The Development of Three Long Universal Nuclear Protein-Coding Locus Markers and Their Application to Osteichthyan Phylogenetics with Nested PCR

por Shen, Xing-Xing, Liang, Dan, Zhang, Peng
Publicado 2012

A Genome-Scale Investigation of How Sequence, Function, and Tree-Based Gene Properties Influence Phylogenetic Inference

por Shen, Xing-Xing, Salichos, Leonidas, Rokas, Antonis
Publicado 2016

Contentious relationships in phylogenomic studies can be driven by a handful of genes

por Shen, Xing-Xing, Hittinger, Chris Todd, Rokas, Antonis
Publicado 2017

Evaluating Fast Maximum Likelihood-Based Phylogenetic Programs Using Empirical Phylogenomic Data Sets

por Zhou, Xiaofan, Shen, Xing-Xing, Hittinger, Chris Todd, Rokas, Antonis
Publicado 2018

Examination of Gene Loss in the DNA Mismatch Repair Pathway and Its Mutational Consequences in a Fungal Phylum

por Phillips, Megan A, Steenwyk, Jacob L, Shen, Xing-Xing, Rokas, Antonis
Publicado 2021

Rooting the Animal Tree of Life

por Li, Yuanning, Shen, Xing-Xing, Evans, Benjamin, Dunn, Casey W, Rokas, Antonis
Publicado 2021

Genomic features and evolution of the conditionally dispensable chromosome in the tangerine pathotype of Alternaria alternata

por Wang, Mingshuang, Fu, Huilan, Shen, Xing‐Xing, Ruan, Ruoxin, Rokas, Antonis, Li, Hongye
Publicado 2019

An investigation of irreproducibility in maximum likelihood phylogenetic inference

por Shen, Xing-Xing, Li, Yuanning, Hittinger, Chris Todd, Chen, Xue-xin, Rokas, Antonis
Publicado 2020

ClipKIT: A multiple sequence alignment trimming software for accurate phylogenomic inference

por Steenwyk, Jacob L., Buida, Thomas J., Li, Yuanning, Shen, Xing-Xing, Rokas, Antonis
Publicado 2020

A Robust Phylogenomic Time Tree for Biotechnologically and Medically Important Fungi in the Genera Aspergillus and Penicillium

por Steenwyk, Jacob L., Shen, Xing-Xing, Lind, Abigail L., Goldman, Gustavo H., Rokas, Antonis
Publicado 2019

Reconstructing the Backbone of the Saccharomycotina Yeast Phylogeny Using Genome-Scale Data

por Shen, Xing-Xing, Zhou, Xiaofan, Kominek, Jacek, Kurtzman, Cletus P., Hittinger, Chris Todd, Rokas, Antonis
Publicado 2016

OrthoSNAP: A tree splitting and pruning algorithm for retrieving single-copy orthologs from gene family trees

por Steenwyk, Jacob L., Goltz, Dayna C., Buida, Thomas J., Li, Yuanning, Shen, Xing-Xing, Rokas, Antonis
Publicado 2022

Recurrent Loss of abaA, a Master Regulator of Asexual Development in Filamentous Fungi, Correlates with Changes in Genomic and Morphological Traits

por Mead, Matthew E, Borowsky, Alexander T, Joehnk, Bastian, Steenwyk, Jacob L, Shen, Xing-Xing, Sil, Anita, Rokas, Antonis
Publicado 2020

FoxO and rotund form a binding complex governing wing polyphenism in planthoppers

por Chen, Sun-Jie, Zhang, Jin-Li, Ma, Wen-Jing, Wu, Hui-Jie, Li, Yang, Shen, Xing-Xing, Xu, Hai-Jun
Publicado 2023

Multiple Reinventions of Mating-type Switching during Budding Yeast Evolution

por Krassowski, Tadeusz, Kominek, Jacek, Shen, Xing-Xing, Opulente, Dana A., Zhou, Xiaofan, Rokas, Antonis, Hittinger, Chris Todd, Wolfe, Kenneth H.
Publicado 2019

The Impact of Natural Selection on the Evolution and Function of Placentally Expressed Galectins

por Ely, Zackery A, Moon, Jiyun M, Sliwoski, Gregory R, Sangha, Amandeep K, Shen, Xing-Xing, Labella, Abigail L, Meiler, Jens, Capra, John A, Rokas, Antonis
Publicado 2019

Genome-scale phylogeny and contrasting modes of genome evolution in the fungal phylum Ascomycota

por Shen, Xing-Xing, Steenwyk, Jacob L., LaBella, Abigail L., Opulente, Dana A., Zhou, Xiaofan, Kominek, Jacek, Li, Yuanning, Groenewald, Marizeth, Hittinger, Chris T., Rokas, Antonis
Publicado 2020

Saccharomycotina yeasts defy longstanding macroecological patterns

por David, Kyle T., Harrison, Marie-Claire, Opulente, Dana A., LaBella, Abigail L., Wolters, John F., Zhou, Xiaofan, Shen, Xing-Xing, Groenewald, Marizeth, Pennell, Matt, Hittinger, Chris Todd, Rokas, Antonis
Publicado 2023

Diverse signatures of convergent evolution in cacti-associated yeasts

por Gonçalves, Carla, Harrison, Marie-Claire, Steenwyk, Jacob L., Opulente, Dana A., LaBella, Abigail L., Wolters, John F., Zhou, Xiaofan, Shen, Xing-Xing, Groenewald, Marizeth, Hittinger, Chris Todd, Rokas, Antonis
Publicado 2023

Evidence for loss and reacquisition of alcoholic fermentation in a fructophilic yeast lineage

por Gonçalves, Carla, Wisecaver, Jennifer H, Kominek, Jacek, Oom, Madalena Salema, Leandro, Maria José, Shen, Xing-Xing, Opulente, Dana A, Zhou, Xiaofan, Peris, David, Kurtzman, Cletus P, Hittinger, Chris Todd, Rokas, Antonis, Gonçalves, Paula
Publicado 2018