Persistent functional and taxonomic groups dominate an 8,000-year sedimentary sequence from Lake Cadagno, Switzerland by Paula Rodriguez, Jasmine S. Berg, Longhui Deng, Longhui Deng, Hendrik Vogel, Michal Okoniewski, Mark A. Lever, Mark A. Lever, Cara Magnabosco

“…Despite these dramatic changes in taxonomic community composition and sediment geochemistry throughout the sediment core, higher-order functional categories and metabolic marker gene abundances remain relatively consistent and indicate a microbial community capable of carbon fixation, fermentation, dissimilatory sulfate reduction and dissimilatory nitrate reduction to ammonium. …”
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Large scale loss of data in low-diversity illumina sequencing libraries can be recovered by deferred cluster calling. by Felix Krueger, Simon R Andrews, Cameron S Osborne

“…Massively parallel DNA sequencing is capable of sequencing tens of millions of DNA fragments at the same time. …”
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Genotyping-by-Sequencing of the regional Pacific abalone (Haliotis discus) genomes reveals population structures and patterns of gene flow. by Bo-Hye Nam, Hyaekang Kim, Donghyeok Seol, Heebal Kim, Eun Soo Noh, Eun Mi Kim, Jae Koo Noh, Young-Ok Kim, Jung Youn Park, Woori Kwak

“…Continuous monitoring of the present genetic status is essential to preserve the genetic resource of wild populations. In this study, we sequenced regional Pacific abalone Haliotis discus samples from three different locations around the Korean peninsula to assess population structure, utilizing Genotyping-by-Sequencing (GBS) method. …”
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Codon Usage in Signal Sequences Affects Protein Expression and Secretion Using Baculovirus/Insect Cell Expression System. by Yalan Wang, Yuanhui Mao, Xiaodong Xu, Shiheng Tao, Hongying Chen

“…By introducing synonymous mutations into the coding sequences of GP64sp and FibHsp signal peptides, the influences of mRNA secondary structure and codon usage of signal sequences on protein expression and secretion were investigated using baculovirus/insect cell expression system. …”
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Distribution and amplification of interstitial telomeric sequences (ITSs) in Australian dragon lizards support frequent chromosome fusions in Iguania. by Kornsorn Srikulnath, Bhumika Azad, Worapong Singchat, Tariq Ezaz

“…Telomeric sequences are generally located at the ends of chromosomes; however, they can also be found in non-terminal chromosomal regions when they are known as interstitial telomeric sequences (ITSs). …”
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A Compressed Sequence Tag Index for Fast Peptide Retrieval and Efficient Storage in Protein Identification Search Engines by Xiaoyu Xie, Yuyue Feng, Piyu Zhou, Di Zhang, Lijin Yao, Haipeng Wang

“…This algorithm utilizes the sequence tag index constructed by STIP for peptide sequence retrieval. …”
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18S rDNA next-generation sequencing uncovers the biodiversity of Gastrointestinal parasites in Tibetan grazing ruminants in China by Siran Wu, Ying Zhong, Haitao Li, Chen Tang, Bin Zhang, Runhui Zhang

“…Juveniles and adults shared the similar species of parasites. A significant reduction in helminth diversity and infection prevalence was documented during autumn. …”
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Myeloid dendritic cells and periodontal disease association: integrated study of single-cell sequencing and Mendelian randomization analysis by ChengJi Shi, XinYi Ou, XiaoXu Lei, LiJuan Huang, ShuHao Xu, Wei Li, Xi Zhao

“…Despite advancements in therapeutic interventions and an enhanced understanding of its pathophysiology, emerging techniques such as single-cell RNA sequencing (scRNA-seq) and Mendelian randomization (MR) present new opportunities for precision medicine in the management of periodontal disease.MethodsData derived from the GSE152042 dataset underwent rigorous quality control, normalization, and dimensionality reduction using Seurat and the MonacoImmuneData framework. …”
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16S rRNA Sequencing and Metabolomics to Analyze Correlation Between Fecal Flora and Metabolites of Squabs and Parent Pigeons by Xiaobin Li, Shengchen Zheng, Haiying Li, Jiajia Liu, Fan Yang, Xiaoyu Zhao, Yafei Liang

“…Fecal samples were collected at 15 days of age, and differences in the microbiota and metabolites between the two groups were analyzed using 16S rRNA sequencing and LC-MS/MS. The results showed the following: (1) Squabs exhibited significantly lower α diversity, with a reduction in their Chao1 index and observed OTUs compared to the parent pigeons. (2) Firmicutes dominated the fecal microbiota in both groups, but parent pigeon feces showed a notably higher abundance of Proteobacteria. …”
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Variants in Nucleotide Sequences; Gene Expression; and Hematological, Immune, and Antioxidant Biomarkers Linked to Pneumonia Risk in Holstein Calves by Ahmed El-Sayed, Attia Eissa, Doaa Ebrahim, Ahmed Ateya, Hossam Gadalla, Hanan M. Alharbi, Khairiah M. Alwutayd, Manal A. Babaker, Aya Aly Elzeer

“…The pneumonic and healthy calves were found to differ in the nucleotide sequences of the genes under analysis. In pneumonic calves, a substantial (<i>p</i> ˂0.05) reduction was detected in RBCs, Hb count, PCV%, and lymphocytes count, and a notable (<i>p</i> ˂ 0.05) increase in WBCs and neutrophil count was correlated with healthy control calves. …”
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An advanced 10K SNP panel for genotyping tomato (Solanum lycopersicum L.) via targeted genome sequencing by Yawo Mawunyo Nevame Adedze, Yanfen Xu, Song Liu, Yaran Zhao, Changjuan Mo, Renxu Zhang, Jiahui Dong, Haofa Lan, Jingjing Huang, Xingming Chen, Xuefei Gao, Qingzhen Yin, Jianan Zhang

“…IntroductionRecent breakthroughs in genomics have facilitated the identification of single nucleotide polymorphisms (SNPs) and small insertions-deletions (InDels). With the reduction in sequencing costs, a variety of genotyping tools have emerged for genetic analysis in plants. …”
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Evaluation of the loading capacity and patterns of packaged DNA in AAV genomes of different sizes using long-read sequencing by Mitsuki Kosaka, Ai Fujita Sajiki, Kosuke Fujita, Kazuhisa Yamada, Kenichi Kawano, Kiichi Hirazawa, Tsuyoshi Matsuno, Masahiko Takada, Nobuhiro Shimozawa, Ken-ichi Inoue, Kenya Yuki, Koji M. Nishiguchi

“…Herein, nanopore long-read sequencing was used to evaluate genomic integrity in AAV vectors harboring genomes of various sizes. …”
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Refinement of the Reference Viral Database (RVDB) for improving bioinformatics analysis of virus detection by high-throughput sequencing (HTS) by Pei-Ju Chin, Jaysheel D. Bhavsar, Trent J. Bosma, Madolyn L. MacDonald, Shawn W. Polson, Arifa S. Khan

“…Additionally, the use of animals is discouraged by the global 3 R’s initiative for replacement, reduction, and refinement. High-throughput or next-generation sequencing (HTS/NGS) technologies can rapidly detect known and novel viruses in biological materials. …”
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Integration of single-cell sequencing and drug sensitivity profiling reveals an 11-gene prognostic model for liver cancer by Qunfang Zhou, Jingqiang Wu, Jiaxin Bei, Zixuan Zhai, Xiuzhen Chen, Wei Liang, Jing Meng, Mingyu Liu

“…Results Dimensionality reduction and clustering of 34 single-cell samples identified five subgroups, with epithelial cells further classified. …”
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Analysis and validation of characteristic genes in RNA sequencing datasets from heart failure patients based on multiple algorithms by Yuxuan Li, Ying Bai, Wujiao Wang, Zhaotian Ma, Peng Li, Dong Li, Sinai Li, Jialin Jin, Jialin Jin, Qian Lin

“…Single-cell data dimensionality reduction, clustering, and visualization were achieved using Principal component analysis (PCA) and uniform manifold approximation and projection (UMAP). …”
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Whole-genome sequencing and metagenomics reveal diversity and prevalence of Listeria spp. from soil in the Nantahala National Forest by Jia Wang, Claire N. Schamp, Lauren K. Hudson, Harleen K. Chaggar, Daniel W. Bryan, Katie N. Garman, Mark Radosevich, Thomas G. Denes

“…Recently, metagenomic sequencing has also been explored as a tool for the detection of Listeria spp. in environmental samples. …”
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Single-cell RNA sequencing uncovers abnormal Sertoli-cell elevation and testicular niche impairment in the transfemales’s testis by Jun Yu, Longfei Hu, Huixia Li, Xiaofeng Li, Chaoye Ma, Ting Jiang, Yongxin Liu, Xue Wang, Xia Li, Liandong Zuo, Haocheng Lin, Wenming Xu, Yiwen Zhou, Yang Liu, Hao Chen

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Joint analysis of single-cell RNA sequencing and bulk transcriptome reveals the heterogeneity of the urea cycle of astrocytes in glioblastoma by Minfeng Tong, Qi Tu, Lude Wang, Huahui Chen, Xing Wan, Zhijian Xu

“…Background: Glioblastoma (GB) is incurable with a dismal prognosis. Single-cell RNA sequencing (scRNA-seq) is a pivotal tool for studying tumor heterogeneity. …”
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In Vitro Study Comparing SARS-CoV-2 Ancestral and Omicron Lineages Sequence &amp; Neutralization Differences by Ms Ashley Burroughs, Dr Clinton Paden, Neha Mittal, Juan Castro, Peter Cook, Sandra Lester, Heather Hicks, Dr. Azaibi Tamin, Fatimah Dawood, Jennifer DeCuir, Diya Surie, Dr. Melissa M Coughlin, Dr. Jennifer L. Harcourt, Dr. Natalie J. Thornburg, Dr. Lydia J. Atherton

“…This study compared sequence changes in the spike protein of SARS-CoV-2 between ancestral WA1/2020 and Omicron lineages and evaluated the impact of those sequence differences on neutralization. …”
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Forest fragmentation in the Brazilian Amazon: Trends and conservation strategies by Pedro Trejo, Claudia Azevedo-Ramos, Felipe Lenti

“…The trajectory of forest fragmentation (sequence, permanence, and location) offers valuable insights for shaping environmental strategies. …”
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