The Dictyostelium discoideum genome lacks significant DNA methylation and uncovers palindromic sequences as a source of false positives in bisulfite sequencing
- Robert A Drewell, Tayla C Cormier, Jacob L Steenwyk, …, Javier F Tabima, Jacqueline M Dresch, Denis A Larochelle
- None, 10.1093/nargab/lqad035
COVID-19-Associated Pulmonary Aspergillosis Isolates Are Genomically Diverse but Similar to Each Other in Their Responses to Infection-Relevant Stresses
- Matthew E Mead, PatrÃcia Alves de Castro, Jacob L Steenwyk, …, Antonis Rokas, Gustavo H Goldman, Sara Gago
- Microbiol Spectr, 10.1128/spectrum.05128-22
Extensive non-coding sequence divergence between the major human pathogen Aspergillus fumigatus and its relatives
- Alec Brown, Matthew E Mead, Jacob L Steenwyk, …, Jacob L Steenwyk, Gustavo H Goldman, Antonis Rokas
- None, 10.3389/ffunb.2022.802494
A global phylogenomic analysis of the shiitake genus Lentinula
- Sean Sierra-Patev, Byoungnam Min, Miguel Naranjo-Ortiz, …, Kazuhisa Terashima, Igor V Grigoriev, David Hibbett
- Proc Natl Acad Sci U S A, 10.1073/pnas.2214076120
The evolution of the gliotoxin biosynthetic gene cluster in Penicillium fungi
- Charu Balamurugan, Jacob L Steenwyk, Gustavo H Goldman, …, Jacob L Steenwyk, Gustavo H Goldman, Antonis Rokas
- None, 10.1101/2023.01.17.524442
The dawn of relaxed phylogenetics
- Jacob L Steenwyk, Antonis Rokas, Jacob L Steenwyk, Antonis Rokas, Jacob L Steenwyk, Antonis Rokas
- PLoS Biol, 10.1371/journal.pbio.3001998
Contrasting modes of macro and microsynteny evolution in a eukaryotic subphylum
- Yuanning Li, Hongyue Liu, Jacob L Steenwyk, …, Tao Zhao, Chris Todd Hittinger, Antonis Rokas
- Curr Biol, 10.1016/j.cub.2022.10.025
OrthoSNAP: A tree splitting and pruning algorithm for retrieving single-copy orthologs from gene family trees
- Jacob L Steenwyk, Dayna C Goltz, Thomas J Buida, Yuanning Li, Xing-Xing Shen, Antonis Rokas
- PLoS Biol, 10.1371/journal.pbio.3001827
Examination of Genome-Wide Ortholog Variation in Clinical and Environmental Isolates of the Fungal Pathogen Aspergillus fumigatus
- Maria Augusta C Horta, Jacob L Steenwyk, Matthew E Mead, …, Toni Gabaldón, Antonis Rokas, Gustavo H Goldman
- mBio, 10.1128/mbio.01519-22
BioKIT: a versatile toolkit for processing and analyzing diverse types of sequence data
- Jacob L Steenwyk, Thomas J Buida, Carla Gonçalves, …, Maria Hadjifrangiskou, Yuanning Li, Antonis Rokas
- Genetics, 10.1093/genetics/iyac079
An orthologous gene coevolution network provides insight into eukaryotic cellular and genomic structure and function
- Jacob L Steenwyk, Megan A Phillips, Feng Yang, …, Judith Berman, Chris Todd Hittinger, Antonis Rokas
- Sci Adv, 10.1126/sciadv.abn0105
Resistance-Guided Mining of Bacterial Genotoxins Defines a Family of DNA Glycosylases
- Noah P Bradley, Katherine L Wahl, Jacob L Steenwyk, Antonis Rokas, Brandt F Eichman
- mBio, 10.1128/mbio.03297-21
Regulation of gliotoxin biosynthesis and protection in Aspergillus species
- PatrÃcia Alves de Castro, Ana Cristina Colabardini, MaÃsa Moraes, …, Agostinho Carvalho, Laure N A Ries, Gustavo H Goldman
- PLoS Genet, 10.1371/journal.pgen.1009965