Mi, K., Li, Z., Zhou, T., Yi, H., & Xu, C.* (2026). Evolutionary analyses of intact full-length transcriptomes support the nonadaptive hypothesis of transcript diversity. Phenomics. In press
Sarker, B., Zhou,
T., Deng, X., Zhang, L., Zhao, X., Huang, W., Yi, H., Jiang,
H.*, & Xu, C.* (2026). APAdeg enhances differentially
expressed gene inference by leveraging site-specific signals
in APA-seq data. Briefings in Bioinformatics, 27(3),
bbag295.B
Mi, K., Guan, L.,
Sarker, B., Song, S., Zhou, T., Yi, H., Zhang, J.* & Xu,
C.* (2026). Transcript diversity reflects
deleterious RNA processing errors shaped by population size
in metazoans. PLOS Biology, 24(3), e3003671.
Lu, W., Liao, B.,
Li, Z., Li, Y., Li, J., Mao, L., Zhou, T., Shi, H., Yu,
D*., Xu, C*., & Chen, Z*. (2026). Single-cell RNA
sequencing reveals the heterogeneity and microenvironment of
temporal bone squamous cell carcinoma. Clinical and
experimental otorhinolaryngology, 10.21053/ceo.2025-00324.
Deng, X.*, Zhao, J., Zhou, T., Xu, C.*, & Sugiyama, T. * (2026). Chromatin and RNA-mediated regulation of cellular quiescence in Schizosaccharomyces pombe. Fungal Biology Reviews, 58, 100516.
Zhou, T., Zhou, E.,
Lu, W., Zou, J., Zhang, J., Li, C., Shen, H., Xu, C., Shen,
Y., Li, J., Zhu, H., Xu, C., Yi, H.*, Yin, S.*, &
Huang, W.*(2026). Cancer burden among adults aged 65 years
and older in Asia, 1990-2023: a systematic analysis of the
Global Burden of Disease Study 2023.npj aging.
Qi, F., Xiao, Y.,
Zhang, S., Chen, Y., Qiao, M.,Xu, C., Zhang, K. Q.*,
& Liang, L. M.* (2026). A Rab GTPase-Activating Protein
Links Secondary Metabolism and Virulence in the
Nematophagous Fungus Purpureocillium lavendulum. Journal of
agricultural and food chemistry, 74(18), 14471–14482.
Zhou, T., Li, Z.,
Huang,W., Zhou, E., Jiang, Y., Bai, Y., Xu, C., Lu, W., Su,
K., Xu, C*, Yi, H* .(2025). Genome-Wide Analyses
Identify circAQR, A circular RNA Suppressing Proliferation
but Promoting Migration and Invasion in Thyroid Cancer. npj
Precision Oncology, 9(1), 171.
Zhang, L., Deng, X.,
Ma, W., Zhou, T., & Xu, C*. (2025). Regulation and
functions of alternative polyadenylation in fungi. Mycology,
1-16.
Li, Z., Mi, K., &
Xu, C*. (2025). Most m5C modifications in mammalian
mRNAs are nonadaptive. Molecular Biology and Evolution,
42(1), msaf008.
Li, Z., Sarker, B.,
Zhao, F., Zhou, T., Zhang, J*., & Xu, C*. (2024).
COL: a method for identifying putatively functional circular
RNAs. Journal of genetics and genomics, S1673-8527.
Zhou, T., Li, Z.,
Jiang, Y., Su, K., Xu, C*. and Yi, H.*, 2024.
Emerging roles of circular RNAs in regulating the hallmarks
of thyroid cancer. Cancer Gene Therapy, pp.1-10.
Xu, C*.,
Kadosh, D., Sun, D., Zeng, G., & Gao, Y. Z. (2023).
Omics-originated exploration of pathogenic patterns and
molecular mechanisms in human and animal fungal pathogens.
Frontiers in Microbiology, 14.
Hao, Y., Shao, L.,
Hou, J., Zhang, Y., Ma, Y., Liu, J., Xu, C., Chen,
F., Cao, L.H. and Ping, Y., 2023. Resveratrol and Sir2
reverse sleep and memory defects induced by amyloid
precursor protein. Neuroscience Bulletin, 39(7),
pp.1117-1130.
Xu, H., Li, C.,
Xu, C., & Zhang, J. (2023). Chance promoter
activities illuminate the origins of eukaryotic intergenic
transcriptions. Nature Communications, 14(1), 1826.
Zhang, J., & Xu,
C.(2022) Gene product diversity: adaptive or not?
Trends in Genetics, 38(11):1112-1122.
Xu, C. & J.
Zhang (2021) Mammalian circular RNAs result largely from
splicing errors. Cell Reports, 36(4), 109439.
Xu, C. , &
Zhang, J. (2020). Mammalian alternative translation
initiation is mostly nonadaptive. Molecular Biology and
Evolution. Mar 7. pii: msaa063. doi: 10.1093/molbev/msaa063.
Xu, C. , &
Zhang, J. (2020) A different perspective on alternative
cleavage and polyadenylation. Nature Review Genetics, doi:
10.1038/s41576-019-0198-z
Xu, C. ,
Park, J. K., & Zhang, J. (2019). Evidence that alternative
transcriptional initiation is largely nonadaptive. PLoS
biology, 17(3), e3000197.
Zhang, Q., Chen, X.,
Xu, C. , Zhao, H., Zhang, X., Zeng, G., ... & Meng,
Y. (2019). Horizontal gene transfer allowed the emergence of
broad host range entomopathogens. Proceedings of the
National Academy of Sciences, 116(16), 7982-7989.
Xu, C. , &
Zhang, J. (2018). Alternative Polyadenylation of Mammalian
Transcripts Is Generally Deleterious, Not Adaptive. Cell
systems, 6 (6), 734-742.e4
Zeng, G., Chen, X.,
Zhang, X., Zhang, Q.,Xu, C. , Mi, W., ..., & Fang, W.
(2017). Genome-wide identification of pathogenicity,
conidiation and colony sectorization genes in Metarhizium
robertsii. Environmental microbiology, 19(10), 3896-3908.
Liu, R.
+, Xu, C. +, Zhang, Q., Wang,
S., & Fang, W. (2017). Evolution of the chitin synthase gene
family correlates with fungal morphogenesis and adaption to
ecological niches. Scientific Reports. 7:44527
Guo, N., Qian, Y.,
Zhang, Q., Chen, X., Zeng, G., Zhang, X., ... Xu, C.,
Raymond J. St. Leger & Fang, W. (2017). Alternative
transcription start site selection in Mr-OPY2 controls
lifestyle transitions in the fungus Metarhizium robertsii.
Nature Communications, 8(1), 1565.
Xu, C., Liu,
R., Zhang, Q., Chen, X., Qian, Y., & Fang, W. (2017). The
diversification of evolutionarily conserved MAPK cascades
correlates with the evolution of fungal species and
development of lifestyles. Genome biology and evolution,
evw051.
Chen, X.
+, Xu, C. +, Qian, Y., Liu, R.,
Zhang, Q., Zeng, G., ... & Fang, W. (2016). MAPK
cascade‐mediated regulation of pathogenicity, conidiation
and tolerance to abiotic stresses in the entomopathogenic
fungus Metarhizium robertsii. Environmental microbiology.
18(3), 1048–1062
Mao, Y., Zhang, Y.,
Xu, C., & Qiu, Y. (2016). Comparative transcriptome
resources of two Dysosma species (Berberidaceae) and
molecular evolution of the CYP719A gene in Podophylloideae.
Molecular ecology resources. 16(1), 228-241.
Xu, C.,
Zhang, X., Qian, Y., Chen, X., Liu, R., Zeng, G., ... &
Fang, W. (2014). A High-Throughput Gene Disruption
Methodology for the Entomopathogenic Fungus Metarhizium
robertsii. PloS one, 9(9), e107657.
Zhao, H., Xu,
C., Lu, H. L., Chen, X., Leger, R. J. S., & Fang, W.
(2014). Host-to-Pathogen Gene Transfer Facilitated Infection
of Insects by a Pathogenic Fungus. PLoS pathogens, 10(4),
e1004009.
Shi, W., Guo, Y.,
Xu, C., Tan, S., Miao, J., Feng, Y., ... & Fang, W.
(2014). Unveiling the mechanism by which microsporidian
parasites prevent locust swarm behavior. Proceedings of the
National Academy of Sciences, 111(4), 1343-1348.
Xu, C., Liu,
L., Zhang, Z., Jin, D., Qiu, J., & Chen, M. (2013).
Genome-scale metabolic model in guiding metabolic
engineering of microbial improvement. Applied microbiology
and biotechnology, 97(2), 519-539.
Xu, C., Zhao, C., He, W., & Qiu, J (2011). Selection of Bacillus cereus resisting to jingangmycin aqua. Acta Agriculturae Zhejiangensis,2011,23(6):1187-1191.
