Horizontal Gene Transfer and Fusion Spread Carotenogenesis Among Diverse Heterotrophic Protists
- Mariana Rius, Joshua S Rest, Gina V Filloramo, …, Anna M G Novák Vanclová, John M Archibald, Jackie L Collier
- Genome Biol Evol, 10.1093/gbe/evad029
HSDecipher: A pipeline for comparative genomic analysis of highly similar duplicate genes in eukaryotic genomes
- Xi Zhang, Yining Hu, Zhenyu Cheng, …, Yining Hu, Zhenyu Cheng, John M Archibald
- STAR Protoc, 10.1016/j.xpro.2022.102014
Gene loss, pseudogenization, and independent genome reduction in non-photosynthetic species of Cryptomonas (Cryptophyceae) revealed by comparative nucleomorph genomics
- Jong Im Kim, Goro Tanifuji, Minseok Jeong, Woongghi Shin, John M Archibald
- BMC Biol, 10.1186/s12915-022-01429-6
A phylogenomically informed five-order system for the closest relatives of land plants
- Sebastian Hess, Shelby K Williams, Anna Busch, …, Henrik Buschmann, Klaus von Schwartzenberg, Jan de Vries
- Curr Biol, 10.1016/j.cub.2022.08.022
Evolutionary Dynamics and Lateral Gene Transfer in Raphidophyceae Plastid Genomes
- Jong Im Kim, Bok Yeon Jo, Myung Gil Park, Yeong Du Yoo, Woongghi Shin, John M Archibald
- None, 10.3389/fpls.2022.896138
TreeTuner: A pipeline for minimizing redundancy and complexity in large phylogenetic datasets
- Xi Zhang, Yining Hu, Laura Eme, …, Gina V Filloramo, Klaas J van Wijk, John M Archibald
- STAR Protoc, 10.1016/j.xpro.2022.101175
The Earth BioGenome Project 2020: Starting the clock
- Harris A Lewin, Stephen Richards, Erez Lieberman Aiden, …, Huanming Yang, Anne D Yoder, Guojie Zhang
- Proc Natl Acad Sci U S A, 10.1073/pnas.2115635118
Why sequence all eukaryotes?
- Mark Blaxter, John M Archibald, Anna K Childers, …, Tandy Warnow, Guojie Zhang, Harris A Lewin
- Proc Natl Acad Sci U S A, 10.1073/pnas.2115636118
Standards recommendations for the Earth BioGenome Project
- Mara K N Lawniczak, Richard Durbin, Paul Flicek, …, He Zhang, Harris A Lewin, Stephen Richards
- Proc Natl Acad Sci U S A, 10.1073/pnas.2115639118
Submergence of the filamentous Zygnematophyceae Mougeotia induces differential gene expression patterns associated with core metabolism and photosynthesis
- Janine M R Fürst-Jansen, Sophie de Vries, Maike Lorenz, Klaus von Schwartzenberg, John M Archibald, Jan de Vries
- Protoplasma, 10.1007/s00709-021-01730-1
Genomic analysis finds no evidence of canonical eukaryotic DNA processing complexes in a free-living protist
- Eelco C Tromer, Bruce A Curtis, Jon Jerlström-Hultqvist, …, John M Archibald, Alastair G B Simpson, Andrew J Roger
- Nat Commun, 10.1038/s41467-021-26077-2
RNA-Seq analysis reveals potential regulators of programmed cell death and leaf remodelling in lace plant (Aponogeton madagascariensis)
- Nathan M Rowarth, Bruce A Curtis, Anthony L Einfeldt, John M Archibald, Christian R Lacroix, Arunika H L A N Gunawardena
- BMC Plant Biol, 10.1186/s12870-021-03066-7
Re-examination of two diatom reference genomes using long-read sequencing
- Gina V Filloramo, Bruce A Curtis, Emma Blanche, John M Archibald
- BMC Genomics, 10.1186/s12864-021-07666-3