Publications

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Journal Articles

Longitudinal plasma proteomics predict phenoconversion to clinically manifest ALS

Published in Nature Medicine, 2026

A longitudinal proteomic study identifying a 19-protein plasma panel that predicts phenoconversion to clinical ALS up to 5 years in advance, outperforming neurofilament light chain alone.

Recommended citation: Ran X., Wuu J., Qin Z.S., McDermott M.P., Cooper-Knock J., Li Y., Granit V., Grignon A.L., Lin E., Fernandez M.C., Colato D., Carberry N., Lill C.M., Piazza P., Malaspina A., & Benatar M. (2026). "Longitudinal plasma proteomics predict phenoconversion to clinically manifest ALS." Nature Medicine.
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An Analytic Pipeline to Obtain Reliable Genetic Ancestry Estimates from Tumor-Derived RNA Sequencing Data

Published in Cancer Epidemiology, Biomarkers & Prevention, 2025

A computational pipeline using tumor RNASeq data accurately estimates global genetic ancestry in the absence of germline DNA.

Recommended citation: Johnson C.E., Ran X., Wrobel J., Davidson N.R., Greene C.S., Epstein M.P., Marks J.R., Peres L.C., Doherty J.A., & Schildkraut J.M. (2025). "An Analytic Pipeline to Obtain Reliable Genetic Ancestry Estimates from Tumor-Derived RNA Sequencing Data." Cancer Epidemiology, Biomarkers & Prevention. PMID:40622249
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Gut Microbiota Modulation by Inulin Improves Metabolism and Ovarian Function in Polycystic Ovary Syndrome

Published in Advanced Science, 2025

Inulin reshapes the gut microbiota to enhance metabolic health and ovarian function in PCOS patients and mouse models.

Recommended citation: Geng L., Yang X., Sun J., Ran X., Zhou D., Ye M., Wen L., Wang R., & Chen M. (2025). “Gut Microbiota Modulation by Inulin Improves Metabolism and Ovarian Function in Polycystic Ovary Syndrome.” Advanced Science. doi:10.1002/advs.202412558
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Bile acid–gut microbiota imbalance in cholestasis and its long-term effect in mice

Published in mSystems, 2024

This study demonstrates that temporary hepatic cholestasis in mice induces persistent gut microbiota dysbiosis, characterized by reduced diversity, overgrowth of pathobionts, and sustained inflammation post-recovery.

Recommended citation: Yang X., Xu Y., Li J., Ran X., Gu Z., Song L., Zhang L., Wen L., Ji G., & Wang R. (2024). “Bile acid–gut microbiota imbalance in cholestasis and its long-term effect in mice.” mSystems, 9(7):e00127-24.
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Conference Papers

LLMBDC: Language Model for Biological Domains Oriented Clustering of Gene Ontology

Published in BIOKDD 2026 (KDD Workshop), 2026

A training-free LLM framework using zero-shot semantic reasoning to cluster Gene Ontology terms into interpretable biological domains, outperforming six existing approaches on Alzheimer's disease and Fragile X syndrome datasets.

Recommended citation: Ran X., Xu J., Jin P., Qin Z., Wen Z., & Lu J. (2026). "LLMBDC: Language Model for Biological Domains Oriented Clustering of Gene Ontology." arXiv:2608.00099.
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Predict Opioid-using Pharmacists from the Prescribing Practices Based on SVM Classification Model

Published in Atlantis Press SARL (ASSEHR), 2022

A support vector machine model achieves 85% accuracy in predicting pharmacists’ propensity to prescribe opioids using CMS prescribing data.

Recommended citation: Ran, X. (2022). “Predict Opioid-using Pharmacists from the Prescribing Practices Based on SVM Classification Model.” In: Proceedings of the International Conference on Applied Science, Engineering and Healthcare Research (ASSEHR). Atlantis Press SARL. doi:10.2991/assehr.k.220110.050
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Ximing Ran