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
A high-quality genome of the dobsonfly Neoneuromus ignobilis reveals molecular convergences in aquatic insects
- Xing-Zhou Ma, Zi-Qi Wang, Xi-Qian Ye, …, Pu Tang, Xingxing Shen, Xue-Xin Chen
- Genomics, 10.1016/j.ygeno.2022.110437
HGT is widespread in insects and contributes to male courtship in lepidopterans
- Yang Li, Zhiguo Liu, Chao Liu, …, Antonis Rokas, Jianhua Huang, Xing-Xing Shen
- Cell, 10.1016/j.cell.2022.06.014
Fusarium fruiting body microbiome member Pantoea agglomerans inhibits fungal pathogenesis by targeting lipid rafts
- Sunde Xu, Yong-Xin Liu, Tomislav Cernava, …, Yunlong Yu, Yang Bai, Yun Chen
- Nat Microbiol, 10.1038/s41564-022-01131-x
Examination of Gene Loss in the DNA Mismatch Repair Pathway and Its Mutational Consequences in a Fungal Phylum
- Megan A Phillips, Jacob L Steenwyk, Xing-Xing Shen, Antonis Rokas
- Genome Biol Evol, 10.1093/gbe/evab219
PhyloFisher: A phylogenomic package for resolving eukaryotic relationships
- Alexander K Tice, David Žihala, Tomáš Pánek, …, Jürgen F H Strassert, Martin KolÃsko, Matthew W Brown
- PLoS Biol, 10.1371/journal.pbio.3001365
Rooting the Animal Tree of Life
- Yuanning Li, Xing-Xing Shen, Benjamin Evans, Casey W Dunn, Antonis Rokas
- Mol Biol Evol, 10.1093/molbev/msab170
Dissecting Incongruence between Concatenation- and Quartet-Based Approaches in Phylogenomic Data
- Xing-Xing Shen, Jacob L Steenwyk, Antonis Rokas
- Syst Biol, 10.1093/sysbio/syab011
A genome-scale phylogeny of the kingdom Fungi
- Yuanning Li, Jacob L Steenwyk, Ying Chang, …, Chris Todd Hittinger, Xing-Xing Shen, Antonis Rokas
- Curr Biol, 10.1016/j.cub.2021.01.074
PhyKIT: a broadly applicable UNIX shell toolkit for processing and analyzing phylogenomic data
- Jacob L Steenwyk, Thomas J Buida, Abigail L Labella, …, Yuanning Li, Xing-Xing Shen, Antonis Rokas
- Bioinformatics, 10.1093/bioinformatics/btab096
ClipKIT: A multiple sequence alignment trimming software for accurate phylogenomic inference
- Jacob L Steenwyk, Thomas J Buida, Yuanning Li, Xing-Xing Shen, Antonis Rokas
- PLoS Biol, 10.1371/journal.pbio.3001007
An investigation of irreproducibility in maximum likelihood phylogenetic inference
- Xing-Xing Shen, Yuanning Li, Chris Todd Hittinger, Xue-Xin Chen, Antonis Rokas
- Nat Commun, 10.1038/s41467-020-20005-6
Feature frequency profile-based phylogenies are inaccurate
- Yuanning Li, Kyle T David, Xing-Xing Shen, Jacob L Steenwyk, Kenneth M Halanych, Antonis Rokas
- Proc Natl Acad Sci U S A, 10.1073/pnas.2013143117
Genome-scale phylogeny and contrasting modes of genome evolution in the fungal phylum Ascomycota
- Xing-Xing Shen, Jacob L Steenwyk, Abigail L LaBella, …, Marizeth Groenewald, Chris T Hittinger, Antonis Rokas
- Sci Adv, 10.1126/sciadv.abd0079
Recurrent Loss of abaA, a Master Regulator of Asexual Development in Filamentous Fungi, Correlates with Changes in Genomic and Morphological Traits
- Matthew E Mead, Alexander T Borowsky, Bastian Joehnk, …, Xing-Xing Shen, Anita Sil, Antonis Rokas
- Genome Biol Evol, 10.1093/gbe/evaa107