Inhibitory Effects of Apigenin on Tumor Carcinogenesis by Altering the Gut Microbiota by Shichang Bian, Hongjuan Wan, Xinyan Liao, Weisheng Wang

“…Using 16S rRNA high-throughput sequencing of fecal samples, the composition of gut microbiota was significantly affected by apigenin. …”
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Nature of viruses and the radical change in viral taxonomy by V. V. Makarov, L. P. Buchatsky

“…A short report is devoted to the radical changes in the taxonomy of viruses. The metagenomic sequencing has revealed the presence of a vast variety of viruses in diverse environmental samples without any connections with banal parasitism, infectivity, or pathogenicity. …”
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Association of PIK3CA somatic mutations with clinicopathological parameters in breast cancer by Gizem Teoman, Zeynep Turkmen Usta, Zeynep Sagnak Yilmaz, Sevdegul Aydin Mungan, Ismail Saygin

“…We conducted a mutational investigation of the PIK3CA gene using next-generation sequencing (NGS) in a sample of 100 cases of primary breast cancer. …”
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MAGEB2-Mediated Degradation of EGR1 Regulates the Proliferation and Apoptosis of Human Spermatogonial Stem Cell Lines by Xueheng Zhao, Zenghui Huang, Yongzhe Chen, Qianyin Zhou, Fang Zhu, Huan Zhang, Dai Zhou

“…Here, we analyzed normal human testis single-cell sequencing data from the GEO dataset (GSE149512 and GSE112013). …”
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Comparative metagenomics reveals the metabolic flexibility of coastal prokaryotic microbiomes contributing to lignin degradation by Qiannan Peng, Lu Lin

“…Using read-based analysis, 16S rRNA amplicon and metagenomic sequencing suggested that these consortia possessed varied taxonomic compositions, yet similar functional traits. …”
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Acute Necrotizing Fasciitis Caused by Rhizopus Infection in a Patient with Diabetes and Pulmonary Tuberculosis: A Case Report by Huang X, Qiu J, Pan L, Wang C, Tang C

“…Metagenomic next-generation sequencing (mNGS) facilitated a swift diagnosis, identifying R. oryzae in blood and drainage samples. …”
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Transformation of brain myeloid cell populations by SIV in rhesus macaques revealed by multiomics by Xiaoke Xu, Meng Niu, Benjamin G. Lamberty, Katy Emanuel, Moses Jedd Facun Apostol, Howard S. Fox

“…Given the gaps in our knowledge on how these cells respond in vivo to CNS infection, we perform single-cell multiomic sequencing, including gene expression and ATAC-seq, on myeloid cells from the brains of rhesus macaques with SIV-induced encephalitis (SIVE) as well as uninfected controls. …”
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Nocardia thailandica Brain Abscess in an Immunocompromised Patient by Muhammad Effendi, Samad Tirmizi, Dayna McManus, Anita J. Huttner, David R. Peaper, Jeffrey E. Topal

“…Upon identification by 16S rDNA sequencing, the organism causing infection was identified to be N. thailandica. …”
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Ontology-based expansion of virtual gene panels to improve diagnostic efficiency for rare genetic diseases by Jaemoon Shin, Toyofumi Fujiwara, Hirotomo Saitsu, Atsuko Yamaguchi

“…Abstract Background Virtual Gene Panels (VGP) comprising disease-associated causal genes are utilized in the diagnosis of rare genetic diseases to evaluate candidate genes identified by whole-genome and whole-exome sequencing. VGPs generated by the PanelApp software were utilized in a UK 100,000 Genome Project pilot study to filter candidate genes, thus enhancing diagnostic efficiency for rare diseases. …”
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Molecular Characterization of Chicken Anemia Virus Circulating in Chicken Flocks in Egypt by Mohammed AboElkhair, Alaa G. Abd El-Razak, Abd Elnaby Y. Metwally

“…In the present study, four nucleotide sequences of detected CAV were genetically characterized. …”
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Regulation of Long Noncoding RNAs Responsive to Phytoplasma Infection in Paulownia tomentosa by Guoqiang Fan, Yabing Cao, Zhe Wang

“…Here, whole-genome identification of lncRNAs, based on strand-specific RNA sequencing, from four Paulownia tomentosa samples, was performed and identified 3689 lncRNAs. …”
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Using GIS-Based Tools for the Optimization of Solid Waste Collection and Transport: Case Study of Sfax City, Tunisia by Amjad Kallel, Mohamed Moncef Serbaji, Moncef Zairi

“…The actual state (Scenario S0) was evaluated, and by modifying its particular parameters, other scenarios were generated and analyzed to identify optimal routes: S1, route optimized with the same working resources (change of stops sequencing only); S2, route optimized with change of vehicles; and S3, route optimized with change of collection method (vehicles and reallocation of bins). …”
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Characterization of a pleomorphic rhabdomyosarcoma cell line by Sandra Stickler, Clemens Lang, Maximilian Rieche, Marie-Therese Eggerstorfer, Martin Hohenegger, Maximilian Hochmair, Gerhard Hamilton

“…Results of the novel functional BH1522 tests corroborate published tumor sequencing data that demonstrated alterations in receptor tyrosine kinase/MAPK, PI3K/AKT and mutated p53 as suspected drivers of malignant growth.…”
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Integrating Prior Knowledge Using Transformer for Gene Regulatory Network Inference by Guangzheng Weng, Patrick Martin, Hyobin Kim, Kyoung Jae Won

“…Here, this work presents GRNPT, a novel Transformer‐based framework that integrates large language model (LLM) embeddings from publicly accessible biological data and a temporal convolutional network (TCN) autoencoder to capture regulatory patterns from single‐cell RNA sequencing (scRNA‐seq) trajectories. GRNPT significantly outperforms both supervised and unsupervised methods in inferring GRNs, particularly when training data is limited. …”
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An Independent Prognostic Model Based on Ten Autophagy-Related Long Noncoding RNAs in Pancreatic Cancer Patients by Jiahui Tian, Chunyan Fu, Xuan Zeng, Xiaoxiao Fan, Yi Wu

“…Methods. We obtained RNA sequencing and clinical data of patients from the TCGA website. …”
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Advancing Insights into Large-Artery Stiffening in Humans Through the Application of Multi-omics by Marie-Joe Dib

“…This review aims to (i) provide an overview of insights from genetic research on LAS pathophysiology, and explore the scope of next-generation sequencing methods in the field arterial research; (ii) shed light on the utility of emerging state-of-the-art multi-omics approaches to unravel mechanisms underlying LAS to identify candidate therapeutic targets; (iii) highlight the potential of emerging state-of-the-art integrative multi-omics, motivating their use to address current gaps in understanding sex- and ancestry-specific mechanisms of LAS.…”
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Complete genome of mangrove-derived anti-MRSA streptomycete, Streptomyces pluripotens MUSC 135T by Hooi-Leng Ser, Kok-Gan Chan, Wen-Si Tan, Wai-Fong Yin, Bey-Hing Goh, Nurul-Syakima Ab Mutalib, Learn-Han Lee

“…Thus, the strain was selected for whole genome sequencing as an attempt to explore its bioactive potential. …”
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Gut Inflammation and Immunity: What Is the Role of the Human Gut Virome? by Alfredo Focà, Maria Carla Liberto, Angela Quirino, Nadia Marascio, Emilia Zicca, Grazia Pavia

“…The development of high-throughput sequencing techniques has shown that the human gut microbiome is a complex community in which the virome plays a crucial role into regulation of intestinal immunity and homeostasis. …”
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Causality-driven candidate identification for reliable DNA methylation biomarker discovery by Xinlu Tang, Rui Guo, Zhanfeng Mo, Wenli Fu, Xiaohua Qian

“…The comprehensive reliability of the proposed method was verified by simulations and applications involving various human diseases, sample origins, and sequencing technologies, highlighting its universal biomedical significance. …”
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The role of lipids in promoting hair growth through HIF-1 signaling pathway by Jieun Seo, Kotone Matsumoto, Ayaka Nanmo, Shan Tu, Do-Won Jeong, Yang-Sook Chun, Lei Yan, Tatsuto Kageyama, Junji Fukuda

“…Lipid supplementation in the culture medium upregulated hair growth-related genes and promoted the proliferation of human dermal papilla cells (DPCs). By using RNA-sequencing analysis and HIF-1α knockdown in DPCs, we found that HIF-1α is a potential candidate that governs lipid-reinforced upregulation of trichogenic genes. …”
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