Steven L. Kelly

RECUR identifies recurrent amino acid substitutions in multiple sequence alignments, showing widespread evolution in SARS-CoV-2 S protein with functional implications.

GLADE infers gene gains, losses, and duplications across species and reconstructs ancestral genomes, showing higher accuracy than existing methods in mammalian datasets.

FastSpeciesTree rapidly and accurately infers species trees from large genomic datasets, outperforming existing methods in speed and scalability.

This study identifies a prion-like protein that regulates the 2D-to-3D growth transition in moss by altering cytokinin signaling and participating in liquid-liquid phase separation.

OrthoFinder v3 splits orthogroups at duplications predating the species-tree root, raising OrthoBench accuracy, and assigns extra species to a core run, finishing 1024 species in 128 hours.

This study shows that reducing stomatal density in Arabidopsis thaliana through metabolic engineering improves water-use efficiency and vegetative growth under water-deficit conditions.

This study manipulates brassinosteroid signalling in rice to increase chloroplast area in bundle sheath cells, showing cell-specific control can enhance chloroplast compartment size without severe growth effects.

The paper develops Chloro-Count, a deep learning tool, to quantify chloroplast occupancy in rice bundle sheath cells and shows that OsHAP3H loss increases chloroplast numbers by 50%.

The paper analyzes adaptive evolution in photosystem subunits across 773 angiosperm species, revealing 7% of residues show signs of adaptive evolution and their impact on photosystem II repair.

This paper uses genome editing to relocalize carbonic anhydrase activity in rice, achieving a key step in C4 photosynthesis evolution and revealing a new role for chloroplast CA in photosynthetic induction.

SHOOT is a tool that places query sequences into phylogenetic trees and identifies orthologs, performing as fast as BLAST and as accurately as conventional tree inference.

The paper revisits the Orthobench benchmark to assess orthogroup inference methods using updated phylogenetic analyses and provides an open-source benchmarking suite.

OrthoFinder now infers orthogroups, rooted gene and species trees, duplications and orthologs from proteomes alone, topping Quest for Orthologs accuracy tests while rivaling heuristic tools' speed.

Clust improves co-expression gene clustering by aligning with biological expectations, outperforming existing methods across multiple datasets.

OMGene improves gene models by optimizing evolutionary conservation within orthogroups using RNA-seq data from plants and fungi.

STAG is a method for species tree inference that uses multi-copy gene families, showing higher accuracy and scalability compared to existing methods.

This study shows that the nitrogen cost of transcript sequences is influenced by photosynthetic nitrogen requirements, slowing molecular evolution in plants with higher nitrogen needs.

The paper identifies novel molecular signatures of C4 photosynthesis by analyzing transcriptomes from eighteen independent origins of C4 plants, revealing shared and new metabolic pathways and gene expression responses to low CO2.

OrthoFiller improves genome annotations by identifying and adding missing genes using information from multiple related species.