Genetic Diversity of a Wild <i>Actinidia arguta</i> Population in Changbai Mountain Determined by Simple Sequence Repeat Markers by Xiaowu Sun, Guangli Shi, Songze Li, Jun Ai, Dan Sun, Zhenxing Wang, Peijin Ni, Zhendong Zhang, Shuaiming Chen, Zelong Du, Xiang Li, Fan Zhang

“…In this study, 31 simple sequence repeat (SSR) markers were used to identify 148 wild <i>A. arguta</i> germplasms from six natural populations in Changbai Mountain, China, and the genetic diversity of their leaf quality traits was subsequently evaluated. …”
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Antimicrobial strategies of lower respiratory tract infections in immunocompromised patients based on metagenomic next-generation sequencing: a retrospective study by Beibei Meng, Haichao Liu, Qinliang Wu, Lei Qu, Congzheng Mao, Fang Yang, Tianzhou Lan, Juan Fang, Zhenhong Hu, Yao Fang

“…The objective of this study is to evaluate the clinical applicability of metagenomic next-generation sequencing (mNGS) in the diagnosis and management of LRTI, as well as its impact on empirical antibacterial therapy for patients with varying immune statuses. …”
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Prevalence and Whole Genome Sequence Analysis of Mycoplasma bovis Isolates From Bulk Tank Milk of Dairy Farms in Tennessee, USA by Aga E. Gelgie, Benti D. Gelalcha, Daniel Christensen, Trevor Freeman, Jonathan E. Beever, Oudessa Kerro Dego

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Identification of cuproptosis-related genes in chronic apical periodontitis based on bulk and single-cell RNA sequencing analyses and experimental validation by Caiyi Zhang, Jie Zhao, Keqing Pan, Lingshuang Liu, Mengyu Jiao, Changqing Yuan, Chunyan Wan

“…Additionally, Receiver Operating Characteristic (ROC) curves were employed to evaluate the discriminatory ability of gene features. …”
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Epidemiological and molecular characterization of Enterobius vermicularis cases in Mersin, Turkey: An analysis based on mitochondrial DNA cox1 gene sequences by Harun Gülbudak, Seda Tezcan Ülger, Taylan Bozok, Gönül Aslan

“…DNA was isolated from 30 positive samples via the phenol–chloroform method, and nested PCR products of the cox1 gene were sequenced. Phylogenetic analyses were performed using GenBank sequences. …”
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In Silico Analysis of Cross-Species Sequence Variability in Host Interferon Antiviral Pathway Proteins and SARS-CoV-2 Susceptibility by Sally A. Mayasich, Peter G. Schumann, Maxwell Botz, Carlie A. LaLone

“…The SARS-CoV-2 spike protein binds to the host’s angiotensin converting enzyme 2 (ACE2) cell surface receptor to gain entry into the cell. ACE2 protein sequence conservation has therefore been evaluated across species, and species with amino acid substitutions in ACE2 were ranked low for susceptibility to SARS-CoV-2 infection. …”
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Single-Cell RNA Sequencing on Formalin-Fixed and Paraffin-Embedded (FFPE) Tissue Identified Multi-Ciliary Cells in Breast Cancer by Silvia González-Martínez, José Palacios, Irene Carretero-Barrio, Val F. Lanza, Mónica García-Cosío Piqueras, Tamara Caniego-Casas, David Hardisson, Isabel Esteban-Rodríguez, Javier Cortés, Belén Pérez-Mies

“…The purpose of this study was to evaluate the suitability of formalin-fixed and paraffin-embedded (FFPE) samples and fixed fresh (FF) samples for single-cell RNA sequencing (scRNAseq). …”
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Predicting the clinical subcutaneous absorption rate constant of monoclonal antibodies using only the primary sequence: a machine learning approach by Ronghua Bei, Justin Thomas, Shiven Kapur, Mahlet Woldeyes, Adam Rauk, Jason Robarge, Jiangyan Feng, Kaoutar Abbou Oucherif

“…Taken altogether, this study reports the development, validation, benchmarking, and interpretation of a model that can predict the clinical ka of a mAb using its primary sequence as the only input.…”
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An innovative fungal-specific targeted next-generation sequencing method: analytical performance and a single-center prospective clinical study by Ruixuan Wang, Shitong Cheng, Wei Du, Fengshuo Sun, Yang Gao, Zheming Zhu, Chuan He, Jingjing Chen, Sufei Tian, Yunzhuo Chu, Gang Zhou, Hui Miao, Lifeng Li, Xiaolong Dong, Xiaoxu Han

“…While metagenomic next-generation sequencing (mNGS) is widely utilized, it is expensive and affected by host DNA interference. …”
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The clinical management and efficacy of metagenomic next-generation sequencing in patients with pyogenic spinal infection: a single-center cohort study by Maoyang Qi, Yueqi Du, Jian Guan, Jiao Ma, Wenwen Li, Zan Chen, Wanru Duan

“…Abstract Objective This study aims to evaluate the clinical management and effectiveness of metagenomic next-generation sequencing (mNGS) in patients with pyogenic spinal infections. …”
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A Customized Next-Generation Sequencing-Based Panel to Identify Novel Genetic Variants in Dementing Disorders: A Pilot Study by Giuseppe Lanza, Francesco Calì, Mirella Vinci, Filomena Irene Ilaria Cosentino, Mariangela Tripodi, Rosario Sebastiano Spada, Mariagiovanna Cantone, Rita Bella, Teresa Mattina, Raffaele Ferri

“…The advancements in the next-generation sequencing (NGS) techniques have allowed for rapid, efficient, and cost-time-effective genetic variant detection. …”
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Identifying a prognostic signature for clear cell renal cell carcinoma: the convergence of single-cell and bulk sequencing with machine learning by Yude Hong, Xiao Hu, Libo Chen, Mingyong Li, Mingxiao Zhang, Weiming Deng

“…Various methods were used to evaluate immune cell infiltration and biological characteristics. …”
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Unveiling macrophage dynamics and efferocytosis-related targets in diabetic kidney disease: insights from single-cell and bulk RNA-sequencing by Binshan Zhang, Yunqi Wu, Zhongli Wang, Suhua Gao, Hongyan Liu, Yao Lin, Pei Yu, Pei Yu

“…Differential expression genes (DEGs) from macrophage subgroups and bulk RNA-sequencing were used to identify shared hub genes. The NephroseqV5 platform was employed to evaluate the clinical significance, and the expression of key molecules was validated in DKD tissues.ResultsMacrophage infiltration rose in DKD, causing inflammation through the release of chemokines. …”
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A retrospective analysis comparing metagenomic next-generation sequencing with conventional microbiology testing for the identification of pathogens in patients with severe infecti... by Fei Hou, Fei Hou, Yanting Qiao, Yuanyuan Qiao, Ya Shi, Mingrui Chen, Min Kong, Min Kong, Xiaohang Hu, Liqing Jiang, Xiaowei Liu

“…IntroductionThe application value of metagenomic next-generation sequencing (mNGS) in detecting pathogenic bacteria was evaluated to promote the rational and accurate use of antibiotics. …”
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PRONAME: a user-friendly pipeline to process long-read nanopore metabarcoding data by generating high-quality consensus sequences by Benjamin Dubois, Mathieu Delitte, Salomé Lengrand, Claude Bragard, Anne Legrève, Frédéric Debode

“…Evaluations using a mock community have shown that PRONAME delivers consensus sequences demonstrating at least 99.5% accuracy with standard settings (and up to 99.7%), making it a robust tool for genomic analysis of complex multi-species communities.ConclusionPRONAME meets the challenges of long-read Nanopore data processing, offering greater accuracy and versatility than existing pipelines. …”
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Identification of a rare variant in TNNT3 responsible for familial dilated cardiomyopathy through whole-exome sequencing and in silico analysis by Motahareh Jadidi, Vida Babaali, Kolsoum InanlooRahatloo, Najmeh Salehi, Reza Mollazadeh

“…Co-segregation analysis was conducted using Sanger sequencing. Protein structure modeling and protein–protein interaction evaluations were performed using AlphaFold3 and HADDOCK2.4, respectively. …”
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Development of a quantitative PMA-16S rRNA gene sequencing workflow for absolute abundance measurements of seawater microbial communities by Marie C. Thomas, Gretel Waugh, Katarina Damjanovic, Inka Vanwonterghem, Nicole S. Webster, Andrew P. Negri, Heidi M. Luter

“…Incorporating microbial community responses into these evaluations requires establishing sensitivity thresholds based on the absolute abundance of viable taxa. …”
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A systematic review of the microbiome of Hyalomma Koch, 1844 ticks using next-generation sequencing of the 16S ribosomal RNA gene by Mohamad Taha Al Masri, Mohammad Ali Al-Deeb

“…The search covered studies published between 2014 and 2024 employing 16S ribosomal RNA gene sequencing to analyze microbiomes of Hyalomma ticks within the MENA region. …”
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Ventricular function assessment using an ultrafast spoiled gradient echo sequence with an intravascular blood pool contrast agent in pediatric patients. by Tayaba Miah, Rithvik Gunda, Gerald Greil, Mohammad Hussain, Qing Zou

“…Paired t-tests were used to assess significant differences in volumetric values (end-diastolic and end-systolic) between T1-TFE and bSSFP sequences. A Bland-Altman analysis evaluated potential bias and agreement between these sequences.…”
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Uncovering dendritic cell specific biomarkers for diagnosis and prognosis of cardiomyopathy using single cell RNA sequencing and comprehensive bioinformatics analysis by Md. Mizanur Rahman, Md Habibur Rahman, Md. Arju Hossain, Kh Mujahidul Islam, Prosenjit Saha Apu, Mahfuj Khan, Md Golam Kibria, Siddique Akber Ansari, Mahammad Humayoo

“…Two RNAseq datasets GSE65446 and GSE155495 also were evaluated to identify significant biomarkers in cardiomyopathy, and 123 mutual DEGs appeared between scRNAseq and RNAseq datasets. …”
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