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, Laurence J Zwiebel* (2013). Antennal transcriptome profiles of anopheline mosquitoes reveal human host olfactory specialization in Anopheles gambiae. BMC Genomics, 14:749. 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, 6(10):2883-96. DOI: 10.1093/gbe/evu231.PDF
Xiaofan Zhou, Antonis Rokas, Shelley L. Berger, Jürgen Liebig, Anandasankar Ray, 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*, Antonis Rokas* (2016). In Silico Whole Genome Sequencer and Analyzer (iWGS). G3, 6(11):3655-3662. DOI: 10.1534/g3.116.034249PDF
Xin Yi#, Jiangwei Qi#, Xiaofan Zhou#, Meiying Hu, Guohua Zhong* (2017). Differential expression of chemosensory-protein genes in midguts in response to diet of Spodoptera litura. Sci Rep, 7(1):296. 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*, Antonis Rokas* (2018). Tempo and Mode of Genome Evolution in the Budding Yeast Subphylum. Cell, 175(6):1533-1545.e20. DOI: 10.1016/j.cell.2018.10.023PDF
Xiaofan Zhou, Xing-Xing Shen, Chris Todd Hittinger, 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, 20(5):1072. DOI:10.3390/ijms20051072PDF
Xiaofan Zhou, Sarah Lutteropp, Lucas Czech, Alexandros Stamatakis, Moritz von Looz, Antonis Rokas* (2020). Quartet-Based Computations of Internode Certainty Provide Robust Measures of Phylogenetic Incongruence. Syst Biol, 69(2):308–324. DOI:10.1093/sysbio/syz058PDF
Yanqiu He#, Xiaofan Zhou#, Jieling Li, Huaping Li, Yunfeng Li*, Yanfang Nie* (2021). In Vitro Secretome Analysis Suggests Differential Pathogenic Mechanisms between Fusarium oxysporum f. sp. cubense Race 1 and Race 4. Biomolecules, 11(9):1353. DOI: 10.3390/biom11091353PDF
Ming Hu#, Chuhao Li#, Xiaofan Zhou#, Yang Xue, Si Wang, Anqun Hu, Shanshan Chen, Xiuwen Mo, 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
Pankaj Bhatt#, Xiaofan Zhou#, Yaohua Huang, Wenping Zhang, Shaohua Chen* (2021). Characterization of the role of esterases in the biodegradation of organophosphate, carbamate, and pyrethroid pesticides. J Hazard Mater, 411:125026. DOI: 10.1016/j.jhazmat.2020.125026PDF
Tiantian Yan#, Xiaofan Zhou#, Jieling Li#, Guanjun Li, Yali Zhao, Haojie Wang, Huaping Li*, Yanfang Nie*, Yunfeng Li* (2022). FoCupin1, a Cupin_1 domain-containing protein, is necessary for the virulence of Fusarium oxysporum f. sp. cubense tropical race 4. Front Microbiol, 13:1001540. DOI: 10.3389/fmicb.2022.1001540PDF
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. Fundamental Res, 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. DOI: 10.1093/sysbio/sya031PDF
Ren Ren, Yazhou Sun, Yue Zhao, David Geiser, Hong Ma*, 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*, Guohua Zhong* (2019). Characterizing potential repelling volatiles for “push-pull” strategy against stem borer：a case study in Chilo auricilius. BMC Genomics, 20(1):751. DOI: 10.1186/s12864-019-6112-4PDF
Yue Zhong#, Meixin Yan#, Jinyan Jiang#, Zhihan Zhang, Junjun Huang, Lianhui Zhang, Yinyue Deng*, Xiaofan Zhou*, Fei He* (2019). Mycophenolic Acid as a Promising Fungal Dimorphism Inhibitor to Control Sugar Cane Disease Caused by Sporisorium scitamineum. J Agric Food Chem, 67(1):112-119. DOI: 10.1021/acs.jafc.8b04893PDF
Li Zheng, Jun-jian Situ, Qing-feng Zhu, Ping-gen Xia, Yin Zheng, Hong-xia Liu, Xiaofan Zhou*, Zide Jiang* (2019). Identification of volatile organic compounds for the biocontrol of postharvest litchi fruit pathogen Peronophythora litchii. Postharvest Biol Technol, 155:37-46. DOI: 10.1016/j.postharvbio.2019.05.009PDF
Tian Ye#, Tian Zhou#, Xudan Xu#, Wenping Zhang, Xinghui Fan, Sandhya Mishra, Lianhui Zhang, Xiaofan Zhou*, 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, 21(18):6729. DOI :10.3390/ijms21186729 www.mdpi.com/journal/ijmsPDF
Xudan Xu#, Tian Ye#, Wenping Zhang, Tian Zhou, Xiaofan Zhou*, Weijun Dai*, 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, 22(18):9862. DOI: 10.3390/ijms22189862PDF
Ming Hu, Chuhao Li, Yang Xue, Anqun Hu, Shanshan Chen, Yufan Chen, Guangtao Lu, Xiaofan Zhou*, Jianuan Zhou* (2021). Isolation, characterization, and genomic investigation of a phytopathogenic strain of Stenotrophomonas maltophilia. Phytopathology, 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*, 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, 13:821895. 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*, Yunfeng Li* (2022). A novel elicitor MoVcpo is necessary for the virulence of Magnaporthe oryzae and triggers rice defense responses. Front Plant Sci, 13:1018616. 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, Xiaofan Zhou* (2022). Isolation and Genome Analysis of Pectobacterium colocasium sp. nov. and Pectobacterium aroidearum, Two New Pathogens of Taro. Front Plant Sci, 13:852750. DOI: 10.3389/fpls.2022.852750PDF
Chenxing Tan, Chuhao Li, Ming Hu , Anqun Hu, Yang Xue, Xiaofan Zhou*, Jianuan Zhou* (2022). Comparative Pathogenomic Analysis of Two Banana Pathogenic Dickeya Strains Isolated from China and the Philippines. Int J Mol Sci, 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, 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, 23(1):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*, Jihua Wang* (2022). The genome of Eustoma grandiflorum reveals the whole‐genome triplication event. Plant Biotechnol J, 20(10):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*, 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. Plant J, 112(3):630-645. DOI: 10.1111/tpj.15968PDF
Siliang Zuo, Linghui Xu, Huiyan Zhang, Meiqian Jiang, Sifeng Wu, Lian-Hui Zhang, Xiaofan Zhou*, Junxia Wang* (2024). FlgI Is a Sec-Dependent Effector of Candidatus Liberibacter asiaticus That Can Be Blocked by Small Molecules Identified Using a Yeast Screen. Plants, 13(2):318. DOI: 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*, 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, 21(8):1066-1089. DOI: 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(1):45. DOI: 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*, Liangsheng Zhang* (2025). The genome of giant waterlily provides insights into the origin of angiosperms, leaf gigantism, and stamen function innovation. Plant Commun, 6(6):101342. DOI: 10.1016/j.xplc.2025.101342PDF
Xiaoqing Wang#, Hongyu Shi#, Xiaoyan Wu, Xuemei Chen, Shaobo Liu, Qinglin Yu, Lian-Hui Zhang*, Xiaofan Zhou* (2025). Microbial diversity in coastal Casuarina equisetifolia forest and its potential in counteracting bacterial wilt infections. Pest Manag Sci, 81(8):4621-4634. DOI: 10.1002/ps.8822PDF
Alexandra Surcel, Xiaofan Zhou, Li Quan, Hong Ma* (2008). Long-term maintenance of stable copy number in the eukaryotic SMC family - origin of a vertebrate meiotic SMC1 and fate of recent segmental duplicates. J Syst Evol, 46(3):405–423. DOI: 10.3724/SP.J.1002.2008.08031PDF
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*, Randen L Patterson* (2013). Reevaluation of the evolutionary events within recA-RAD51 phylogeny. BMC Genomics, 14:240. DOI: 10.1186/1471-2164-14-240PDF
David C Rinkera, R Jason Pitts, Xiaofan Zhou, Eunho Suh, Antonis Rokas, Laurence J Zwiebel* (2013). Blood meal-induced changes to antennal transcriptome profiles reveal shifts in odor sensitivities in the malaria vector mosquito Anopheles gambiae. Proc Natl Acad Sci U S A, 110(20):8260-8265. DOI: 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, Nora J Besansky* (2015). Highly evolvable malaria vectors: the genomes of 16 Anopheles mosquitoes. Science, 347(6217):1258522. 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, 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 Rep, 16(7):2003-2016. DOI: 10.1016/j.celrep.2016.07.032PDF
Xing-Xing Shen, Xiaofan Zhou, Jacek Kominek, Cletus P. Kurtzman*, Chris Todd Hittinger*, Antonis Rokas* (2016). Reconstructing the Backbone of the Saccharomycotina Yeast Phylgoeny Using Genome-Scale Data. G3, 6(12):3927-3939. DOI: 10.1534/g3.116.034744PDF
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*, Claude Desplan* (2017). An Engineered orco Mutation Produces Aberrant Social Behavior and Defective Neural Development in Ants. Cell, 170(4):736-747.e9. DOI: 10.1016/j.cell.2017.06.051PDF
Sha Jin, Xiaofan Zhou, Feng Gu, Guohua Zhong, 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. Nat Commun, 8(1):297. 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. Sci Rep,7(1):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, 7:e33034. DOI: 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. Nat Commun, 9(1):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, 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: 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, Chris Todd Hittinger* (2019). Eukaryotic acquisition of a bacterial operon. Cell, 176(6):1356-1366.e10. DOI: 10.1016/j.cell.2019.01.034PDF
Tadeusz Krassowski, Jacek Kominek, Xing-Xing Shen, Dana A Opulente, Xiaofan Zhou, Antonis Rokas, Chris Todd Hittinger, Kenneth H Wolfe* (2019). Multiple reinventions of mating-type switching during budding yeast evolution. Curr Biol, 29(15):2555-2562.e8. DOI: 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, 120(5):7309-7322. 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. DOI: 10.1371/journal.pbio.3000255PDF
Hua Yan#, Shadi Jafari#, Gregory Pask, Xiaofan Zhou, Danny Reinberg and Claude Desplan* (2020). Evolution, developmental expression and function of odorant receptors in insects. J Exp Biol, 223:jeb208215. DOI: 10.1242/jeb.208215PDF
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(7788):79-84. DOI: 10.1038/s41586-019-1852-5PDF
Lingxiao Yang, Danyan Su1, Xin Chang, Charles SP Foster, Linhua Sun, Chien-Hsun Huang, Xiaofan Zhou, Liping Zeng, Hong Ma, Bojian Zhong* (2020). Phylogenomic insights into deep phylogeny of Angiosperms based on broad nuclear gene sampling. Plant Commun, 1(2):100027. DOI: 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(45):eabd0079. 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(12):e0020221. DOI: 10.1128/AEM.00202-21PDF
Wen Li, Peng Li, Xiaofan Zhou, Junjian Situ, Yiming Lin, Jiahui Qiu, Yuling Yuan, Pinggen Xi, Zide Jiang*, 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*, Chris Todd Hittinger* (2021). Repeated horizontal gene transfer of GALactose metabolism genes violates Dollo's law of irreversible loss. Genetics, 217(2):iyaa012. DOI: 10.1093/genetics/iyaa012PDF
Danyan Su#, Lingxiao Yang#, Xuan Shi, Xiaoya Ma, Xiaofan Zhou, S. Blair Hedges, 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 fumigatus. Microbiol Spectr, 9(1):e0001021. DOI: 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(15):e0032522. DOI: 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, Antonis Rokas* (2022). Contrasting modes of macro and microsynteny evolution in a eukaryotic subphylum. Curr Biol, 32(24):5335-5343.e4. DOI: 10.1016/j.cub.2022.10.025PDF
Peiyi Ye#, Xia Li#, Binbin Cui#, Shihao Song#, Fangfang Shen, Xiayu Chen, Gerun Wang, Xiaofan Zhou, Yinyue Deng* (2022). Proline utilization A controls bacterial pathogenicity by sensing its substrate and cofactors. Commun Biol, 5(1):496. DOI: 10.1038/s42003-022-03451-4PDF
Jinli Yan, Nuoqiao Lin, Xiaoqing Wang, Xuemei Chen, Huishan Wang, Qiqi Lin, Xiaofan Zhou, Lianhui Zhang*, Lisheng Liao* (2022). Markerless gene deletion in Ralstonia solanacearum based on its natural transformation competence. Front Microbiol, 13:977580. DOI: 10.3389/fmicb.2022.977580PDF
Mingfa Lv#, Sixuan Ye#, Ming Hu, Yang Xue, Zhibin Liang, Xiaofan Zhou, Lianhui Zhang*, Jianuan Zhou* (2022). Two-component system ArcBA modulates cell motility and biofilm formation in Dickeya oryzae. Front Plant Sci, 13:1033192. DOI: 10.3389/fpls.2022.1033192PDF
Yu Shi, Xiaobei Yang, Xiaoxin Ye, Jiaying Feng, Tianfang Cheng, Xiaofan Zhou, Ding Xiang Liu, Linghui Xu*, Junxia Wang* (2022). The Methyltransferase HemK Regulates the Virulence and Nutrient Utilization of the Phytopathogenic Bacterium Xanthomonas citri subsp. citri. Int J Mol Sci, 23(7):3931. DOI: 10.3390/ijms23073931PDF
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, 23(10):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. Science, 377(6610):1092-1099. 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, Liangsheng Zhang* (2023). Genome and whole-genome resequencing of Cinnamomum camphora elucidate its dominance in subtropical urban landscapes. BMC Biol, 21(1):192. DOI: 10.1186/s12915-023-01692-1PDF
Junjian Situ#*, Xinning Zhang#, Xiaofan Zhou, Zijing Zhang, Pinggen Xi, Guanghui Kong, Zide Jiang* (2023). The ankyrin repeat-containing protein PlANK1 mediates mycelial growth, oospore development, and virulence in Peronophythora litchii.Phytopathol Res, 5:54. DOI: 10.1186/s42483-023-00211-yPDF
Danlu Han, Wenliang Li, Zhuangwei Hou, Chufang Lin, Yun Xie, Xiaofan Zhou, Yuan Gao, Junwen Huang, Jianbin Lai, Li Wang, Liangsheng Zhang*, Chengwei Yang* (2023). The chromosome-scale assembly of the Salvia rosmarinus genome provides insight into carnosic acid biosynthesis. Plant J, 113(4):819-832. DOI: 10.1111/tpj.16087PDF
Peng Li, Wen Li, Xiaofan Zhou, Junjian Situ, Lizhu Xie, Pinggen Xi, Bo Yang, Guanghui Kong* and Zide Jiang* (2023). Peronophythora litchii RXLR effector P. litchii avirulence homolog 202 destabilizes a host ethylene biosynthesis enzyme. Plant Physiol, 193(1):756-774. DOI: 10.1093/plphys/kiad311PDF
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Bryan Zavala*, Lauren Dineen, Kaitlin J. Fisher, Dana A. Opulente, Marie-Claire Harrison, John F. Wolters, Xing-Xing Shen, Xiaofan Zhou, Marizeth Groenewald, Chris Todd Hittinger, Antonis Rokas, Abigail Leavitt LaBella* (2024). Genomic factors shaping codon usage across the Saccharomycotina subphylum. G3, 14(11):jkae207. DOI: 10.1093/g3journal/jkae207PDF
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, 10(12):868. DOI: 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, Chris Todd Hittinger* (2024). Functional and evolutionary integration of a fungal gene with a bacterial operon. Mol Biol Evol, 41(4):msae045. DOI: 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(1):8412. DOI: 10.1038/s41467-024-52639-1PDF
Jingyang Sun#, Yonglin Li#, Li Zheng, Daipeng Chen, Xiaofan Zhou, Peng Li* (2024). The first complete genome of Robbsia andropogonis reveals its arsenal of virulence system causing leaf spot disease of areca palm. Phytopathol Res, 6:51. DOI: 10.1186/s42483-024-00269-2PDF
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: 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*, 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: 10.1073/pnas.2315314121PDF
Kyle T David, Marie-Claire Harrison, Dana A Opulente, Abigail L LaBella, John F Wolters, Xiaofan Zhou, Xing-Xing Shen, Marizeth Groenewald, Matt Pennell, Chris Todd Hittinger, Antonis Rokas* (2024). Saccharomycotina yeasts defy long-standing macroecological patterns. Proc Natl Acad Sci U S A, 121(10):e2316031121. DOI: 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 CˇCadež, Diego Libkind, Jeremy H DeVirgilio, Amanda Beth Hulfachor, Cletus P Kurtzman, José Paulo Sampaio, Paula Gonçalves, Xiaofan Zhou, Xing-Xing Shen, Marizeth Groenewald, Antonis Rokas*, Chris Todd Hittinger* (2024). Genomic factors shape carbon and nitrogen metabolic niche breadth across Saccharomycotina yeasts. Science, 384(6694):eadj4503. 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, 41(10):615-628. DOI: 10.1002/yea.3981PDF
Wenjuan Chen, Xiaofang Luo, Xuanrui Zhang, Kalpana Bhatt, Shaofang Chen, Mohamed A. Ghorab, Xiaofan Zhou, Yaohua Huang* (2025). Elucidating the kinetics and mechanisms of tetramethrin biodegradation by the fungal strain Neocosmospora sp. AF3. Microb Cell Fact, 24(1):124. DOI: 10.1186/s12934-025-02747-4PDF
Yaohua Huang#, Shunkang Zhou#, Wenjuan Chen#, Xiaofan Zhou, Shaofang Chen, Haoran Song, Zhenchen Yan, Sandhya Mishra, Mohamed A. Ghorab, Pankaj Bhatt, Shaohua Chen* (2025). Mechanistic insights into D-cyphenothrin biodegradation by Rhodococcus ruber Y14 and its potential for bioremediation of pyrethroid-polluted environment. Chem Eng J, 506:160030. DOI: 10.1016/j.cej.2025.160030PDF
Carla Gonçalves#, Jacob L Steenwyk#, David C Rinker, Dana A Opulente, Abigail L LaBella, Marie-Claire Harrison, John F Wolters, Xiaofan Zhou, Xing-Xing Shen, Shay Covo, Marizeth Groenewald, Chris Todd Hittinger, Antonis Rokas* (2025). Stable Hypermutators Revealed by the Genomic Landscape of Genes Involved in Genome Stability Among Yeast Species. Mol Biol Evol, 42(11):msaf285. DOI: 10.1093/molbev/msaf285PDF
Kyle T David, Joshua G Schraiber, Johnathan G Crandall, Abigail L Labella, Dana A Opulente, Marie-Claire Harrison, John F Wolters, Xiaofan Zhou, Xing-Xing Shen, Marizeth Groenewald, Chris Todd Hittinger*, Matt Pennell*, Antonis Rokas* (2025). Convergent expansions of keystone gene families drive metabolic innovation in Saccharomycotina yeasts. Proc Natl Acad Sci U S A, 122(23):e2500165122. DOI: 10.1073/pnas.2500165122PDF
Ruyue Zhang, Liming Wang, Shuo Tian, Yang Liu, Yunlan Jiang, Xiaofan Zhou, Ding Yang*, Xingyue Liu*, Yuyu Wang* (2025). Inconsistent performance of multi-type genomic data in phylogenomics of neuropteridan insects, with solutions toward conflicting results. Proc Natl Acad Sci U S A, 122(23):e2500165122. DOI: 10.1111/syen.12684PDF
Max A B Haase*, Luciana Lazar-Stefanita, Lyam Baudry, Aleksandra Wudzinska, Xiaofan Zhou, Antonis Rokas, Chris Todd Hittinger, Boris Pfander, Andrea Musacchio, Jef D Boeke* (2026). Ancient co-option of LTR retrotransposons as yeast centromeres. Nature, 651(8107):1004-1011. DOI: 10.1038/s41586-025-10092-0PDF
Fei Fu#, Xingyu Yu#, Xiaojing Lin#, Jianhao Lin, Yang Xue, Ming Hu, Huilin Chen, Yizhen Deng, Gan Sha, Tong Zhang, Xiaofan Zhou, Xuefeng Qu, Jianuan Zhou* (2026). Comparative genomic analysis of three Enterobacter strains associated with rice leaf wilt disease. Phytopathol Res, 8:2. DOI: 10.1186/s42483-025-00389-3PDF
Xiaoyu Xie#, Yuting Ye#, Yuqing Qi#, Zehao Liu, Yang Xue, Yunliu Ouyang, Shilin Zhang, Xiaoyuan Chen, Lianhui Zhang, Xiaofan Zhou, Jianuan Zhou*, Ming Hu* (2026). Broad-Spectrum Quorum Quenching and Biocontrol Potential of Pseudomonas procumbens sp. nov. and Pseudomonas polia sp. nov. via Degradation of Multiple Quorum Sensing Molecules. J Agric Food Chem, 74(10):8578-8594. DOI: 10.1021/acs.jafc.5c18073PDF
Marie-Claire Harrison#, David C Rinker#, Abigail L LaBella, Dana A Opulente, John F Wolters, Xiaofan Zhou, Xing-Xing Shen, Marizeth Groenewald, Chris Todd Hittinger, Antonis Rokas* (2026). Machine learning identifies novel signatures of antifungal drug resistance in Saccharomycotina yeasts. PLoS Genet, 22(3):e1012091. DOI: 10.1371/journal.pgen.1012091PDF
Yuwei Liang*, Xin Geng, Yijun Shen, Kuang Sheng, Xinyi Zhou, Danqing Li, Xiuyun Wang, Chuan Dong, Xiaofan Zhou, Liangsheng Zhang*, Jiasheng Wu*, Chengjun Zhang* (2026). Tandem duplication underlies diversification of the gymnosperm-specific TPS-d subfamily. Hortic Res, in press. DOI: 10.1093/hr/uhag195PDF