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Loop profile: 1251165

Keywords

Phylogenetics, Evolutionary Biology, Genomics, Insects, Structural Genomics

Countries

China

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Employment (3)

Zhejiang University: Hangzhou, Zhejiang, CN

2025-03-01 to present | Professor (Institute of Insect Sciences)
Employment
Source: Self-asserted source
Xing-Xing Shen

Zhejiang University: Hangzhou, Zhejiang, CN

2019-12-03 to 2025-02-28 | Assistant Professor (Institute of Insect Sciences)
Employment
Source: Self-asserted source
Xing-Xing Shen

Vanderbilt University: Nashville, TN, US

2014-12-01 to 2019-11-30 | PostDoctoral Fellow (Biological Science)
Employment
Source: Self-asserted source
Xing-Xing Shen

Education and qualifications (2)

Sun Yat-Sen University: Guangzhou, Guangdong, CN

2009-09-01 to 2014-06-28 | Ph.D (School of Life Science)
Education
Source: Self-asserted source
Xing-Xing Shen

Hainan University: Haikou, CN

2005-09-01 to 2009-06-30 | B.S. (School of Agriculture)
Education
Source: Self-asserted source
Xing-Xing Shen

Works (50 of 55)

Items per page:
Page 1 of 2

Genomic factors limiting the diversity of Saccharomycotina plant pathogens

2025-02-28 | Preprint
DOI: 10.1101/2025.02.27.640420
Contributors: Sun Lee; Caroline West; Dana A. Opulente; Marie-Claire Harrison; John F. Wolters; Xing-Xing Shen; Xiaofan Zhou; Marizeth Groenewald; Chris Todd Hittinger; Antonis Rokas et al.
Source: check_circle
Crossref

A critical evaluation of deep-learning based phylogenetic inference programs using simulated datasets

Journal of Genetics and Genomics
2025-01 | Journal article
DOI: 10.1016/j.jgg.2025.01.006
Contributors: Yixiao Zhu; Yonglin Li; Chuhao Li; Xing-Xing Shen; Xiaofan Zhou
Source: check_circle
Crossref

Genomic factors shaping codon usage across the Saccharomycotina subphylum

G3: Genes, Genomes, Genetics
2024-11-06 | Journal article
DOI: 10.1093/g3journal/jkae207
Contributors: Bryan Zavala; Lauren Dineen; Kaitlin J Fisher; Dana A Opulente; Marie-Claire Harrison; John F Wolters; Xing-Xing Shen; Xiaofan Zhou; Marizeth Groenewald; Chris Todd Hittinger et al.
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Crossref

Post‐transfer adaptation of HGT‐acquired genes and contribution to guanine metabolic diversification in land plants

New Phytologist
2024-10 | Journal article
DOI: 10.1111/nph.20040
Contributors: Jun‐Jie Wu; Qian‐Wen Deng; Yi‐Yang Qiu; Chao Liu; Chen‐Feng Lin; Ya‐Lu Ru; Yue Sun; Jun Lai; Lu‐Xian Liu; Xing‐Xing Shen et al.
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Crossref

The Influence of the Number of Tree Searches on Maximum Likelihood Inference in Phylogenomics

Systematic Biology
2024-10-30 | Journal article
DOI: 10.1093/sysbio/syae031
Contributors: Chao Liu; Xiaofan Zhou; Yuanning Li; Chris Todd Hittinger; Ronghui Pan; Jinyan Huang; Xue-xin Chen; Antonis Rokas; Yun Chen; Xing-Xing Shen et al.
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Crossref

Convergent expansions of keystone gene families drive metabolic innovation in a major eukaryotic clade

2024-07-23 | Preprint
DOI: 10.1101/2024.07.22.604484
Contributors: Kyle T David; Joshua G Schraiber; Johnathan G. Crandall; Abigail Leavitt LaBella; Dana A Opulente; Marie-Claire Harrison; John F Wolters; Xiaofan Zhou; Xing-Xing Shen; Marizeth Groenewald et al.
Source: check_circle
Crossref

Identification of a longevity gene through evolutionary rate covariation of insect mito-nuclear genomes

Nature Aging
2024-06-04 | Journal article | Author
DOI: 10.1038/s43587-024-00641-z
Part of ISSN: 2662-8465
Contributors: Mei Tao; Jiani Chen; Chunlai Cui; Yandong Xu; Jingxiu Xu; Zheyi Shi; Jiaqi Yun; Junwei Zhang; Guo-Zheng Ou; Chao Liu et al.
Source: Self-asserted source
Xing-Xing Shen

Genomic factors shaping codon usage across the Saccharomycotina subphylum

2024-05-24 | Preprint
DOI: 10.1101/2024.05.23.595506
Contributors: Bryan Zavala; Lauren Dineen; Kaitlin J. Fisher; Dana A. Opulente; Marie-Claire Harrison; John F. Wolters; Xing-Xing Shen; Xiaofan Zhou; Marizeth Groenewald; Chris Todd Hittinger et al.
Source: check_circle
Crossref

Identification of miRNA858 long-loop precursors in seed plants

The Plant Cell
2024-05-01 | Journal article
DOI: 10.1093/plcell/koad315
Contributors: Wen-qiu Wang; Xiao-fen Liu; Yong-jing Zhu; Jia-zhen Zhu; Chao Liu; Zhi-ye Wang; Xing-Xing Shen; Andrew C Allan; Xue-ren Yin
Source: check_circle
Crossref

Machine learning enables identification of an alternative yeast galactose utilization pathway

Proceedings of the National Academy of Sciences
2024-04-30 | Journal article
DOI: 10.1073/pnas.2315314121
Contributors: Marie-Claire Harrison; Emily J. Ubbelohde; Abigail L. LaBella; Dana A. Opulente; John F. Wolters; Xiaofan Zhou; Xing-Xing Shen; Marizeth Groenewald; Chris Todd Hittinger; Antonis Rokas
Source: check_circle
Crossref

Functional and Evolutionary Integration of a Fungal Gene With a Bacterial Operon

Molecular Biology and Evolution
2024-04-02 | Journal article
DOI: 10.1093/molbev/msae045
Contributors: Liang Sun; Kyle T David; John F Wolters; Steven D Karlen; Carla Gonçalves; Dana A Opulente; Abigail Leavitt LaBella; Marizeth Groenewald; Xiaofan Zhou; Xing-Xing Shen et al.
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Crossref

Saccharomycotina yeasts defy long-standing macroecological patterns

Proceedings of the National Academy of Sciences
2024-03-05 | Journal article
DOI: 10.1073/pnas.2316031121
Contributors: 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 et al.
Source: check_circle
Crossref

Incongruence in the phylogenomics era

Nature Reviews Genetics
2023-12 | Journal article
DOI: 10.1038/s41576-023-00620-x
Contributors: Jacob L. Steenwyk; Yuanning Li; Xiaofan Zhou; Xing-Xing Shen; Antonis Rokas
Source: check_circle
Crossref

A genome-scale Opisthokonta tree of life: toward phylogenomic resolution of ancient divergences

2023-09-21 | Preprint
DOI: 10.1101/2023.09.20.556338
Contributors: Hongyue Liu; Jacob L. Steenwyk; Xiaofan Zhou; Darrin T. Schultz; Kevin M. Kocot; Xing-Xing Shen; Antonis Rokas; Yuanning Li
Source: check_circle
Crossref

Diverse signatures of convergent evolution in cacti-associated yeasts

2023-09-17 | Preprint
DOI: 10.1101/2023.09.14.557833
Contributors: Carla Gonçalves; Marie-Claire Harrison; Jacob L. Steenwyk; Dana A. Opulente; Abigail L. LaBella; John F. Wolters; Xiaofan Zhou; Xing-Xing Shen; Marizeth Groenewald; Chris Todd Hittinger et al.
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Crossref

Saccharomycotina yeasts defy longstanding macroecological patterns

2023-08-31 | Preprint
DOI: 10.1101/2023.08.29.555417
Contributors: 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 et al.
Source: check_circle
Crossref

Temporal transcriptomics provides insights into host‒pathogen interactions: a case study of Didymella pinodella and disease-resistant and disease-susceptible pea varieties

Crop Health
2023-08-10 | Journal article
DOI: 10.1007/s44297-023-00005-w
Contributors: Chao Liu; Xingmin Han; Jacob L. Steenwyk; Xing-Xing Shen
Source: check_circle
Crossref

Machine learning illuminates how diet influences the evolution of yeast galactose metabolism

2023-07-23 | Preprint
DOI: 10.1101/2023.07.20.549758
Contributors: Marie-Claire Harrison; Emily J. Ubbelohde; Abigail L. LaBella; Dana A. Opulente; John F. Wolters; Xiaofan Zhou; Xing-Xing Shen; Marizeth Groenewald; Chris Todd Hittinger; Antonis Rokas
Source: check_circle
Crossref

How has horizontal gene transfer shaped the evolution of insect genomes?

Environmental Microbiology
2023-03 | Journal article
DOI: 10.1111/1462-2920.16311
Contributors: Chao Liu; Yang Li; Yun Chen; Xue‐xin Chen; Jianhua Huang; Antonis Rokas; Xing‐Xing Shen
Source: check_circle
Crossref

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

Cell
2022-08-04 | Journal article
DOI: 10.1016/j.cell.2022.06.014
Part of ISSN: 0092-8674
Contributors: Xing-Xing Shen
Source: Self-asserted source
Xing-Xing Shen

Defining upstream enhancing and inhibiting sequence patterns for plant peroxisome targeting signal type 1 using large‐scale in silico and in vivo analyses

The Plant Journal
2022-07 | Journal article
DOI: 10.1111/tpj.15840
Contributors: Qianwen Deng; He Li; Yanlei Feng; Ruonan Xu; Weiran Li; Rui Zhu; Delara Akhter; Xingxing Shen; Jianping Hu; Hangjin Jiang et al.
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Crossref

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

Nature Microbiology
2022-05-26 | Journal article
DOI: 10.1038/s41564-022-01131-x
Contributors: Sunde Xu; Yong-Xin Liu; Tomislav Cernava; Hongkai Wang; Yaqi Zhou; Tie Xia; Shugeng Cao; Gabriele Berg; Xing-Xing Shen; Ziyue Wen et al.
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Crossref

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

2021-11-02 | Preprint
DOI: 10.1101/2021.10.30.466607
Contributors: Jacob L. Steenwyk; Dayna C. Goltz; Thomas J. Buida, III; Yuanning Li; Xing-Xing Shen; Antonis Rokas
Source: check_circle
Crossref

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

Genome Biology and Evolution
2021-10-01 | Journal article
DOI: 10.1093/gbe/evab219
Contributors: Megan A Phillips; Jacob L Steenwyk; Xing-Xing Shen; Antonis Rokas; Kenneth Wolfe
Source: check_circle
Crossref

Rooting the Animal Tree of Life

Molecular Biology and Evolution
2021-09-27 | Journal article
DOI: 10.1093/molbev/msab170
Contributors: Yuanning Li; Xing-Xing Shen; Benjamin Evans; Casey W Dunn; Antonis Rokas; Koichiro Tamura
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Crossref

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

Bioinformatics
2021-08-25 | Journal article
DOI: 10.1093/bioinformatics/btab096
Contributors: Jacob L Steenwyk; Thomas J Buida, III; Abigail L Labella; Yuanning Li; Xing-Xing Shen; Antonis Rokas; Russell Schwartz
Source: check_circle
Crossref

Examination of gene loss in the DNA mismatch repair pathway and its mutational consequences in a fungal phylum

2021-04-14 | Preprint
DOI: 10.1101/2021.04.13.439724
Contributors: Megan A Phillips; Jacob L Steenwyk; Xing-Xing Shen; Antonis Rokas
Source: check_circle
Crossref

Feature frequency profile-based phylogenies are inaccurate

Proceedings of the National Academy of Sciences
2020-12-15 | Journal article
DOI: 10.1073/pnas.2013143117
Contributors: Yuanning Li; Kyle T. David; Xing-Xing Shen; Jacob L. Steenwyk; Kenneth M. Halanych; Antonis Rokas
Source: check_circle
Crossref

An investigation of irreproducibility in maximum likelihood phylogenetic inference

Nature Communications
2020-11-30 | Journal article
DOI: 10.1038/s41467-020-20005-6
Contributors: Xing-Xing Shen; Yuanning Li; Chris Todd Hittinger; Xue-xin Chen; Antonis Rokas
Source: check_circle
Crossref

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

Science Advances
2020-11-06 | Journal article
DOI: 10.1126/sciadv.abd0079
Contributors: Xing-Xing Shen; Jacob L. Steenwyk; Abigail L. LaBella; Dana A. Opulente; Xiaofan Zhou; Jacek Kominek; Yuanning Li; Marizeth Groenewald; Chris T. Hittinger; Antonis Rokas
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Crossref

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

2020-10-28 | Preprint
DOI: 10.1101/2020.10.27.358143
Contributors: Jacob L. Steenwyk; Thomas J. Buida, III; Abigail L. Labella; Yuanning Li; Xing-Xing Shen; Antonis Rokas
Source: check_circle
Crossref

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

Genome Biology and Evolution
2020-07-01 | Journal article
DOI: 10.1093/gbe/evaa107
Contributors: Matthew E Mead; Alexander T Borowsky; Bastian Joehnk; Jacob L Steenwyk; Xing-Xing Shen; Anita Sil; Antonis Rokas; Jason E Stajich
Source: check_circle
Crossref

Feature Frequency Profile-based phylogenies are inaccurate

2020-06-30 | Preprint
DOI: 10.1101/2020.06.28.176479
Contributors: Yuanning Li; Kyle T. David; Xing-Xing Shen; Jacob L. Steenwyk; Kenneth M. Halanych; Antonis Rokas
Source: check_circle
Crossref

ClipKIT: a multiple sequence alignment-trimming algorithm for accurate phylogenomic inference

2020-06-10 | Preprint
DOI: 10.1101/2020.06.08.140384
Contributors: Jacob L. Steenwyk; Thomas J. Buida, III; Yuanning Li; Xing-Xing Shen; Antonis Rokas
Source: check_circle
Crossref

Disentangling biological and analytical factors that give rise to outlier genes in phylogenomic matrices

2020-04-21 | Preprint
DOI: 10.1101/2020.04.20.049999
Contributors: Joseph F. Walker; Xing-Xing Shen; Antonis Rokas; Stephen A. Smith; Edwige Moyroud
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Crossref

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

mBio
2019-08-27 | Journal article
DOI: 10.1128/mBio.00925-19
Contributors: Jacob L. Steenwyk; Xing-Xing Shen; Abigail L. Lind; Gustavo H. Goldman; Antonis Rokas; Jon P. Boyle
Source: check_circle
Crossref

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

PLOS Biology
2019-05-21 | Journal article
DOI: 10.1371/journal.pbio.3000255
Contributors: Jacob L. Steenwyk; Sophien Kamoun; Dana A. Opulente; Jacek Kominek; Xing-Xing Shen; Xiaofan Zhou; Abigail L. Labella; Noah P. Bradley; Brandt F. Eichman; Neža Čadež et al.
Source: check_circle
Crossref

Eukaryotic Acquisition of a Bacterial Operon

Cell
2019-03 | Journal article
DOI: 10.1016/j.cell.2019.01.034
Part of ISSN: 0092-8674
Source: Self-asserted source
Xing-Xing Shen

Structural Biology of the HEAT-Like Repeat Family of DNA Glycosylases

BioEssays
2018-11 | Journal article
DOI: 10.1002/bies.201800133
Part of ISSN: 0265-9247
Source: Self-asserted source
Xing-Xing Shen

Tempo and Mode of Genome Evolution in the Budding Yeast Subphylum

Cell
2018-11 | Journal article
DOI: 10.1016/j.cell.2018.10.023
ISSN: 0092-8674
Source: Self-asserted source
Xing-Xing Shen

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

Proceedings of the National Academy of Sciences
2018-10-23 | Journal article
DOI: 10.1073/pnas.1806268115
Part of ISSN: 0027-8424
Part of ISSN: 1091-6490
Source: Self-asserted source
Xing-Xing Shen

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

Nature Communications
2018-05-14 | Journal article
DOI: 10.1038/s41467-018-04374-7
Contributors: 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 et al.
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Crossref

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

eLife
2018-04-12 | Journal article
DOI: 10.7554/elife.33034
Part of ISSN: 2050-084X
Source: Self-asserted source
Xing-Xing Shen

Selective base excision repair of DNA damage by the non‐base‐flipping DNA glycosylase AlkC

The EMBO Journal
2018-01-04 | Journal article
DOI: 10.15252/embj.201797833
Part of ISSN: 0261-4189
Part of ISSN: 1460-2075
Part of ISSN: 0261-4189
Part of ISSN: 1460-2075
Source: Self-asserted source
Xing-Xing Shen

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

Molecular plant pathology
2017-10-31 | Journal article
DOI: 10.1111/mpp.12848
Source: Self-asserted source
Xing-Xing Shen

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

Molecular Biology and Evolution
2017-05 | Journal article
DOI: 10.1093/molbev/msx302
Source: Self-asserted source
Xing-Xing Shen

Evaluating fast maximum likelihood-based phylogenetic programs using empirical phylogenomic data sets

2017-05-25 | Preprint
DOI: 10.1101/142323
Contributors: Xiaofan Zhou; Xingxing Shen; Chris Todd Hittinger; Antonis Rokas
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Crossref

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

Nature Ecology & Evolution
2017-04 | Journal article
DOI: 10.1038/s41559-017-0126
PMID: 28812701
Source: Self-asserted source
Xing-Xing Shen

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

G3
2016-09 | Journal article
DOI: 10.1534/g3.116.034744
PMID: 27672114
Source: Self-asserted source
Xing-Xing Shen

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

Genome Biology and Evolution
2016-08 | Journal article
DOI: 10.1093/gbe/evw179
PMID: 27492233
Source: Self-asserted source
Xing-Xing Shen
Items per page:
Page 1 of 2

Peer review (6 reviews for 3 publications/grants)

Review activity for Nature (1)
Review activity for Nature communications (4)
Review activity for Nature ecology & evolution. (1)
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