Bioinformatics Laboratory Publications
Publications
2022 Publications
Chen Y, Qin Y, Fu Y, Gao Z, Deng Y*. Integrated Analysis of Bulk RNA-Seq and Single-Cell RNA-Seq Unravels the Influences of SARS-CoV-2 Infections to Cancer Patients. Int J Mol Sci. 2022 Dec 10;23(24):15698. doi: 10.3390/ijms232415698. PMID: 36555339; PMCID: PMC9779348.
Yu Z, Chen S, Tang Z, Tang Y, Ling Z, Wang H, Gong T, Gao Z, Devendra G, Huang G, Chen W, Deng Y*. Mitochondria-derived small RNAs as diagnostic biomarkers in lung cancer patients through a novel ratio-based expression analysis methodology. Genes Dis. 2022 Aug 7;10(3):1055-1061. doi: 10.1016/j.gendis.2022.07.013. PMID: 37396544; PMCID: PMC10308114.
Awad CS, Deng Y, Kwagyan J, Roche-Lima A, Tchounwou PB, Wang Q, Idris MY. Summary of Year-One Effort of the RCMI Consortium to Enhance Research Capacity and Diversity with Data Science. Int J Environ Res Public Health. 2022 Dec 24;20(1):279. doi: 10.3390/ijerph20010279. PMID: 36612607; PMCID: PMC9819075.
Ryon KA, Tierney BT, Frolova A, Kahles A, Desnues C, Ouzounis C, Gibas C, Bezdan D, Deng Y, He D, Dias-Neto E, Elhaik E, Afshin E, Grills G, Iraola G, Suzuki H, Werner J, Udekwu K, Schriml L, Bhattacharyya M, Oliveira M, Zambrano MM, Hazrin-Chong NH, Osuolale O, ?abaj PP, Tiasse P, Rapuri S, Borras S, Pozdniakova S, Shi T, Sezerman U, Rodo X, Sezer ZH, Mason CE. A history of the MetaSUB consortium: Tracking urban microbes around the globe. iScience. 2022 Oct 20;25(11):104993. doi: 10.1016/j.isci.2022.104993. PMID: 36299999; PMCID: PMC9589169.
Salami Ghaleh S, Rahimian K, Mahmanzar M, Mahdavi B, Tokhanbigli S, Mollapour Sisakht M, Farhadi A, Mousakhan Bakhtiari M, Lee Kuehu D, Deng Y*. SARS-CoV-2 Non-Structural Protein 1(NSP1) Mutation Virulence and Natural SelectionTrends in the Six Continents. bioRxiv [Preprint]. 2022 Jul 25:2022.07.22.501212. doi: 10.1101/2022.07.22.501212. PMID: 35923310; PMCID.
Mahmanzar M, Houseini ST, Rahimian K, Namini AM, Gholamzad A, Tokhanbigli S, Sisakht MM, Farhadi A, Kuehu DL, Deng Y*. The First Geographic Identification by Country of Sustainable Mutations of SARS-COV2 Sequence Samples: Worldwide Natural Selection Trends. bioRxiv [Preprint]. 2022 Jul 19:2022.07.18.500565. doi: 10.1101/2022.07.18.500565. PMID: 35898341; PMCID: PMC9327626.
Gao Z, Jijiwa M, Nasu M, Borgard H, Gong T, Xu J, Chen S, Fu Y, Chen Y, Hu X, Huang G, Deng Y*. Comprehensive landscape of tRNA-derived fragments in lung cancer. Mol Ther Oncolytics. 2022 Jul 6;26:207-225. doi:10.1016/j.omto.2022.07.002. PMID: 35892120; PMCID: PMC9307607.
Genomic Data Science Community Network (Deng Y is one of co-authors). Diversifying the genomic data science research community. Genome Res. 2022 Jul 20. doi: 10.1101/gr.276496.121. Epub ahead of print. PMID: 35858750.
Adhikari B, Lee CN, Khadka VS, Deng Y, Fukumoto G, Thorne M, Caires K, Odani J, Mishra B. RNA-Sequencing based analysis of bovine endometrium during the maternal recognition of pregnancy. BMC Genomics. 2022 Jul 7;23(1):494. doi: 10.1186/s12864-022-08720-4. PMID: 35799127; PMCID: PMC9264496.
Zhang W, Yang Y, Xiang Z, Cheng J, Yu Z, Wang W, Hu L, Ma F, Deng Y, Jin Z, Hu X. MRTF-A-mediated protection against amyloid-?-induced neuronal injury correlates with restoring autophagy via miR-1273g-3p/mTOR axis in Alzheimer models. Aging (Albany NY). 2022 May 23;14(10):4305-4325. doi: 10.18632/aging.203883. Epub 2022 May 23. PMID: 35604830.
Chen S, Gao Z, Hu L, Zuo Y, Fu Y, Wei M, Zitello E, Huang G, Deng Y*. Association of Septic Shock with Mortality in Hospitalized COVID-19 Patients in Wuhan, China. Adv Virol. 2022 Apr 23;2022:3178283. doi: 10.1155/2022/3178283. PMID: 35502304; PMCID: PMC9056262.
Irwin SV, Deardorff LM, Deng Y, Fisher P, Gould M, June J, Kent RS, Qin Y, Yadao F. Sulfite preservatives effects on the mouth microbiome: Changes in viability, diversity and composition of microbiota. PLoS One. 2022 Apr 7;17(4). doi: 10.1371/journal.pone.0265249. PMID: 35390016; PMCID: PMC8989357.
Kumar R, Deng Y, Fan JB, Wei L. Editorial: Early Detection and Diagnosis of Cancer. Front Genet. 2022 Mar 14;13:875421. doi: 10.3389/fgene.2022.875421. PMID: 35360854; PMCID: PMC8963914.
Urena F, Ma C, Hoffmann FW, Nunes LGA, Urschitz J, Moisyadi S, Khadka VS, Deng Y, Hoffmann PR. T cell activation decreases microRNA-15a/16 levels to promote MEK1-ERK1/2-Elk1 signaling and promote proliferative capacity. J Biol Chem. 2022 Jan 24:101634. doi: 10.1016/j.jbc.2022.101634. Epub ahead of print. PMID: 35085550.