scRNA seq of an F1 cross of Marek’s disease resistant and susceptible chickens identifies allele specific expression signatures enriched in transcription modulators by Deborah Velez-Irizarry, Hans Cheng, Cari Hearn

“…These results show that functional variants associated with susceptibility to MD may have a bigger impact in subsets of immune cell types, and by characterizing the transcriptomes of these subtypes we can unravel molecular signatures specific to MD genomic resistance.…”
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Orientin Reduces the Effects of Repeated Procedural Neonatal Pain in Adulthood: Network Pharmacology Analysis, Molecular Docking Analysis, and Experimental Validation by Dong-Dong Guo, Hai-Yan Huang, Hai-E. Liu, Kun Liu, Xing-Jing Luo

“…A protein-protein interaction (PPI) network was constructed, and Gene Ontology (GO) and Kyoto Encyclopedia of Genes and Genomes (KEGG) enrichment analyses were performed to explore the potential mechanism of action. …”
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Molecular mechanisms and therapeutic strategies of Naegleria fowleri Carter (1970): a review of the fatal brain-eating amoeba by N. Datta

“…With the advances in genomic and proteomic technologies, new opportunities have emerged to explore the molecular biology of N. fowleri and its host response. …”
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Identification and Verification of Hub Mitochondrial Dysfunction Genes in Osteoarthritis Based on Bioinformatics Analysis by Hui Niu, Xingxing Deng, Qian Zhang, Yijun Zhao, Jinfeng Wen, Wenyu Li, Huan Liu, Xiong Guo, Cuiyan Wu

“…Gene ontology (GO) and Kyoto encyclopedia of genes and genomes pathways were analyzed for DEMDFGs. The hub genes were determined by WGCNA and LASSO regression analysis. …”
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Gut microbiome-derived bacterial extracellular vesicles in patients with solid tumours by Surbhi Mishra, Mysore Vishakantegowda Tejesvi, Jenni Hekkala, Jenni Turunen, Niyati Kandikanti, Anna Kaisanlahti, Marko Suokas, Sirpa Leppä, Pia Vihinen, Hanne Kuitunen, Kaisa Sunela, Jussi Koivunen, Arja Jukkola, Ilja Kalashnikov, Päivi Auvinen, Okko-Sakari Kääriäinen, T. Peñate Medina, O. Peñate Medina, Juha Saarnio, Sanna Meriläinen, Tero Rautio, Raila Aro, Reetta Häivälä, Juho Suojanen, Mikael Laine, Pande Putu Erawijattari, Leo Lahti, Peeter Karihtala, Terhi S. Ruuska, Justus Reunanen

“…Objectives: Analyzing the functionality of bEVs using (meta)genomics and proteomics could highlight the unique aspects of host–gut microbiome interactions in solid tumor patients. …”
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The <i>Meq</i> Genes of Nigerian Marek’s Disease Virus (MDV) Field Isolates Contain Mutations Common to Both European and US High Virulence Strains by Joseph N. Patria, Luka Jwander, Ifeoma Mbachu, Levi Parcells, Brian Ladman, Jakob Trimpert, Benedikt B. Kaufer, Phaedra Tavlarides-Hontz, Mark S. Parcells

“…These sequences included partial whole genomes as well as targeted sequences of the <i>meq</i> oncogenes from these strains. …”
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Driving effect of P16 methylation on telomerase reverse transcriptase-mediated immortalization and transformation of normal human fibroblasts by Xuehong Zhang, Paiyun Li, Ying Gan, Shengyan Xiang, Liankun Gu, Jing Zhou, Xiaorui Zhou, Peihuang Wu, Baozhen Zhang, Dajun Deng, Jing Ni

“…P16 inactivation is frequently accompanied by telomerase reverse transcriptase (TERT) amplification in human cancer genomes. P16 inactivation by DNA methylation often occurs automatically during immortalization of normal cells by TERT. …”
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RNA-Sequence Reveals the Regulatory Mechanism of miR-149 on Osteoblast Skeleton under Mechanical Tension by Yifan Wang, Guanyin Zhu, Fang Pei, Yigan Wang, Jun Liu, Caixia Lu, Zhihe Zhao

“…Gene Ontology (GO) and Kyoto Encyclopedia of Genes and Genomes (KEGG) were used for enrichment analysis. …”
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Biomedical and candidate SN P markers of chronopathologies can significantly change affinity of ТАТА -binding protein for human gene promoters by D. A. Rasskazov, N. L. Podkolodnyy, O. A. Podkolodnaya, N. N. Podkolodnaya, V. V. Suslov, L. K. Savinkova, P. M. Ponomarenko, M. P. Ponomarenko

“…Computational analysis of millions of unannotated SNPs from the 1000 Genomes Project may speed up the search for biomedical SNP markers. …”
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Screening and Functional Pathway Analysis of Pulmonary Genes Associated with Suppression of Allergic Airway Inflammation by Adipose Stem Cell-Derived Extracellular Vesicles by Sung-Dong Kim, Shin Ae Kang, Yong-Wan Kim, Hak Sun Yu, Kyu-Sup Cho, Hwan-Jung Roh

“…Enrichment analysis based on the Gene Ontology (GO) database and Kyoto Encyclopedia of Genes and Genomes (KEGG) pathway analysis were also performed to further identify the function of DEGs. …”
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Comprehensive analysis of mRNA and miRNA differential expression profiles in the hypothalamus-pituitary-gonadal axis in laying and broodiness period of Wanxi white geese by Xinwei Tong, Xiaojin Li, Yuhua Wang, Fei Xie, Ruidong Li, Man Ren, Qianqian Hu, Shenghe Li

“…Gene ontology (GO) and Kyoto Encyclopedia of Genes and Genomes (KEGG) functional enrichment analysis showed that differentially expressed genes (DEGs) and differentially expressed miRNAs (DEMs) were significantly enriched in hormone level regulation, cell communication, calcium signaling pathway, GnRH signaling pathway, MAPK signaling pathway, Wnt signaling pathway, and other processes. …”
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Exploring the functional role of POU5F1 using CRISPR RNP electroporation of zygote (CRISPR-EZ) in buffaloes by Meeti Punetha, Dharmendra Kumar, Suman Choudhary, Sheetal Saini, Kamlesh Kumari Bajwa, Surabhi Sharma, Manu Mangal, P. S. Yadav, T. K. Datta

“…We developed an easy and straightforward protocol for gene editing, which could serve as a valuable method for studying the functional genomics of the buffalo embryos. …”
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Dietary antioxidant consumption and the risk of type 2 diabetes in South Korean adults: a prospective cohort study based on the Health Examinees study by Sangah Shin, Li-Juan Tan, Su Bin Hwang, Shinyoung Jun, Hyojee Joung

“…This study aimed to identify the association between dietary antioxidant consumption and the incidence of type 2 diabetes (T2D) mellitus (defined using the Korean Diabetes Association criteria) in South Korean adults.Design Baseline and follow-up data from the Health Examinees (HEXA) study, a large-scale community-based genomic cohort study conducted in South KoreaSetting A South Korean community.Participants A total of 20 594 participants, aged 40–79 years, who participated in the baseline and follow-up surveys of the HEXA study were included. …”
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Prognostic significance of neutrophil extracellular trap-related genes in childhood acute lymphoblastic leukemia: insights from multi-omics and in vitro experiment by Cheng Chen, Yu Ma, Yadai Gao, Huiqing Ge, Xiaochun Zhang

“…Background This study aimed to develop a prognostic model based on extracellular trap-related genes (NETRGs) for patients with cALL.Methods Data from the TARGET-ALL-P2 and TARGET-ALL-P3 cohorts in the Genomic Data Commons database, the transcriptome dataset GSE26713, the single-cell transcriptome dataset GSE130116 from the Gene Expression Omnibus database and 306 NETRGs identified were analysed. …”
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Insights into incompatible plasmids in multidrug-resistant Raoultella superbugs by Jiao Feng, Changxin Wu, Dongsheng Zhou, Lingfei Hu, Kai Mu, Zhe Yin

“…This study aims to elucidate the genomic features of novel incompatible plasmids in MDR Raoultella by presenting 13 complete plasmid sequences from four isolates, along with an analysis of 16 related plasmids from GenBank. …”
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Sangre Por Salud (SPS) Biobank: cohort profile by Richard R Sharp, Euijung Ryu, Janet E Olson, Karen Meagher, James R Cerhan, Davinder Singh, Suzette Bielinski, Emmil Zarrugh, Marlene E Girardo, Giovanna Moreno Garzon, Valentina Hernandez, Sharon Levey, Crystal Gonzalez, Daniela B Pompa, Gabriel Q Shaibi, Lawrence Mandarino, Steven Thibodeau, Elena De Filippis

“…Additionally, we plan to obtain a more comprehensive genomic analysis on the entire cohort, ensuring greater research interest and investigation into the underlying genetic factors that contribute to disease susceptibility in this cohort.…”
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A ribodepletion and tagging protocol to multiplex samples for RNA-seq based virus detection: application to the cassava virome by Daniel H. Otron, Justin S. Pita, Murielle Hoareau, Fidèle Tiendrébéogo, Jean-Michel Lett, Pierre Lefeuvre

“…After confirming that the protocol was suitable for ribodepletion, we demonstrated it was possible to detect RNA and DNA viruses via identification of near full-size genomes. Additional phylogenetic analyses confirmed the presence of begomoviruses and ipomoviruses responsible for CMD and CBSD, respectively. …”
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Parental conflicts and resource sharing: Evolutionary trade-off by Ruby Dhar, Arun Kumar, Subhradip Karmakar

“…There is a hypothetical scenario in which parents can influence gene expression in embryos directly. Similar to genomic imprinting, this may happen as a result of sexual selection in males competing with other males to gain more resources for their offspring from their mothers. …”
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ASSOCIATION BETWEEN POLYMORPHISMS IN GENES ENCODING 2′-5′-OLIGOADENYLATE SYNTHETASES AND THE HUMORAL IMMUNE RESPONSE UPON VACCINATION AGAINST TICK-BORNE ENCEPHALITIS by N. S. Yudin, A. V. Igoshin, S. L. Lutova, Ya. Gon, M. I. Voevoda, V. A. Belyavskaya

“…Levels of specific IgG antibodies against tick-borne encephalitis virus and interleukin 4 (IL-4) were analyzed. Genomic DNA samples were genotyped for the SNPs rs2285932, rs2072136, rs1293762, rs15895 and rs1732778 in genes encoding 2’-5’-oligoadenylate synthetases OAS2 and OAS3. …”
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Identification of core biomarkers for tuberculosis progression through bioinformatics analysis and in vitro research by Zhanpeng Chen, Qiong Wang, Quan Ma, Jinyun Chen, Xingxing Kong, Yuqin Zeng, Lanlan Liu, Shuihua Lu, Xiaomin Wang

“…Kyoto Encyclopedia of Genes and Genomes (KEGG) enrichment analysis indicated that these genes are primarily associated with fatty acid degradation, pyruvate metabolism, arginine and proline metabolism, as well as cholesterol metabolism signaling pathways. …”
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