Publications

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Lab members are indicated in bold. # co-first author, * corresponding author.

Preprints/Submitted articles

30.Liu H.#, Steenwyk JL#, Schultz D, Kocot KM, Zhou X, Shen XX, Zhao T, Rokas A.*, Li Y*. A genome-scale Opisthokonta tree of life: toward phylogenomic resolution of ancient divergences.

Research articles

2023

32.Steenwyk JL, Y. Li, X. Zhou, XX Shen, Rokas A.*2023. Incongruence in the phylogenomics era. Nature Reviews Genetics. 27:1-7
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31.M. Groenewald*, C.T. Hittinger, K. Bensch, D.A. Opulente, X.-X. Shen, Li Y., C. Liu, A.L. LaBella, X. Zhou, S. Limtong, S. Jindamorakot, P. Gonçalves, V. Robert, K.H. Wolfe, C.A. Rosa, T. Boekhout, N. Čadež, G. Péter, J.P. Sampaio, M.-A. Lachance, A.M. Yurkov, H.-M. Daniel, M. Takashima, K. Boundy-Mills, D. Libkind, K. Aoki, T. Sugita, A. Rokas. 2023. A genome-informed higher rank classification of the biotechnologically important fungal subphylum Saccharomycotina. Studies in Mycology.
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2022

30.Li Y.,* Liu H., Steenwyk JL, LaBella AL, Harrison MC, Groenewald M, Zhou X, Shen XX, Zhao T, Hittinger CT, Rokas A.* 2022. Contrasting modes of macro and microsynteny evolution in a eukaryotic subphylum. Current Biology 29:S0960-9822(22)01670-0.
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29.Steenwyk JL,* Goltz DC, Buida TJ III, Li Y., Shen XX, Antonis Rokas.* 2022. OrthoSNAP: A tree splitting and pruning algorithm for retrieving single-copy orthologs from gene family trees. PLOS Biology 20(10): e3001827.
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28.Li Y., Altamia MA., Shipway JR., Brugler MR., Bernardino AF., de Brito TL., Lin Z., da Silva Oliveira FA., Sumida P., Smith CR., Trindade-Silva A, Halanych KM.*, Distel DL.* 2022. Contrasting Modes of Mitochondrial Genome Evolution in Sister Taxa of Wood-Eating Marine Bivalves (Teredinidae and Xylophagaidae). Genome Biology and Evolution 14(6):evac089.
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27.He C., Liu J.*, Wang R., Li Y., Zheng Q., Jiao F., He C., Shi Q., Xu Y., Zhang R., Thomas H., et al. 2022. Metagenomic evidence for the microbial transformation of carboxyl-rich alicyclic molecules: A long-term macrocosm experiment. Water Research 216, 118281.
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26.Steenwyk, J. L.*, T. J. Buida III, C. Goncalves, D. C. Goltz, G. H. Morales, M. E. Mead, A. L. LaBella, C. M. Chavez, J. E. Schmitz, M. Hadjifrangiskou, Y. Li, & A. Rokas*. 2022. BioKIT: a versatile toolkit for processing and analyzing diverse types of sequence data. Genetics 221(3):iyac079.
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25.Liu D., Chen J., Wang Y., Meng Y., Li Y., Huang R., Xia Y., Liu H., Jiao N., Xun L., Liu J.* 2022. Synechococcus sp. PCC7002 Uses Peroxiredoxin to Cope with Reactive Sulfur Species Stress. Mbio e01039-22.
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2021

24.Li Y., Shen X.-X., Evans B., Dunn C.W.*, Rokas A.* 2021. Rooting the animal tree of life. Molecular Biology and Evolution 38: 4322–4333.
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23.Li Y., Steenwyk J., Chang Y., Wang Y., James T.Y., Stajich J.E., Spatafora J.W., Groenewald M., Dunn C., Hittinger C.T., Shen X.-X.*, Rokas A.* 2021. A genome-scale phylogeny of the kingdom Fungi. Current Biology 31: 1653-1665.
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22. Novitsky V., Steingrimsson J., Howison M., Dunn C., Gillani, F.S. Manne, A., Li Y., Spence M. Parillo, Z., Fulton J. and Marak T., 2021. Longitudinal typing of molecular HIV clusters in a statewide epidemic. AIDS 35(11):1711-1722.
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21. Steenwyk, J. L., M. E. Mead, P. A. Castro, C. Valero, A. Damasio, R. A. C. Santos, A. L. LaBella, Y. Li, S. L. Knowles, H. A. Raja, N. H. Oberlies, X. Zhou, O. A. Cornely, F. Fuchs, P. Koehler*, G. H. Goldman*, & A. Rokas*, 2021. Genomic and phenotypic analysis of COVID-19-associated pulmonary aspergillosis isolates of Aspergillus fumigatus. Microbiology Spectrum 9(1): e00010-21.
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20. Steenwyk J., Buida III T.J., LaBella A.L., Li Y., Shen X.-X., Rokas A. 2021. PhyKIT: a UNIX shell toolkit for processing and analyzing phylogenomic data. Bioinformatics 37(16):2325-2331.
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2020

19. Shen X.-X.*, Li Y., Hittinger C., Chen X., Rokas A.* 2020. An investigation of irreproducibility in maximum likelihood phylogenetic inference. Nature Communications 11:6096.
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The story behind the paper in Nature Ecology & Evolution blog

18. Steenwyk J., Buida III T.J., Li Y., Shen X.-X., Rokas A. 2020. ClipKIT: a multiple sequence alignment-trimming algorithm for accurate phylogenomic inference. PLoS Biology 18: e3001007.
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17. Li Y.#, David K.T.#, Shen X.-X., Steenwyk J., Halanych K.M., Rokas A. 2020. Feature Frequency Profile-based phylogenies are inaccurate. Proc. Natl. Acad. Sci. USA in press.
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16. Shen X.-X.*, Steenwyk J., LaBella A., Opulente D., Zhou X., Kominek J., Li Y., Groenewald M., Hittinger C., Rokas A.* 2020. Genome-scale phylogeny and contrasting modes of genome evolution in the fungal phylum Ascomycota. Science Advances 6(45):eabd0079.
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genome assemblies and annotations

15. Novitsky V., Steingrimsson J.A., Howison M., Gillani F.S., Li Y., Manne A., Fulton J., Spence M., Parillo Z., Marak T. and Chan P.A., 2020. Empirical comparison of analytical approaches for identifying molecular HIV-1 clusters. Scientific Reports 10(1):1-11.
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14. Kantor R., Fulton J.P., Steingrimsson J., Novitsky V., Howison M., Gillani F., Li Y., Manne A., Parillo Z., Spence M. and Marak T., 2020. Challenges in evaluating the use of viral sequence data to identify HIV transmission networks for public health. Statistical Communications in Infectious Diseases 12(S1).
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13. Kong L.#, Li Y.#, Kocot K.M., Yang Y., Qi L., Li Q. and Halanych K.M.*, 2020. Mitogenomics reveals phylogenetic relationships of Arcoida (Mollusca, Bivalvia) and multiple independent expansions and contractions in mitochondrial genome size. Molecular Phylogenetics and Evolution 150, p.106857.
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12. Zhou Y.*, Li Y., Cheng H., Halanych K.M. and Wang C.*, 2020. The mitochondrial genome of the bone-eating worm Osedax rubiplumus (Annelida, Siboglinidae). Mitochondrial DNA Part B 5(3):2267-2268.
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11. Zhou Y., Wang, Y. Li, Y., Shen C., Liu Z. and Wang C., 2020. First report of Osedax in the Indian Ocean indicative of trans-oceanic dispersal through the Southern Ocean. Marine Biodiversity 50(1):1-9.
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10. Li Y., Tassia M.G., Waits D.S., Bogantes V.E., David K.T. and Halanych K.M., 2019. Genomic adaptations to chemosymbiosis in the deep-sea seep-dwelling tubeworm Lamellibrachia luymesi. BMC Biology 17(1):1-14.
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9. Voight J.R., Marshall B.A., Judge J., Halanych K.M., Li Y., Bernardino A.F., Grewe F. and Maddox J.D., 2019. Life in wood: preliminary phylogeny of deep-sea wood-boring bivalves (Xylophagaidae), with descriptions of three new genera and one new species. Journal of Molluscan Studies 85(2):1-9.
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8. Li Y.*, Kocot K.M., Tassia M.G., Cannon J.T., Bernt M. and Halanych K.M.*, 2019. Mitogenomics reveals a novel genetic code in Hemichordata. Genome Biology and Evolution 11(1):29-409.
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7. Galaska M.P., Li Y., Kocot K.M., Mahon A.R. and Halanych K.M.*, 2019. Conservation of mitochondrial genome arrangements in brittle stars (Echinodermata, Ophiuroidea). Molecular Phylogenetics and Evoluion 30, pp.115-120.
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6. Li N., Bao L., Zhou T., Yuan Z., Liu S., Dunham R., Li Y., Wang K., Xu X., Jin Y. and Zeng Q., 2018. Genome sequence of walking catfish (Clarias batrachus) provides insights into terrestrial adaptation. Proc. Natl. Acad. Sci. USA 19(1):1-16.
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5. Li Y.*, Liles M.R. and Halanych K.M.*, 2018. Endosymbiont genomes yield clues of tubeworm success. The ISME journal 12(11):2785-2795.
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4. Bernardino A.F., Li, Y., Smith C.R. and Halanych K.M., 2017. Multiple introns in a deep-sea Annelid (Decemunciger: Ampharetidae) mitochondrial genome. Scientific Reports 7(1):1-8.
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3. Li Y.*, Kocot K.M., Whelan N.V., Santos S.R., Waits D.S., Thornhill D.J. and Halanych K.M.*, 2017. Phylogenomics of tubeworms (Siboglinidae, Annelida) and comparative performance of different reconstruction methods. Zoologica Scripta 46(2):200-213.
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2. Waits D.S., Santos S.R., Thornhill D.J., Li Y. and Halanych K.M.*, 2016. Evolution of sulfur binding by hemoglobin in Siboglinidae (Annelida) with special reference to bone-eating worms, Osedax. Journal of molecular evolution 82(4-5):219-229.
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1. Li Y., Kocot K.M., Schander C., Santos S.R., Thornhill D.J. and Halanych K.M., 2015. Mitogenomics reveals phylogeny and repeated motifs in control regions of the deep-sea family Siboglinidae (Annelida). Molecular Phylogenetics and Evolution 85:221-229.
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