Kelly, Steven

OrthoFinder: phylogenetic orthology inference for comparative genomics

Emms, D. M., & Kelly, S. (2019) · Genome Biology

Genomics and Phylogenetic StudiesChromosomal and Genetic Variations

Cited by 7,676

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

Emms, D. M., & Kelly, S. (2015) · Genome Biology

Genomics and Phylogenetic StudiesChromosomal and Genetic Variations

Cited by 3,408

STAG: Species Tree Inference from All Genes

Emms, D. M., & Kelly, S. (2018) · bioRxiv (Cold Spring Harbor Laboratory)

Genomics and Phylogenetic StudiesEvolution and Paleontology Studies

Cited by 332

STRIDE: Species Tree Root Inference from Gene Duplication Events

Emms, D. M., & Kelly, S. (2017) · Molecular Biology and Evolution

Genomics and Phylogenetic StudiesProtist diversity and phylogeny

Cited by 311

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

Kelly, S., & Maini, P. K. (2013) · PLoS ONE

Genomics and Phylogenetic StudiesFractal and DNA sequence analysis

Cited by 73

SHOOT: phylogenetic gene search and ortholog inference

Emms, D. M., & Kelly, S. (2022) · Genome Biology

Genomics and Phylogenetic StudiesFractal and DNA sequence analysis

Cited by 67

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

Bouvier, J. W., Emms, D. M., Rhodes, T., Bolton, J. S., Brasnett, A., Eddershaw, A., Nielsen, J. R., Unitt, A., Whitney, S. M., & Kelly, S. (2021) · Molecular Biology and Evolution

Photosynthetic Processes and MechanismsEvolution and Genetic Dynamics

Cited by 65

The economics of organellar gene loss and endosymbiotic gene transfer

Kelly, S. (2021) · Genome Biology

Protist diversity and phylogenyEvolution and Genetic Dynamics

Cited by 62

The economics of organellar gene loss and endosymbiotic gene transfer

Kelly, S. (2020) · Genome biology

Protist diversity and phylogenyEvolution and Genetic Dynamics

Cited by 62

Ten Years of Collaborative Progress in the Quest for Orthologs

Linard, B., Ebersberger, I., McGlynn, S. E., Glover, N., Mochizuki, T., Patricio, M., Lecompte, O., Nevers, Y., Thomas, P. D., Gabaldón, T., et al. (2021) · Molecular Biology and Evolution

Genomics and Phylogenetic StudiesBioinformatics and Genomic Networks

Cited by 45

Benchmarking Orthogroup Inference Accuracy: Revisiting Orthobench

Emms, D. M., & Kelly, S. (2020) · Genome Biology and Evolution

Genomics and Phylogenetic StudiesChromosomal and Genetic Variations

Cited by 36

OrthoFinder: improved phylogenetic orthology inference with enhanced accuracy and scalability

Emms, D. M., Liu, Y., Belcher, L., Holmes, J., & Kelly, S. (2026) · Nature Methods

Genomics and Phylogenetic StudiesBioinformatics and Genomic Networks

Cited by 25

Publishing ethics in the era of paper mills

Hackett, R., & Kelly, S. (2020) · Biology Open

Publishing and Scholarly CommunicationAcademic integrity and plagiarism

Cited by 22

Response to Tcherkez and Farquhar: Rubisco adaptation is more limited by phylogenetic constraint than by catalytic trade-off

Bouvier, J. W., & Kelly, S. (2023) · Journal of Plant Physiology

Photosynthetic Processes and MechanismsPlant Water Relations and Carbon Dynamics

Cited by 11