Scientific Publications
Active Learning: The Almost Silver Bullet
2020 Dec 16 KSE 2020
Eric Hicks, Quang Tran, Kriangsiri Malasri, Nam Sy Vo, Vinhthuy Phan
Despite its clear benefits, Active Learning (AL) has gone widely unused in favor of traditional teaching models, due to AL's higher costs. With the increased prevalence of software based teaching aids, many of these barriers have been removed and new Active Learning strategies can be more easily implemented. We show that AL can be utilized in the classroom to improve work efficiency, better use TAs, and achieve positive gains in student performance and understanding using integrated lab work.
Read full articleiBRAB: In silico based-designed broad-spectrum Fab against H1N1 influenza A virus
2020 Dec 31 PLOS ONE
Do, P. C, Nguyen, T. H, Vo, U. H, Le, L
Influenza virus A is a significant agent involved in the outbreak of worldwide epidemics, causing millions of fatalities around the world by respiratory diseases and seasonal illness. Many projects had been conducting to investigate recovered infected patients for therapeutic vaccines that have broad-spectrum activity. With the aid of the computational approach in biology, the designation for a vaccine model is more accessible. We developed an in silico protocol called iBRAB to design a broad-reactive Fab on a wide range of influenza A virus. The Fab model was constructed based on sequences and structures of available broad-spectrum Abs or Fabs against...
Read full articleAnalysis of Periodontal Conditions in the Provinces of Vietnam: Results From the National Dental Survey
2022 Jan 9 ASIA PAC J PUBLIC HEALTH
Nguyen Thi Hong Minh, Tran Cao Binh, Trinh Dinh Hai, Nguyen Thuy Duong, Quang-Thanh Bui
Nationwide dental health surveys are crucial for providing essential information on dental health and dental condition-related problems in the community. However, the relationship between periodontal conditions and sociodemographic data has not been well investigated in Vietnam. With data from the National Oral Health Survey in 2019, we performed several machine learning methods on this dataset to investigate the impacts of sociodemographic features on gingival bleeding, periodontal pockets, and Community Periodontal Index. From the experiments, LightGBM produced a maximum AUC (area under the curve) value of 0.744. The other models in descending order were logistic regression (0.705), logiboost (0.704), and random...
Read full articleLiquid biopsy to characterize cell-free DNA in detecting and monitoring of cancers
2019 Dec 31 JOURNAL OF RESEARCH AND DEVELOPMENT ON INFORMATION AND COMMUNICATION TECHNOLOGY, 2019
Tran N. Nguyen
Liquid biopsy, a concept introduced approximately a decade ago, refers to noninvasive approaches that have become the focus of biomedical research. In clinical oncology and research, the term liquid biopsy is used in a broad sense as the sampling and analysis of analytes including cell-free DNA from various accessible biological fluids for diagnosis, prognosis and prediction of a therapeutic response. This technology has the potential to be used in tracking the genomic evolution of tumors over time. It may also have therapeutic implications in terms of its ability to detect actionable events or resistant subclonal populations while avoiding the need...
Read full articleUnveiling Prognostics Biomarkers of Tyrosine Metabolism Reprogramming in Liver Cancer by Cross-platform Gene Expression Analyses
2020 Jun 15 PLOS ONE, 2020
Nguyen TN, Nguyen HQ, Le D-H
Tyrosine is mainly degraded in the liver by a series of enzymatic reactions. Abnormal expression of the tyrosine catabolic enzyme tyrosine aminotransferase (TAT) has been reported in patients with hepatocellular carcinoma (HCC). Despite this, aberration in tyrosine metabolism has not been investigated in cancer development. In this work, we conduct comprehensive cross-platform study to obtain foundation for discoveries of potential therapeutics and preventative biomarkers of HCC. We explore data from The Cancer Genome Atlas (TCGA), Gene Expression Omnibus (GEO), Gene Expression Profiling Interactive Analysis (GEPIA), Oncomine and Kaplan Meier plotter (KM plotter) and performed integrated analyses to evaluate the clinical...
Read full articleMeta-analysis of computational methods for breast cancer classification
2020 Jun 26 INT. J. INTELLIGENT INFORMATION AND DATABASE SYSTEMS, 2019
Tri-Cong Pham, Chi-Mai Luong, Antoine Doucet, Van-Dung Hoang, Diem-Phuc Tran, Le Duc-Hau
Tyrosine is mainly degraded in the liver by a series of enzymatic reactions. Abnormal expression of the tyrosine catabolic enzyme tyrosine aminotransferase (TAT) has been reported in patients with hepatocellular carcinoma (HCC). Despite this, aberration in tyrosine metabolism has not been investigated in cancer development. In this work, we conduct comprehensive cross-platform study to obtain foundation for discoveries of potential therapeutics and preventative biomarkers of HCC. We explore data from The Cancer Genome Atlas (TCGA), Gene Expression Omnibus (GEO), Gene Expression Profiling Interactive Analysis (GEPIA), Oncomine and Kaplan Meier plotter (KM plotter) and performed integrated analyses to evaluate the clinical...
Read full articleIntegrative transcriptomic analysis for linking acute stress responses to squamous cell carcinoma development
2020 Oct 14 SCIENTIFIC REPORTS 10, 17209 (2020)
Tran N. Nguyen, Kimal Rajapakshe, Courtney Nicholas, Leticia Tordesillas, Erik A. Ehli, Christel M. Davis, Cristian Coarfa, Elsa R. Flores, Sally E. Dickinson, Clara Curiel-Lewandrowski, Kenneth Y. Tsai
Cutaneous squamous cell carcinoma (cuSCC) is the second most common skin cancer and commonly arises in chronically UV-exposed skin or chronic wounds. Since UV exposure and chronic wounds are the two most prominent environmental factors that lead to cuSCC initiation, we undertook this study to test whether more acute molecular responses to UV and wounding overlapped with molecular signatures of cuSCC. We reasoned that transcriptional signatures in common between acutely UV-exposed skin, wounded skin, and cuSCC tumors, might enable us to identify important pathways contributing to cuSCC. We performed transcriptomic analysis on acutely UV-exposed human skin and integrated those findings...
Read full articleIntegrative Transcriptomic Analysis Identifies Drivers of Squamous Cell Carcinoma Development
2020 Oct 14 SCIENTIFIC REPORTS, 2020
Tran N. Nguyen, Kimal Rajapakshe, Courtney Nicholas, Leticia Tordesillas, Cristian Coarfa, Elsa R. Flores, Sally Dickinson, Clara Curiel-Lewandrowski, Kenneth Y. Tsai
Cutaneous squamous cell carcinoma (cuSCC) is the second most common skin cancer and commonly arises in chronically UV-exposed skin or chronic wounds. Since UV exposure and chronic wounds are the two most prominent environmental factors that lead to cuSCC initiation, we undertook this study to test whether more acute molecular responses to UV and wounding overlapped with molecular signatures of cuSCC. We reasoned that transcriptional signatures in common between acutely UV-exposed skin, wounded skin, and cuSCC tumors, might enable us to identify important pathways contributing to cuSCC. We performed transcriptomic analysis on acutely UV-exposed human skin and integrated those findings...
Read full articleMulti-Omics Analysis Detects Novel Prognostic Subgroups of Breast Cancer
2020 Oct 15 FRONT. GENET. 11:574661. (2020)
Nguyen Q-H, Nguyen H, Nguyen T, Le D-H
The unprecedented proliferation of recent large-scale and multi-omics databases of cancers has given us many new insights into genomic and epigenomic deregulation in cancer discovery in general. However, we wonder whether or not there exists a systematic connection between copy number aberrations (CNA) and methylation (MET)? If so, what is the role of this connection in breast cancer (BRCA) tumorigenesis and progression? At the same time, the PAM50 intrinsic subtypes of BRCA have gained the most attention from BRCA experts. However, this classification system manifests its weaknesses including low accuracy as well as a possible lack of association with biological...
Read full articleImproving existing analysis pipeline to identify and analyze cancer driver genes using multi-omics data
2020 Nov 25 SCIENTIFIC REPORTS, 2020
Quang-Huy Nguyen, Le Duc-Hau
The cumulative of genes carrying mutations is vital for the establishment and development of cancer. However, this driver gene exploring research line has selected and used types of tools and models of analysis unsystematically and discretely. Also, the previous studies may have neglected low-frequency drivers and seldom predicted subgroup specificities of identified driver genes. In this study, we presented an improved driver gene identification and analysis pipeline that comprises the four most widely focused analyses for driver genes: enrichment analysis, clinical feature association with expression profiles of identified driver genes as well as with their functional modules, and patient stratification...
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