Sitemap
A concise index of the public pages and selected publications on this site. An XML sitemap is also available.
Pages
Bioinformatics at the intersection of data, software, and biology
Shaojun Xie builds reproducible bioinformatics tools for sequencing, single-cell, and multi-omics data.
Projects
Selected bioinformatics software and workflow engineering projects.
Publications
Comparative analyses for plant virus-based cancer immunotherapy drug development
Published in Cell Biomaterials, 2025
Comparative molecular analyses supporting plant virus-based cancer immunotherapy development.
Recommended citation: Omole, A. O., Newton, H. S., Cedrone, E., Nematpour, K., Xie, S., et al. (2025). Cell Biomaterials, 1(6), 100095.
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Nanoparticles may influence mast cells gene expression profiles without affecting their degranulation function
Published in Nanomedicine: Nanotechnology, Biology and Medicine, 2025
Transcriptomic analysis of nanoparticle-associated changes in mast-cell gene expression.
Recommended citation: Newton, H. S., Cedrone, E., Grunberger, J., Xie, S., et al. (2025). Nanomedicine, 66, 102818.
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Diversity and selection analyses identify transmission-blocking antigens as the optimal vaccine candidates in Plasmodium falciparum
Published in eBioMedicine, 2024
Population-genomic analysis of diversity and selection in candidate Plasmodium falciparum vaccine antigens.
Recommended citation: Ciubotariu, I. I., Broyles, B. K., Xie, S., et al. (2024). eBioMedicine, 106, 105227.
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Transgenerational increases in DNA methylation in Arabidopsis plants defective in active DNA demethylation
Published in Proceedings of the National Academy of Sciences, 2024
Analysis of transgenerational methylation changes caused by defects in active DNA demethylation.
Recommended citation: Tang, K., Zhu, X., Xie, S., Lang, Z., & Zhu, J.-K. (2024). PNAS, 121(22), e2320468121.
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Aging and obesity prime the methylome and transcriptome of adipose stem cells for disease and dysfunction
Published in The FASEB Journal, 2023
Integrated methylome and transcriptome analysis of adipose stem cells in aging and obesity.
Recommended citation: Xie, S., Choudhari, S., Wu, C.-L., Abramson, K., Corcoran, D., Gregory, S. G., Thimmapuram, J., Guilak, F., & Little, D. (2023). The FASEB Journal, 37(3), e22785.
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ViewBS: a powerful toolkit for visualization of high-throughput bisulfite sequencing data
Published in Bioinformatics, 2018
A command-line toolkit for summarizing and visualizing bisulfite sequencing data.
Recommended citation: Huang, X., Zhang, S., Li, K., Thimmapuram, J., & Xie, S. (2018). Bioinformatics, 34(4), 708–709.
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Transcriptome-wide high-throughput deep m6A-seq reveals unique differential m6A methylation patterns between three organs in Arabidopsis thaliana
Published in Genome Biology, 2015
Transcriptome-wide analysis of organ-specific m6A methylation patterns in Arabidopsis.
Recommended citation: Wan, Y., Tang, K., Zhang, D., Xie, S., Zhu, X., Wang, Z., & Lang, Z. (2015). Genome Biology, 16, 272.
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Genome-wide high resolution parental-specific DNA and histone methylation maps uncover patterns of imprinting regulation in maize
Published in Genome Research, 2014
High-resolution parental-specific epigenomic maps of imprinting regulation in maize.
Recommended citation: Zhang, M., Xie, S., Dong, X., et al. (2014). Genome Research, 24(1), 167–176.
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