Publications

Research Publications & Preprints

Publication Overview

A complete and up-to-date list of my publications is available on my Google Scholar profile. Below are selected publications organized by research topics and fields, with first-author papers highlighted at the beginning of each category.

๐Ÿ”ฌ Viromics & Phage Biology

Unveiling the Hidden Role of Aquatic Viruses in Hydrocarbon Pollution Bioremediation
Ru, J., Xue, J., Sun, J., et al. | Journal of Hazardous Materials, 2023
Abstract: This study reveals that aquatic viruses encode hydrocarbon degradation genes, suggesting their potential role in environmental bioremediation and highlighting the under-characterized global virosphere. Read Paper โ†’

ViroProfiler: A Containerized Bioinformatics Pipeline for Viral Metagenomic Data Analysis
Ru, J., Khan Mirzaei, M., Xue, J., et al. | Gut Microbes, 2023
Abstract: ViroProfiler is a containerized bioinformatics workflow for analyzing viral metagenomic data, ensuring computational reproducibility and facilitating collaborative research in viromics. Read Paper โ†’

TCMSP: A Database of Systems Pharmacology for Drug Discovery from Herbal Medicines
Ru, J., Li, P., Wang, J., et al. | Journal of Cheminformatics, 2014
Abstract: TCMSP is a comprehensive systems pharmacology platform that integrates pharmacochemistry, ADME properties, drug targets, and interaction networks for accelerating drug discovery from traditional Chinese medicine. Read Paper โ†’

Bacteria and Bacteriophage Consortia Are Associated with Protective Intestinal Metabolites in Patients Receiving Stem Cell Transplantation
Thiele Orberg, E., Meedt, E., Hiergeist, A., Xue, J., Heinrich, P., Ru, J., et al. | Nature Cancer, 2024
Abstract: This study identifies a microbiome signature associated with protective immunomodulatory metabolites and provides a rationale for considering metabolite-producing consortia as microbiome-based therapies in stem cell transplantation. Read Paper โ†’

Helicobacter pylori Infection Alters Gut Virome by Expanding Temperate Phages Linked to Increased Risk of Colorectal Cancer
Luo, S., Ru, J., Khan Mirzaei, M., et al. | Gut, 2024
Abstract: This research demonstrates that H. pylori infection expands temperate phages in the gut, potentially contributing to colorectal cancer development through virus-bacteria interactions. Read Paper โ†’

Gut Virome Profiling Identifies an Association between Temperate Phages and Colorectal Cancer Promoted by Helicobacter pylori Infection
Luo, S., Ru, J., Mirzaei, M. K., et al. | Gut Microbes, 2023
Abstract: This study demonstrates that H. pylori infection expands temperate phages in the gut, potentially contributing to colorectal cancer development through virus-bacteria interactions. Read Paper โ†’

Altered Virome Structure and Function Characterization in Helicobacter pylori-Driven Colorectal Carcinogenesis and H. pylori Eradication
Luo, S., Xue, J., Ru, J., et al. | bioRxiv, 2022
Abstract: This preprint investigates the role of gut virome alterations in H. pylori-driven colorectal cancer and the long-term impact of antibiotic treatment on viral communities. Read Paper โ†’

Replidec: Use Naive Bayes Classifier to Identify Virus Lifecycle from Metagenomics Data
Peng, X., Ru, J., Mirzaei, M. K., et al. | bioRxiv, 2022
Abstract: Replidec is a novel tool for identifying phage replication cycles (virulent, temperate, chronic) in viral sequences using machine learning approaches. Read Paper โ†’

Differences in Gut Virome Related to Barrett Esophagus and Esophageal Adenocarcinoma
Ma, T., Ru, J., Xue, J., et al. | Microorganisms, 2021
Abstract: This study reveals differences in gut phage community composition and functional traits between esophageal disease patients and healthy controls. Read Paper โ†’

Challenges of Studying the Human Virome โ€“ Relevant Emerging Technologies
Mirzaei, M. K., Xue, J., Costa, R., Ru, J., et al. | Trends in Microbiology, 2021
Abstract: This review discusses the challenges and emerging technologies for studying the human virome, particularly in the context of disease research. Read Paper โ†’

Bacteriophages Isolated from Stunted Children Can Regulate Gut Bacterial Communities in an Age-Specific Manner
Mirzaei, M. K., Khan, M. A. A., Ghosh, P., Taranu, Z. E., Taguer, M., Ru, J., et al. | Cell Host & Microbe, 2020
Abstract: This study demonstrates that phages from stunted children can regulate gut bacterial communities in an age-specific manner, highlighting the role of viruses in microbiome development. Read Paper โ†’

๐Ÿงฌ Bioinformatics & Computational Biology

SVLearn: A Dual-Reference Machine Learning Approach Enables Accurate Cross-Species Genotyping of Structural Variants
Yang, Q., Sun, J., Wang, X., Ru, J., et al. | Nature Communications, 2025
Abstract: SVLearn introduces a machine-learning approach for genotyping bi-allelic structural variations, significantly outperforming existing tools with precision improvements of up to 15.61% for insertions and 13.75% for deletions in repetitive regions. Read Paper โ†’

PyPropel: A Python-based Tool for Efficiently Processing and Characterising Protein Data
Sun, J., Ru, J., Cribbs, A. P., et al. | BMC Bioinformatics, 2025
Abstract: PyPropel addresses the need for robust bioinformatics tools to facilitate efficient characterization and annotation of protein sequences for functional studies in the era of exponential metagenomic data growth. Read Paper โ†’

TMKit: A Python Interface for Computational Analysis of Transmembrane Proteins
Sun, J., Kulandaisamy, A., Ru, J., et al. | Briefings in Bioinformatics, 2023
Abstract: TMKit is an open-source Python programming interface specifically designed for processing transmembrane protein data, enabling database wrangling, feature engineering, and protein-protein interaction interface visualization. Read Paper โ†’

DeepdlncUD: Predicting Regulation Types of Small Molecule Inhibitors on Modulating lncRNA Expression by Deep Learning
Sun, J., Si, S., Ru, J., et al. | Computers in Biology and Medicine, 2023
Abstract: DeepdlncUD integrates predictions from nine deep learning algorithms to infer the regulation types of small molecules on modulating lncRNA expression, outperforming existing methods in accuracy and performance. Read Paper โ†’

DeepsmirUD: Prediction of Regulatory Effects on microRNA Expression Mediated by Small Molecules Using Deep Learning
Sun, J., Ru, J., Ramos-Mucci, L., et al. | International Journal of Molecular Sciences, 2023
Abstract: DeepsmirUD is the first cross-platform prediction tool to infer small-molecule-mediated regulatory effects on miRNA expression, powered by 12 cutting-edge deep-learning frameworks. Read Paper โ†’

๐Ÿฆ  Environmental Microbiology & Systems Biology

Temperature Response of Planktonic Microbiota in Remote Alpine Lakes
Jiang, Y., Huang, H., Ma, T., Ru, J., et al. | Frontiers in Microbiology, 2019
Abstract: This study investigates bacterial response to global temperature rise in alpine lakes, revealing the role of water temperature in shaping microbial community composition and metabolic activities. Read Paper โ†’

Long-Term and High-Concentration Heavy-Metal Contamination Strongly Influences the Microbiome and Functional Genes in Yellow River Sediments
Chen, Y., Jiang, Y., Huang, H., Mou, L., Ru, J., et al. | Science of The Total Environment, 2018
Abstract: This research reveals how long-term heavy metal contamination shapes microbial communities and functional genes in river sediments, highlighting adaptation mechanisms to environmental stress. Read Paper โ†’

Toxic/Bioactive Peptide Synthesis Genes Rearranged by Insertion Sequence Elements Among the Bloom-Forming Cyanobacteria Planktothrix
Entfellner, E., Li, R., Jiang, Y., Ru, J., et al. | Frontiers in Microbiology, 2022
Abstract: This study investigates the role of insertion sequence elements in genomic rearrangements and the distribution of toxic/bioactive peptide synthesis pathways in cyanobacteria. Read Paper โ†’

๐Ÿ’Š Systems Pharmacology & Drug Discovery

Large-Scale Exploration and Analysis of Drug Combinations
Li, P., Huang, C., Fu, Y., Wang, J., Wu, Z., Ru, J., et al. | Bioinformatics, 2015
Abstract: This study presents a systems pharmacology framework (PreDCs) for predicting drug combinations using probability ensemble approach, achieving high specificity and sensitivity in combination efficacy prediction. Read Paper โ†’

Large-Scale Direct Targeting for Drug Repositioning and Discovery
Zheng, C., Guo, Z., Huang, C., Wu, Z., Li, Y., Chen, X., Fu, Y., Ru, J., et al. | Scientific Reports, 2015
Abstract: This research develops a novel algorithm (WES) for identifying drug direct targets based on large-scale drug-target relationships, providing a potential in silico model for drug repositioning. Read Paper โ†’

Insights from Systems Pharmacology into Cardiovascular Drug Discovery and Therapy
Li, P., Fu, Y., Ru, J., Huang, C., et al. | BMC Systems Biology, 2014
Abstract: This study demonstrates how systems-level information can be used to interrogate features of cardiovascular disease for better understanding of pathogenesis and identification of new drug targets. Read Paper โ†’

Small Molecule-Mediated Targeting of microRNAs for Drug Discovery: Experiments, Computational Techniques, and Disease Implications
Sun, J., Xu, M., Ru, J., James-Bott, A., et al. | European Journal of Medicinal Chemistry, 2023
Abstract: This comprehensive review outlines biological and computational applications in miRNA-targeted drug discovery, along with their disease implications and clinical significance. Read Paper โ†’

๐Ÿงช Translational Research & Disease Mechanisms

Single-Cell RNA Sequencing Reveals Intrahepatic Signature Related to Pathobiology of Duck Hepatitis A Virus Type 3 (DHAV-3) Infection
Zhang, Y., Ding, D., Li, S., Pan, Q., Ru, J., et al. | Poultry Science, 2025
Abstract: This study profiles the transcriptome of 1.4 million cells from DHAV-3 susceptible and resistant ducklings, revealing inflammatory immune signatures and cell communications underlying viral pathogenesis. Read Paper โ†’

Genomic Landscape and Regulation of RNA Editing in Pekin Ducks Susceptible to Duck Hepatitis A Virus Genotype 3 Infection
Zhao, H., Wu, Z., Wang, Z., Ru, J., et al. | International Journal of Molecular Sciences, 2024
Abstract: This study profiles dynamic RNA editing events in liver tissue during DHAV-3 infection, revealing their potential to tune physiological processes and contribute to host differential susceptibility to viral infection. Read Paper โ†’

Targeted Therapy for EWS-FLI1 in Ewing Sarcoma
Gong, H., Xue, B., Ru, J., et al. | Cancers, 2023
Abstract: This review describes EWS-FLI1 protein partners and downstream pathways, as well as related target therapies for the treatment of Ewing sarcoma, a rare pediatric malignancy. Read Paper โ†’

Transient Mild Photothermia Improves Therapeutic Performance of Oral Nanomedicines with Enhanced Accumulation in The Colitis Mucosa
Ma, Y., Gou, S., Zhu, Z., Sun, J., Shahbazi, M. A., Si, T., Xu, C., Ru, J., et al. | Advanced Materials, 2023
Abstract: This study demonstrates that transient mild photothermia enhances the therapeutic outcomes of oral nanomedicines against ulcerative colitis by improving drug accumulation and cellular processes. Read Paper โ†’

๐Ÿ“Š Research Impact

  • Total Publications: 30+ peer-reviewed articles and preprints
  • High-Impact Journals: Nature Cancer, Gut, Nature Communications, Bioinformatics, Advanced Materials
  • Research Areas: Viromics, Phage Biology, Bioinformatics, Systems Pharmacology, Environmental Microbiology, Translational Research
  • Citations: 1000+ (Google Scholar)
  • h-index: 15
  • First Author Papers: 3 publications where you are the lead author
  • Collaborative Research: Extensive international collaborations in computational biology and microbiology
  • Research Breadth: Spans from fundamental viromics to translational applications in disease research

View complete publication list on Google Scholar โ†’