Research

Publications

• Ruan P., and Wang S. (2021). DiSNEP: a Disease-Specific gene Network Enhancement to improve Prioritizing candidate disease genes. Briefings in Bioinformatics, 22(4), bbaa241.
• Ruan P., Wang S., and Liang H. (2020). mirPLS: A Partial Linear Structure Identifier Method for Cancer Subtyping Using MicroRNAs. Bioinformatics, 36(19), 4902-4909.
• Ruan, P., Wang, Y., Shen, R., and Wang, S. (2019). Using Association Signal Annotations to Boost Similarity Network Fusion. Bioinformatics, 35(19): 3718-3726.
• Huang, H., Shangguan, J., Ruan, P., and Liang, H. (2019). Bi-level Feature Selection in High Dimensional AFT Models with Applications to a Genomic Study. Statistical Applications in Genetics and Molecular Biology.
• Wang, Y., Qian, M., Ruan, P., Teschendorff, A. E., and Wang, S. (2018). Detection of Epigenetic Field Defects Using a Weighted Epigenetic Distance-based Method. Nucleic Acids Research, 47(1), e6-e6.
• Ruan, P., Shen, J., Santella, R. M., Zhou, S., and Wang, S. (2016). NEpiC: a Network-Assisted Algorithm for Epigenetic Studies Using Mean and Variance Combined Signals. Nucleic Acids Research, 44(16), e134-e134.

Software

DiSNEP:

• R package for an improved analytical tool for prioritizing genes associated with diseases using gene network information.
• Reference: Ruan, P. and Wang S. DiSNEP: a Disease-Specific gene Network Enhancement to improve Prioritizing candidate disease genes. Accepted by Briefings in Bioinformatics.

mirPLS:

• R package for a partial linear structure identifier algorithm identifying non-linearly outcome-associated miRNAs for cancer subtyping.
• Reference: Ruan, P., Wang, S. and Liang, H. mirPLS: A Partial Linear Structure Identifier Method for Cancer Subtyping Using MicroRNAs. Bioinformatics, btaa606.

abSNF:

• R package for an algorithm using association signal annotation to boost similarity network fusion for diseases subtyping.
• Reference: Ruan, P., Wang, Y., Shen, R., and Wang, S. (2019). Using Association Signal Annotations to Boost Similarity Network Fusion. Bioinformatics, 35(19): 3718-3726.

NEpiC:

• R package for a biological network assisted greedy algorithm for identifying epigenetic biomarkers.
• Reference: Ruan, P., Shen, J., Santella, R. M., Zhou, S., and Wang, S. (2016) NEpiC: a Network-Assisted Algorithm for Epigenetic Studies Using Mean and Variance Combined Signals. Nucleic Acids Research, 44(16), e134-e134.