2024
47.Chen W, Yan M, Chen S, Sun J, Wang J, Meng D, Li J, Zhang L, Guo L#. (2024) The complete genome assembly of Nicotiana benthamiana reveals genetic and epigenetic landscape of centromeres. Nature Plants. https://doi.org/10.1038/s41477-024-01849-y
46.Yang B, Meng T, Wang X, Li J, Zhao S, Wang Y, Yi S, Zhou Y, Zhang Y, Li L#, Guo L#. (2024) CAT Bridge: an efficient toolkit for compound-transcript association mining from multi-omics data. GigaScience. https://doi.org/10.1093/gigascience/giae083
45.Tanvir R, Guo L, Wu H, Li L# (2024). Special Issue: Manipulation/regulation of secondary metabolites in medicinal plants. Plant Physiology and Biochemistry. https://doi.org/10.1016/j.plaphy.2024.108549.
44.Chen H, Wang J, Wang X, Peng C, Chang X, Chen Z, Yang B, Wang XR, Qiu J, Guo L# and Lu Y#. (2024) Identification of Key Genes Controlling Sugar and Organic Acid Accumulation in Wampee Fruit (Clausena lansium) via Genome Assembly and Genome-wide Association Analysis. Journal of Agricultural and Food Chemistry. https://doi.org/10.1021/acs.jafc.4c04830
43.Wang, H., Yao, G., Chen, W. et al. A gap-free genome assembly of Fusarium oxysporum f. sp. conglutinans, a vascular wilt pathogen.Sci Data 11, 925 (2024). https://doi.org/10.1038/s41597-024-03763-6
42.Wang K*, Jin J*, Wang J*, Wang X, Sun J, Meng D, Wang X, Guo L#. (2024 ) The complete telomere-to-telomere genome assembly of lettuce. Plant Communications. doi: 10.1016/j.xplc.2024.101011.
41.Chen W*, Wang X*, Sun J*, Wang X*, Zhu Z*, Ayhan DH, Yi S, Yan M, Zhang L, Meng T, Mu Y, Li J, Meng D, Bian J, Wang K, Wang L, Chen S, Chen R, Jin J, Li B, Zhang X, Deng XW, He H#, Guo L#. (2024) Two telomere-to-telomere gapless genomes reveal insights into Capsicum evolution and capsaicinoid biosynthesis. Nature Communications. 15, 4295. https://doi.org/10.1038/s41467-024-48643-0
40. Meng T, Jiao H, Zhang Y, Zhou Y, Chen S, Wang X, Yang B, Sun J, Geng X, Ayhan, DH and Guo L#. (2024) FoPGDB: a pangenome database of Fusarium oxysporum, a cross-kingdom fungal pathogens. Database. https://doi.org/10.1093/database/baae017
39. Wang XR*, Zhang L*, Yao G, Wang XF, Yi S, Meng T, Meng D, Chen W#, Guo L#. (2024) De novo chromosome-level genome assembly of Chinese motherwort (Leonurus japonicus). Scientific Data. https://doi.org/10.1038/s41597-023-02901-w.
2023
38. Wang X*, Li H*, Shen T, Wang X, Yi S, Meng T, Sun J, Wang X, Qu X, Chen S#, Guo L#. (2023) A near-complete genome sequence of einkorn wheat provides insight into the evolution of wheat A subgenomes. Plant Communications. doi: 10.1016/j.xplc.2023.100768.
37. Yao, G., Chen, W., Sun, J., Wang, X., Wang, H., Meng, T., Zhang, L., & Guo, L. (2023). Gapless genome assembly of Fusarium verticillioides, a filamentous fungus threatening plant and human health. Scientific data, 10(1), 229. https://doi.org/10.1038/s41597-023-02145-8
36. Jia, Y., Xu, Y., Wang, B., Guo, L., Guo, M., Che, X., & Ye, K. (2023). The tissue-specific chromatin accessibility landscape of Papaver somniferum. Frontiers in genetics, 14, 1136736. https://doi.org/10.3389/fgene.2023.1136736
2022
35. Liu H, Wang H, Liao XL, Gao B, Lu X, Sun D, Gong W, Zhong J, Zhu H, Pan X, Guo L#, Deng XW# and Zhou Q#. (2022) Mycoviral gene integration converts a plant pathogenic fungus into a biocontrol agent Proc Natl Acad Sci USA. 119(50): e2214096119
34. Guo L*#, Yao Hui*, Chen W*, Wang X, Ye P, Xu Z, Zhang S, Wu H#. (2022) Natural products of medicinal plants: biosynthesis and bioengineering in post-genomic era, Horticulture Research. Vol.9: uhac223.
33. Wang J*, Li J*, Li Z, Liu B, Zhang L, Guo D, Huang S, Qian W#, Guo L#. (2022) Genomic insights into longan evolution from a chromosome-level genome assembly and population genomics of longan accessions. Horticulture Research. Vol. 9: uhac021.
32. Xu T, Yang X, Jia Y, Li Z, Tang G, Li X, Wang B, Wang T, Lin J, Guo L, Ye K. (2022) A global survey of the transcriptome of the opium poppy (Papaver somniferum) based on single-molecule long-read isoform sequencing. The Plant Journal doi: 10.1111/tpj.15689.
31. Jia Y*, Chen S, Chen W, Zhang P, Su Z, Zhang L, Xu M and Guo L# (2022) A chromosome-level reference genome of Chinese balloon flower (Platycodon grandiflorus).Frontiers in Genetics.13:869784. doi: 10.3389/fgene.2022.869784.
2021
30. Yang X*, Gao S*, Guo L*, Wang B, Jia Y, Zhou J, Che Y, Jia P, Lin J, Xu T, Sun J, Ye K#. (2021) Three chromosome-scale Papaver genomes reveal punctuated patchwork evolution of the morphinan and noscapine biosynthesis pathway. Nature Communications. 12:6030.
29. Kang Y*, Ji X*, Guo L*, Xia H*, Yang X, Xie Z, Shi X, Wu R, Feng D, Wang C, Chen M, Zhang W, Wei H, Guan Y, Ye K#, Zhao G#. (2021) Cerebrospinal fluid from healthy pregnant women does not harbor a detectable microbial community. Microbiol Spectrum. doi: 10.1128/Spectrum.00769-21.
28. Lin J*, Yang X*, Kosters W, Xu T, Jia Y, Wang S, Zhu Q, Ryan M, Guo L, Zhang C, Lee C, Devine SE, Eichler EE, Ye K#; Human Genome Structural Variation Consortium.(2021) Mako: a graph-based pattern growth approach to detect complex structural variants. Genomics, Proteomics & Bioinformatics. doi:10.1016/j.gpb.2021.03.007
27. Chen Y*, Feng W, Ye K, Guo L, Xia H, Guan Y, Chai L, Shi W, Zhai C, Wang J, Yan X, Wang Q, Zhang Q, Li C, Liu P, Li M#. (2021) Application of metagenomic next-generation sequencing in the diagnosis of pulmonary infectious pathogens from bronchoalveolar lavage samples. Frontiers in Cellular and Infection Microbiology. doi: 10.3389/fcimb.2021.541092
26. Guo L*, Yu H*, Wang B*, Vescio K, Delulio G, Yang H, Berg A, Zhang L, Edel-Hermann V, Steinberg C, Kistler HC, Ma LJ# (2021) Metatranscriptomic comparison of endophytic and pathogenic Fusarium-Arabidopsis interactions reveals plant transcriptional plasticity. Molecular Plant-Microbe Interactions. 34(9):1071-1083
25. Yang H, Wang D, Guo L, Pan H, Yvon R, Garman S, Wu HM, Cheung AY#. (2021) Malectin/Malectin-like domain-containing proteins: A repertoire of cell surface molecules with broad functional potential. The Cell Surface. doi: 10.1016/j.tcsw.2021.100056.
2020
24. Shao C*, Xiang D*, Wei H*, Liu S, Yi G, Lyu S#, Guo L#, Li C#. (2020) Predicting virulence of Fusarium oxysporum f. sp. cubense based on the production of mycotoxin using a linear regression model. Toxins. 12: 254.
23. Wang B, Yu H, Jia Y, Dong Q, Steinberg C, Alabouvette CL, Edel-Hermann V, Kistler HC, Ye K#, Ma LJ#, and Guo L##. (2020) Chromosome-scale genome assembly of Fusarium oxysporum strain Fo47, a fungal endophyte and biocontrol agent. Molecular Plant-Microbe Interactions. 33(9), p.1108-1111
22. Guo L*#, Ji M*, and Ye K#. (2020) Dynamic network inference and association computation discover gene modules regulating virulence, mycotoxin production and sexual reproduction in Fusarium graminearum. BMC Genomics. 21:179
21. Fokkens L*, Guo L*, Dora S, Wang B, Ye K#, Sánchez-Rodríguez C#, Croll D#. (2020) A chromosome-scale genome assembly for the Fusarium oxysporum strain Fo5176 to establish a model Arabidopsis-fungal pathosystem. G3: Genes, Genomes, Genetics. 10(10), p.3549-3555
20. Wang B*, Guo L*, Ye K#, Wang L# (2020) Chromosome-scale genome assembly of Talaromyces rugulosus strain W13939, a mycoparasitic fungus and promising biocontrol agent. Molecular Plant-Microbe Interactions. 33(12):1446-1450.
19. Jia P, Yang X, Guo L, Liu B, Lin J, Liang H, Sun J, Zhang C, Ye K#. (2020) MSIsensor-pro: fast, accurate, and matched-normal-sample-free detection of microsatellite instability. Genomics, Proteomics & Bioinformatics. 18(1): p65-71.
18. Yang X, Xu T, Jia P, Xia H, Guo L, Ye K#. (2020) Transportation, Germs, Culture: A Dynamic Graph Model of 2019-nCoV Spread. Quantitative Biology. 8(3): 238–244
17. Zhang Y*, Yang H*, Turra D, Zhou S, Ayhan DH, DeIulio GA, Guo L, Broz K, Wiederhold N, Coleman JJ, Donnell KO, Youngster I, McAdam AJ, Savinov S, Shea T, Young S, Zeng Q, Rep M, Pearlman E, Schwartz DC, Di Pietro A, Kistler HC, Ma LJ#. The genome of opportunistic fungal pathogen Fusarium oxysporum carries a unique set of lineage-specific chromosomes. Communications Biology, 3(1): p. 50.
16. Zhao G, Guo L, Zhang Y, Gao L, Ma LJ#. (2020). Identifying TF binding motifs from partial target gene sets and its application to regulatory network inference. IEEE/ACM Transactions on Computational Biology and Bioinformatics. 17(4): 1211-1221
2019
15. Guo L, Ye K#. (2019) Mapping genome variants sheds light on genetic and phenotypic differentiation in Chinese. Genomics, Proteomics & Bioinformatics. 17(3): p226-228
14. Chaisson, M.J.P.*, A.D. Sanders*, X. Zhao*, A. Malhotra, D. Porubsky, T. Rausch, E.J. Gardner, O. Rodriguez,Guo L, R.L. Collins, X. Fan, J. Wen, R.E. Handsaker, S. Fairley, Z.N. Kronenberg, X. Kong, F. Hormozdiari, D. Lee, A.M. Wenger, A. Hastie, D. Antaki, P. Audano, H. Brand, S. Cantsilieris, H. Cao, E. Cerveira, C. Chen, X. Chen, C.-S. Chin, Z. Chong, N.T. Chuang, C.C. Lambert, D.M. Church, L. Clarke, A. Farrell, J. Flores, T. Galeev, D. Gorkin, M. Gujral, V. Guryev, W. Haynes Heaton, J. Korlach, S. Kumar, J.Y. Kwon, J.E. Lee, J. Lee, W.-P. Lee, S.P. Lee, S. Li, P. Marks, K. Viaud-Martinez, S. Meiers, K.M. Munson, F. Navarro, B.J. Nelson, C. Nodzak, A. Noor, S. Kyriazopoulou-Panagiotopoulou, A. Pang, Y. Qiu, G. Rosanio, M. Ryan, A. Stutz, D.C.J. Spierings, A. Ward, A.E. Welch, M. Xiao, W. Xu, C. Zhang, Q. Zhu, X. Zheng-Bradley, E. Lowy, S. Yakneen, S. McCarroll, G. Jun, L. Ding, C.L. Koh, B. Ren, P. Flicek, K. Chen, M.B. Gerstein, P.-Y. Kwok, P.M. Lansdorp, G. Marth, J. Sebat, X. Shi, A. Bashir, K. Ye, S.E. Devine, M. Talkowski, R.E. Mills, T. Marschall, J.O. Korbel#, E.E. Eichler#, and C. Lee# (2019). Multi-platform discovery of haplotype-resolved structural variation in human genomes. Nature Communications. 10:1784
13. Gao S, Gold SE, Wisecaver JH, Zhang Y, Guo L, Ma LJ, Rokas A, Glenn AE#. (2019). Genome-wide analysis of Fusarium verticillioides reveals potential contribution of horizontal gene transfer to the expansion of metabolism. Fungal Genetics and Biology. 128:60-73.
2018
12. Guo L*, Winzer T*, Yang X*, Li Y*, Ning Z*, He Z, Teodor R, Lu Y, Bowser TA, Graham IA#, Ye K# (2018) The opium poppy genome and morphinan production. Science. 362(6412): p. 343-347.
11. Deiulio GA, Guo L, Zhang Y, Goldberg JM, Kistler HC, Ma LJ#. (2018). Kinome expansion in the Fusarium oxysporum species complex driven by accessory chromosomes. mSphere 3: e00231-18. doi.org/10.1128/mSphere .00231-18.
10. Zhang Y, Guo L, Ma LJ#. (2018) A computational protocol to analyze metatranscriptomic data capturing fungal–host interactions. Wenbo Ma and Thomas Wolpert (eds.), Plant Pathogenic Fungi and Oomycetes. Methods in Molecular Biology. 1848:207-233
9. Ye K#, Guo L, Yang X, Lamijer EW, Raine K, Ning Z. (2018) Split-Read Indel and Structural Variant Calling Using PINDEL. Derek Bickhart (ed.), Copy Number Variants: Methods and Protocols, Methods in Molecular Biology.1833:95-105.
2016
8. Guo L, Zhao G, Gao L, Xu JR, Kistler HC, Ma LJ#. (2016) Compartmentalized gene regulatory network of a pathogenic fungus Fusarium graminearum. New Phytologist. 211(2): 527-541.
7. Guo L, Breakspear A, Zhao G, Gao L, Kistler HC, Xu JR, Ma LJ#. (2016) Conservation and divergence of the cyclic adenosine monophosphate–protein kinase A (cAMP–PKA) pathway in two plant-pathogenic fungi: Fusarium graminearum and F. verticillioides. Molecular Plant Pathology 17(2): 196-209.
6. Guo L, Allen KS, Deiulio GA, Zhang Y, Wick RL, Ma LJ# (2016) A de-novo-assembly-based pipeline for data mining in plant obligate parasite metatranscriptomic studies. Frontiers in Plant Science. 7: 925
5. Guo L, Wenner N, Kuldau GA#. (2016) FvSO regulates vegetative hyphal fusion, asexual growth, fumonisin B1 production, and virulence in Fusarium verticillioides. Fungal Biology 119(12): 1158-1169.
2015
4. Guo L, Blatt A, Geiser D, Jiménez-Gasco MDM, and Kuldau, GA#. (2015) Mating type and spore killing characterization of Fusarium verticillioides strains. Mycological Progress. 14: 1-6.
3. Guo L and Ma LJ# (2014) Fusarium graminearum Genomics and Beyond. Genomics of Plant-Associated Fungi: Monocot Pathogens, eds Dean RA, Lichens-Park A, & Kole C (Springer Berlin Heidelberg), pp 103-122.
2. Wyenandt CA#, Simon JE#, Pyne RM, Homa K, McGrath MT, Zhang S, Raid RN, Ma LJ, Wick R, Guo L, Madeiras, Angela M. (2015) Basil Downy Mildew (Peronospora belbahrii): Discoveries and Challenges Relative to Its Control. Phytopathology 105(7): 885-894.
2014
1. Zhao G, Guo L, Ma LJ, Gao L# (2014) Inferring regulatory networks through orthologous gene mapping. 2013 IEEE International Conference on Bioinformatics and Biomedicine (BIBM), Shanghai China, pp 76-83. DOI: 10.1109/BIBM.2013.673273