Xing‐Xing Shen

Research interests

Publications

• Genomic factors shape carbon and nitrogen metabolic niche breadth across Saccharomycotina yeasts

  Science · 2024 · https://doi.org/10.1126/science.adj4503

• Incongruence in the phylogenomics era

  Nature Reviews Genetics · 2023 · https://doi.org/10.1038/s41576-023-00620-x

• A genome-informed higher rank classification of the biotechnologically important fungal subphylum Saccharomycotina

  Studies in Mycology · 2023 · https://doi.org/10.3114/sim.2023.105.01

• HGT is widespread in insects and contributes to male courtship in lepidopterans

  Cell · 2022 · https://doi.org/10.1016/j.cell.2022.06.014

• Fusarium fruiting body microbiome member Pantoea agglomerans inhibits fungal pathogenesis by targeting lipid rafts

  Nature Microbiology · 2022 · https://doi.org/10.1038/s41564-022-01131-x

• A genome-scale phylogeny of the kingdom Fungi

  Current Biology · 2021 · https://doi.org/10.1016/j.cub.2021.01.074

• Rooting the Animal Tree of Life

  Molecular Biology and Evolution · 2021 · https://doi.org/10.1093/molbev/msab170

• PhyloFisher: A phylogenomic package for resolving eukaryotic relationships

  PLoS Biology · 2021 · https://doi.org/10.1371/journal.pbio.3001365

• PhyKIT: a broadly applicable UNIX shell toolkit for processing and analyzing phylogenomic data

  Bioinformatics · 2021 · https://doi.org/10.1093/bioinformatics/btab096

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

  PLoS Biology · 2020 · https://doi.org/10.1371/journal.pbio.3001007

• Prickly waterlily and rigid hornwort genomes shed light on early angiosperm evolution

  Nature Plants · 2020 · https://doi.org/10.1038/s41477-020-0594-6

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

  Science Advances · 2020 · https://doi.org/10.1126/sciadv.abd0079

• Eukaryotic Acquisition of a Bacterial Operon

  Cell · 2019 · https://doi.org/10.1016/j.cell.2019.01.034

• Extensive loss of cell-cycle and DNA repair genes in an ancient lineage of bipolar budding yeasts

  PLoS Biology · 2019 · https://doi.org/10.1371/journal.pbio.3000255

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

  mBio · 2019 · https://doi.org/10.1128/mbio.00925-19

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

  eLife · 2018 · https://doi.org/10.7554/elife.33034

• Tempo and Mode of Genome Evolution in the Budding Yeast Subphylum

  Cell · 2018 · https://doi.org/10.1016/j.cell.2018.10.023

• Functional and evolutionary characterization of a secondary metabolite gene cluster in budding yeasts

  Proceedings of the National Academy of Sciences · 2018 · https://doi.org/10.1073/pnas.1806268115

• Evolutionary instability of CUG-Leu in the genetic code of budding yeasts

  Nature Communications · 2018 · https://doi.org/10.1038/s41467-018-04374-7

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

  Molecular Biology and Evolution · 2017 · https://doi.org/10.1093/molbev/msx302

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

  Nature Ecology & Evolution · 2017 · https://doi.org/10.1038/s41559-017-0126

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

  G3 Genes Genomes Genetics · 2016 · https://doi.org/10.1534/g3.116.034744

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

  Genome Biology and Evolution · 2016 · https://doi.org/10.1093/gbe/evw179

• Multiple Genome Alignments Facilitate Development of NPCL Markers: A Case Study of Tetrapod Phylogeny Focusing on the Position of Turtles

  Molecular Biology and Evolution · 2011 · https://doi.org/10.1093/molbev/msr148

Current projects

No projects listed.