Ruidong Li

Publications

# These authors contributed equally; * Corresponding author

2024

1. Huang, H.-C.^#, Li, R.^#, Huang., H., Liu, S.-W., Wan, C., Chaudhuri, S., Yue, L., Wong, T., Dominical, V., Yen, R., Ngo, O., Bui, N., Stoppler, H., Yi, T., Suthram, S., Li, L., Sun, K.-H., 2024. Single-cell sequencing of full-length transcripts and T-cell receptors with automated high-throughput Smart-seq3. BMC Genomics. (IF: 3.5)
2. Yin, W., Chen, G., Li, Y., Li, R., Jia, Z., Zhong, C., Wang, S., Mao, X., Cai, Z., Deng, J., Zhong, W.-D., Pan, B., Lu, J., 2024. Identification of a 9-gene signature to enhance biochemical recurrence prediction in primary prostate cancer: A benchmarking study using ten machine learning methods and twelve patient cohorts. Cancer Letters. (IF: 9.1)

2023

1. Yu, L., Li, R. et al., 2023. An integrated model of splice variants and gene expression profiles to predict clinical outcomes in chronic lymphocytic leukemia. (Submitted)
2. Yu, L., Li, R. et al., 2023. A Hierarchical Multi-Omics Prognostic Model Reveals the Relevance of Human Papillomavirus to Prostate Cancer. (Submitted)
3. Chen, W., Yu, L., Li, R. et al. 2023. Can blood cell genome represent germline cell genome? (Submitted)
4. Yin, W., Chen, G., Li, Y., Li, R. et al. 2023. Identification of a 9-Gene Signature for Accurately Predicting Biochemical Recurrence in Primary Prostate Cancer: A Benchmarking Study Using Ten Machine Learning Methods and Twelve Patient Cohorts. (Submitted)

2022

1. Li, R.^*, Zhu, J., Zhong, W.-D., Jia, Z.^*, 2022. Comprehensive evaluation of machine learning models and gene expression signatures for prostate cancer prognosis using large population cohorts. Cancer Research. (IF: 13.31.)
2. Liu, S., Chen, M., Li, R., Li, W., Gal-On, A., Jia, Z., Ding, S., 2022. Identification of positive and negative regulators of antiviral RNA interference in Arabidopsis thaliana. Nature Communications. (IF: 17.69)
3. Wang, W., Yuan, D., Jiang, K., Li, R. et al., 2022. Genome-Wide CRISPR-Cas9 Screening and Identification of Potential Genes Promoting Prostate Cancer Growth and Metastasis. Current Cancer Drug Targets. (IF: 2.3)
4. Qu, H.^#, Li, R.^# et al., 2022. IIIandMe: An Algorithm for Chromosome-scale Haplotype Determination Using Genome-wide Variants of Three Haploid Reproductive Cells. bioRxiv.

2021

1. Li, R.^*, Qu, H., Wang, S., Chater, J.M., Wang, X., Cui, Y., Yu, L., Zhou, R., Jia, Q., Traband, R., Wang, M., Xie, W., Yuan, D., Zhu, J., Zhong, W.D., Jia, Z.^*, 2021. CancerMIRNome: an interactive analysis and visualization database for miRNome profiles of human cancer. Nucleic Acids Research. (IF: 19.16)
2. Li, R.^#, Liclican, A.^#, Xu, Y., Pitts, J., Niu, C., Zhang, J., Kim, C., Zhao, X., Soohoo, D., Babusis, D., Yue, Q., Ma, B., Murray, B., Subramanian, R., Xie, X., Zou, J., Bilello, J., Li, L., Schultz, B.E., Sakowicz, R., Smith, B., Shi, P., Murakami, E., Feng, J.Y., 2021. Key Metabolic Enzymes Involved in Remdesivir Activation in Human Lung Cells. Antimicrobial Agents and Chemotherapy. (IF: 5.94)
3. Shi, X.^#, Li, R.^#, Zhai, J.^#, Chen, M., Huang, K., Zheng, Z., Chen, Z., Dong, X., Liu, X., Lu, D., Feng, S., Diao, D., Ren, P., Liu, Z., Morahan, G., Cai, K., 2021. The First Comprehensive Database of Germline Pathogenic Variants in East Asian Cancer Patients. Database. (IF: 4.46)
4. Luo, G.^#, Shen, L.^#, Zhao, S.^#, Li, R.^#, Song, Y., Song, S., Yu, K., Yang, W., Li, X., Sun, J., Wang, Y., Gao, C., Liu, D., Zhang, A., 2021. Genome-wide identification of seed storage protein gene regulators in wheat through co-expression analysis. The Plant Journal. (IF: 7.09)
5. Huang, C., Rangel, D.S., Qin, X., Bui, C., Li, R., Jia, Z., Cui, X., and Jin, H., 2021. The chromatin remodeling protein BAF60/SWP73A regulates the plant immune receptor NLRs. Cell Host & Microbe. (IF: 31.32)
6. Li, R.^*, Zhu, J., Zhong, W.-D., Jia, Z.^*, 2021. PCaDB - a comprehensive and interactive database for transcriptomes from prostate cancer population cohorts. bioRxiv.

2020

1. Li, R.^#, Qu, H.^#, Chen, J., Wang, S., Chater, J.M., Zhang, L., Wei, J., Zhang, Y., Xu, C., Zhong, W.D., Zhu, J., Lu, J., Feng, Y., Chen, W., Ma, R., Ferrante, S.P., Roose, M.L., and Jia, Z., 2020. Inference of Chromosome-length Haplotypes Using Genomic Data of Three or a Few More Single Gametes. Molecular Biology and Evolution. (IF: 8.80)
2. Li, R.^#, Wang, S.^#, Cui, Y.^#, Qu, H., Chater, J.M., Zhang, L., Wei, J., Wang, M., Xu, Y., Yu, L., Lu, J., Feng, Y., Zhou, R., Huang, Y., Ma, R., Zhu, J., Zhong, W., and Jia, Z., 2020. Extended Application of Genomic Selection to Screen Multi-Omics Data for Prognostic Signatures of Prostate Cancer. Briefings in Bioinformatics. (IF: 13.99)
3. Shi, X.^#, Li, R.^#, Dong, X., Chen, A.M., Liu, X., Lu, D., Feng, S., Wang, H., and Cai, K., 2020. An Immune-associated gene classifier for lung adenocarcinoma prognosis. Journal of Translational Medicine. (IF: 8.44)
4. Gao, X.^#, Huang, Z.^#, Guan, C.^#, Feng, C.^#, Li, R.^#, Xie, H.^#, Que, R., Den, B., Cao, P., Li, M., Lu, J., Huang, Y., Li, M., Yang, W., Yang, X., Wen, C., Liang, X., Yang, Q., Chao, Y., Chan, L., Yenari, A.M., Jin, K., Chaudhuri, R.K., Zhang, J., Tan, EK., and Wang, Q., 2020. Multi-modal analysis identifies SVT genes associated with Parkinson’s disease. Briefings in Bioinformatics. (IF: 13.99)
5. Wang, M., Li, R., Xu, S., 2020. Deshrinking Ridge Regression for Genome-wide Association Studies. Bioinformatics (IF: 6.93)
6. Wang, S., Xu, Y., Qu, H., Cui, Y., Li, R., Chater J., Yu, Li., Zhou, R., Ma, R., Huang, Y. Qiao, Y., Hu X., Xie, W., Jia, Z., 2020. Boosting Predictabilities of Agronomic Traits in Rice using Bivariate Genomic Selection. Briefings in Bioinformatics. (IF: 13.99)
7. Jiao, M., Li, J., Zhang, Q., Xu, Xiu., Li, R., Dong, P., Meng, Chun., Li, Y., Wang, L., Qi, W., Kang, K., Wang, H., and Wang, T., 2020. Identification of four potential biomarkers associated with coronary artery disease in non-diabetic patients by Gene Co-expression Network Analysis. Frontiers in Genetics. (IF: 4.77)
8. Chater, J., Duong, F., Alas, M., Yip, M., Zib, A., Luu, I., Carrillo-Kashani, A., Wang, S., Li, R., Qu, H., Merhaut, D., Jia, Z., 2020. Postharvest Quality of Imported, Domestic and Minimally Processed Pomegranate Fruit. International Journal of Fruit Science. (IF: 1.53)

2019

1. Cui, Y.^#, Li, R.^#, Li, G.^#, Zhang, F., Zhu, T., Zhang, Q., Ali, J., Li, Z. and Xu, S., 2019. Hybrid Breeding of Rice via Genomic Selection. Plant Biotechnology Journal. (IF: 13.26)
2. Kang, K.^#, Li, J.^#, Li, R.^#, Xu, X., Liu, J., Qin, L., Huang, T., Wu, J., Jiao, M., Wei, M., Wang, H., Wang, T., and Zhang, Q., 2019. Potentially critical roles of NDUFB5, TIMMDC1,and VDAC3 in the progression of septic cardiomyopathy through integrated bioinformatics analysis. DNA and Cell Biology. (IF: 3.55)
3. Dai, X., Gonzalez, G., Li, L., Li, J., You, C., Miao, W., Hu, J., Fu, L., Zhao, Y., Li, R., Li, L., Chen, X., Xu, Y., Gu, W., Wang, Y., 2019. YTHDF2 Binds to 5-Methylcytosine in RNA and Modulates the Maturation of Ribosomal RNA. Analytical Chemistry. (IF: 8.01)
4. Wang, T., Zheng, X., Li, R., Liu, X., Wu, J., Zhong, X., Zhang, W., Liu, Y., He, X., Liu, W. and Wang, H., 2019. Integrated bioinformatic analysis reveals YWHAB as a novel diagnostic biomarker for idiopathic pulmonary arterial hypertension. Journal of Cellular Physiology. (IF: 6.51)
5. Jia, Z., Zhu, J., Zhuo, Y., Li, R., Qu, H., Wang, S., Lu, J., Chater, J.M., Ma, R., Liu, Z., and Cai, Z., 2019. Offsetting Expression Profiles of Prognostic Markers in Prostate Tumor versus its Microenvironment. Frontiers in Oncology. (IF: 5.74)
6. Wei, J., Xie, W., Li, R., Wang, S., Qu, H., Ma, R., Zhou, X. and Jia, Z., 2019. Analysis of trait heritability in functionally partitioned rice genome. Heredity. (IF: 3.83)
7. Wang, S., Wei, J., Li, R., Qu, H., Chater, J.M., Ma, R., Li, Y., Xie, W. and Jia, Z., 2019. Identification of optimal prediction models using multi-omic data for selecting hybrid rice. Heredity. (IF: 3.83)
8. Zhou, T., Lin, W., Zhu, Q., Renaud, H., Liu, X., Li, R., Tang, C., Ma, C., Rao, T., Tan, Z. and Guo, Y., 2019. The role of PEG3 in the occurrence and prognosis of colon cancer. OncoTargets and Therapy. (IF: 4.35)

2018

1. Li, R.^#, Qu, H.^#, Wang, S., Wei, J., Zhang, L., Ma, R., Lu, J., Zhu, J., Zhong, W.D. and Jia, Z., 2018. GDCRNATools: an R/Bioconductor package for integrative analysis of lncRNA, miRNA and mRNA data in GDC. Bioinformatics, 34(14), pp.2515-2517. (IF: 6.93)
2. Wei, J., Wang, A., Li, R., Qu, H. and Jia, Z., 2018. Metabolome-wide association studies for agronomic traits of rice. Heredity, 120(4), p.342. (IF: 3.83)
3. Lu, J., Dong, W., He, H., Han, Z., Zhuo, Y., Mo, R., Liang, Y., Zhu, J., Li, R., Qu, H., Zhang, L., Wang, S., Ma, R., Jia, Z. and Zhong, W., 2018. Autophagy induced by overexpression of DCTPP1 promotes tumor progression and predicts poor clinical outcome in prostate cancer. International Journal of Biological Macromolecules, 118, pp.599-609. (IF: 8.03)

2015

1. Gu, W., Gallagher, G.R., Dai, W., Liu, P., Li, R., Trombly, M.I., Gammon, D.B., Mello, C.C., Wang, J.P. and Finberg, R.W., 2015. Influenza A virus preferentially snatches noncoding RNA caps. RNA, 21(12), pp.2067-2075. (IF: 5.64)