The case for development of a core outcome set (COS) and supplemental reporting guidelines for influenza vaccine challenge trial research in swine by Sheila Keay, Famke Alberts, Annette M. O’Connor, Robert Friendship, Terri O’Sullivan, Zvonimir Poljak

“…The checklist serves two purposes: as a reminder of details essential to report for inclusion of findings in meta-analyses and sub-group meta-analyses (e.g., antigenic or genomic descriptions of influenza vaccine and challenge viruses), and as an aid to help synthesis researchers fully characterize and comprehensively include studies in reviews.…”
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Natural population cohort study on long-lived adults: West China longevity and ageing procedure (WCLAP) by Li Wang, Yan Zhang, Qiukui Hao, Xiaoyan Chen, Birong Dong, Yan He, Meijuan Chen, Jirong Yue, Xiaochu Wu, Tianyao Zhang, Yan She, Yanling Gao, Yiping Deng

“…Analysis of biological samples facilitates biological characterisation at the microscopic level through proteomics, metabolomics, genomics and other techniques. Baseline data, group-level follow-up data and microbiological examination data are integrated together to provide an evaluation tool, exploring sarcopenia, disability, dementia, caregiver burden, ageing biomarkers and other influencing factors.Trial registration numbers 2018-463; ChiCTR1900020754.…”
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Promoter Methylation Precedes Chromosomal Alterations in Colorectal Cancer Development by Sarah Derks, Cindy Postma, Peter T. M. Moerkerk, Sandra M. van den Bosch, Beatriz Carvalho, Mario A. J. A. Hermsen, Walter Giaretti, James G. Herman, Matty P. Weijenberg, Adriaan P. de Bruïne, Gerrit A. Meijer, Manon van Engeland

“…Chromosomal alterations were evaluated by comparative genomic hybridization. Results: Our data demonstrate that nonprogressed adenomas, progressed adenomas and carcinomas show similar frequencies of promoter methylation for the majority of the genes. …”
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Genetic polymorphism of modern common flax (Linum usitatissimum L.) cultivars developed at Russian breeding centers using SSR markers by T. A. Bazanov, I. V. Ushchapovskii, V. A. Lemesh, M. V. Bahdanava, A. V. Lahunovskaya

“…Molecular identification of plant genomes, based on the use of DNA markers, is becoming a reliable tool for cultivar identification. …”
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Identification of a new alphacoronavirus (Coronaviridae: <i>Alphacoronavirus</i>) associated with the greater horseshoe bat (<i>Rhinolophus ferrumequinum</i>) in the south of Europ... by Sergey V. Lenshin, Tatyana V. Vishnevskaya, Alexey V. Romashin, Yulia I. Bulycheva, Oleg I. Vyshemirsky, Sophya A. Solovyeva, Asya K. Gitelman, Alexey S. Pazilin, Dmitry K. Lvov, Ben Hu, Zheng-Li Shi, Sergey V. Alkhovsky

“…Fecal samples were collected from bats inhabiting caves on the southern macroslope of the Greater Caucasus (Sochi-Adler region) during 2020, 2021, and 2024. Viral genomes were detected and analyzed using high-throughput sequencing (NGS) and RT-PCR. …”
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Actively protective combinatorial analysis: A scalable novel method for detecting variants that contribute to reduced disease prevalence in high-risk individuals by J Sardell, S Das, K Taylor, C Stubberfield, A Malinowski, M Strivens, S Gardner

“…We show how this can be used to identify mechanisms in the background of normal cellular biology that work to slow or stop progression of complex, chronic diseases.Actively protective combinatorial analysis identifies combinations of features that contribute to reducing risk of disease in individuals who remain healthy even though their genomic profile suggests that they have high risk of developing disease. …”
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DNA Amplifications and Aneuploidy, High Proliferative Activity and Impaired Cell Cycle Control Characterize Breast Carcinomas with Poor Prognosis by Harald Blegen, John S. Will, B. Michael Ghadimi, Hesed‐Padilla Nash, Anders Zetterberg, Gert Auer, Thomas Ried

“…In order to explore whether specific cytogenetic abnormalities can be used to stratify tumors with a distinctly different clinical course, we performed comparative genomic hybridization (CGH) of tumors from patients who were diagnosed with metastatic disease after an interval of less than 2 years or who remained free from distant metastases for more than 10 years. …”
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Decoding the trajectory of antibiotic resistance genes in saline and alkaline soils: Insights from different fertilization regimes by Dandan Zhang, Jie Li, Guilong Zhang, Yan Xu

“…Indoor experiments demonstrated that there was a survival trade-off between the growth of resistant bacteria and the evolution of antibiotic resistance in salinity and alkalinity environments. Meta-genomic and Meta-transcriptomic analysis consistently demonstrated bacterial antibiotic resistance was primarily associated with pyruvate, energy and lipid metabolic pathways. …”
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Identification of Host–Protein Interaction Network of Canine Parvovirus Capsid Protein VP2 in F81 Cells by Hongzhuan Zhou, Huanhuan Zhang, Xia Su, Fuzhou Xu, Bing Xiao, Jin Zhang, Qi Qi, Lulu Lin, Kaidi Cui, Qinqin Li, Songping Li, Bing Yang

“…Subsequently, the protein Interaction Network (PPI), the annotation of gene ontology (GO) and the database of Kyoto Encyclopedia of Genes and Genomes (KEGG) were constructed for in-depth analysis. …”
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Orthoweb: a software package for evolutionary analysis of gene networks by R. A. Ivanov, A. M. Mukhin, F. V. Kazantsev, Z. S. Mustafin, D. A. Afonnikov, Y. G. Matushkin, S. A. Lashin

“…Furthermore, it offers tools for SNP enrichment analysis, enabling the users to assess the evolutionary significance of genetic variants within specific genomic regions. A key feature of Orthoweb is its ability to integrate these indices with gene network analysis. …”
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Nuclear Intron Sequence Variation of the <i>Bulinus globosus</i> Complex (Mollusca: Planorbidae): Implications for Molecular Systematic Analyses by Chairat Tantrawatpan, Kotchaphon Vaisusuk, Chrysantus M. Tanga, Warayutt Pilap, Naruemon Bunchom, Ross H. Andrews, Tongjit Thanchomnang, Wanchai Maleewong, Weerachai Saijuntha

“…A total of 81 <i>B. globosus</i> snails were collected from three different localities in Kwale County, Kenya. Genomic diversity, heterozygosity, DNA recombination, and haplotype network were calculated using AkInt3 sequences. …”
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Interplay of aurora kinase a functional residues and Epstein-barr Nuclear Antigen 1 in Epstein-barr virus associated Gastric cancer using AGS cells by Nidhi Varshney, Siddharth Singh, Meenakshi Kandpal, Vaishali Saini, Erle S. Roberston, Hem Chandra Jha

“…Aurora Kinase A is a major mitotic protein kinase that regulates mitotic progression; overexpression and hyperactivation of AURKA commonly promote genomic instability in many tumours. However, the relationship of functional residues of AURKA and EBV in gastric cancer progression remains unknown. …”
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Oral phenotype and scoring of vascular Ehlers–Danlos syndrome: a case–control study by Lisa Golmard, Ariane Berdal, François Côme Ferré, Michael Frank, Bruno Gogly, Adrien Naveau, Hafida Chérifi, Joseph Emmerich, Frédérick Gaultier, Xavier Jeunemaitre, Benjamin P J Fournier

“…COL3A1 mutations were identified by direct sequencing of genomic or complementary DNA.Results Prevalence of gingival recession was low among patients with vEDS, as for periodontitis. …”
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Detection and Characterization of Shiga Toxin Producing Escherichia coli, Salmonella spp., and Yersinia Strains from Human, Animal, and Food Samples in San Luis, Argentina by Gabriela Isabel Favier, Cecilia Lucero Estrada, Teresa Inés Cortiñas, María Esther Escudero

“…The antimicrobial susceptibility of all the strains was studied, the genomic relationships among isolates of the same species were determined by PFGE, and the potencial virulence of Y. enterocolitica strains was analyzed. …”
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Habitat fragmentation increases the risk of local extinction of small reptiles: A case study on Phrynocephalus przewalskii by Cui Yang, Yue Qi, Jiayuan Guo, Liangfei Peng, Neng Xiong, Wenya Zhang, Wei Zhao

“…Results showed that individuals in highly fragmented areas exhibited smaller body size, higher reproductive investment, and lower genetic diversity. Genomic analyses revealed significantly fewer SNPs, INDELs, and SVs in the highly fragmented area compared to others, with the slowest linkage disequilibrium decay rate, indicating strong environmental pressure. …”
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Leveraging Single-Cell Multi-Omics to Decode Tumor Microenvironment Diversity and Therapeutic Resistance by Hussein Sabit, Borros Arneth, Timothy M. Pawlik, Shaimaa Abdel-Ghany, Aysha Ghazy, Rawan M. Abdelazeem, Amany Alqosaibi, Ibtesam S. Al-Dhuayan, Jawaher Almulhim, Noof A. Alrabiah, Ahmed Hashash

“…These technologies are able to integrate data from molecular genomic, transcriptomic, proteomics, and metabolomics studies of cells at a single-cell resolution scale that give rise to the full cellular and molecular complexity in the TME. …”
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Deciphering the nature and statistical optimization of antimicrobial metabolites of two endophytic bacilli by Raghda S. Isleem, Ahmed M. Eid, Saad El-Din Hassan, Khaled M. Aboshanab, Ghadir S. El-Housseiny

“…Both bacterial isolates displayed antioxidant and antiviral activity and mild cytotoxic action. Genomic sequence and antiSMASH analysis showed that the biosynthetic gene clusters of bacillomycin, mycosubtilin, fengycin, and macrolactin H in B. velezensis CCASU-C6 and bacillibactin and Macrolactin H in B. subtilis CCASU-C11 showed 100% conservation.…”
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The technology landscape for detection of DNA methylation in cancer liquid biopsies by Isabelle Neefs, Joe Ibrahim, Marc Peeters, Guy Van Camp, Ken Op de Beeck

“…The first methods were established for DNA methylation detection in genomic DNA, while new methods have focused more on compatibility with the emerging interest of cell-free DNA (cfDNA) from liquid biopsies. …”
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Multigene Panel Testing in Turkish Hereditary Cancer Syndrome Patients by Esra ARSLAN ATES, Ayberk TURKYILMAZ, Ceren ALAVANDA, Ozlem YILDIRIM, Ahmet Ilter GUNEY

“…In addition, 25 HCS-related genes were sequenced using a multigene panel, and variations were classified according to the American College of Medical Genetics and Genomics (ACMG) criteria. In total, 218 HCS patients predominantly with breast, colorectal, ovarian, gastric, and endometrium cancers were included. …”
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DHX37 Impacts Prognosis of Hepatocellular Carcinoma and Lung Adenocarcinoma through Immune Infiltration by Yanni Xu, Qiongchao Jiang, Hejun Liu, Xiaoyun Xiao, Dinghong Yang, Phei Er Saw, Baoming Luo

“…Coexpression genes, Gene Ontology (GO) and Kyoto Encyclopedia of Genes and Genomes (KEGG), and fundamental regulators were performed via LinkedOmics. …”
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