Article
Medicine, General & Internal
Lorenzo Spirito, Rufina Maturi, Sara Carmela Credendino, Celeste Manfredi, Davide Arcaniolo, Marco De Martino, Francesco Esposito, Luigi Napolitano, Francesco Di Bello, Alfredo Fusco, Pierlorenzo Pallante, Marco De Sio, Gabriella De Vita
Summary: Bladder cancer (BC) is the tenth most common cancer, with urothelial carcinoma representing about 90% of all BC. The role of lncRNAs in BC development has emerged, but it is still poorly explored. This study investigated the expression of four lncRNA genes in BC, showing differential expression between normal tissue, benign lesions, and cancers. These lncRNAs could potentially be used as markers for BC diagnosis and follow-up.
Article
Cell Biology
Shumei Zhang, Haoran Jiang, Bo Gao, Wen Yang, Guohua Wang
Summary: This study used gene expression profiles to screen differentially expressed genes in breast cancer patients and normal samples. Functional and pathway enrichment analysis revealed important pathways and functions related to breast cancer. By constructing a gene interaction network, potential diagnostic markers for breast cancer were identified, and a predictive model was constructed to validate their diagnostic ability.
FRONTIERS IN CELL AND DEVELOPMENTAL BIOLOGY
(2022)
Article
Computer Science, Software Engineering
T. Harbig, M. Witte Paz, K. Nieselt
Summary: Analysis pipelines in genomics, transcriptomics, and proteomics often produce lists of genes that overlap only partially or not at all and are too large for manual comparison. This paper presents GO-Compass, a visual analytics tool that reduces the redundancy and improves interpretability of gene lists by using semantic similarity. GO-Compass offers interactive visualizations, such as hierarchical clustering, treemaps, heatmaps, and bar charts, to facilitate the comparison of GO terms and gene information.
COMPUTER GRAPHICS FORUM
(2023)
Article
Nutrition & Dietetics
Ali Mahmoudi, Stephen L. Atkin, Nikita G. Nikiforov, Amirhossein Sahebkar
Summary: This study investigated the effect of curcumin on critical genes and pathways related to diabetes. The results showed that curcumin targeted several important genes involved in diabetes and may have potential as a therapeutic agent for diabetes.
Article
Nutrition & Dietetics
Ali Mahmoudi, Alexandra E. Butler, Muhammed Majeed, Maciej Banach, Amirhossein Sahebkar
Summary: Curcumin may improve or inhibit the progression of NAFLD by modulating genes and proteins associated with the disease, specifically targeting stress and lipid metabolism pathways.
Article
Immunology
Raushan Kumar Chaudhary, L. Ananthesh, Prakash Patil, Uday Venkat Mateti, Sanjit Sah, Aroop Mohanty, Rama S. Rath, Bijaya Kumar Padhi, Sumira Malik, Kadhim Hussein Jassim, Moustafa A. Al-Shammari, Yasir Waheed, Prakasini Satapathy, Joshuan J. Barboza, Alfonso J. Rodriguez-Morales, Ranjit Sah
Summary: This study identified key genes and pathways associated with H5N1 infection in humans through protein-protein interaction and functional enrichment analysis. These hub genes and pathways play important roles in the diagnosis, prognosis, and treatment of H5N1 infection.
Article
Biochemistry & Molecular Biology
Wen Chen, Jing Li, Shulan Huang, Xiaodeng Li, Xuan Zhang, Xiang Hu, Shuanglin Xiang, Changning Liu
Summary: Gene co-expression network analysis is widely used in gene function annotation, but there is a lack of effective cross-platform analysis tools. To address this issue and make it easier for biologists to build and predict gene co-expression networks, a command-line toolkit called GCEN has been developed using C++. With its efficient and user-friendly design, GCEN allows researchers to perform gene co-expression network analysis without requiring sophisticated programming skills, especially in the context of RNA-Seq research and lncRNA function annotation.
CURRENT ISSUES IN MOLECULAR BIOLOGY
(2022)
Article
Public, Environmental & Occupational Health
Xue-Meng Gao, Xiu-Hua Zhou, Meng-Wei Jia, Xiao-Zhuo Wang, Dan Liu
Summary: When the body damages its own tissues in response to an infection, sepsis develops. Understanding the molecular mechanisms of sepsis and identifying potential molecular targets for treatment is crucial. We used WGCNA analysis to construct two modules, the light-green GSE131761 module and the blue GSE137342 module, which showed the strongest links to sepsis. Gene ontology analysis revealed that genes in the light-green module were involved in inflammatory response, while genes in the blue module were associated with proteasomal protein catabolic process. Additionally, two hub genes, ANKRD22 and VNN1, were identified as crucial genes in sepsis etiology.
PREVENTIVE MEDICINE
(2023)
Article
Oncology
Diego A. Pedroza, Matthew Ramirez, Venkatesh Rajamanickam, Ramadevi Subramani, Victoria Margolis, Tugba Gurbuz, Adriana Estrada, Rajkumar Lakshmanaswamy
Summary: Our study reveals that therapeutic targeting of PGRMC1 in aggressive breast cancers leads to the activation of miRNAs targeting overexpressed genes and deactivation of miRNAs with oncogenic potential.
FRONTIERS IN ONCOLOGY
(2021)
Article
Mathematical & Computational Biology
Matti Hoch, Suchi Smita, Konstantin Cesnulevicius, David Lescheid, Myron Schultz, Olaf Wolkenhauer, Shailendra Gupta
Summary: Complex diseases pose a challenge due to their multifaceted nature and heterogeneous data. Disease maps provide a standardized representation of molecular interactions, disease-related processes, and phenotypes. We propose a two-dimensional enrichment analysis approach to infer downstream and upstream elements using network topology parameters and molecular perturbations. Our approach is implemented in the MINERVA platform, enabling experimental data mapping and prediction of regulatory interactions. We demonstrate the utility of our approach in analyzing RNA-seq datasets and identifying enriched processes and transcription factors.
NPJ SYSTEMS BIOLOGY AND APPLICATIONS
(2022)
Article
Agronomy
Jing Guo, Xiuli Song, Shiqi Sun, Baihui Shao, Bo Tao, Lili Zhang
Summary: This study focused on selecting potato varieties with tolerance and sensitivity to bentazone, determining key genes involved in tolerance, and providing a theoretical basis for selecting stress-resistant resources in the future. The research found that tolerant potato plants showed a significantly higher photosynthetic rate and experienced faster degradation of bentazone compared to sensitive plants, with specific genes such as PPO, AOMT3, RBCS-C, and CHS2 identified as contributing to bentazone tolerance.
Article
Biotechnology & Applied Microbiology
Swetha Kumar, Venkata Gayatri Dhara, Linda D. Orzolek, Haiping Hao, Abbie J. More, Eduardo Catchon Lau, Michael J. Betenbaugh
Summary: The study found that plant-based hydrolysates, such as cottonseed hydrolysate, can positively impact CHO cell growth and productivity by upregulating transcription and translation, and affecting pathways related to the cell cycle and metabolism.
APPLIED MICROBIOLOGY AND BIOTECHNOLOGY
(2021)
Article
Immunology
Nikita R. Raje, Janelle R. Noel-MacDonnell, Katherine A. Shortt, Nicole M. Gigliotti, Marcia A. Chan, Daniel P. Heruth
Summary: The phenotypic variations of chromosome 22q11.2 deletion syndrome (22qDS) are not well explained. This study investigated gene expression in T cells of individuals with and without 22qDS, and found differentially expressed genes associated with T cell counts and markers. This suggests an important role of T cells in defective communication in 22qDS.
JOURNAL OF IMMUNOLOGY
(2022)
Article
Biology
Ambritha Balasundaram, C. George Priya Doss
Summary: This study identified differentially expressed genes in non-small cell lung cancer (NSCLC) and constructed a circRNA-miRNA-mRNA regulatory network to explore the potential mechanism of NSCLC.
COMPUTERS IN BIOLOGY AND MEDICINE
(2023)
Article
Computer Science, Interdisciplinary Applications
Cheng Chen, Lingyun Luo, Chunlei Zheng, Pingjian Ding, Huan Liu, Hanyu Luo
Summary: This study proposes a machine-learning-based framework for auditing gene ontology by predicting and validating the relationships between concepts. By uncovering potential errors through predicting and validating the relationships in the gene ontology, this approach can help improve the quality and accuracy of the ontology.
JOURNAL OF BIOMEDICAL INFORMATICS
(2023)
Article
Fisheries
Wen-Sing Liang, Tsuei-Yun Fang, Hong-Ting Lin, Tristan C. Liu, Wen-Jung Lu, Wen-Shyong Tzou, Shye-Jye Tang, Fu-Pang Lin, Shiu-Mei Liu, Chorng-Liang Pan
Article
Engineering, Biomedical
Pei-Xin Lai, Chung-Wein Chen, Shih-Chun Wei, Tzu-Yu Lin, Hong-Jyuan Jian, Irving Po-Jung Lai, Ju-Yi Mao, Pang-Hung Hsu, Han-Jia Lin, Wen-Shyong Tzou, Shiow-Yi Chen, Scott G. Harroun, Jui-Yang Lai, Chih-Ching Huang
Article
Biochemistry & Molecular Biology
Jing Hou, Heping Zheng, Wen-Shyong Tzou, David R. Cooper, Maksymilian Chruszcz, Mahendra D. Chordia, Keehwan Kwon, Marek Grabowski, Wladek Minor
Article
Biochemical Research Methods
Tun-Wen Pai, Kuan-Hung Li, Cing-Han Yang, Chin-Hwa Hu, Han-Jia Lin, Wen-Der Wang, Yet-Ran Chen
BMC BIOINFORMATICS
(2018)
Article
Mathematical & Computational Biology
Chien-Ming Chen, Tun-Wen Pai, Chia-Sheng Chuang, Jhen-Li Huang, Wen-Shyong Tzou, Chin-Hua Hu
INTERNATIONAL JOURNAL OF DATA MINING AND BIOINFORMATICS
(2014)
Article
Biochemical Research Methods
Wen-Shyong Tzou, Ying-Tsang Lo, Tun-Wen Pai, Chin-Hwa Hu, Chung-Hao Li
JOURNAL OF COMPUTATIONAL BIOLOGY
(2014)
Article
Multidisciplinary Sciences
Huang-Wei Lien, Rey-Yue Yuan, Chih-Ming Chou, Yi-Chung Chen, Chin-Chun Hung, Chin-Hwa Hu, Sheng-Ping L. Hwang, Pung-Pung Hwang, Chia-Ning Shen, Chih-Lung Chen, Chia-Hsiung Cheng, Chang-Jen Huang
SCIENTIFIC REPORTS
(2016)
Article
Biochemistry & Molecular Biology
Yi-Chen Lin, Chang-Yi Wu, Chin-Hwa Hu, Tun-Wen Pai, Yet-Ran Chen, Wen-Der Wang
Article
Biochemistry & Molecular Biology
Hsin-Yu Chung, Bo-An Lin, Yi-Xuan Lin, Chen-Wei Chang, Wen-Shyong Tzou, Tun-Wen Pei, Chin-Hwa Hu
Summary: Research demonstrates that Hif1 alpha acts downstream of Meis1 to mediate gata1 expression in zebrafish embryos, impacting erythropoiesis. Meis1 and Hif1 alpha form a hierarchical regulatory network, activating gata1 transcription through direct interactions, ensuring the generation of primitive erythrocytes.
Article
Biochemistry & Molecular Biology
Han-Hsiang Chen, Chin-Jung Lin, Anisha Anand, Han-Jia Lin, Hung-Yun Lin, Ju-Yi Mao, Pei-Hua Wang, Yufeng Jane Tseng, Wen-Shyong Tzou, Chih-Ching Huang, Robert Y. L. Wang
Summary: This study synthesized Cur carbon quantum dots (Cur-CQDs) with higher water solubility and lower cytotoxicity, which showed superior antiviral activity against Japanese encephalitis virus (JEV) infection. The researchers found that Cur-CQDs effectively bound to the E protein of JEV and prevented viral entry into host cells. They also identified specific mutations in the E protein that play a key role in Cur-CQDs binding. This research suggests that the E protein of flaviviruses can be a potential target for the development of CQD-based inhibitors to prevent or treat viral infections.
JOURNAL OF BIOLOGICAL CHEMISTRY
(2022)
Article
Engineering, Multidisciplinary
Chi-Fu Chou, Han-Jia Lin, Chih-Yu Tsai, Tzung-Yi Lin, Hsin-Yu Chung, Chia-Yin Chiang, Chung-Hao Li, Tun-Wen Pai, Chin-Hwa Hu, Wen-Shyong Tzou
JOURNAL OF MARINE SCIENCE AND TECHNOLOGY-TAIWAN
(2016)