Bioinformatics Laboratory Publications
Publications
2023 Publications
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: PMC10800799.
Liu S, Zhong H, Zhu J, Wu Y, Deng Y, Wu L. Regulome-wide association study identifies genetically driven accessible regions associated with pancreatic cancer risk. Int J Cancer. 2024 Feb 15;154(4):670-678. doi: 10.1002/ijc.34761. Epub 2023 Oct 18. PMID: 37850323; PMCID: PMC10842605.
Gao Z, Khadka VS, Deng Y*, Ju J. A novel approach to evaluate the expression and functions of microRNAs in colorectal cancer. Int J Mol Sci. 2019 Dec 15;20(24). doi:10.3390/ijms20246244. PMID: 31847119; PMCID: PMC6943741.
Nakatsu K, Jijiwa M, Khadka V, Nasu M, Deng Y*. sRNAfrag: a pipeline and suite of tools to analyze fragmentation in small RNA sequencing data. Brief Bioinform. 2023 Nov 22;25(1). doi: 10.1093/bib/bbad515. PMID: 38243693; PMCID: PMC10796253.
Nasu M, Khadka VS, Jijiwa M, Kobayashi K, Deng Y*. Exploring Optimal Biomarker Sources: A Comparative Analysis of Exosomes and Whole Plasma in Fasting and Non-Fasting Conditions for Liquid Biopsy Applications. Int J Mol Sci. 2023 Dec 27;25(1):371. doi: 10.3390/ijms25010371. PMID: 38203541; PMCID: PMC10779159.
Yin H, Sui Z, Wang Y, Liu D, Wang Q, Wang Y, Sun L, Wen X, Deng Y*, Hongwei 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 & Diseases. 2023, 101171. doi.org/10.1016/j.gendis.2023.101171.
Liu D, Bae YE, Zhu J, Zhang Z, Sun Y, Deng Y, Wu C, Wu L. Splicing transcriptome-wide association study to identify splicing events for pancreatic cancer risk. Carcinogenesis. 2023 Sep 28. doi: 10.1093/carcin/bgad069. Epub ahead of print. PMID: 37769343.
Yoon H, Dean LS, Jiyarom B, Khadka V, Deng Y, Nerurukar VR, Chow DC, Shikuma CM, Devendra G, Koh Y, Park J. Single-cell RNA sequencing reveals characteristics of myeloid cells in pulmonary post-acute sequelae of SARS-CoV-2. bioRxiv [Preprint]. 2023 Aug 2:2023.07.31.551349. doi:10.1101/2023.07.31.551349. PMID: 37577518; PMCID: PMC10418075.
Sun Y, Bae YE, Zhu J, Zhang Z, Zhong H, Cheng C, Deng Y, Wu C, Wu L. A Splicing Transcriptome-Wide Association Study Identifies Candidate Altered Splicing for Prostate Cancer Risk. OMICS. 2023 Jul 25. doi:10.1089/omi.2023.0065. Epub ahead of print. PMID: 37486714.
Rahimian K, Arefian E, Mahdavi B, Mahmanzar M, Kuehu DL, Deng Y*. SARS2Mutant: SARS-CoV-2 amino-acid mutation atlas database. NAR Genom Bioinform. 2023 Apr 24;5(2). doi: 10.1093/nargab/lqad037. PMID: 37101659; PMCI PMC10124966.
Khadka VS, Nasu M, Deng Y*, Jijiwa M. Circulating microRNA Biomarker for Detecting Breast Cancer in High-Risk Benign Breast Tumors. Int J Mol Sci. 2023 Apr 20;24(8):7553. doi: 10.3390/ijms24087553. PMID: 37108716; PMCID.
Burkhart JG, Wu G, Song X, Raimondi F, McWeeney S, Wong MH, Deng Y*. Biology-inspired graph neural network encodes reactome and reveals biochemical reactions of disease. Patterns (N Y). 2023 May 22;4(7):100758. doi:10.1016/j.patter.2023.100758. PMID: 37521042; PMCID: PMC10382942.
Maison DP, Deng Y, Gerschenson M. SARS-CoV-2 and the host-immune response. Front Immunol. 2023 Jun 19;14:1195871. doi: 10.3389/fimmu.2023.1195871. PMID: 37404823; PMCID: PMC10315470.
Nerurkar PV, Yokoyama J, Ichimura K, Kutscher S, Wong J, Bittenbender HC and Deng Y. Roasting and Brewing Methods Differentially Modulate Global Metabolomics, Lipidomics, Biogenic Amines, Mineral Contents and Antioxidant Capacity of Hawaii-Grown Coffee. Metabolites 2023, 13(3), 412. doi: 10.3390/metabo13030412.
Abbasian MH, Mahmanzar M, Rahimian K, Mahdavi B, Tokhanbigli S, Moradi B, Sisakht MM, Deng Y*. Global landscape of SARS-CoV-2 mutations and conserved regions. J Transl Med. 2023 Feb 25;21(1):152. doi: 10.1186/s12967-023-03996-w. PMID: 36841805; PMCID: PMC9958328.
Yang WS, Caliva MJ, Khadka VS, Tiirikainen M, Matter ML, Deng Y, Ramos JW. RSK1 and RSK2 serine/threonine kinases regulate different transcription programs in cancer. Front Cell Dev Biol. 2023 Jan 4;10:1015665. doi:10.3389/fcell.2022.1015665. PMID: 36684450; PMCID: PMC9845784.
Nguyen TB, Lac Q, Abdi L, Banerjee D, Deng Y, Zhang Y. Harshening stem cell research and precision medicine: The states of human pluripotent cells stem cell repository diversity, and racial and sex differences in transcriptomes. Front Cell Dev Biol. 2023 Jan 4;10:1071243. doi: 10.3389/fcell.2022.1071243. PMID:36684445; PMCID: PMC9848738.
Ghaleh SS, Rahimian K, Mahmanzar M, Mahdavi B, Tokhanbigli S, Sisakht MM, Farhadi A, Bakhtiari MM, Kuehu DL, Deng Y*. SARS-CoV-2 Non-structural protein 1(NSP1) mutation virulence and natural selection: Evolutionary trends in the six continents. Virus Res. 2023 Jan 2;323:199016. doi: 10.1016/j.virusres.2022.199016. PMID: 36473671; PMCID.
Fu Y, Wu K, Wang Z, Yang H, Chen Y, Wu L, Yanagihara R, Hedges JR, Wang H, Deng Y*; N3C consortium. Effectiveness of various COVID-19 vaccine regimens among 10.4 million patients from the National COVID Cohort Collaborative during Pre-Delta to Omicron periods – United States, 11 December 2020 to 30 June 2022. Vaccine. 2023 Sep 21(23)01025-3. doi: 10.1016/j.vaccine.2023.08.069. Epub ahead of print. PMID: 37741761.