Steven Kelly

Genome Biol· August 2015

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