Bioinformatics Laboratory Publications
Publications
2024 Publications
Shen Y, Zheng X, Hu Y, Deng Y, Xiong Q. Editorial: Bile acids in obesity-related diseases. Front Endocrinol (Lausanne). 2024 Dec 23;15:1518604. doi: 10.3389/fendo.2024.1518604. PMID: 39786024; PMCID: PMC10601567.
Jung SY, Yu H, Deng Y, Pellegrini M. DNA-methylation age and accelerated epigenetic aging in blood as a tumor marker for predicting breast cancer susceptibility. Aging (Albany NY). 2024 Dec 5;16. doi: 10.18632/aging.206169. Online ahead of print. PMID: 39642870; PMCID: PMC10521234.
Panee J, Qin Y, Deng Y. Associations of Chronic Marijuana Use with Changes in Salivary Microbiome. Microorganisms. 2024 Nov 6;12(11):2244. doi: 10.3390/microorganisms12112244. PMID: 39597633; PMCID: PMC10512644.
Panee J, Qin Y, Deng Y. Associations of Chronic Marijuana Use with Changes in Salivary Microbiome. Microorganisms. 2024 Nov 6;12(11):2244. doi: 10.3390/microorganisms12112244. PMID: 39597633; PMCID: PMC10512644.
Yu J, Zhu J, Zhong H, Zhang Z, Liu J, Lin X, Zeng G, Zhang M, Wu C, Deng Y, Sun Y, Wu L. Age-Related Hearing Impairment: Genome and Blood Methylome Data Integration Reveals Candidate Epigenetic Biomarkers. OMICS. 2024 Dec;28(12):620-631. doi: 10.1089/omi.2024.0172. Epub 2024 Nov 25. PMID: 39585213.
Chen S, Liu F, Fu Y, Deng CK, Borgia JA, Ayman AG, Nasu M, Jijiwa M, Yang H, Gong T, Wang J, Ling Z, Wang X, Wang H, Chu Q, Deng Y. A prospective multi-cohort study identifies and validates a 5-gene peripheral blood signature predictive of immunotherapy response in non-small cell lung cancer. Mol Cancer. 2024 Nov 6;23(1):247. doi: 10.1186/s12943-024-02160-2. PMID: 39506771; PMCID: PMC10511567.
Rai SK, Du W, Zhang J, Yu H, Deng Y, Fei P. Somatic gene mutations involved in DNA damage response/Fanconi anemia signaling are tissue- and cell-type specific in human solid tumors. Front Med (Lausanne). 2024 Oct 3;11:1462810. doi: 10.3389/fmed.2024.1462810. PMID: 39421870; PMCID: PMC10421567.
Liu S, Zhu J, Green D, Zhong H, Long Q, Wu C, Wang L, Deng Y, Wu L. Integrating Multi-Omics Data to Uncover Prostate Tissue DNA Methylation Biomarkers and Target Genes for Prostate Cancer Risk. Mol Carcinog. 2024 Oct 14. doi: 10.1002/mc.23828. Online ahead of print. PMID: 39400371.
Liu S, Zhu J, Zhong H, Wu C, Xue H, Darst BF, Guo X, Durda P, Tracy RP, Liu Y, Johnson WC, Taylor KD, Manichaikul AW, Goodarzi MO, Gerszten RE, Clish CB, Chen YI, Highland H, Haiman CA, Gignoux CR, Lange L, Conti DV, Raffield LM, Wilkens L, Marchand LL, North KE, Young KL, Loos RJ, Buyske S, Matise T, Peters U, Kooperberg C, Reiner AP, Yu B, Boerwinkle E, Sun Q, Rooney MR, Echouffo-Tcheugui JB, Daviglus ML, Qi Q, Mancuso N, Li C, Deng Y, Manning A, Meigs JB, Rich SS, Rotter JI, Wu L. Identification of proteins associated with type 2 diabetes risk in diverse racial and ethnic populations. Diabetologia. 2024 Dec;67(12):2754-2770. doi: 10.1007/s00125-024-06277-3. Epub 2024 Sep 30. PMID: 39349773.
Zhou Y, Zhang S, Qiu G, Wang X, Yonemura A, Xu H, Cui G, Deng S, Chun J, Chen N, Xu M, Song X, Wang J, Xu Z, Deng Y, Evert M, Calvisi DF, Lin S, Wang H, Chen X. TSC/mTORC1 mediates mTORC2/AKT1 signaling in c-MYC-induced murine hepatocarcinogenesis via centromere protein M. J Clin Invest. 2024 Sep 26;134(22):e174415. doi: 10.1172/JCI174415. PMID: 39325536; PMCID: PMC10491277.
Abbasian MH, Rahimian K, Mahmanzar M, Bayat S, Kuehu DL, Sisakht MM, Moradi B, Deng Y. Comparative Atlas of SARS-CoV-2 Substitution Mutations: A Focus on Iranian Strains Amidst Global Trends. Viruses. 2024 Aug 20;16(8):1331. doi: 10.3390/v16081331. PMID: 39205305; PMCID: PMC10410537.
Kuehu DL, Fu Y, Nasu M, Yang H, Khadka VS, Deng Y. Effects of Heat-Induced Oxidative Stress and Astaxanthin on the NF-kB, NFE2L2 and PPAR? Transcription Factors and Cytoprotective Capacity in the Thymus of Broilers. Curr Issues Mol Biol. 2024 Aug 22;46(8):9215-9233. doi: 10.3390/cimb46080544. PMID: 39194761.
Yin H, Sui Z, Wang Y, Liu D, Wang Q, Wang Y, Sun L, Li J, Li Z, Liu Y, Guo S, Wang W, Yin H, Liu P, Zhang K, Zhang H, Liu Y, Liu Y, Zhou Q, Wei D, Zhang H, Wang S, Ning Y, Geng S, Wen X, Deng Y, Wang H, Wang Y. The efficacy and safety of NeuroWell antidepressant dietary supplement, Deanxit, and their combination in the treatment of mild-to-moderate depression: A randomized clinical trial. Genes Dis. 2023 Dec 13;11(6):101171. doi: 10.1016/j.gendis.2023.101171. Epub 2024 Nov. PMID: 39104421; PMCID: PMC10401456.
Qin Y, Maggio A, Hawkins D, Beaudry L, Kim A, Pan D, Gong T, Fu Y, Yang H, Deng Y. Whole-genome bisulfite sequencing data analysis learning module on Google Cloud Platform. Brief Bioinform. 2024 Jul 23;25(Suppl 1):bbae236. doi: 10.1093/bib/bbae236. PMID: 39041913; PMCID: PMC10451433.
Feng Z, Fu Y, Deng Y. Enhancing visibility and inclusivity of queer scientists to advance equality in academia. Patterns (N Y). 2024 Jun 14;5(6):101008. doi: 10.1016/j.patter.2024.101008. eCollection 2024 Jun. PMID: 39005484; PMCID: PMC10421456.
Kuehu DL, Fu Y, Nasu M, Yang H, Khadka VS, Deng Y. Use of Microalgae-Derived Astaxanthin to Improve Cytoprotective Capacity in the Ileum of Heat-Induced Oxidative Stressed Broilers. Animals (Basel). 2024 Jun 29;14(13):1932. doi: 10.3390/ani14131932. PMID: 38998041; PMCID: PMC10401345.
Dekyi, Xiao Y, Wang X, Feng S, Wang Y, Liao L, Wang S, Deng Y, Zheng J, Zhao D. Predominance of A2063G mutant strains in the Mycoplasma pneumoniae epidemic in children: A clinical and epidemiological study in 2023 in Wuhan, China. Int J Infect Dis. 2024 Aug;145:107074. doi: 10.1016/j.ijid.2024.107074. Epub 2024 May 9. PMID: 38734057.
Zhu J, Wu K, Liu S, Masca A, Zhong H, Yang T, Ghoneim DH, Surendran P, Liu T, Yao Q, Liu T, Fahle S, Butterworth A, Alam MA, Vadgama JV, Deng Y, Deng HW, Wu C, Wu Y, Wu L. Proteome-wide association study and functional validation identify novel protein markers for pancreatic ductal adenocarcinoma. Gigascience. 2024 Jan 2;13:giae012. doi: 10.1093/gigascience/giae012. PMID: 38608280; PMCID: PMC10301389.
Huo M, Rai SK, Nakatsu K, Deng Y, Jijiwa M. Subverting the Canon: Novel Cancer-Promoting Functions and Mechanisms for snoRNAs. Int J Mol Sci. 2024 Mar 2;25(5):2923. doi: 10.3390/ijms25052923. PMID: 38474168; PMCID: PMC10251473. Review.
Chen Y, Gao Z, Mohd-Ibrahim I, Yang H, Wu L, Fu Y, Deng Y. Pan-cancer analyses of bromodomain containing 9 as a novel therapeutic target reveals its diagnostic, prognostic potential and biological mechanism in human tumours. Clin Transl Med. 2024 Feb;14(2):e1543. doi: 10.1002/ctm2.1543. PMID: 38303608; PMCID: PMC10201368.
Yoon H, Dean LS, Jiyarom B, Khadka VS, Deng Y, Nerurkar VR, Chow DC, Shikuma CM, Devendra G, Koh Y, Park J. Single-cell RNA sequencing reveals characteristics of myeloid cells in post-acute sequelae of SARS-CoV-2 patients with persistent respiratory symptoms. Front Immunol. 2024 Jan 8;14:1268510. doi: 10.3389/fimmu.2023.1268510. PMID: 38259488; PMCID: PMC10151367.