Xing-Xing Shen - Publications

Affiliations: 
2014-2019 Biology Sciences Vanderbilt University, Nashville, TN 
Area:
evolutionary biology,phylogenetics,evolutionary genomics
Website:
https://xingxingshen.github.io/

33 high-probability publications. We are testing a new system for linking publications to authors. You can help! If you notice any inaccuracies, please sign in and mark papers as correct or incorrect matches. If you identify any major omissions or other inaccuracies in the publication list, please let us know.

Year Citation  Score
2021 Li Y, Shen XX, Evans B, Dunn CW, Rokas A. Rooting the animal tree of life. Molecular Biology and Evolution. PMID 34097041 DOI: 10.1093/molbev/msab170  1
2021 Haase MAB, Kominek J, Opulente DA, Shen XX, LaBella AL, Zhou X, DeVirgilio J, Hulfachor AB, Kurtzman CP, Rokas A, Hittinger CT. Repeated horizontal gene transfer of GALactose metabolism genes violates Dollo's law of irreversible loss. Genetics. 217. PMID 33724406 DOI: 10.1093/genetics/iyaa012  1
2021 Shen XX, Steenwyk JL, Rokas A. Dissecting incongruence between concatenation- and quartet-based approaches in phylogenomic data. Systematic Biology. PMID 33616672 DOI: 10.1093/sysbio/syab011  1
2021 Li Y, Steenwyk JL, Chang Y, Wang Y, James TY, Stajich JE, Spatafora JW, Groenewald M, Dunn CW, Hittinger CT, Shen XX, Rokas A. A genome-scale phylogeny of the kingdom Fungi. Current Biology : Cb. PMID 33607033 DOI: 10.1016/j.cub.2021.01.074  1
2021 Steenwyk JL, Buida TJ, Labella AL, Li Y, Shen XX, Rokas A. PhyKIT: a broadly applicable UNIX shell toolkit for processing and analyzing phylogenomic data. Bioinformatics (Oxford, England). PMID 33560364 DOI: 10.1093/bioinformatics/btab096  1
2020 Steenwyk JL, Buida TJ, Li Y, Shen XX, Rokas A. ClipKIT: A multiple sequence alignment trimming software for accurate phylogenomic inference. Plos Biology. 18: e3001007. PMID 33264284 DOI: 10.1371/journal.pbio.3001007  1
2020 Shen XX, Li Y, Hittinger CT, Chen XX, Rokas A. An investigation of irreproducibility in maximum likelihood phylogenetic inference. Nature Communications. 11: 6096. PMID 33257660 DOI: 10.1038/s41467-020-20005-6  1
2020 Li Y, David KT, Shen XX, Steenwyk JL, Halanych KM, Rokas A. Feature frequency profile-based phylogenies are inaccurate. Proceedings of the National Academy of Sciences of the United States of America. PMID 33234569 DOI: 10.1073/pnas.2013143117  1
2020 Shen XX, Steenwyk JL, LaBella AL, Opulente DA, Zhou X, Kominek J, Li Y, Groenewald M, Hittinger CT, Rokas A. Genome-scale phylogeny and contrasting modes of genome evolution in the fungal phylum Ascomycota. Science Advances. 6. PMID 33148650 DOI: 10.1126/sciadv.abd0079  1
2020 Mead ME, Borowsky AT, Joehnk B, Steenwyk JL, Shen XX, Sil A, Rokas A. 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. PMID 32442273 DOI: 10.1093/Gbe/Evaa107  1
2020 Yang Y, Sun P, Lv L, Wang D, Ru D, Li Y, Ma T, Zhang L, Shen X, Meng F, Jiao B, Shan L, Liu M, Wang Q, Qin Z, et al. Prickly waterlily and rigid hornwort genomes shed light on early angiosperm evolution. Nature Plants. PMID 32094642 DOI: 10.1038/S41477-020-0594-6  0.8
2019 Ely ZA, Moon JM, Sliwoski GR, Sangha AK, Shen XX, Labella AL, Meiler J, Capra JA, Rokas A. The impact of natural selection on the evolution and function of placentally expressed galectins. Genome Biology and Evolution. PMID 31504490 DOI: 10.1093/Gbe/Evz183  1
2019 Krassowski T, Kominek J, Shen XX, Opulente DA, Zhou X, Rokas A, Hittinger CT, Wolfe KH. Multiple Reinventions of Mating-type Switching during Budding Yeast Evolution. Current Biology : Cb. PMID 31353182 DOI: 10.1016/J.Cub.2019.06.056  1
2019 Wang M, Fu H, Shen XX, Ruan R, Rokas A, Li H. Genomic features and evolution of the conditionally dispensable chromosome in the tangerine pathotype of Alternaria alternata. Molecular Plant Pathology. PMID 31297970 DOI: 10.1111/Mpp.12848  1
2019 Steenwyk JL, Shen XX, Lind AL, Goldman GH, Rokas A. A Robust Phylogenomic Time Tree for Biotechnologically and Medically Important Fungi in the Genera and . Mbio. 10. PMID 31289177 DOI: 10.1128/Mbio.00925-19  1
2019 Steenwyk JL, Opulente DA, Kominek J, Shen XX, Zhou X, Labella AL, Bradley NP, Eichman BF, Čadež N, Libkind D, DeVirgilio J, Hulfachor AB, Kurtzman CP, Hittinger CT, Rokas A. Extensive loss of cell-cycle and DNA repair genes in an ancient lineage of bipolar budding yeasts. Plos Biology. 17: e3000255. PMID 31112549 DOI: 10.1371/Journal.Pbio.3000255  1
2019 Kominek J, Doering DT, Opulente DA, Shen XX, Zhou X, DeVirgilio J, Hulfachor AB, Groenewald M, Mcgee MA, Karlen SD, Kurtzman CP, Rokas A, Hittinger CT. Eukaryotic Acquisition of a Bacterial Operon. Cell. PMID 30799038 DOI: 10.1016/J.Cell.2019.01.034  1
2018 Shen XX, Opulente DA, Kominek J, Zhou X, Steenwyk JL, Buh KV, Haase MAB, Wisecaver JH, Wang M, Doering DT, Boudouris JT, Schneider RM, Langdon QK, Ohkuma M, Endoh R, et al. Tempo and Mode of Genome Evolution in the Budding Yeast Subphylum. Cell. PMID 30415838 DOI: 10.1016/J.Cell.2018.10.023  1
2018 Krause DJ, Kominek J, Opulente DA, Shen XX, Zhou X, Langdon QK, DeVirgilio J, Hulfachor AB, Kurtzman CP, Rokas A, Hittinger CT. Functional and evolutionary characterization of a secondary metabolite gene cluster in budding yeasts. Proceedings of the National Academy of Sciences of the United States of America. PMID 30297402 DOI: 10.1073/Pnas.1806268115  1
2018 Shi R, Shen XX, Rokas A, Eichman BF. Structural Biology of the HEAT-Like Repeat Family of DNA Glycosylases. Bioessays : News and Reviews in Molecular, Cellular and Developmental Biology. PMID 30264543 DOI: 10.1002/Bies.201800133  1
2018 Krassowski T, Coughlan AY, Shen XX, Zhou X, Kominek J, Opulente DA, Riley R, Grigoriev IV, Maheshwari N, Shields DC, Kurtzman CP, Hittinger CT, Rokas A, Wolfe KH. Evolutionary instability of CUG-Leu in the genetic code of budding yeasts. Nature Communications. 9: 1887. PMID 29760453 DOI: 10.1038/S41467-018-04374-7  1
2018 Gonçalves C, Wisecaver JH, Kominek J, Oom MS, Leandro MJ, Shen XX, Opulente DA, Zhou X, Peris D, Kurtzman CP, Hittinger CT, Rokas A, Gonçalves P. Evidence for loss and reacquisition of alcoholic fermentation in a fructophilic yeast lineage. Elife. 7. PMID 29648535 DOI: 10.7554/Elife.33034  1
2018 Gonçalves C, Wisecaver JH, Kominek J, Oom MS, Leandro MJ, Shen X, Opulente DA, Zhou X, Peris D, Kurtzman CP, Hittinger CT, Rokas A, Gonçalves P. Author response: Evidence for loss and reacquisition of alcoholic fermentation in a fructophilic yeast lineage Elife. DOI: 10.7554/Elife.33034.033  1
2017 Zhou X, Shen X, Hittinger CT, Rokas A. Evaluating fast maximum likelihood-based phylogenetic programs using empirical phylogenomic data sets. Molecular Biology and Evolution. PMID 29177474 DOI: 10.1093/Molbev/Msx302  1
2017 Shi R, Mullins EA, Shen XX, Lay KT, Yuen PK, David SS, Rokas A, Eichman BF. Selective base excision repair of DNA damage by the non-base-flipping DNA glycosylase AlkC. The Embo Journal. PMID 29054852 DOI: 10.15252/Embj.201797833  1
2017 Shen XX, Hittinger CT, Rokas A. Contentious relationships in phylogenomic studies can be driven by a handful of genes. Nature Ecology & Evolution. 1: 126. PMID 28812701 DOI: 10.1038/S41559-017-0126  1
2016 Shen XX, Zhou X, Kominek J, Kurtzman CP, Hittinger CT, Rokas A. Reconstructing the Backbone of the Saccharomycotina Yeast Phylogeny Using Genome-Scale Data. G3 (Bethesda, Md.). PMID 27672114 DOI: 10.1534/G3.116.034744  1
2016 Shen XX, Salichos L, Rokas A. A genome-scale investigation of how sequence-, function-, and tree-based gene properties influence phylogenetic inference. Genome Biology and Evolution. PMID 27492233 DOI: 10.1093/Gbe/Evw179  1
2015 Shen XX, Liang D, Chen MY, Mao RL, Wake DB, Zhang P. Enlarged Multilocus Dataset Provides Surprisingly Younger Time of Origin for the Plethodontidae, the Largest Family of Salamanders. Systematic Biology. PMID 26385618 DOI: 10.1093/Sysbio/Syv061  1
2013 Shen XX, Liang D, Feng YJ, Chen MY, Zhang P. A versatile and highly efficient toolkit including 102 nuclear markers for vertebrate phylogenomics, tested by resolving the higher level relationships of the caudata. Molecular Biology and Evolution. 30: 2235-48. PMID 23827877 DOI: 10.1093/Molbev/Mst122  1
2013 Liang D, Shen XX, Zhang P. One thousand two hundred ninety nuclear genes from a genome-wide survey support lungfishes as the sister group of tetrapods. Molecular Biology and Evolution. 30: 1803-7. PMID 23589454 DOI: 10.1093/Molbev/Mst072  1
2012 Shen XX, Liang D, Zhang P. The development of three long universal nuclear protein-coding locus markers and their application to osteichthyan phylogenetics with nested PCR. Plos One. 7: e39256. PMID 22720083 DOI: 10.1371/Journal.Pone.0039256  1
2011 Shen XX, Liang D, Wen JZ, Zhang P. Multiple genome alignments facilitate development of NPCL markers: a case study of tetrapod phylogeny focusing on the position of turtles. Molecular Biology and Evolution. 28: 3237-52. PMID 21680872 DOI: 10.1093/Molbev/Msr148  1
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