Xiaofan Zhou#, Jesse D. Slone#; Antonis Rokas; Shelley L. Berger; Jürgen Liebig; Anandasankar Ray; Danny Reinberg; Laurence J. Zwiebel* (2012). Phylogenetic and Transcriptomic Analysis of Chemosensory Receptors in a Pair of Divergent Ant Species Reveals Sex-Specific Signatures of Odor Coding. PLoS Genet 8(8): e1002930. doi:10.1371/journal.pgen.1002930PDF
David C Rinker#, Xiaofan Zhou#, Ronald Jason Pitts, The AGC Consortium, Antonis Rokas and Laurence J Zwiebel* (2013). Antennal transcriptome profiles of anopheline mosquitoes reveal human host olfactory specialization in Anopheles gambiae. BMC Genomics 14, 749 (2013). doi: 10.1186/1471-2164-14-749PDF
Xiaofan Zhou#, David C. Rinker#, Ronald Jason Pitts, Antonis Rokas, Laurence J. Zwiebel* (2014). Divergent and Conserved Elements Comprise the Chemoreceptive Repertoire of the Nonblood-Feeding Mosquito Toxorhynchites amboinensis. Genome Biol Evol. 2014 Oct 16;6(10):2883-96. doi: 10.1093/gbe/evu231.PDF
Xiaofan Zhou, Antonis Rokas, Shelley L. Berger, Jürgen Liebig, Anandasankar Ray, and Laurence J. Zwiebel* (2015). Chemoreceptor Evolution in Hymenoptera and Its Implications for the Evolution of Eusociality. Genome Biol. Evol. 7(8):2407–2416. doi:10.1093/gbe/evv149PDF
Xiaofan Zhou, David Peris, Jacek Kominek, Cletus P. Kurtzman, Chris Todd Hittinger* and Antonis Rokas* (2016). In Silico Whole Genome Sequencer and Analyzer (iWGS). G3.doi: 10.1534/g3.116.034249PDF
Xin Yi#, Jiangwei Qi#, Xiaofan Zhou#, Mei Ying Hu & Guo Hua Zhong* (2017). Differential expression of chemosensory-protein genes in midguts in response to diet of Spodoptera litura. Sci Rep 7, 296 (2017). DOI:10.1038/s41598-017-00403-5PDF
Xing-Xing Shen#, Dana A. Opulente#, Jacek Kominek#, Xiaofan Zhou#, Jacob L. Steenwyk, Kelly V. Buh, Max A.B. Haase, Jennifer H. Wisecaver, Mingshuang Wang, Drew T. Doering, James T. Boudouris, Rachel M. Schneider, Quinn K. Langdon, Moriya Ohkuma, Rikiya Endoh, Masako Takashima, Ri-ichiroh Manabe, Neža Čadež, Diego Libkind, Carlos A. Rosa, Jeremy DeVirgilio, Amanda Beth Hulfachor, Marizeth Groenewald, Cletus P. Kurtzman, Chris Todd Hittinger*, and Antonis Rokas* (2018). Tempo and Mode of Genome Evolution in the Budding Yeast Subphylum. Cell 175, 1533—1545.e1—e11, November 29, 2018. doi: 10.1016/j.cell.2018.10.023PDF
Xiaofan Zhou, Xing-Xing Shen, Chris Todd Hittinger, and Antonis Rokas* (2018). Evaluating Fast Maximum Likelihood-Based Phylogenetic Programs Using Empirical Phylogenomic Data Sets. Mol. Biol. Evol. 35(2):486–503 doi:10.1093/molbev/msx302PDF
Yuyu Wang#, Xiaofan Zhou#, Liming Wang, Xingyue Liu*, Ding Yang* and Antonis Rokas* (2019). Gene Selection and Evolutionary Modeling Affect Phylogenomic Inference of Neuropterida Based on Transcriptome Data. Int. J. Mol. Sci. 2019, 20, 1072 doi:10.3390/ijms20051072PDF
Xiaofan Zhou, Sarah Lutteropp, Lucas Czech, Alexandros Stamatakis, Moritz von Looz, and Antonis Rokas* (2020). Quartet-Based Computations of Internode Certainty Provide Robust Measures of Phylogenetic Incongruence. Syst. Biol. 69(2):308–324, 202 DOI:10.1093/sysbio/syz058PDF
Yanqiu He#, Xiaofan Zhou#, Jieling Li, Huaping Li, Yunfeng Li* and Yanfang Nie* (2021). In Vitro Secretome Analysis Suggests Differential Pathogenic Mechanisms between Fusarium oxysporum f. sp. cubense Race 1 and Race 4. Biomolecules 2021, 11, 1353. doi: 10.3390/biom11091353PDF
Ming Hu#, Chuhao Li#, Xiaofan Zhou#, Yang Xue, Si Wang, Anqun Hu, Shanshan Chen, Xiuwen Mo and Jianuan Zhou* (2021). Microbial Diversity Analysis and Genome Sequencing Identify Xanthomonas perforans as the Pathogen of Bacterial Leaf Canker of Water Spinach (Ipomoea aquatic). Front. Microbiol. 12:752760. doi: 10.3389/fmicb.2021.752760PDF
Lin Chen#, Chengyu Li#, Bijun Li#, Xiaofan Zhou#, Yulin Bai, Xiaoqing Zou, Zhixiong Zhou, Qian He, Baohua Chen, Mei Wang, Yaguo Xue, Zhou Jiang, Jianxin Feng, Tao Zhou, Zhanjiang Liu*, Peng Xu* (2024). Evolutionary divergence of subgenomes in common carp provides insights into speciation and allopolyploid success. FundamentalResearch 4(2024)589–602. doi: 10.1016/j.fmre.2023.06.011PDF
Chao Liu#, Xiaofan Zhou#, Yuanning Li, Chris Todd Hittinger, Ronghui Pan, Jinyan Huang, Xue-xin Chen, Antonis Rokas, Yun Chen, and Xing-Xing Shen* (2024). The Influence of the Number of Tree Searches on Maximum Likelihood Inference in Phylogenomics. Syst. Biol. 73(5):807–822, 20 doi.org/10.1093/sysbio/sya031PDF
Ren Ren, Yazhou Sun, Yue Zhao, David Geiser, Hong Ma* and Xiaofan Zhou* (2016). Phylogenetic Resolution of Deep Eukaryotic and Fungal Relationships Using Highly Conserved Low-Copy Nuclear Genes. Genome Biol. Evol. 8(9):2683—2701. doi:10.1093/gbe/evw196PDF
Xin Yi, Song Shi, Peidan Wang, Yaoyao Chen, Qiqi Lu, Tianyi Wang, Xiaofan Zhou* and Guohua Zhong* (2019). Characterizing potential repelling volatiles for “push-pull” strategy against stem borer：a case study in Chilo auricilius. BMC Genomics 20, 751 (2019). doi: 10.1186/s12864-019-6112-4PDF
Tian Ye#, Tian Zhou#, Xudan Xu#, Wenping Zhang, Xinghui Fan, Sandhya Mishra, Lianhui Zhang, Xiaofan Zhou* and Shaohua Chen* (2020). Whole-Genome Sequencing Analysis of Quorum Quenching Bacterial Strain Acinetobacter lactucae QL-1 Identifies the FadY Enzyme for Degradation of the Diffusible Signal Factor. Int. J. Mol. Sci. 2020, 21, 6729 doi:10.3390/ijms21186729 www.mdpi.com/journal/ijmsPDF
Xudan Xu#, Tian Ye#, Wenping Zhang, Tian Zhou, Xiaofan Zhou*, Weijun Dai* and Shaohua Chen* (2021). Identification of FadT as a Novel Quorum Quenching Enzyme for the Degradation of Diffusible Signal Factor in Cupriavidus pinatubonensis Strain HN-2. Int. J. Mol. Sci. 2021, 22, 9862. doi: 10.3390/ijms22189862PDF
Ming Hu, Chuhao Li, Yang Xue, Anqun Hu, Shanshan Chen, Yufan Chen, Guangtao Lu, Xiaofan Zhou* and Jianuan Zhou* (2021). Isolation, characterization, and genomic investigation of a phytopathogenic strain of Stenotrophomonas maltophilia. Phytopathology 2021 111:11, 2088-2099 doi: 10.1094/PHYTO-11-20-0501-RPDF
Yang Liu#, Stephen Dela Ahator#, Huishan Wang, Qishun Feng, Yinuo Xu, Chuhao Li, Xiaofan Zhou* and Lian-Hui Zhang* (2022). Microevolution of the mexT and lasR Reinforces the Bias of Quorum Sensing System in Laboratory Strains of Pseudomonas aeruginosa PAO1. Front. Microbiol., 12 April 2022 doi: 10.3389/fmicb.2022.821895PDF
Yanfang Nie#, Guanjun Li#, Jieling Li, Xiaoshu Zhou, Yanzhi Zhang, Qingchuan Shi, Xiaofan Zhou*, Huaping Li*, Xiao-Lin Chen* and Yunfeng Li* (2022). A novel elicitor MoVcpo is necessary for the virulence of Magnaporthe oryzae and triggers rice defense responses. Front. Plant Sci., 17 October 2022 doi: 10.3389/fpls.2022.1018616PDF
Jianuan Zhou#, Ming Hu#, Anqun Hu#, Chuhao Li, Xinyue Ren, Min Tao, Yang Xue, Shanshan Chen, Chongzhi Tang, Yiwu Xu, Lianhui Zhang and Xiaofan Zhou* (2022). Isolation and Genome Analysis of Pectobacterium colocasium sp. nov. and Pectobacterium aroidearum, Two New Pathogens of Taro. Front. Plant Sci., 26 April 2022 doi: 10.3389/fpls.2022.852750PDF
Chenxing Tan, Chuhao Li, Ming Hu , Anqun Hu, Yang Xue, Xiaofan Zhou* and Jianuan Zhou* (2022). Comparative Pathogenomic Analysis of Two Banana Pathogenic Dickeya Strains Isolated from China and the Philippines. Int. J. Mol. Sci. 2022, 23(21), 12758; doi: 10.3390/ijms232112758PDF
Ming Hu, Yang Xue, Chuhao Li, Mingfa Lv, Lianhui Zhang, Matthew R. Parsek, Guangtao Lu, Xiaofan Zhou*, Jianuan Zhou* (2022). 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. Microbiol Spectr. 2022 Feb 23;10(1):e0159021. doi: 10.1128/spectrum.01590-21PDF
Mingfa Lv#, Yufan Chen#, Ming Hu, Qinglin Yu, Cheng Duan, Sixuan Ye, Jinfeng Ling, Jianuan Zhou, Xiaofan Zhou*, Lianhui Zhang* (2022). OhrR is a central transcriptional regulator of virulence in Dickeya zeae. Mol Plant Pathol. 2022;23:45–59. DOI: 10.1111/mpp.13141PDF
Yuwei Liang#, Fan Li#, Qiang Gao#, Chunlian Jin, Liqing Dong, Qi Wang, Min Xu, Fuhui Sun, Bo Bi, Peng Zhao, Shenchong Li, Jiwei Ruan, Xiaofan Zhou*, Liangsheng Zhang* and Jihua Wang* (2022). The genome of Eustoma grandiflorum reveals the whole‐genome triplication event. Plant Biotechnology Journal (2022) 20, pp. 1856–1858 doi: 10.1111/pbi.13899PDF
Peng Yang, Hai-Ying Zhao, Jie-Shu Wei, Yuan-Yuan Zhao, Xiao-Jing Lin, Jing Su, Fang-Ping Li, Meng Li, Dong-Ming Ma, Xu-Kai Tan, Hui-Lin Liang, Ye-Wen Sun, Ruo-Ting Zhan, Guo-Zhen He*, Xiao-Fan Zhou* and Jin-Fen Yang* (2022). Chromosome-level genome assembly and functional characterization of terpene synthases provide new insights into the volatile terpenoid biosynthesis of Wurfbainia villosa. The Plant Journal (2022) 112, 630–645 doi: 10.1111/tpj.15968PDF
Xiaoqing Wang, Chuhao Li, Shaohua Huang, Huagui Gao, Yonglin Li, Xuemei Chen, Liangzhou Huang, Jianhua Luo, LianHui Zhang* and Xiaofan Zhou* (2024). Pathogenic and Comparative Genomic Analysis of Ralstonia pseudosolanacearum Isolated from Casuarina. Plant Disease 2024 108:2809-2819 doi.org/10.1094/PDIS-01-24-0118-REPDF
Siliang Zuo, Linghui Xu, Huiyan Zhang, Meiqian Jiang, Sifeng Wu, Lian-Hui Zhang, Xiaofan Zhou* and Junxia Wan* (2024). FlgI Is a Sec-Dependent Effector of Candidatus Liberibacter asiaticus That Can Be Blocked by Small Molecules Identified Using a Yeast Screen. Plants 2024, 13, 318. doi.org/10.3390/plants13020318PDF
Bo Feng#, Yonglin Li#, Biyang Xu#, Hongyue Liu, Jacob L Steenwyk, Kyle T Davi, Xiaolin Tian, Carla Gonçalves, Dana A Opulente, Abigail L LaBella, Marie-Claire Harrison, John F Wolters, Shengyuan Shao, Zhaohao Chen, Kaitlin J Fisher, Marizeth Groenewald, Chris Todd Hittinger, Xing-Xing Shen, Shengying Li, Antonis Rokas*, Xiaofan Zhou* and Yuanning Li* (2025). Unique trajectory of gene family-evolution from genomic analysis of nearly all known species in an ancient yeast lineage. Mol Syst Biol(2025)21: 1066 - 1089 doi.org/10.1038/s44320-025-00118-0PDF
Yuwei Liang#, Qiang Gao#, Fan Li#, Yunpeng Du#, Jian Wu#, Wenqiang Pan, Shaokun Wang, Xiuhai Zhang, Mingfang Zhang, Xiaoming Song, Linlin Zhong, Fan Zhang, Yan Li, Zhiwei Wang, Danqing Li, Qing Duan, Shenchong Li, Chunlian Jin, Peihua Zhang, Yang Gu, Zhong-Hua Chen, Klaus F. X. Mayer*, Xiaofan Zhou*, Jihua Wang* & Liangsheng Zhang* (2025). The giant genome of lily provides insights into the hybridization of cultivated lilies. Nat Commun 16, 45 (2025). doi.org/10.1038/s41467-024-55545-8PDF
Xiaohui Wen#, Yuwei Liang#, Hongyan Shan#, Xiaojun Chang#, Xiaoming Song#, Shaoqin Shen, Yanhong Fu, Dan Chen, Fei Chen, Yueqing Li, Qian Guan, Qiang Gao, Qi Wang, Yonglin Li, Zhengjia Wang, Hongzhi Kong, Huan Liu*, Xiang Gao*, Xiaofan Zhou*, Chris Thorogood* and Liangsheng Zhang* (2025). The genome of giant waterlily provides insights into the origin of angiosperms, leaf gigantism, and stamen function innovation. Plant Commun. doi.org/10.1016/j.xplc.2025.101342PDF
Xiaoqing Wang#, Hongyu Shi#, Xiaoyan Wu, Xuemei Chen, Shaobo Liu, Qinglin Yu, Lian-Hui Zhang* and Xiaofan Zhou* (2025). Microbial diversity in coastal Casuarina equisetifolia forest and its potential in counteracting bacterial wilt infections. Pest Manag Sci 2025 DOI 10.1002/ps.8822PDF
Danhua Jiang, Changsong Yin, Aiping Yu, Xiaofan Zhou, Wanqi Liang, Zheng Yuan, Yun Xu, Qingbo Yu, Tieqiao Wen, Dabing Zhang* (2006). Duplication and expression analysis of multicopy miRNA gene family members in Arabidopsis and rice. Cell Res 16, 507–518 (2006). doi.org/10.1038/sj.cr.7310062PDF
Sree V Chintapalli#, Gaurav Bhardwaj#, Jagadish Babu, Loukia Hadjiyianni, Yoojin Hong, George K Todd, Casey A Boosalis, Zhenhai Zhang, Xiaofan Zhou, Hong Ma, Andriy Anishkin, Damian B van Rossum* and Randen L Patterson* (2013). Reevaluation of the evolutionary events within recA-RAD51 phylogeny. BMC Genomics 14, 240 (2013). doi.org/10.1186/1471-2164-14-240PDF
David C. Rinkera, R. Jason Pitts, Xiaofan Zhou, Eunho Suh, Antonis Rokas, and Laurence J. Zwiebel* (2013). Blood meal-induced changes to antennal transcriptome profiles reveal shifts in odor sensitivities in the malaria vector mosquito Anopheles gambiae. Natl. Acad. Sci. U.S.A. 110 (20) 8260-8265, doi.org/10.1073/pnas.1302562110PDF
Daniel E. Neafsey#*, Robert M. Waterhouse#, Mohammad R. Abai, Sergey S. Aganezov, Max A. Alekseyev, James E. Allen, James Amon, Bruno Arcà, Peter Arensburger, Gleb Artemov, Lauren A. Assour, Hamidreza Basseri, Aaron Berlin, Bruce W. Birren, Stephanie A. Blandin, Andrew I. Brockman, Thomas R. Burkot, Austin Burt, Clara S. Chan, Cedric Chauve, Joanna C. Chiu, Mikkel Christensen, Carlo Costantini, Victoria L. M. Davidson, Elena Deligianni, Tania Dottorini, Vicky Dritsou, Stacey B. Gabriel, Wamdaogo M. Guelbeogo, Andrew B. Hall, Mira V. Han, Thaung Hlaing, Daniel S. T. Hughes, Adam M. Jenkins, Xiaofang Jiang, Irwin Jungreis, Evdoxia G. Kakani, Maryam Kamali, Petri Kemppainen, Ryan C. Kennedy, Ioannis K. Kirmitzoglou, Lizette L. Koekemoer, Njoroge Laban, Nicholas Langridge, Mara K. N. Lawniczak, Manolis Lirakis, Neil F. Lobo, Ernesto Lowy, Robert M. MacCallum, Chunhong Mao, Gareth Maslen, Charles Mbogo, Jenny McCarthy, Kristin Michel, Sara N. Mitchell, Wendy Moore, Katherine A. Murphy, Anastasia N. Naumenko, Tony Nolan, Eva M. Novoa, Samantha O’Loughlin, Chioma Oringanje, Mohammad A. Oshaghi, Nazzy Pakpour, Philippos A. Papathanos, Ashley N. Peery, Michael Povelones, Anil Prakash, David P. Price, Ashok Rajaraman, Lisa J. Reimer, David C. Rinker, Antonis Rokas, Tanya L. Russell, N’Fale Sagnon, Maria V. Sharakhova, Terrance Shea, Felipe A. Simão, Frederic Simard, Michel A. Slotman, Pradya Somboon, Vladimir Stegniy, Claudio J. Struchiner, Gregg W. C. Thomas, Marta Tojo, Pantelis Topalis, José M. C. Tubio, Maria F. Unger, John Vontas, Catherine Walton, Craig S. Wilding, Judith H. Willis, Yi-Chieh Wu, Guiyun Yan, Evgeny M. Zdobnov, Xiaofan Zhou, Flaminia Catteruccia, George K. Christophides, Frank H. Collins, Robert S. Cornman, Andrea Crisanti, Martin J. Donnelly, Scott J. Emrich, Michael C. Fontaine, William Gelbart, Matthew W. Hahn, Immo A. Hansen, Paul I. Howell, Fotis C. Kafatos, Manolis Kellis, Daniel Lawson, Christos Louis, Shirley Luckhart, Marc A. T. Muskavitch, José M. Ribeiro, Michael A. Riehle, Igor V. Sharakhov, Zhijian Tu, Laurence J. Zwiebel, and Nora J. Besansky* (2015). Highly evolvable malaria vectors - the genomes of 16 Anopheles mosquitoes. Science347,1258522(2015).DOI:10.1126/science.1258522PDF
Yue Zhao, Qi Liu, Pankaj Acharya, Kristy R. Stengel, Quanhu Sheng, Xiaofan Zhou, Hojoong Kwak, Melissa A. Fischer, James E. Bradner, Stephen A. Strickland, Sanjay R. Mohan, Michael R. Savona, Bryan J. Venters, Ming-Ming Zhou, John T. Lis, and Scott W. Hiebert* (2016). High-Resolution Mapping of RNA Polymerases Identifies Mechanisms of Sensitivity and Resistance to BET Inhibitors in t(8;21) AML. Cell Reports 16, 2003–2016, August 16, 2016 doi.org/10.1016/j.celrep.2016.07.032PDF
Hua Yan, Comzit Opachaloemphan, Giacomo Mancini, Huan Yang, Matthew Gallitto, Jakub Mlejnek, Alexandra Leibholz, Kevin Haight, Majid Ghaninia, Lucy Huo, Michael Perry, Jesse Slone, Xiaofan Zhou, Maria Traficante, Clint A. Penick, Kelly Dolezal, Kaustubh Gokhale, Kelsey Stevens, Ingrid Fetter-Pruneda, Roberto Bonasio, Laurence J. Zwiebel, Shelley L. Berger*, Jürgen Liebig*, Danny Reinberg* and Claude Desplan* (2017). An Engineered orco Mutation Produces Aberrant Social Behavior and Defective Neural Development in Ants. Cell Volume 170, Issue 4p736-747.e9August 10, 2017 DOI: 10.1016/j.cell.2017.06.051PDF
Sha Jin, Xiaofan Zhou, Feng Gu, Guohua Zhong, and Xin Yi* (2017). Olfactory plasticity variation in the expression of chemosensory receptors in Bactrocera dorsalis in different physiological states. Front. Physiol. 8:672. doi: 10.3389/fphys.2017.00672PDF
Gregory M. Pask, Jesse D. Slone, Jocelyn G. Millar, Prithwiraj Das, Jardel A. Moreira, Xiaofan Zhou, Jan Bello, Shelley L. Berger, Roberto Bonasio, Claude Desplan, Danny Reinberg, Jürgen Liebig, Laurence J. Zwiebel & Anandasankar Ray* (2017). Specialized odorant receptors in social insects that detect cuticular hydrocarbon cues and candidate pheromones. Nature Communications volume 8, Article number: 297 (2017) DOI: 10.1038/s41467-017-00099-1PDF
Liyuan Zhao, Xiaofan Zhou, Antonis Rokas & Roger D. Con* (2017). Functional variants of the melanocortin-4 receptor associated with the Odontoceti and Mysticeti suborders of cetaceans. SCIENTIFIC RepoRts 7: 5684 DOI:10.1038/s41598-017-05962-1PDF
Carla Gonc ̧alves, Jennifer H Wisecaver, Jacek Kominek, Madalena Salema Oom, Maria Jose ́ Leandro, Xing-Xing Shen, Dana A Opulente, Xiaofan Zhou, David Peris, Cletus P Kurtzman, Chris Todd Hittinger, Antonis Rokas, Paula Gonc ̧alves* (2018). Evidence for loss and reacquisition of alcoholic fermentation in a fructophilic yeast lineage. eLife 2018;7:e33034. DOI: doi.org/10.7554/eLife.33034PDF
Tadeusz Krassowski#, Aisling Y. Coughlan#, Xing-Xing Shen, Xiaofan Zhou, Jacek Kominek, Dana A. Opulente, Robert Riley, Igor V. Grigoriev, Nikunj Maheshwari, Denis C. Shields, Cletus P. Kurtzman, Chris Todd Hittinger, Antonis Rokas & Kenneth H. Wolfe* (2018). Evolutionary instability of CUG-Leu in the genetic code of budding yeasts. NATURE COMMUNICATIONS (2018) 9:1887 DOI: 10.1038/s41467-018-04374-7PDF
David J. Krausea, Jacek Komineka, Dana A. Opulentea, Xing-Xing Shen, Xiaofan Zhou, Quinn K. Langdon, Jeremy DeVirgilio, Amanda Beth Hulfachor, Cletus P. Kurtzman, Antonis Rokas and Chris Todd Hittinger* (2018). Functional and evolutionary characterization of a secondary metabolite gene cluster in budding yeasts. Proc. Natl. Acad. Sci. U.S.A. 115 (43) 11030-11035 doi.org/10.1073/pnas.1806268115PDF
Jacek Kominek#, Drew T. Doering#, Dana A. Opulente, Xing-Xing Shen, Xiaofan Zhou, Jeremy DeVirgilio, Amanda B. Hulfachor, Marizeth Groenewald, Mcsean A. Mcgee, Steven D. Karlen, Cletus P. Kurtzman, Antonis Rokas, and Chris Todd Hittinger* (2019). Eukaryotic acquisition of a bacterial operon. Cell 176, 1–11 March 7, 2019 doi.org/10.1016/j.cell.2019.01.034PDF
Tadeusz Krassowski, Jacek Kominek, Xing-Xing Shen, Dana A. Opulente, Xiaofan Zhou, Antonis Rokas, Chris Todd Hittinger and Kenneth H. Wolfe* (2019). Multiple reinventions of mating-type switching during budding yeast evolution. Current Biology 29, 1–8 August 5, 2019 doi.org/10.1016/j.cub.2019.06.056PDF
Susu Zhang, Yue Zhao, Tiffany M. Heaster, Melissa A. Fischer, Kristy R. Stengel, Xiaofan Zhou, Haley Ramsey, Ming‐Ming Zhou, Michael R. Savona, Melissa C. Skala, Scott W. Hiebert* (2019). BET inhibitors reduce cell size and induce reversible cell cycle arrest in AML. J Cell Biochem. 2018;1-14. DOI: 10.1002/jcb.280PDF
Jacob L. Steenwyk, Dana A. Opulente, Jacek Kominek, Xing-Xing Shen, Xiaofan Zhou, Abigail L. Labella, Noah P. Bradley, Brandt F. Eichman, Nezˇa Čadezˇ, Diego Libkind, Jeremy DeVirgilio, Amanda Beth Hulfachor, Cletus P. Kurtzman, Chris Todd Hittinger*, Antonis Rokas* (2019). Extensive loss of cell-cycle and DNA repair genes in an ancient lineage of bipolar budding yeasts. PLoS Biol 17(5): e3000255. 10.1371/journal.pbio.3000255PDF
Liangsheng Zhang#*, Fei Chen#, Xingtan Zhang#, Zhen Li#, Yiyong Zhao#, Rolf Lohaus#, Xiaojun Chang#, Wei Dong, Simon Y. W. Ho, Xing Liu, Aixia Song, Junhao Chen, Wenlei Guo, Zhengjia Wang, Yingyu Zhuang, Haifeng Wang, Xuequn Chen, Juan Hu, Yanhui Liu, Yuan Qin, Kai Wang, Shanshan Dong, Yang Liu, Shouzhou Zhang, Xianxian Yu, Qian Wu, Liangsheng Wang, Xueqing Yan, Yuannian Jiao, Hongzhi Kong, Xiaofan Zhou, Cuiwei Yu, Yuchu Chen, Fan Li, Jihua Wang, Wei Chen, Xinlu Chen, Qidong Jia, Chi Zhang, Yifan Jiang, Wanbo Zhang, Guanhua Liu, Jianyu Fu, Feng Chen, Hong Ma, Yves Van de Peer & Haibao Tang (2020). The water lily genome and the early evolution of flowering plants. Nature 577, 79–84 (2020). doi.org/10.1038/s41586-019-1852-5PDF
Lingxiao Yang, Danyan Su1, Xin Chang, Charles S.P. Foster, Linhua Sun, Chien-Hsun Huang, Xiaofan Zhou, Liping Zeng, Hong Ma and Bojian Zhong* (2020). Phylogenomic insights into deep phylogeny of Angiosperms based on broad nuclear gene sampling. Plant Communications 1, 100027, March 2020 doi.org/10.1016/j.xplc.2020.100027PDF
Xing-Xing Shen*, Jacob L. Steenwyk, Abigail L. LaBella, Dana A. Opulente, Xiaofan Zhou, Jacek Kominek, Yuanning Li, Marizeth Groenewald, Chris T. Hittinger, Antonis Rokas* (2020). Genome-scale phylogeny and contrasting modes of genome evolution in the fungal phylum Ascomycota. Sci. Adv.6,eabd0079(2020). DOI:10.1126/sciadv.abd0079PDF
Kai Wang#, Xia Li#, Chunxi Yang, Shihao Song, Chaoyu Cui, Xiaofan Zhou, Yinyue Deng* (2021). A LysR Family Transcriptional Regulator Modulates Burkholderia cenocepacia Biofilm Formation and Protease Production. Appl Environ Microbiol 87:e00202-21. doi.org/10.1128/AEM.00202-21PDF
Wen Li, Peng Li, Xiaofan Zhou, Junjian Situ, Yiming Lin, Jiahui Qiu, Yuling Yuan, Pinggen Xi, Zide Jiang* and Guanghui Kong* (2021). A Cytochrome B 5-Like HemeSteroid Binding Domain Protein, PlCB5L1, Regulates Mycelial Growth, Pathogenicity and Oxidative Stress Tolerance in Peronophythora litchii. Front. Plant Sci. 12:783438. doi: 10.3389/fpls.2021.783438PDF
Max A. B. Haase#, Jacek Kominek#, Dana A. Opulente, Xing-Xing Shen, Abigail L. LaBella, Xiaofan Zhou, Jeremy DeVirgilio, Amanda Beth Hulfachor, Cletus P. Kurtzman, Antonis Rokas* and Chris Todd Hittinger* (2021). Repeated horizontal gene transfer of GALactose metabolism genes violates Dollo's law of irreversible loss. Genetics, Volume 217, Issue 2, February 2021, iyaa012 DOI: 10.1093/genetics/iyaa012PDF
Danyan Su#, Lingxiao Yang#, Xuan Shi, Xiaoya Ma, Xiaofan Zhou, S. Blair Hedges, and Bojian Zhong* (2021). Large-scale phylogenomic analyses reveal the monophyly of bryophytes and Neoproterozoic origin of land plants. Mol. Biol. Evol. 38(8):3332–3344 doi:10.1093/molbev/msab106PDF
Jacob L. Steenwyk, Matthew E. Mead, Patrícia Alves de Castro, Clara Valero, André Damasio, Renato A. C. dos Santos, Abigail L. Labella, Yuanning Li, Sonja L. Knowles, Huzefa A. Raja, Nicholas H. Oberlies, Xiaofan Zhou, Oliver A. Cornely, Frieder Fuchs, Philipp Koehler*, Gustavo H. Goldman*, Antonis Rokas* (2021). Genomic and Phenotypic Analysis of COVID-19-Associated Pulmonary Aspergillosis Isolates of Aspergillus fumigatu. Microbiol Spectr 9:e00010-21. 10.1128/Spectrum.00010-21PDF
Jinli Yan#, Peng Li#, Xiaoqing Wang, Minya Zhu, Hongyu Shi, Guohui Yu, Xuemei Chen, Huishan Wang, Xiaofan Zhou, Lisheng Liao*, Lianhui Zhang* (2022). RasI-R Quorum Sensing System Controls the Virulence of Ralstonia solanacearum Strain EP1. Appl Environ Microbiol 88:e00325-22. doi.org/10.1128/aem.00325-22PDF
Yuanning Li*, Hongyue Liu, Jacob L. Steenwyk, Abigail L. LaBella, Marie-Claire Harrison, Marizeth Groenewald, Xiaofan Zhou, Xing-Xing Shen, Tao Zhao, Chris Todd Hittinger and Antonis Rokas* (2022). Contrasting modes of macro and microsynteny evolution in a eukaryotic subphylum. Current Biology 32, 1—9 December 19, 2022 doi.org/10.1016/j.cub.2022.10.025PDF
Shanshan Chen#, Ming Hu#, Anqun Hu, Yang Xue, Si Wang, Fan Liu, Chuhao Li, Xiaofan Zhou, Jianuan Zhou* (2022). The integration host factor regulates multiple virulence pathways in bacterial pathogen Dickeya zeae MS2. Mol Plant Pathol. 2022;23:1487–1507. DOI: 10.1111/mpp.13244PDF
Hua Yan#, Comzit Opachaloemphan#, Francisco Carmona-Aldana#, Giacomo Mancini, Jakub Mlejnek, Nicolas Descostes, Bogdan Sieriebriennikov, Alexandra Leibholz, Xiaofan Zhou, Long Ding, Maria Traficante, Claude Desplan*, Danny Reinberg* (2022). Insulin signaling in the long-lived reproductive caste of ants. Science377,1092-1099(2022). DOI:10.1126/science.abm8767PDF
Danqing Li#, Han‑Yang Lin#, Xiuyun Wang#, Bo Bi, Yuan Gao, Lingmei Shao, Runlong Zhang, Yuwei Liang, Yiping Xia, Yun‑Peng Zhao, Xiaofan Zhou and Liangsheng Zhang* (2023). Genome and whole-genome resequencing of Cinnamomum camphora elucidate its dominance in subtropical urban landscapes. BMC Biology (2023) 21:192 doi.org/10.1186/s12915-023-01692-1PDF
M. Groenewald*, C.T. Hittinger, K. Bensch1, D.A. Opulente, X.-X. Shen, Y. Li5, 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 105: 1–22. doi: 10.3114/sim.2023.105.01PDF
Na Zhang#, Xinyang Li#, Liangping Ming, Wenda Sun, Xiaofang Xie, Cailing Zhi, Xiaofan Zhou, Yanhua Wen, Zhibin Liang* and Yizhen Deng* (2024). Comparative Genomics and Pathogenicity Analysis of Three Fungal Isolates Causing Barnyard Grass Blast. J. Fungi 2024, 10, 868.doi.org/10.3390/jof10120868PDF
Liang Sun, Kyle T. David, John F. Wolters, Steven D. Karlen, Carla Gonçalves, Dana A. Opulente, Abigail Leavitt LaBella, Marizeth Groenewald, Xiaofan Zhou, Xing-Xing Shen, Antonis Rokas and Chris Todd Hittinger* (2024). Functional and evolutionary integration of a fungal gene with a bacterial operon. Mol. Biol. Evol. 41(4):msae045 doi.org/10.1093/molbev/msae045PDF
Jacob L. Steenwyk, Sonja Knowles, Rafael W. Bastos, Charu Balamurugan, David Rinker, Matthew E. Mead, Christopher D. Roberts, Huzefa A. Raja, Yuanning Li, Ana Cristina Colabardini, Patrícia Alves de Castro, Thaila Fernanda dos Reis, Adiyantara Gumilang, María Almagro-Molto, Alexandre Alanio, Dea Garcia-Hermoso, Endrews Delbaje, Laís Pontes, Camila Figueiredo Pinzan, Angélica Zaninelli Schreiber, David Canóvas, Rafael Sanchez Luperini, Katrien Lagrou, Egídio Torrado, Fernando Rodrigues, Nicholas H. Oberlies, Xiaofan Zhou, Gustavo H. Goldman* & Antonis Rokas* (2024). Evolutionary origin and population diversity of a cryptic hybrid pathogen. Nat Commun 15, 8412 (2024). doi.org/10.1038/s41467-024-52639-1PDF
Carla Gonçalves, Marie-Claire Harrison, Jacob L. Steenwyk, Dana A. Opulente, Abigail L. LaBella, John F. Wolters, Xiaofan Zhou, Xing-Xing Shen, Marizeth Groenewald, Chris Todd Hittinger, Antonis Rokas* (2024). Diverse signatures of convergent evolution in cactus-associated yeasts. PLoS Biol 22(9):e3002832. doi.org/10.1371/journal.pbio.3002832PDF
Marie- Claire Harrison, Emily J. Ubbelohde, Abigail L. LaBellaa, Dana A. Opulenteb, John F. Wolters, Xiaofan Zhou, Xing-Xing Shen, Marizeth Groenewald, Chris Todd Hittinger* and Antonis Rokas* (2024). Machine learning enables identification of an alternative yeast galactose utilization pathway. Proc. Natl. Acad. Sci. U.S.A. 121 (18) e2315314121 doi.org/10.1073/pnas.2315314121PDF
Marie Claire Harrison, Emily J. Ubbelohde, Abigail L. LaBella, Dana A. Opulente, John F. Wolters, Xiaofan Zhou, Xing Xing Shen, Marizeth Groenewald, Chris Todd Hittinger, and Antonis Rokas* (2024). Saccharomycotina yeasts defy long-standing macroecological patterns. Proc. Natl. Acad. Sci. U.S.A. 121 (10) e2316031121 doi.org/10.1073/pnas.2316031121PDF
Dana A. Opulente#, Abigail Leavitt LaBella#, Marie-Claire Harrison, John F. Wolters, Chao Liu, Yonglin Li, Jacek Kominek, Jacob L. Steenwyk, Hayley R. Stoneman, Jenna VanDenAvond, Caroline R. Miller, Quinn K. Langdon, Margarida Silva, Carla Gonçalves, Emily J. Ubbelohde, Yuanning Li, Kelly V. Buh, Martin Jarzyna, Max A. B. Haase, Carlos A. Rosa, Neža C ˇadež, Diego Libkind, Jeremy H. DeVirgilio, Amanda Beth Hulfachor, Cletus P. Kurtzman, José Paulo Sampaio, Paula Gonçalves, Xiaofan Zhou, Xingxing Shen, Marizeth Groenewald, Antonis Rokas*, Chris Todd Hittinger* (2024). Genomic factors shape carbon and nitrogen metabolic niche breadth across Saccharomycotina yeasts. Science 384, eadj4503 (2024). DOI:10.1126/science.adj4503PDF
Marie‐Claire Harrison, Dana A. Opulente, John F. Wolters, Xing‐Xing Shen, Xiaofan Zhou, Marizeth Groenewald, Chris Todd Hittinger, Antonis Rokas, Abigail Leavitt LaBella* (2024). Exploring Saccharomycotina Yeast Ecology Through an Ecological Ontology Framework. Yeast, 2024; 41:615–628 doi.org/10.1002/yea.3981PDF
Wen-Juan Chen, Xiaofang Luo, Xuanrui Zhang, Kalpana Bhatt, Shao-Fang Chen, Mohamed A. Ghorab, Xiaofan Zhou and Yaohua Huang* (2025). Elucidating the kinetics and mechanisms of tetramethrin biodegradation by the fungal strain Neocosmospora sp. AF3. Microbial Cell Factories (2025) 24:124 doi.org/10.1186/s12934-025-02747-4PDF