| Year |
Citation |
Score |
| 2025 |
Zhu Y, Li Y, Li C, Shen XX, Zhou X. A critical evaluation of deep-learning based phylogenetic inference programs using simulated data sets. Journal of Genetics and Genomics = Yi Chuan Xue Bao. PMID 39824436 DOI: 10.1016/j.jgg.2025.01.006 |
0.591 |
|
| 2025 |
Liang Y, Gao Q, Li F, Du Y, Wu J, Pan W, Wang S, Zhang X, Zhang M, Song X, Zhong L, Zhang F, Li Y, Wang Z, Li D, ... Zhou X, et al. The giant genome of lily provides insights into the hybridization of cultivated lilies. Nature Communications. 16: 45. PMID 39747119 DOI: 10.1038/s41467-024-55545-8 |
0.445 |
|
| 2024 |
Zhang N, Li X, Ming L, Sun W, Xie X, Zhi C, Zhou X, Wen Y, Liang Z, Deng Y. Comparative Genomics and Pathogenicity Analysis of Three Fungal Isolates Causing Barnyard Grass Blast. Journal of Fungi (Basel, Switzerland). 10. PMID 39728364 DOI: 10.3390/jof10120868 |
0.401 |
|
| 2024 |
Qiu M, Li Y, Liu Q, Zhang X, Huang Y, Guo R, Hu M, Zhou J, Zhou X. sp. nov. and sp. nov., isolated from wilted pepper plants. International Journal of Systematic and Evolutionary Microbiology. 74. PMID 39589767 DOI: 10.1099/ijsem.0.006550 |
0.322 |
|
| 2024 |
Crandall JG, Zhou X, Rokas A, Hittinger CT. Specialization Restricts the Evolutionary Paths Available to Yeast Sugar Transporters. Molecular Biology and Evolution. 41. PMID 39492761 DOI: 10.1093/molbev/msae228 |
0.54 |
|
| 2024 |
Steenwyk JL, Knowles S, Bastos RW, Balamurugan C, Rinker D, Mead ME, Roberts CD, Raja HA, Li Y, Colabardini AC, de Castro PA, Dos Reis TF, Gumilang A, Almagro-Molto M, Alanio A, ... ... Zhou X, et al. Evolutionary origin and population diversity of a cryptic hybrid pathogen. Nature Communications. 15: 8412. PMID 39333551 DOI: 10.1038/s41467-024-52639-1 |
0.804 |
|
| 2024 |
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 cactus-associated yeasts. Plos Biology. 22: e3002832. PMID 39312572 DOI: 10.1371/journal.pbio.3002832 |
0.841 |
|
| 2024 |
Harrison MC, Opulente DA, Wolters JF, Shen XX, Zhou X, Groenewald M, Hittinger CT, Rokas A, LaBella AL. Exploring Saccharomycotina Yeast Ecology Through an Ecological Ontology Framework. Yeast (Chichester, England). PMID 39295298 DOI: 10.1002/yea.3981 |
0.831 |
|
| 2024 |
Liu H, Steenwyk JL, Zhou X, Schultz DT, Kocot KM, Shen XX, Rokas A, Li Y. A taxon-rich and genome-scale phylogeny of Opisthokonta. Plos Biology. 22: e3002794. PMID 39283949 DOI: 10.1371/journal.pbio.3002794 |
0.836 |
|
| 2024 |
Zavala B, Dineen L, Fisher KJ, Opulente DA, Harrison MC, Wolters JF, Shen XX, Zhou X, Groenewald M, Hittinger CT, Rokas A, LaBella AL. Genomic factors shaping codon usage across the Saccharomycotina subphylum. G3 (Bethesda, Md.). PMID 39213398 DOI: 10.1093/g3journal/jkae207 |
0.829 |
|
| 2024 |
Crandall JG, Zhou X, Rokas A, Hittinger CT. Specialization restricts the evolutionary paths available to yeast sugar transporters. Biorxiv : the Preprint Server For Biology. PMID 39091816 DOI: 10.1101/2024.07.22.604696 |
0.54 |
|
| 2024 |
David KT, Schraiber JG, Crandall JG, LaBella AL, Opulente DA, Harrison MC, Wolters JF, Zhou X, Shen XX, Groenewald M, Hittinger CT, Pennell M, Rokas A. Convergent expansions of keystone gene families drive metabolic innovation in a major eukaryotic clade. Biorxiv : the Preprint Server For Biology. PMID 39091791 DOI: 10.1101/2024.07.22.604484 |
0.813 |
|
| 2024 |
Liu C, Zhou X, Li Y, Hittinger CT, Pan R, Huang J, Chen XX, Rokas A, Chen Y, Shen XX. The influence of the number of tree searches on maximum likelihood inference in phylogenomics. Systematic Biology. PMID 38940001 DOI: 10.1093/sysbio/syae031 |
0.79 |
|
| 2024 |
Feng B, Li Y, Liu H, Steenwyk JL, David KT, Tian X, Xu B, Gonçalves C, Opulente DA, LaBella AL, Harrison MC, Wolters JF, Shao S, Chen Z, Fisher KJ, ... Zhou X, et al. Unique trajectory of gene family evolution from genomic analysis of nearly all known species in an ancient yeast lineage. Biorxiv : the Preprint Server For Biology. PMID 38895429 DOI: 10.1101/2024.06.05.597512 |
0.817 |
|
| 2024 |
Zavala B, Dineen L, Fisher KJ, Opulente DA, Harrison MC, Wolters JF, Shen XX, Zhou X, Groenewald M, Hittinger CT, Rokas A, LaBella AL. Genomic factors shaping codon usage across the Saccharomycotina subphylum. Biorxiv : the Preprint Server For Biology. PMID 38826271 DOI: 10.1101/2024.05.23.595506 |
0.831 |
|
| 2024 |
Tang J, Xu J, Liu XH, Lv FZ, Yao QJ, Zhou XF, Lu HY, Yu TM, Jiang ZZ, Jin XZ, Guo F, Yu XJ. Prevalence and genetic diversity of Anaplasma and Ehrlichia in ticks and domesticated animals in Suizhou County, Hubei Province, China. Scientific Reports. 14: 12621. PMID 38824201 DOI: 10.1038/s41598-024-63267-6 |
0.304 |
|
| 2024 |
Wang X, Li C, Huang S, Gao H, Li Y, Chen X, Huang L, Luo J, Zhou X, Zhang L. Pathogenic and Comparative Genomic Analysis of Isolated from . Plant Disease. PMID 38687570 DOI: 10.1094/PDIS-01-24-0118-RE |
0.343 |
|
| 2024 |
Harrison MC, Ubbelohde EJ, LaBella AL, Opulente DA, Wolters JF, Zhou X, Shen XX, Groenewald M, Hittinger CT, Rokas A. Machine learning enables identification of an alternative yeast galactose utilization pathway. Proceedings of the National Academy of Sciences of the United States of America. 121: e2315314121. PMID 38669185 DOI: 10.1073/pnas.2315314121 |
0.828 |
|
| 2024 |
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, ... Zhou X, et al. Genomic factors shape carbon and nitrogen metabolic niche breadth across Saccharomycotina yeasts. Science (New York, N.Y.). 384: eadj4503. PMID 38662846 DOI: 10.1126/science.adj4503 |
0.825 |
|
| 2024 |
Li F, Hou Z, Xu S, Han D, Li B, Hu H, Liu J, Cai S, Gan Z, Gu Y, Zhang X, Zhou X, Wang S, Zhao J, Mei Y, et al. Haplotype-resolved genomes of octoploid species in Phyllanthaceae family reveal a critical role for polyploidization and hybridization in speciation. The Plant Journal : For Cell and Molecular Biology. PMID 38606539 DOI: 10.1111/tpj.16767 |
0.446 |
|
| 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 |
0.825 |
|
| 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 |
0.804 |
|
| 2023 |
Chen L, Li C, Li B, Zhou X, Bai Y, Zou X, Zhou Z, He Q, Chen B, Wang M, Xue Y, Jiang Z, Feng J, Zhou T, Liu Z, et al. Evolutionary divergence of subgenomes in common carp provides insights into speciation and allopolyploid success. Fundamental Research. 4: 589-602. PMID 38933191 DOI: 10.1016/j.fmre.2023.06.011 |
0.341 |
|
| 2023 |
Li X, Yu S, Cheng Z, Chang X, Yun Y, Jiang M, Chen X, Wen X, Li H, Zhu W, Xu S, Xu Y, Wang X, Zhang C, Wu Q, ... Zhou X, et al. Origin and evolution of the triploid cultivated banana genome. Nature Genetics. PMID 38082204 DOI: 10.1038/s41588-023-01589-3 |
0.396 |
|
| 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 |
0.832 |
|
| 2023 |
Liu Q, Li C, Zhang X, Ding M, Liao X, Yan J, Hu M, Yang L, Wang X, Liao L, Li P, Zhou X. PhcX Is a LqsR-family response regulator that contributes to virulence and regulates multiple virulence factors. Mbio. e0202823. PMID 37787568 DOI: 10.1128/mbio.02028-23 |
0.311 |
|
| 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 |
0.839 |
|
| 2023 |
Li D, Lin HY, Wang X, Bi B, Gao Y, Shao L, Zhang R, Liang Y, Xia Y, Zhao YP, Zhou X, Zhang L. Genome and whole-genome resequencing of Cinnamomum camphora elucidate its dominance in subtropical urban landscapes. Bmc Biology. 21: 192. PMID 37697363 DOI: 10.1186/s12915-023-01692-1 |
0.345 |
|
| 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 |
0.804 |
|
| 2023 |
Steenwyk JL, Knowles S, Bastos RW, Balamurugan C, Rinker D, Mead ME, Roberts CD, Raja HA, Li Y, Colabardini AC, de Castro PA, Dos Reis TF, Canóvas D, Sanchez RL, Lagrou K, ... ... Zhou X, et al. Evolutionary origin, population diversity, and diagnostics for a cryptic hybrid pathogen. Biorxiv : the Preprint Server For Biology. PMID 37461539 DOI: 10.1101/2023.07.03.547508 |
0.841 |
|
| 2023 |
Yang P, Ling XY, Zhou XF, Chen YX, Wang TT, Lin XJ, Zhao YY, Ye YS, Huang LX, Sun YW, Qi YX, Ma DM, Zhan RT, Huang XS, Yang JF. Comparing genomes of Fructus Amomi-producing species reveals genetic basis of volatile terpenoid divergence. Plant Physiology. PMID 37427874 DOI: 10.1093/plphys/kiad400 |
0.383 |
|
| 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, ... Zhou X, 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 |
0.826 |
|
| 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 |
0.828 |
|
| 2022 |
He Q, Li J, Liu Q, Li Y, Liao X, Zhou J, Zhou X. Complete genome sequence resource of CL1 causing soft rot disease in (Wampee) in China. Plant Disease. PMID 36444142 DOI: 10.1094/PDIS-10-22-2504-A |
0.409 |
|
| 2022 |
Xu M, Gao Q, Jiang M, Wang W, Hu J, Chang X, Liu D, Liang Y, Jiang Y, Chen F, Li C, Huang H, Chen F, Li F, Trigiano RN, ... ... Zhou X, et al. The nearly complete genome sequence of Jasminum sambac reveals the molecular mechanism underlying the accumulation of jasmonates. Journal of Experimental Botany. PMID 36433929 DOI: 10.1093/jxb/erac464 |
0.397 |
|
| 2022 |
Tan C, Li C, Hu M, Hu A, Xue Y, Zhou X, Zhou J. Comparative Pathogenomic Analysis of Two Banana Pathogenic Strains Isolated from China and the Philippines. International Journal of Molecular Sciences. 23. PMID 36361548 DOI: 10.3390/ijms232112758 |
0.31 |
|
| 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 |
0.836 |
|
| 2022 |
Yan J, Lin N, Wang X, Chen X, Wang H, Lin Q, Zhou X, Zhang L, Liao L. Markerless gene deletion in based on its natural transformation competence. Frontiers in Microbiology. 13: 977580. PMID 36177460 DOI: 10.3389/fmicb.2022.977580 |
0.309 |
|
| 2022 |
Yang P, Zhao HY, Wei JS, Zhao YY, Lin XJ, Su J, Li FP, Li M, Ma DM, Tan XK, Liang HL, Sun YW, Zhan RT, He GZ, Zhou XF, et al. Chromosome-level genome assembly and functional characterization of terpene synthases provide new insights into the volatile terpenoid biosynthesis of Wurfbainia villosa. The Plant Journal : For Cell and Molecular Biology. PMID 36071028 DOI: 10.1111/tpj.15968 |
0.427 |
|
| 2022 |
Liang Y, Li F, Gao Q, Jin C, Dong L, Wang Q, Xu M, Sun F, Bi B, Zhao P, Li S, Ruan J, Zhou X, Zhang L, Wang J. The genome of Eustoma grandiflorum reveals the whole-genome triplication event contributing to ornamental traits in cultivated lisianthus. Plant Biotechnology Journal. PMID 35880287 DOI: 10.1111/pbi.13899 |
0.341 |
|
| 2022 |
Zhou J, Hu M, Hu A, Li C, Ren X, Tao M, Xue Y, Chen S, Tang C, Xu Y, Zhang L, Zhou X. Isolation and Genome Analysis of sp. nov. and , Two New Pathogens of Taro. Frontiers in Plant Science. 13: 852750. PMID 35557713 DOI: 10.3389/fpls.2022.852750 |
0.364 |
|
| 2022 |
Shi Y, Yang X, Ye X, Feng J, Cheng T, Zhou X, Liu DX, Xu L, Wang J. The Methyltransferase HemK Regulates the Virulence and Nutrient Utilization of the Phytopathogenic Bacterium Subsp. . International Journal of Molecular Sciences. 23. PMID 35409293 DOI: 10.3390/ijms23073931 |
0.316 |
|
| 2022 |
Hu M, Xue Y, Li C, Lv M, Zhang L, Parsek MR, Lu G, Zhou X, Zhou J. Genomic and Functional Dissections of Dickeya zeae Shed Light on the Role of Type III Secretion System and Cell Wall-Degrading Enzymes to Host Range and Virulence. Microbiology Spectrum. e0159021. PMID 35107329 DOI: 10.1128/spectrum.01590-21 |
0.341 |
|
| 2021 |
Steenwyk JL, Mead ME, de Castro PA, Valero C, Damasio A, Dos Santos RAC, Labella AL, Li Y, Knowles SL, Raja HA, Oberlies NH, Zhou X, Cornely OA, Fuchs F, Koehler P, et al. Genomic and Phenotypic Analysis of COVID-19-Associated Pulmonary Aspergillosis Isolates of Aspergillus fumigatus. Microbiology Spectrum. e0001021. PMID 34106569 DOI: 10.1128/Spectrum.00010-21 |
0.809 |
|
| 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 |
0.839 |
|
| 2021 |
Gao RF, Wang JY, Liu KW, Yoshida K, Hsiao YY, Shi YX, Tsai KC, Chen YY, Mitsuda N, Liang CK, Wang ZW, Wang Y, Zhang DY, Huang L, Zhao X, ... ... Zhou XF, et al. Comparative analysis of genomes reveals oomycete pathogenesis in crops. Heliyon. 7: e06317. PMID 33665461 DOI: 10.1016/j.heliyon.2021.e06317 |
0.496 |
|
| 2020 |
Yang L, Su D, Chang X, Foster CSP, Sun L, Huang CH, Zhou X, Zeng L, Ma H, Zhong B. Phylogenomic Insights into Deep Phylogeny of Angiosperms Based on Broad Nuclear Gene Sampling. Plant Communications. 1: 100027. PMID 33367231 DOI: 10.1016/j.xplc.2020.100027 |
0.365 |
|
| 2020 |
Hatmaker EA, Zhou X, Mead ME, Moon H, Yu JH, Rokas A. Revised Transcriptome-Based Gene Annotation for Aspergillus flavus Strain NRRL 3357. Microbiology Resource Announcements. 9. PMID 33273000 DOI: 10.1128/MRA.01155-20 |
0.811 |
|
| 2020 |
Steenwyk JL, Mead ME, de Castro PA, Valero C, Damasio A, Dos Santos RAC, Labella AL, Li Y, Knowles SL, Raja HA, Oberlies NH, Zhou X, Cornely OA, Fuchs F, Koehler P, et al. Genomic and phenotypic analysis of COVID-19-associated pulmonary aspergillosis isolates of . Biorxiv : the Preprint Server For Biology. PMID 33173866 DOI: 10.1101/2020.11.06.371971 |
0.819 |
|
| 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 |
0.832 |
|
| 2020 |
Ye T, Zhou T, Xu X, Zhang W, Fan X, Mishra S, Zhang L, Zhou X, Chen S. Whole-Genome Sequencing Analysis of Quorum Quenching Bacterial Strain QL-1 Identifies the FadY Enzyme for Degradation of the Diffusible Signal Factor. International Journal of Molecular Sciences. 21. PMID 32937869 DOI: 10.3390/Ijms21186729 |
0.418 |
|
| 2019 |
Zhang L, Chen F, Zhang X, Li Z, Zhao Y, Lohaus R, Chang X, Dong W, Ho SYW, Liu X, Song A, Chen J, Guo W, Wang Z, Zhuang Y, ... Zhou X, et al. The water lily genome and the early evolution of flowering plants. Nature. PMID 31853069 DOI: 10.1038/S41586-019-1852-5 |
0.396 |
|
| 2019 |
Zhou X, Lutteropp S, Czech L, Stamatakis A, von Looz M, Rokas A. Quartet-based computations of internode certainty provide robust measures of phylogenetic incongruence. Systematic Biology. PMID 31504977 DOI: 10.1093/Sysbio/Syz058 |
0.541 |
|
| 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 |
0.746 |
|
| 2019 |
Liang Z, Huang L, He F, Zhou X, Shi Z, Zhou J, Chen Y, Lv M, Chen Y, Zhang LH. A Substrate-Activated Efflux Pump, DesABC, Confers Zeamine Resistance to Dickeya zeae. Mbio. 10. PMID 31138747 DOI: 10.1128/mBio.00713-19 |
0.314 |
|
| 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 |
0.819 |
|
| 2019 |
Wang Y, Zhou X, Wang L, Liu X, Yang D, Rokas A. Gene Selection and Evolutionary Modeling Affect Phylogenomic Inference of Neuropterida Based on Transcriptome Data. International Journal of Molecular Sciences. 20. PMID 30832228 DOI: 10.3390/Ijms20051072 |
0.731 |
|
| 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 |
0.779 |
|
| 2019 |
Li P, Zhang Y, Sun Y, Wu X, Wang Z, Zhou J, Zhou X. Comparative genomic analysis of subspecies of Pantoea stewartii reveals distinct variations Journal of Plant Pathology. 101: 997-1004. DOI: 10.1007/S42161-019-00328-0 |
0.358 |
|
| 2018 |
Zhang S, Zhao Y, Heaster TM, Fischer MA, Stengel KR, Zhou X, Ramsey H, Zhou MM, Savona MR, Skala MC, Hiebert SW. BET inhibitors reduce cell size and induce reversible cell cycle arrest in AML. Journal of Cellular Biochemistry. PMID 30417424 DOI: 10.1002/Jcb.28005 |
0.316 |
|
| 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 |
0.843 |
|
| 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 |
0.768 |
|
| 2018 |
Wang J, Zhao Y, Zhou X, Hiebert SW, Liu Q, Shyr Y. Nascent RNA sequencing analysis provides insights into enhancer-mediated gene regulation. Bmc Genomics. 19: 633. PMID 30139328 DOI: 10.1186/S12864-018-5016-Z |
0.352 |
|
| 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 |
0.763 |
|
| 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 |
0.826 |
|
| 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 |
0.751 |
|
| 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 |
0.752 |
|
| 2017 |
Yan H, Opachaloemphan C, Mancini G, Yang H, Gallitto M, Mlejnek J, Leibholz A, Haight K, Ghaninia M, Huo L, Perry M, Slone J, Zhou X, Traficante M, Penick CA, et al. An Engineered orco Mutation Produces Aberrant Social Behavior and Defective Neural Development in Ants. Cell. 170: 736-747.e9. PMID 28802043 DOI: 10.1016/J.Cell.2017.06.051 |
0.338 |
|
| 2017 |
Zhao L, Zhou X, Rokas A, Cone RD. Functional variants of the melanocortin-4 receptor associated with the Odontoceti and Mysticeti suborders of cetaceans. Scientific Reports. 7: 5684. PMID 28720755 DOI: 10.1038/S41598-017-05962-1 |
0.567 |
|
| 2017 |
Yi X, Qi J, Zhou X, Hu MY, Zhong GH. Differential expression of chemosensory-protein genes in midguts in response to diet of Spodoptera litura. Scientific Reports. 7: 296. PMID 28331183 DOI: 10.1038/S41598-017-00403-5 |
0.319 |
|
| 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 |
0.823 |
|
| 2016 |
Zhou X, Peris D, Kominek J, Kurtzman CP, Hittinger CT, Rokas A. in silico Whole Genome Sequencer & Analyzer (iWGS): A Computational Pipeline to Guide the Design and Analysis of de novo Genome Sequencing Studies. G3 (Bethesda, Md.). PMID 27638685 DOI: 10.1534/G3.116.034249 |
0.61 |
|
| 2016 |
Ren R, Sun Y, Zhao Y, Geiser D, Ma H, Zhou X. Phylogenetic Resolution of Deep Eukaryotic and Fungal Relationships Using Highly Conserved Low-Copy Nuclear Genes. Genome Biology and Evolution. PMID 27604879 DOI: 10.1093/Gbe/Evw196 |
0.499 |
|
| 2015 |
Wang Y, Zhou X, Yang D, Rokas A. A genome-scale investigation of incongruence in Culicidae mosquitoes. Genome Biology and Evolution. PMID 26608059 DOI: 10.1093/Gbe/Evv235 |
0.774 |
|
| 2015 |
Zhou X, Rokas A, Berger SL, Liebig J, Ray A, Zwiebel LJ. Chemoreceptor Evolution in Hymenoptera and Its Implications for the Evolution of Eusociality. Genome Biology and Evolution. 7: 2407-16. PMID 26272716 DOI: 10.1093/Gbe/Evv149 |
0.59 |
|
| 2015 |
Neafsey DE, Waterhouse RM, Abai MR, Aganezov SS, Alekseyev MA, Allen JE, Amon J, Arcà B, Arensburger P, Artemov G, Assour LA, Basseri H, Berlin A, Birren BW, Blandin SA, ... Zhou X, et al. Mosquito genomics. Highly evolvable malaria vectors: the genomes of 16 Anopheles mosquitoes. Science (New York, N.Y.). 347: 1258522. PMID 25554792 DOI: 10.1126/Science.1258522 |
0.83 |
|
| 2014 |
Zhou X, Rinker DC, Pitts RJ, Rokas A, Zwiebel LJ. Divergent and conserved elements comprise the chemoreceptive repertoire of the nonblood-feeding mosquito Toxorhynchites amboinensis. Genome Biology and Evolution. 6: 2883-96. PMID 25326137 DOI: 10.1093/Gbe/Evu231 |
0.782 |
|
| 2014 |
Zhou X, Rokas A. Prevention, diagnosis and treatment of high-throughput sequencing data pathologies. Molecular Ecology. 23: 1679-700. PMID 24471475 DOI: 10.1111/Mec.12680 |
0.495 |
|
| 2013 |
Rinker DC, Zhou X, Pitts RJ, Rokas A, Zwiebel LJ. Antennal transcriptome profiles of anopheline mosquitoes reveal human host olfactory specialization in Anopheles gambiae. Bmc Genomics. 14: 749. PMID 24182346 DOI: 10.1186/1471-2164-14-749 |
0.79 |
|
| 2013 |
Rinker DC, Pitts RJ, Zhou X, Suh E, Rokas A, Zwiebel LJ. Blood meal-induced changes to antennal transcriptome profiles reveal shifts in odor sensitivities in Anopheles gambiae. Proceedings of the National Academy of Sciences of the United States of America. 110: 8260-5. PMID 23630291 DOI: 10.1073/Pnas.1302562110 |
0.745 |
|
| 2013 |
Chintapalli SV, Bhardwaj G, Babu J, Hadjiyianni L, Hong Y, Todd GK, Boosalis CA, Zhang Z, Zhou X, Ma H, Anishkin A, van Rossum DB, Patterson RL. Reevaluation of the evolutionary events within recA/RAD51 phylogeny. Bmc Genomics. 14: 240. PMID 23574621 DOI: 10.1186/1471-2164-14-240 |
0.424 |
|
| 2012 |
Rokas A, Gibbons JG, Zhou X, Beauvais A, Latgé JP. The diverse applications of RNA-seq for functional genomic studies in Aspergillus fumigatus. Annals of the New York Academy of Sciences. 1273: 25-34. PMID 23230834 DOI: 10.1111/J.1749-6632.2012.06755.X |
0.743 |
|
| 2012 |
Zhou X, Slone JD, Rokas A, Berger SL, Liebig J, Ray A, Reinberg D, Zwiebel LJ. Phylogenetic and transcriptomic analysis of chemosensory receptors in a pair of divergent ant species reveals sex-specific signatures of odor coding. Plos Genetics. 8: e1002930. PMID 22952454 DOI: 10.1371/Journal.Pgen.1002930 |
0.597 |
|
| 2010 |
Zhou X, Lin Z, Ma H. Phylogenetic detection of numerous gene duplications shared by animals, fungi and plants. Genome Biology. 11: R38. PMID 20370904 DOI: 10.1186/Gb-2010-11-4-R38 |
0.515 |
|
| 2009 |
Feng B, Li L, Zhou X, Stanley B, Ma H. Analysis of the Arabidopsis floral proteome: detection of over 2 000 proteins and evidence for posttranslational modifications. Journal of Integrative Plant Biology. 51: 207-23. PMID 19200160 DOI: 10.1111/J.1744-7909.2008.00787.X |
0.308 |
|
| 2007 |
Sun Y, Zhou X, Ma H. Genome‐wide Analysis of Kelch Repeat‐containing F‐box Family Journal of Integrative Plant Biology. 49: 940-952. DOI: 10.1111/J.1744-7909.2007.00498.X |
0.341 |
|
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