First-Author

1.       Yuanning Li, 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:S09609822(22)01670-0.

2.       Yuanning Li, Altamia MA, Shipway JR, Brugler MR, Bernardino AF, de Brito TL, Lin Z, da Silva Oliveira FA, Sumida P, Smith CR, Trindade-Silva A. (2022). Contrasting Modes of Mitochondrial Genome Evolution in Sister Taxa of Wood-Eating Marine Bivalves (Teredinidae and Xylophagaidae). Genome biology and evolution. Jun;14(6):evac089.

3.       Yuanning Li, X. Shen, B. Evans, A. Rokas, C.W. Dunn. (2021). Rooting the animal tree of life. Molecular Biology and Evolution. Msab170.

4.       YuanningLi, J.L.Steenwyk, Y.Chang, Y.Wang, T.Y.James, J.E.Stajich, J.W.Spatafora, M.Groenewald, C.W.Dunn, C.T.Hittinger, X.-X. Shen, A Rokas (2021). A genome-scale phylogeny of the kingdom Fungi. Current Biology. 31, 1653-1665.

5.       Yuanning Li, KT. David, X. Shen, JL. Seenwyk, KM. Halanych, A. Rokas. (2020). Feature Frequency Profile-based phylogenies are inaccurate. Proceedings of the National Academy of Sciences of the United States of America. 117: 31580-31581.

6.       L.Kong*, YuanningLi*, K.M.Kocot, Y.Yang,Q.Li, K.M.Halanych. (2020). Mitogenomics reveals phylogenetic relationships of Arcoida molluscs and multiple independent expansions in mitogenome size. Molecular Phylogenetics and Evolution. 150, 106857. (* Co-first Author)

7.       Yuanning Li, M.G. Tassia, D.S. Waits, V.E. Bogantes, K.T. David, K.M. Halanych. (2019). Genomic adaptations to chemosymbiosis in the deep-sea seep-dwelling tubeworm Lamellibrachia luymesi. BMC Biology. 17(1):19.

8.       Yuanning Li, K.M. Kocot, M.G. Tassia, J.T. Cannon, M. Bernt, K.M. Halanych. (2019). Mitogenomics reveals a novel genetic code in Hemichordata. Genome Biology and evolution. 11(1), 29-40.

9.       Yuanning Li, M.R. Liles, K.M.Halanch. (2018). Endosymbiont genomes yield clues of tubeworm success. The ISME journal. 12(11), p.2785.

10.     Yuanning Li, K.M. Kocot, N.V. Whelan, S.R. Santos, D.S. Waits, K.M. Halanych. (2017). Phylogenomics of tubeworms (Siboglinidae, Annelida) and comparative performance of different reconstruction methods. Zoologica Scripta. 46: 200-213.

11.     Yuanning Li, K.M. Kocot, S.R. Santos, D.J. Thornhill, K.M. Halanych. (2015). Mitogenomics reveals phylogeny and dramatic size variations of control regions in the deep-sea family Siboglinidae (Annelida). Molecular Phylogenetics and Evolution. 85, 221-229.

12.     Yuanning Li, P. Ma, P. Liu, Q. Li. (2012). The genetic diversity and phylogenetic analysis of ITS1 in mitochondrial DNA of four populations of Portunus Trituberculatus. Oceanologia Et Limnologia Sinica. 43(4).

Contributing-Author

1.       Steenwyk JL, Y. Li, X. Zhou, XX Shen, Rokas A. (2023). Incongruence in the phylogenomics era. Nature Reviews Genetics.

2.       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.

3.       Novitsky V, J. Steingrimsson, M. Howison, C. Dunn, F.S. Gillani, A. Manne, Li Y, M. Spence, Z. Parillo, J. Fulton, T. Marak.(2021). Longitudinal typing of molecular HIV clusters in a statewide epidemic. AIDS.(London, England). 1;35(11):1711-1722.

4.       Steenwyk, J. L., M. E. Mead, P. A. Castro, C. Valero, A. Damasio, R. A. C. Santos, A. L. LaBella, Yuanning 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. Microbiol. Spectr. 3;9(1), e0001021.

5.       Steenwyk, J. L., T. J. Buida III, A. L. LaBella, Yuanning Li, X.-X. Shen, A. Rokas (2021). PhyKIT: a broadly applicable UNIX shell toolkit for processing and analyzing phylogenomic data. Bioinformatics. 9;37(16):2325–31.

6.       X. Shen, JL. Seenwyk, AL. LaBella, DA. Opulente, X. Zhou, J. Kominek, Yuanning Li, M. Groenewald, CT. Hittinger, A. Antonis. (2020). Genome-scale phylogeny and contrasting modes of genome evolution in the fungal phylum Ascomycota. Science Advances. 6(45), eabd0079.

7.       JL. Steenwyk, TJ. Buida, Yuanning Li, X. Shen, A. Antonis. (2020). ClipKIT: a multiple sequence alignment-trimming algorithm for accurate phylogenomic inference. Plos Biology. 18(12), e3001007.

8.       Novitsky, V., Steingrimsson, J.A., Howison, M., Gillani, F.S., Yuanning Li., 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), pp.1-11.

9.       Kantor, R., Fulton, J.P., Steingrimsson, J., Novitsky, V., Howison, M., Gillani, F., Yuanning Li, 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).

10.     X. Shen, Yuanning Li, C. Hittinger., X. Chen, A. Antonis. (2020). An investigation of irreproducibility in maximum likelihood phylogenetic inference. Nature Communication.11(1), 1-14.

11.     Y. Zhou, Yuanning Li, C. Shen, K.M. Halanych C. Wang. (2020). The mitochondrial genome of the bone-eating worm Osedax rubiplumus (Annelida, Siboglinidae). Mitochondrial DNA. 50(1), 1-9.

12.     V. Novitsky, J. Steingrimsson, Ma. Howison, F. Gillani, Yuanning Li, A. Manne, J. Fulton, M. Spence, Z. Parillo, T. Marak, P. A. Chan, T. Bertrand, U. Bandy, N. Alexander-Scott, C. W. Dunn, J. Hogan, R. Kantor (2021). Empirical Comparison of Analytical Approaches for Identifying Molecular HIV-1 Clusters. Scientific Reports. 10(1), 1-11.

13.     Y. Zhou, Y. Wang, Yuanning Li, C. Shen, Z. Liu, C. Wang. (2020). First report of Osedax in the Indian Ocean indicative of trans-oceanic dispersal through the Southern Ocean. Marine Biodiversity. 50(1), 1-9.

14.     N. Li, L. Bao, T. Zhou, Z. Yuan, S. Liu, R. Dunham, Yuanning Li, Wang K, Xu X, et al. (2018). Genome sequence of walking catfish (Clarias batrachus) provides insights into terrestrial adaptation. BMC genomics.19(1):952.

15.      J.R. Voight., B.A. Marshall, J. Judge, K.M. Halanych, Yuanning Li, A.F. Bernardino, F. Grewe and J. Maddox. (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), pp.232-243.

16.     P.G. Galaska, Yuanning Li, K.M. Kocot, A.R. Mahon, K.M. Halanych. (2018). Conservation of brittle stars (Ophiuroidea, Echinodermata) mitochondrial genome arrangements. Molecular Phylogenetics and Evolution. 130, pp. 115-120.

17.     A.F. Bernardino, Yuanning Li, C.R. Smith, K.M. Halanych. (2017). Multiple introns in a deep-sea Annelid mitochondrial genome. Scientific Reports 7:4295.

18.     D.S. Waits, S.R. Santos, D.J. Thornhill, Yuanning Li, K.M. Halanych. (2016). Evolution of Sulfur Binding in Hemoglobin in Siboglinidae (Annelida) with Special Reference to Bone Eating Worms, Osedax. Journal of Molecular Evolution. 82: 219-229.

19.     X. Su, G. Wang, J. Feng, J. Yuanning Li. (2011). Genetic diversity of 15 Macrobrachium nipponense populations in Poyang Lake based on microsatellite analysis. Chinese Journal of Ecology. 2011,30(9):2007-2013.