☰

Xing-Xing Shen, Ph.D. - Publications

Affiliations: 
2014-2019 Biology Sciences Vanderbilt University, Nashville, TN 
 2019- Institute of Insect Sciences Zhejiang University, Hangzhou Shi, Zhejiang Sheng, China 
Area:
evolutionary biology, phylogenetics, evolutionary genomics
Website:
https://shenxlab.com/
Tree Info Similar researchers PubMed Report error

47 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
2024 Sun L, David KT, Wolters JF, Karlen SD, Gonçalves C, Opulente DA, LaBella AL, Groenewald M, Zhou X, Shen XX, Rokas A, Hittinger CT. Functional and evolutionary integration of a fungal gene with a bacterial operon. Molecular Biology and Evolution. PMID 38415839 DOI: 10.1093/molbev/msae045  0.809
2024 David KT, Harrison MC, Opulente DA, LaBella AL, Wolters JF, Zhou X, Shen XX, Groenewald M, Pennell M, Hittinger CT, Rokas A. Saccharomycotina yeasts defy long-standing macroecological patterns. Proceedings of the National Academy of Sciences of the United States of America. 121: e2316031121. PMID 38412132 DOI: 10.1073/pnas.2316031121  0.789
2024 Jones RE, Tice AK, Eliáš M, Eme L, Kolísko M, Nenarokov S, Pánek T, Rokas A, Salomaki E, Strassert JFH, Shen XX, Žihala D, Brown MW. Create, Analyze, and Visualize Phylogenomic Datasets Using PhyloFisher. Current Protocols. 4: e969. PMID 38265166 DOI: 10.1002/cpz1.969  0.561
2023 Sun L, David KT, Wolters JF, Karlen SD, Gonçalves C, Opulente DA, LaBella AL, Groenewald M, Zhou X, Shen XX, Rokas A, Hittinger CT. Functional and evolutionary integration of a fungal gene with a bacterial operon. Biorxiv : the Preprint Server For Biology. PMID 38045280 DOI: 10.1101/2023.11.21.568075  0.82
2023 Gonçalves C, Harrison MC, Steenwyk JL, Opulente DA, LaBella AL, Wolters JF, Zhou X, Shen XX, Groenewald M, Hittinger CT, Rokas A. Diverse signatures of convergent evolution in cacti-associated yeasts. Biorxiv : the Preprint Server For Biology. PMID 37745407 DOI: 10.1101/2023.09.14.557833  0.802
2023 David KT, Harrison MC, Opulente DA, LaBella AL, Wolters JF, Zhou X, Shen XX, Groenewald M, Pennell M, Hittinger CT, Rokas A. Saccharomycotina yeasts defy longstanding macroecological patterns. Biorxiv : the Preprint Server For Biology. PMID 37693602 DOI: 10.1101/2023.08.29.555417  0.77
2023 Opulente DA, LaBella AL, Harrison MC, Wolters JF, Liu C, Li Y, Kominek J, Steenwyk JL, Stoneman HR, VanDenAvond J, Miller CR, Langdon QK, Silva M, Gonçalves C, Ubbelohde EJ, ... ... Shen XX, et al. Genomic and ecological factors shaping specialism and generalism across an entire subphylum. Biorxiv : the Preprint Server For Biology. PMID 37425695 DOI: 10.1101/2023.06.19.545611  0.787
2023 Steenwyk JL, Li Y, Zhou X, Shen XX, Rokas A. Incongruence in the phylogenomics era. Nature Reviews. Genetics. PMID 37369847 DOI: 10.1038/s41576-023-00620-x  0.825
2022 Liu C, Li Y, Chen Y, Chen XX, Huang J, Rokas A, Shen XX. How has horizontal gene transfer shaped the evolution of insect genomes? Environmental Microbiology. PMID 36511824 DOI: 10.1111/1462-2920.16311  0.669
2022 Li Y, Liu H, Steenwyk JL, LaBella AL, Harrison MC, Groenewald M, Zhou X, Shen XX, Zhao T, Hittinger CT, Rokas A. Contrasting modes of macro and microsynteny evolution in a eukaryotic subphylum. Current Biology : Cb. PMID 36334587 DOI: 10.1016/j.cub.2022.10.025  0.805
2022 Steenwyk JL, Goltz DC, Buida TJ, Li Y, Shen XX, Rokas A. OrthoSNAP: A tree splitting and pruning algorithm for retrieving single-copy orthologs from gene family trees. Plos Biology. 20: e3001827. PMID 36228036 DOI: 10.1371/journal.pbio.3001827  0.834
2022 Li Y, Liu Z, Liu C, Shi Z, Pang L, Chen C, Chen Y, Pan R, Zhou W, Chen XX, Rokas A, Huang J, Shen XX. HGT is widespread in insects and contributes to male courtship in lepidopterans. Cell. PMID 35853453 DOI: 10.1016/j.cell.2022.06.014  0.619
2021 Phillips MA, Steenwyk JL, Shen XX, Rokas A. Examination of gene loss in the DNA mismatch repair pathway and its mutational consequences in a fungal phylum. Genome Biology and Evolution. PMID 34554246 DOI: 10.1093/gbe/evab219  0.787
2021 Tice AK, Žihala D, Pánek T, Jones RE, Salomaki ED, Nenarokov S, Burki F, Eliáš M, Eme L, Roger AJ, Rokas A, Shen XX, Strassert JFH, Kolísko M, Brown MW. PhyloFisher: A phylogenomic package for resolving eukaryotic relationships. Plos Biology. 19: e3001365. PMID 34358228 DOI: 10.1371/journal.pbio.3001365  0.573
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  0.732
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  0.832
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  0.751
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  0.846
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  0.787
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  0.793
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  0.774
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  0.734
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  0.815
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  0.847
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  0.538
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  0.783
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  0.715
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  0.8
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  0.845
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  0.812
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  0.753
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  0.827
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  0.743
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  0.491
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  0.736
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  0.815
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  0.729
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  0.738
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  0.445
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  0.626
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  0.801
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  0.82
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  0.612
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  0.371
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  0.471
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  0.384
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  0.549
Show low-probability matches.