Risultati della ricerca - Xing‐Xing Shen

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  1. 1
    One Thousand Two Hundred Ninety Nuclear Genes from a Genome-Wide Survey Support Lungfishes as the Sister Group of Tetrapods

    One Thousand Two Hundred Ninety Nuclear Genes from a Genome-Wide Survey Support Lungfishes as the Sister Group of Tetrapods di Dan Liang, Xing‐Xing Shen, Peng Zhang

    Pubblicazione 2013
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  2. 2
    A Genome-Scale Investigation of How Sequence, Function, and Tree-Based Gene Properties Influence Phylogenetic Inference

    A Genome-Scale Investigation of How Sequence, Function, and Tree-Based Gene Properties Influence Phylogenetic Inference di Xing‐Xing Shen, Leonidas Salichos, Antonis Rokas

    Pubblicazione 2016
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  3. 3
    Multiple Genome Alignments Facilitate Development of NPCL Markers: A Case Study of Tetrapod Phylogeny Focusing on the Position of Turtles

    Multiple Genome Alignments Facilitate Development of NPCL Markers: A Case Study of Tetrapod Phylogeny Focusing on the Position of Turtles di Xing‐Xing Shen, Dan Liang, Jianping Wen, Ping Zhang

    Pubblicazione 2011
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  4. 4
    Evaluating Fast Maximum Likelihood-Based Phylogenetic Programs Using Empirical Phylogenomic Data Sets

    Evaluating Fast Maximum Likelihood-Based Phylogenetic Programs Using Empirical Phylogenomic Data Sets di Xiaofan Zhou, Xing‐Xing Shen, Chris Todd Hittinger, Antonis Rokas

    Pubblicazione 2017
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  5. 5
    A robust phylogenomic timetree for biotechnologically and medically important fungi in the genera <i>Aspergillus</i> and <i>Penicillium</i>

    A robust phylogenomic timetree for biotechnologically and medically important fungi in the genera <i>Aspergillus</i> and <i>Penicillium</i> di Jacob L. Steenwyk, Xing‐Xing Shen, Abigail Lind, Gustavo H. Goldman, Antonis Rokas

    Pubblicazione 2018
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  6. 6
    A Robust Phylogenomic Time Tree for Biotechnologically and Medically Important Fungi in the Genera <i>Aspergillus</i> and <i>Penicillium</i>

    A Robust Phylogenomic Time Tree for Biotechnologically and Medically Important Fungi in the Genera <i>Aspergillus</i> and <i>Penicillium</i> di Jacob L. Steenwyk, Xing‐Xing Shen, Abigail Lind, Gustavo H. Goldman, Antonis Rokas

    Pubblicazione 2019
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  7. 7
    ClipKIT: A multiple sequence alignment trimming software for accurate phylogenomic inference

    ClipKIT: A multiple sequence alignment trimming software for accurate phylogenomic inference di Jacob L. Steenwyk, Thomas J. Buida, Yuanning Li, Xing‐Xing Shen, Antonis Rokas

    Pubblicazione 2020
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  8. 8
    An investigation of irreproducibility in maximum likelihood phylogenetic inference

    An investigation of irreproducibility in maximum likelihood phylogenetic inference di Xing‐Xing Shen, Yuanning Li, Chris Todd Hittinger, Xue‐Xin Chen, Antonis Rokas

    Pubblicazione 2020
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  9. 9
    Reconstructing the Backbone of the Saccharomycotina Yeast Phylogeny Using Genome-Scale Data

    Reconstructing the Backbone of the Saccharomycotina Yeast Phylogeny Using Genome-Scale Data di Xing‐Xing Shen, Xiaofan Zhou, Jacek Kominek, Cletus P. Kurtzman, Chris Todd Hittinger, Antonis Rokas

    Pubblicazione 2016
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  10. 10
    OrthoSNAP: A tree splitting and pruning algorithm for retrieving single-copy orthologs from gene family trees

    OrthoSNAP: A tree splitting and pruning algorithm for retrieving single-copy orthologs from gene family trees di Jacob L. Steenwyk, Dayna Goltz, Thomas J. Buida, Yuanning Li, Xing‐Xing Shen, Antonis Rokas

    Pubblicazione 2022
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  11. 11
    PhyKIT: a broadly applicable UNIX shell toolkit for processing and analyzing phylogenomic data

    PhyKIT: a broadly applicable UNIX shell toolkit for processing and analyzing phylogenomic data di Jacob L. Steenwyk, Thomas J. Buida, Abigail L. LaBella, Yuanning Li, Xing‐Xing Shen, Antonis Rokas

    Pubblicazione 2021
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  12. 12
    Functional and evolutionary characterization of a secondary metabolite gene cluster in budding yeasts

    Functional and evolutionary characterization of a secondary metabolite gene cluster in budding yeasts di David Krause, Jacek Kominek, Dana A. Opulente, Xing‐Xing Shen, Xiaofan Zhou, Quinn K. Langdon, Jeremy DeVirgilio, Amanda Beth Hulfachor, Cletus P. Kurtzman, Antonis Rokas, Chris Todd Hittinger

    Pubblicazione 2018
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  13. 13
    Saccharomycotina yeasts defy long-standing macroecological patterns

    Saccharomycotina yeasts defy long-standing macroecological patterns di Kyle T. David, Marie‐Claire Harrison, Dana A. Opulente, Abigail L. LaBella, John F. Wolters, Xiaofan Zhou, Xing‐Xing Shen, Marizeth Groenewald, Matt Pennell, Chris Todd Hittinger, Antonis Rokas

    Pubblicazione 2024
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  14. 14
    Eukaryotic Acquisition of a Bacterial Operon

    Eukaryotic Acquisition of a Bacterial Operon di Jacek Kominek, Drew T. Doering, Dana A. Opulente, Xing‐Xing Shen, Xiaofan Zhou, Jeremy DeVirgilio, Amanda Beth Hulfachor, Marizeth Groenewald, Mcsean A. Mcgee, Steven D. Karlen, Cletus P. Kurtzman, Antonis Rokas, Chris Todd Hittinger

    Pubblicazione 2019
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  15. 15
    Evolutionary instability of CUG-Leu in the genetic code of budding yeasts

    Evolutionary instability of CUG-Leu in the genetic code of budding yeasts di Tadeusz Krassowski, Aisling Y. Coughlan, Xing‐Xing Shen, Xiaofan Zhou, Jacek Kominek, Dana A. Opulente, Robert Riley, Igor V. Grigoriev, Nikunj Maheshwari, Denis C. Shields, Cletus P. Kurtzman, Chris Todd Hittinger, Antonis Rokas, Kenneth H. Wolfe

    Pubblicazione 2018
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  16. 16
    Convergent expansions of keystone gene families drive metabolic innovation in Saccharomycotina yeasts

    Convergent expansions of keystone gene families drive metabolic innovation in Saccharomycotina yeasts di Kyle T. David, Joshua G. Schraiber, Johnathan G. Crandall, Abigail L. LaBella, Dana A. Opulente, Marie‐Claire Harrison, John F. Wolters, Xiaofan Zhou, Xing‐Xing Shen, Marizeth Groenewald, Chris Todd Hittinger, Matthew W. Pennell, Antonis Rokas

    Pubblicazione 2025
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  17. 17
    PhyloFisher: A phylogenomic package for resolving eukaryotic relationships

    PhyloFisher: A phylogenomic package for resolving eukaryotic relationships di Alexander K. Tice, David Žihala, Tomáš Pánek, Robert E. Jones, Eric D. Salomaki, Serafim Nenarokov, Fabien Burki, Marek Eliáš, Laura Eme, Andrew J. Roger, Antonis Rokas, Xing‐Xing Shen, Jürgen F. H. Strassert, Martin Kolísko, Matthew W. Brown

    Pubblicazione 2021
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  18. 18
    Extensive loss of cell-cycle and DNA repair genes in an ancient lineage of bipolar budding yeasts

    Extensive loss of cell-cycle and DNA repair genes in an ancient lineage of bipolar budding yeasts di Jacob L. Steenwyk, Dana A. Opulente, Jacek Kominek, Xing‐Xing Shen, Xiaofan Zhou, Abigail L. LaBella, Noah P. Bradley, Brandt F. Eichman, Neža Čadež, Diego Libkind, Jeremy DeVirgilio, Amanda Beth Hulfachor, Cletus P. Kurtzman, Chris Todd Hittinger, Antonis Rokas

    Pubblicazione 2019
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  19. 19
    Prickly waterlily and rigid hornwort genomes shed light on early angiosperm evolution

    Prickly waterlily and rigid hornwort genomes shed light on early angiosperm evolution di Yongzhi Yang, Pengchuan Sun, Leke Lv, Donglei Wang, Dafu Ru, Ying Li, Tao Ma, Lei Zhang, Xing‐Xing Shen, Fanbo Meng, Beibei Jiao, Lanxing Shan, Man Liu, Qingfeng Wang, Zhiji Qin, Zhenxiang Xi, Xiyin Wang, Charles C. Davis, Jianquan Liu

    Pubblicazione 2020
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  20. 20
    Tempo and Mode of Genome Evolution in the Budding Yeast Subphylum

    Tempo and Mode of Genome Evolution in the Budding Yeast Subphylum di Xing‐Xing Shen, Dana A. Opulente, Jacek Kominek, Xiaofan Zhou, Jacob L. Steenwyk, Kelly V. Buh, Max A. B. Haase, Jennifer H. Wisecaver, Mingshuang Wang, Drew T. Doering, James T. Boudouris, Rachel M. Schneider, Quinn K. Langdon, Moriya Ohkuma, Rikiya Endoh, Masako Takashima, Ri‐Ichiroh Manabe, Neža Čadež, Diego Libkind, Carlos A. Rosa, Jeremy DeVirgilio, Amanda Beth Hulfachor, Marizeth Groenewald, Cletus P. Kurtzman, Chris Todd Hittinger, Antonis Rokas

    Pubblicazione 2018
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