Citations are available at Google Scholar. Lab members are indicated in bold. # co-first author, * corresponding author.
Preprint articles
1. Walker J., Shen X.-X., Rokas A., Smith S., Moyroud E. 2020. Disentangling biological and analytical factors that give rise to outlier genes in phylogenomic matrices. bioRxiv. bioRxiv preprint.
Research articles
2023
45. Liu C., Han X., Steenwyk J.L., Shen X.-X.* 2023. Temporal transcriptomics provides insights into host‒pathogen interactions: a case study of Didymella pinodella and disease-resistant and disease-susceptible pea varieties. Crop Health In press PDF
44. Steenwyk J.L., Li Y., Zhou X., Shen X.-X., Shen X.-X., Rokas A.* 2023. Incongruence in the phylogenomics era. Nature Reviews Genetics In press PDF
43. Chen S.-J., Zhang J.-L., Ma W.-J., Wu H.-J., Li Y., Shen X.-X., Xu H.-J.* 2023. FoxO and rotund form a binding complex governing wing polyphenism in planthoppers. iScience 26:107182. PDF
42. Groenewald M.*, Hittinger C.T., Bensch K., Opulente D.A., Shen X.-X., Li Y., Liu C., LaBella A.L., Zhou X., Limtong S., Jindamorakot S., Gonçalves P., Robert V., Wolfe K.H., Rosa C.A., Boekhout T., Ĉadež N., Péter G., Sampaio J.P., Lachance M.-A., Yurkov A.M., Daniel H.-M., Takashima M., Boundy-Mills K., Libkind D., Aoki K., Sugita T., Rokas A. 2023. A genome-informed higher rank classification of the biotechnologically important fungal subphylum Saccharomycotina. Studies in Mycology 105:1-22. PDF
41. Liu C., Li Y., Chen Y., Chen X.-X., Huang J., Rokas A., Shen X.-X.* 2023. How has horizontal gene transfer shaped the evolution of insect genomes? Environmental Microbiology 25(3):642–645. PDF
2022
40. Li Y.-N.*, Liu H., Steenwyk J.L., LaBella A.L., Harrison M.-C., Groenewald M., Zhou X., Shen X.-X., Zhao T., Hittinger C.T., Rokas A.* 2022. Contrasting modes of macro and microsynteny evolution in a eukaryotic subphylum. Current Biology 32(24):5335-5343. PDF
39. Steenwyk, J.L.*, Goltz, D.C., Buida, T.J., Li, Y., Shen X.-X., and Rokas, A.* 2022. OrthoSNAP: A tree splitting and pruning algorithm for retrieving single-copy orthologs from gene family trees. PLoS biology 20(10):e3001827. PDF
38. Ma, X.-Z., Wang, Z.-Q., Ye, X.-Q., Liu, X.-Y., Tang, P., Shen X.-X., and Chen, X.-X.* 2022. A high-quality genome of the dobsonfly Neoneuromus ignobilis reveals molecular convergences in aquatic insects. Genomics 114(5):110437. PDF
37. Li Y.#, Liu Z.#, Liu C.#, Shi Z., Pang L., Chen C., Chen Y., Pan R., Zhou W., Chen X.-X., Rokas A.*, Huang J.*, Shen X.-X.* 2022. HGT is widespread in insects and contributes to male courtship in lepidopterans. Cell 185(16):2975-2987. PDF Download data and additional figures & tables, HGTfinder
Research Highlights in Nature and Nature Ecology & Evolution
36. Deng Q.#, Li H.#, Feng Y.#, Xu R., Li W., Zhu R., Akhter D., Shen X.-X., Hu J.*, Jiang H.*, Pan R.* 2022. 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 111(2):567-582. PDF
35. Xu S.#, Liu Y.-X.#, Cernava T.#, Wang H., Zhou Y., Xia T., Cao S., Berg G., Shen X.-X., Wen Z., Li C., Qu B., Ruan H., Chai Y., Zhou X., Ma Z., Shi Y., Yu Y.*, Bai Y.*, Chen Y.* 2022. Fusarium fruiting body microbiome member Pantoea agglomerans inhibits fungal pathogenesis by targeting lipid rafts. Nature microbiology 7(6): 831-843. PDF
2021
34. Phillips, M. A., Steenwyk J.*, Shen X.-X., Rokas A.* 2021. Examination of gene loss in the DNA mismatch repair pathway and its mutational consequences in a fungal phylum. Genome Biology and Evolution 13(10):1-12. PDF
33. Tice, A. K.#, D. Žihala#, T. Pánek#, R. E. Jones, E. Salomaki, S. Nenarokov, F. Burki, M. Eliáš, L. Eme, A. J. Roger, A. Rokas, Shen X.-X., J. F. H. Strassert, M. Kolísko, M. W. Brown* 2021. PhyloFisher: A phylogenomic package for resolving eukaryotic relationships. PLoS Biology 19: e3001365. PDF Download PhyloFisher.
32. Li Y., Shen X.-X., Evans B., Dunn C.W.*, Rokas A.* 2021. Rooting the animal tree of life. Molecular Biology and Evolution 38(10):4322-4333. PDF
31. Shen X.-X.*, Steenwyk J., Rokas A. 2021. Dissecting incongruence between concatenation- and quartet-based approaches in phylogenomic data. Systematic Biology 70(5):997-1014. PDF Download data GLS&GQS caculation
30. 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. PDF Download phylogenomic data, genome data.
29. 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. PDF Download PhyKIT.
2020
28. 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. PDF Download data.
27. 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. PDF Download ClipKT.
26. Haase M.A.B.#, Kominek J.#, Opulente D., Shen X.-X., LaBella A., Zhou X., DeVirgilio J., Hulfachor A, Kurtzman C.P., Rokas A.*, Hittinger C.T.* 2020. Repeated horizontal gene transfer of GALactose metabolism genes violates Dollo’s law of irreversible loss. Genetics 217: iyaa012. PDF
25. Li Y.#, Davod 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 117(50):31580-31581. PDF
24. 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. PDF Download phylogenomic data, genome assemblies and annotations.
23. Mead M.#, Borowsky A.#, Joehnk B., Steenwyk J., Shen X.-X., Sil A., Rokas A.* 2020. 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 12(7):1119–1130. PDF
22. Yang Y., Sun P., Lv L., Wang D., Ru D., Li Y., Ma T., Zhang L., Shen X.-X., Meng F., Jiao B., Shan L., Liu M., Wang Q., Qin Z., Xi Z., Wang X., Davis C.C., Liu J.* 2020. Prickly waterlily and rigid hornwort genomes shed light on early angiosperm evolution. Nature Plants 6(3):215–222. PDF
Commentary in Nature Plants
Before 2020
21. Ely Z.A., Moon J.M., Sliwoski G.R., Sangha A.K., Shen X.-X., Labella A.L., Meiler J., Capra J.A., Rokas A.* 2019. The impact of natural selection on the evolution and function of placentally expressed galectins. Genome Biology and Evolution 11(9):2574–2592 PDF
20. Krassowski, T., J. Kominek, Shen X.-X., D. A. Opulente, X. Zhou, A. Rokas, C. T. Hittinger, Wolfe K.H.* 2019. Multiple Reinventions of Mating-type Switching during Budding Yeast Evolution. Current Biology 29(15):2555–2562. PDF
Commentary in Current Biology
19. Wang M., Fu H., Shen X.-X., Ruan R., Rokas A., Li H.* 2019. Genomic features and evolution of the conditionally dispensable chromosome in the tangerine pathotype of Alternaria and alternata. Mol. Plant Pathol. 20(10): 1425–1438. PDF
18. Steenwyk, J. L., Shen X.-X., A. L. Lind, G. G. Goldman, Rokas A. 2019.* A robust phylogenomic timetree for biotechnologically and medically important fungi in the genera Aspergillus and Penicillium. mBio 10: 1-25. PDF
17. Steenwyk, J. L., D. A. Opulente, J. Kominek, Shen X.-X., X. Zhou, A. L. Labella, N. P. Bradley, B. F. Eichman, N. Čadež, D. Libkind, J. DeVirgilio, A. B. Hulfachor, Kurtzman C.P., Hittinger C.T., Rokas A.* 2019. Extensive loss of cell cycle and DNA repair genes in an ancient lineage of bipolar budding yeasts. PLoS Biology 17: e3000255. PDF
16. Kominek J.#, Doering D.T.#, Opulente D., Shen X.-X., Zhou X., Jeremy D., Hulfachor A.B., Groenewald M., Mcgee M., Karlen S., Kurtzman C.P., Rokas A., Hittinger C.T.* 2019. Eukaryotic acquisition of a bacterial operon. Cell 176: 1356-1366. PDF
Commentary in Cell
15. Shen X.-X.#, Opulente D.A.#, Kominek J.#, Zhou X.#, Steenwyk J., Buh K.V., Haase M., Wisecaver J.H., Wang M., Doering D.T., Boudouris J., Schneider R., Langdon Q.K., Ohkuma M., Endoh R., Takashima M., Manabe R., Čadež N., Libkind D., Rosa C., DeVirgilio J., Hulfachor A., Groenewald M., Kurtzman C.P., Hittinger C.T.*, Rokas A.* 2018. The tempo and mode of genome evolution in the budding yeast subphylum. Cell 175: 1533-1545. PDF Download data
Featured article on the homepage of the US Department of Energy Office of Science on December 4 2018
The story behind the paper in Nature Ecology & Evolution blog
14. Krause D.J., Kominek J., Opulente D.A., Shen X.-X., Zhou X., Langdon Q.K., DeVirgilio J., Hulfachor A., Kurtzman C.P., Rokas A., Hittinger C.T.* 2018. Functional and evolutionary characterization of a secondary metabolite gene cluster in budding yeasts. Proc. Natl. Acad. Sci. USA 115: 11030-11035. PDF
13. Shi R., Shen X.-X., Rokas A., Eichman B.F.* 2018. Structural biology of the HEAT-like repeat family of DNA glycosylases. BioEssays 40: 1800133. PDF
12. Krassowski T., Coughlan A.Y., Shen X.-X., Zhou X., Kominek J., Opulente D.A., Riley R., Grigoriev I. V., Maheshwari N., Shields D.C., Kurtzman C.P., Hittinger C.T., Rokas A., Wolfe K.H.* 2018. Evolutionary instability of CUG-Leu in the genetic code of budding yeasts. Nature Communications 9: 1887. PDF
11. Gonçalves C., Wisecaver J.H., Kominek J., Oom M.S., Leandro M.J., Shen X.-X., Opulente D.A., Zhou X., Peris D., Kurtzman C.P., Hittinger C.T., Rokas A., Gonçalves P.* 2018. Evidence for loss and adaptive reacquisition of alcoholic fermentation in an early-derived fructophilic yeast lineage. eLife 7: e33034. PDF
10. Zhou X., Shen X.-X., Hittinger C.T., Rokas A.* 2018. Evaluating Fast Maximum Likelihood-Based Phylogenetic Programs Using Empirical Phylogenomic Data Sets. Molecular Biology and Evolution 35(2): 486-503. PDF Download data
9. Shi R., Mullins E.A., Shen X.-X., Lay K.T., Yuen P.K., David S.S., Rokas A., Eichman B.F.* 2018. Selective base excision repair of DNA damage by the non-base-flipping DNA glycosylase AlkC. EMBO Journal 37: 63-74. PDF
8. Shen X.-X., Hittinger C. T., Rokas A.* 2017. Contentious relationships in phylogenomic studies can be driven by a handful of genes. Nature Ecology and Evolution 1: 0126. PDF Download data Phylogenetic signal parser v1.1
One of 12 evolutionary biological papers in 2017 and 2018 (Nature Ecol & Evol's 2nd Anniversary)
One of 10 editors’ and readers’ favourites in 2017 (Nature Ecol & Evol's 1st Anniversary)
The story behind the paper in Nature Ecology & Evolution blog
7. Shen X.-X., Zhou X., Kominek J., Kurtzman C. P., Hittinger C. T., Rokas A.* 2016. Reconstructing the backbone of the Saccharomycotina yeast phylogeny using genome-scale data. G3: Genes | Genomes | Genetics 6: 3927-3939. PDF Download data
One of the most cited papers in G3 (G3 10th Anniversary)
6. Shen X.-X., Salichos L., Rokas A.* 2016. A genome-scale investigation of how sequence-, function-, and tree-based gene properties influence phylogenetic inference. Genome Biology and Evolution 8(8): 2565–2580. PDF Download data
5. Shen X.-X., Liang D., Chen M.Y., Mao R.L., Wake D.B., Zhang P.* 2016. Enlarged Multilocus Dataset Provides Surprisingly Younger Time of Origin for the Plethodontidae, the Largest Family of Salamanders. Systematic Biology 65(1): 66-81. PDF Download data
4. Shen X.-X., Liang D., Feng Y.J., Chen M.Y., Zhang P.* 2013. 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(10): 2235-2248. PDF Download data
3. Liang D.#, Shen X.-X.#, Zhang P.* 2013. 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(8): 1803-1807. PDF Download data
2. Shen X.-X.#, Liang D.#, Zhang P.* 2012. The Development of Three Long Universal Nuclear Protein-Coding Locus Markers and Their Application to Osteichthyan Phylogenetics with Nested PCR. PLoS ONE 7(6): e39256.62. PDF Download data
1. Shen X.-X., Liang D, Wen J.Z., Zhang P.* 2011. 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(12): 3237-3252. PDF Download data