Bioinformatics Laboratory Publications
Publications
2025 Publications
Feng Z, Nasu M, Devendra G, Abdul-Ghani AA, Chan OTM, Borgia JA, Gao Z, Zhang H, Chen Y, Gong T, Luo G, Yang H, Wu L, Fu Y, Deng Y. Liquid biopsy diagnostics for non-small cell lung cancer via elucidation of tRNA signatures. Commun Med (Lond). 2025 Aug 21;5(1):364. doi: 10.1038/s43856-025-01068-2. PMID: 40841456; PMCID: PMC12003961.
Manzoor F, Gupta V, Pinky L, Wang Z, Chen Z, Deng Y, Neupane S. A Systematic Review of Multimodal Deep Learning and Machine Learning Fusion Techniques for Prostate Cancer Classification. medRxiv [Preprint]. 2025 Aug 11:2025.08.07.25333235. doi: 10.1101/2025.08.07.25333235. PMID: 40832371; PMCID: PMC12000971.
Allan NP, Torres A, Corley MJ, Yamamoto BY, Balaan C, Yamauchi Y, Peres R, Qin Y, Khadka VS, Deng Y, Ward MA, Maunakea AK. Pre-Conception Maternal Obesity Confers Autism Spectrum Disorder-like Behaviors in Mice Offspring Through Neuroepigenetic Dysregulation. Cells. 2025 Aug 5;14(15):1201. doi: 10.3390/cells14151201. PMID: 40801633; PMCID: PMC11984043.
Maison DP, Khadka VS, Mohd-Ibrahim I, Peluso MJ, Henrich TJ, Deng Y, Gerschenson M. Peripheral immune progression to long COVID is associated with mitochondrial gene transcription: A meta-analysis. Mitochondrion. 2025 Jul 28;85:102072. doi: 10.1016/j.mito.2025.102072. PMID: 40738238; PMCID: PMC11952111.
Gao Z, Nasu M, Devendra G, Abdul-Ghani AA, Herrera AJ, Borgia JA, Seder CW, Kuehu DL, Feng Z, Chen Y, Gong T, Zhang Z, Chan O, Yang H, Yu J, Fu Y, Wu L, Deng Y. A robust machine learning model based on ribosomal-subunit-derived piRNAs for diagnostic potential of nonsmall cell lung cancer across multicentre, large-scale of sequencing data. Clin Transl Med. 2025 Aug;15(8):e70418. doi: 10.1002/ctm2.70418. PMID: 40714929.
Higa L, Deng Y. Highlighting the achievements and impact of women in data science. Patterns (N Y). 2025 Jun 13;6(6):101263. doi: 10.1016/j.patter.2025.101263. PMID: 40575125; PMCID: PMC11885936.
Marcantonio E, Burger AD, Chang KH, Hoffmann FW, Fu Y, Khadka VS, Smagghe BJ, Deng Y, Hoffmann PR, Prisic S. Zinc-limited Mycobacterium tuberculosis stimulate distinct responses in macrophages compared with standard zinc-replete bacteria. Infect Immun. 2025 Feb 4:e0057824. doi: 10.1128/iai.00578-24. Online ahead of print. PMID: 39903447.
Zhong H, Zhu J, Liu S, Zhou D, Long Q, Wu C, Zhao B, Cheng C, Yang Y, Wu Q, Wu Y, Li C, Wang Z, Wu J, Guo X, Zhi D, Deng Y, Wu L. Linking DNA methylation in brain regions to Alzheimer’s disease risk: a Mendelian randomization study. Hum Mol Genet. 2025 Jun 4;34(12):1026-1033. doi: 10.1093/hmg/ddaf053. PMID: 40267236.
Yang C, Gao M, Wang Y, Jiang T, Ma Y, Si X, Deng Y, Liu Y, Mo M, Xiao X, Wang F, Yang Y. Low-Frequency Optical Signal Enhancement Device Combines CRISPR-Based Assay for Portable S. pneumoniae Detection. Anal Chem. 2025 Apr 22;97(15):8553-8563. doi: 10.1021/acs.analchem.5c00634. Epub 2025 Apr 9. PMID: 40203058.
Tokhanbigli S, Salami Ghaleh S, Rahimian K, Mahmanzar M, Bayat S, Ahangarzadeh S, Moradi B, Mahmanzar R, Wang Y, Oliver BGG, Deng Y. Intersecting SARS-CoV-2 spike mutations and global vaccine efficacy against COVID-19. Front Immunol. 2025 Mar 7;16:1435873. doi: 10.3389/fimmu.2025.1435873. PMID: 40124365; PMCID: PMC11835654.
Wang J, Katsaros D, Wang Z, Ma L, Casetta E, Fei P, Denti P, Grimaudo I, Chen S, Deng Y, Yu H. Mitochondrial tRNA fragment, mt-tRF-Tyr-GTA-001 (tRF-21-X3OJI8EWB), in breast cancer and its potential clinical implications. Breast Cancer Res Treat. 2025 Jun;211(3):675-685. doi: 10.1007/s10549-025-07682-x. Epub 2025 Mar 18. PMID: 40102335.
Maison DP, Tasissa H, Deitchman A, Peluso MJ, Deng Y, Miller FD, Henrich TJ, Gerschenson M. COVID-19 clinical presentation, management, and epidemiology: a concise compendium. Front Public Health. 2025 Jan 31;13:1498445. doi: 10.3389/fpubh.2025.1498445. PMID: 39957982; PMCID: PMC11787481. Review.
Marcantonio E, Burger AD, Chang KH, Hoffmann FW, Fu Y, Khadka VS, Smagghe BJ, Deng Y, Hoffmann PR, Prisic S. Zinc-limited Mycobacterium tuberculosis stimulate distinct responses in macrophages compared with standard zinc-replete bacteria. Infect Immun. 2025 Feb 4:e0057824. doi: 10.1128/iai.00578-24. Online ahead of print. PMID: 39903447.
Sun Y, Zhu J, Zhong H, Zhang Z, Wang F, Nakamura A, Liu Y, Liu J, Yu J, Zeng G, Lin X, Zhou D, Wu C, Wang L, Deng Y, Wu L. Transcriptome-Wide Association Study Identified Novel Blood Tissue Gene Biomarkers for Prostate Cancer Risk. Prostate. 2025 Jan 29:e24859. doi: 10.1002/pros.24859. Online ahead of print. PMID: 39878408.