Review
Biochemistry & Molecular Biology
Monikaben Padariya, Alicja Sznarkowska, Sachin Kote, Maria Gomez-Herranz, Sara Mikac, Magdalena Pilch, Javier Alfaro, Robin Fahraeus, Ted Hupp, Umesh Kalathiya
Summary: IRDS genes, a subgroup of ISGs, are upregulated in cancer types, promoting resistance to chemotherapy and radiotherapy. Strategies to suppress these genes and induce sensitivity were discussed, along with their associated pathways and regulators. Targeting IRDS genes may offer an efficient strategy to resensitize tumor cells and enhance anti-cancer treatment outcomes.
Article
Biology
Chun-Yan Cui, Xiao Liu, Ming-Hui Peng, Qing Liu, Ying Zhang
Summary: The study identified key genes and signaling pathways related to neuropathic pain using bioinformatics technology, providing potential targets for the targeted therapy of neuropathic pain.
COMPUTERS IN BIOLOGY AND MEDICINE
(2022)
Article
Biochemistry & Molecular Biology
He Zhu, Bei Wen, Li Xu, Yuguang Huang
Summary: CRPS is a chronic pain disorder with no established treatment. This study identified key genes and pathways associated with CRPS through bioinformatics analysis. The findings suggest that targeting excessive inflammation may offer new therapeutic methods for CRPS and related disorders.
Article
Biochemical Research Methods
Mustafa Coskun, Mehmet Koyuturk
Summary: Using node similarity-based convolution matrices in GCNs can significantly improve the link prediction performance of GCN-based embeddings. Experimental results in biomedical networks show that this approach can enhance the performance of link prediction.
Article
Biochemical Research Methods
Hyun-Myung Woo, Byung-Jun Yoon
Summary: MONACO is a novel and versatile network alignment algorithm that achieves highly accurate pairwise and multiple network alignments through iterative optimal matching of 'local' neighborhoods around focal nodes. Extensive performance assessments on real and synthetic networks, where the ground truth is known, show that MONACO consistently outperforms all other state-of-the-art network alignment algorithms in terms of accuracy, coherence, and topological quality of the aligned network regions. Despite the significantly enhanced alignment accuracy, MONACO remains computationally efficient and scales well with increasing size and number of networks.
Article
Genetics & Heredity
Christelle Adolphe, Angli Xue, Atefeh Taherian Fard, Laura A. Genovesi, Jian Yang, Brandon J. Wainwright
Summary: The study identified 71 BCC susceptibility loci and 46 functional candidate susceptibility genes through GWAS, indicating that increased risk of BCC is associated with decreased expression of some susceptibility genes and increased expression of others. Pathway analysis revealed enrichment of cell cycle, cell death, and immune regulation processes in BCC susceptibility, with genes linked to T-Reg cell biology showing global enrichment.
Article
Biotechnology & Applied Microbiology
Siwei Bi, Ruiqi Liu, Beiyi Wu, Linfeng He, Jun Gu
Summary: This study identified several hub genes with significant differential expression, revealed important pathways in the development of keloids, and predicted miRNA-hub gene interactions. The results provide insights for future therapeutic strategies.
BIOMED RESEARCH INTERNATIONAL
(2021)
Article
Biochemical Research Methods
Kerr Ding, Sheng Wang, Yunan Luo
Summary: This article introduces a new approach to biological network alignment called GraNA, which utilizes deep learning and functional correspondence between proteins across species to predict functional relatedness. GraNA performs well on multiple tasks and successfully discovers functionally replaceable human-yeast protein pairs documented in previous studies.
Article
Biotechnology & Applied Microbiology
Vindhya Mohindra, Labrechai Mog Chowdhury, Nishita Chauhan, Alisha Paul, Rajeev Kumar Singh, Basdeo Kushwaha, Rajesh Kumar Maurya, Kuldeep K. Lal, J. K. Jena
Summary: In this study, large-scale gill transcriptome analyses revealed differentially expressed genes (DEGs) in Tenualosa ilisha (Hilsa shad) in different salinity regions. The DEGs were mapped into various pathways, including focal adhesion and PI3K-Akt signaling pathways. The expression of certain osmoregulatory genes and other specific genes varied in different habitats. The results provide valuable information about the molecular mechanisms regulating water homeostasis in gills and potential bio-markers for adaptation to environmental changes.
MARINE BIOTECHNOLOGY
(2023)
Article
Endocrinology & Metabolism
Harish Joshi, Basavaraj Vastrad, Nidhi Joshi, Chanabasayya Vastrad, Anandkumar Tengli, Iranna Kotturshetti
Summary: This study aimed to diagnose differentially expressed genes associated with obesity development, identifying important DEGs that may serve as novel biomarkers or potential therapeutic targets. Through bioinformatics analysis, a set of key hub genes related to obesity were identified, providing reliable molecular biomarkers for screening and diagnosis, prognosis, and potential therapeutic intervention for obesity.
FRONTIERS IN ENDOCRINOLOGY
(2021)
Article
Gastroenterology & Hepatology
Rui Zhong, Xujuan Luo, Jin Xu, Xin Jiang, Yongfeng Yan, Xiaomin Shi, Yan Peng, Xiaowei Tang, Xiangsheng Fu
Summary: This study investigates differentially expressed genes in acute pancreatitis (AP) and identifies CDH1 and VCL as potential key genes regulated by MAZ in AP.
Article
Endocrinology & Metabolism
Nan Wang, Linfeng Wei, Die Liu, Quyan Zhang, Xiaobo Xia, Lexi Ding, Siqi Xiong
Summary: Through bioinformatics analysis, this study identified 23 potential autophagy-related genes in diabetic retinopathy (DR), among which the down-regulated expression of MAPK3 may affect the occurrence and development of DR by regulating autophagy. This provides a novel insight into the pathogenesis of DR.
FRONTIERS IN ENDOCRINOLOGY
(2022)
Article
Psychiatry
Ester Anton-Galindo, Judit Cabana-Dominguez, Barbara Torrico, Roser Corominas, Bru Cormand, Noelia Fernandez-Castillo
Summary: This study demonstrates the pleiotropic contribution of dopaminergic and serotonergic genes to addiction and related behaviors, such as anxiety, irritability, neuroticism, and risk-taking behavior, highlighting the role of dopamine genes in the co-occurrence of these phenotypes.
FRONTIERS IN PSYCHIATRY
(2023)
Article
Genetics & Heredity
Hadi Rezaeeyan, B. Fatemeh Nobakht M. Gh, Masoud Arabfard
Summary: This study investigated COPD, asthma, IPF, and MLD, identifying 22 shared genes and related inflammatory pathways. By understanding the shared genes and pathways, this research can contribute to understanding the pathogenesis of these diseases and designing preventive and therapeutic strategies.
BMC MEDICAL GENOMICS
(2023)
Article
Genetics & Heredity
Vimaladhasan Senthamizhan, Balaraman Ravindran, Karthik Raman
Summary: Essential gene prediction models traditionally rely on sequence-based features, but this study showed the importance of network-based features for accurate predictions. The NetGenes database, containing essential gene predictions for over 2,700 bacteria, offers various features for each gene, including essentiality scores, annotations, and feature vectors.
FRONTIERS IN GENETICS
(2021)
