Bioinformatics Laboratory Publications
Publications
2020 Publications
Wen Z, Huang Y, Ling Z, Chen J, Wei X, Su R, Tang Z, Wen Z, Deng Y, Hu Z. Lack of Efficacy of Combined Carbohydrate Antigen Markers for Lung Cancer Diagnosis. Dis Markers. 2020 Dec 10;2020:4716793. doi: 10.1155/2020/4716793. PMID: 33488842; PMCID: PMC7787803.
Zhang F, Wu X, Chen W, Deng Y. Editorial: Cancer Informatics Toward Precision Medicine. Front Med (Lausanne). 2020 Nov 25;7:576611. doi: 10.3389/fmed.2020.576611. PMID: 33330533; PMCID: PMC7732532.
Fu Y, Ling Z, Arabnia H, Deng Y. Current trend and development in bioinformatics research. BMC Bioinformatics. 2020 Dec 3;21(Suppl 9):538. doi: 10.1186/s12859-020-03874-y. PMID: 33272214; PMCID: PMC7713158.
Yu Z, Fu Y, Ai J, Zhang J, Huang G, Deng Y. Development of predictive models to distinguish metals from non-metal toxicants, and individual metal from one another. BMC Bioinformatics. 2020 Dec 3;21(Suppl 9):239. doi: 10.1186/s12859-020-3525-7. PMID: 33272211; PMCID: PMC7712572.
Rodriguez RM, Khadka VS, Menor M, Hernandez BY, Deng Y. Tissue-associated microbial detection in cancer using human sequencing data. BMC Bioinformatics. 2020 Dec 3;21(Suppl 9):523. doi: 10.1186/s12859-020-03831-9. PMID: 33272199; PMCID: PMC7713026.
Hu X, Xiang Z, Zhang W, Yu Z, Xin X, Zhang R, Deng Y, Yuan Q. Protective effect of DLX6-AS1 silencing against cerebral ischemia/reperfusion induced impairments. Aging (Albany NY). 2020 Nov 18;12. doi: 10.18632/aging.104070. Epub ahead of print. PMID: 33216728.
Li X, Bu S, Pan RR, Zhou C, Qu K, Ying X, Zhong J, Xiao J, Yuan Q, Zhang S, Tipton L, Wang Y, Deng Y, Duan S. The values of AHCY and CBS promoter methylation on the diagnosis of cerebral infarction in Chinese Han population. BMC Med Genomics. 2020 Nov 2;13(1):163. doi: 10.1186/s12920-020-00798-7. PMID: 33138824; PMCID: PMC7607831.
Guo R, Chen Y, Borgard H, Jijiwa M, Nasu M, He M, Deng Y. The Function and Mechanism of Lipid Molecules and Their Roles in The Diagnosis and Prognosis of Breast Cancer. Molecules. 2020 Oct 21;25(20):4864. doi: 10.3390/molecules25204864. PMID: 33096860; PMCID: PMC7588012.
Chen X, Zhu Y, Jijiwa M, Nasu M, Ai J, Dai S, Jiang B, Zhang J, Huang G, Deng Y. Identification of plasma lipid species as promising diagnostic markers for prostate cancer. BMC Med Inform Decis Mak. 2020 Sep 24;20(Suppl 9):223. doi: 10.1186/s12911-020-01242-7. PMID: 32967667; PMCID: PMC7513490.
Williams AL, Khadka VS, Anagaran MCT, Lee K, Avelar A, Deng Y, Shohet RV. miR-125 family regulates XIRP1 and FIH in response to myocardial infarction. Physiol Genomics. 2020 Jul 27. doi: 10.1152/physiolgenomics.00041.2020. Epub ahead of print. PMID: 32716698.
Zhao T, Khadka VS, Deng Y. Identification of lncRNA biomarkers for lung cancer through integrative cross-platform data analyses. Aging (Albany NY). 2020 Jul 16;12. doi: 10.18632/aging.103496. Epub ahead of print. PMID: 32675385.
Chng KR, Li C, Bertrand D, Ng AHQ, Kwah JS, Low HM, Tong C, Natrajan M, Zhang MH, Xu L, Ko KKK, Ho EXP, Av-Shalom TV, Teo JWP, Khor CC; MetaSUB Consortium, Deng Y, Chen SL, Mason CE, Ng OT, Marimuthu K, Ang B, Nagarajan N. Cartography of opportunistic pathogens and antibiotic resistance genes in a tertiary hospital environment. Nat Med. 2020 Jun 8. doi: 10.1038/s41591-020-0894-4. PMID: 32514171.
Xie G, Wang X, Wei R, Wang J, Zhao A, Chen T, Wang Y, Zhang H, Xiao Z, Liu X, Deng Y, Wong L, Rajani C, Kwee S, Bian H, Gao X, Liu P, Jia W. Serum metabolite profiles are associated with the presence of advanced liver fibrosis in Chinese patients with chronic hepatitis B viral infection. BMC Med. 2020 Jun 5;18(1):144. doi: 10.1186/s12916-020-01595-w. PMID: 32498677.
Hu L, Chen S, Fu Y, Gao Z, Long H, Wang JM, Ren HW, Zuo Y, Li H, Wang J, Xu QB, Yu WX, Liu J, Shao C, Hao JJ, Wang CZ, Ma Y, Wang Z, Yanagihara R, Deng Y. Risk Factors Associated with Clinical Outcomes in 323 COVID-19 Hospitalized Patients in Wuhan, China. Clin Infect Dis. 2020 May 3. doi: 10.1093/cid/ciaa539. Epub ahead of print. PMID: 32361738; PMCID: PMC7197620.
Rodriguez RM, Hernandez BY, Menor M, Deng Y, Khadka VS. The landscape of bacterial presence in tumor and adjacent normal tissue across 9 major cancer types using TCGA exome sequencing. Comput Struct Biotechnol J. 2020 Mar 13;18:631-641. doi: 10.1016/j.csbj.2020.03.003. PMID: 32257046; PMCID: PMC7109368.
Itami Y, Miyake M, Ohnishi S, Tatsumi Y, Gotoh D, Hori S, Morizawa Y, Iida K, Ohnishi K, Nakai Y, Inoue T, Anai S, Tanaka N, Fujii T, Shimada K, Furuya H, Khadka VS, Deng Y, Fujimoto K. Disabled Homolog 2 (DAB2) Protein in Tumor Microenvironment Correlates with Aggressive Phenotype in Human Urothelial Carcinoma of the Bladder. Diagnostics (Basel). 2020 Jan 20;10(1). doi: 10.3390/diagnostics10010054. PMID: 31968685.
Marikawa Y, Chen HR, Menor M, Deng Y, Alarcon VB. Exposure-based assessment of chemical teratogenicity using morphogenetic aggregates of human embryonic stem cells. Reprod Toxicol. 2020 Jan;91:74-91. doi: 10.1016/j.reprotox.2019.10.004. PMID: 31711903; PMCID: PMC6980740.