Investigating the Pulmonary Host Response of <i>Acinetobacter baumannii</i> Infection-Associated Pneumonia by Metagenomic Next-Generation Sequencing by Mu-Jung Chou, Chih-Hung Cheng, Hui-Ching Wang, Ming-Ju Tsai, Chau-Chyun Sheu, Wei-An Chang

“…<b>Background:</b> For investigating the host response in <i>Acinetobacter baumannii</i> associated pneumonia, we analyzed the host genetic sequences obtained from metagenomic next-generation sequencing (mNGS). …”
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Evaluation of controls, quality control assays, and protocol optimisations for PacBio HiFi sequencing on diverse and challenging samples by Iraad F. Bronner, Emma Dawson, Naomi Park, Olaf Piepenburg, Michael A. Quail

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Single-cell RNA sequencing reveals the heterogeneity and interactions of immune cells and Müller glia during zebrafish retina regeneration by Hui Xu, Lining Cao, Yuxi Chen, Cuiping Zhou, Jie Xu, Zhuolin Zhang, Xiangyu Li, Lihua Liu, Jianfeng Lu

“…Here, we used single-cell RNA sequencing to investigate the cell heterogeneity and interactions of MG and immune cells in the regenerating zebrafish retina. …”
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Validation of Simple Sequence Length Polymorphism Regions of Commonly Used Mouse Strains for Marker Assisted Speed Congenics Screening by Channabasavaiah B. Gurumurthy, Poonam S. Joshi, Scott G. Kurz, Masato Ohtsuka, Rolen M. Quadros, Donald W. Harms, K. C. Kent Lloyd

“…Traditionally, the technique is performed by analyzing PCR amplified regions of simple sequence length polymorphism (SSLP) markers between the recipient and donor strains: offspring with the highest number of markers showing the recipient genome across all chromosomes is chosen for the next generation. …”
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Exploring changes in metabolites and fecal microbiota of advanced gastric cancer based on plasma metabolomics and 16S rDNA sequencing by Xinyi Feng, Yu Zhang, Jun Feng, Zhongjun Li, Zhi Zhang, Lin Zhu, Ruoyu Zhou, Haibo Wang, Xiaojun Dai, Yanqing Liu

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Decision-Making on the Solution of a Stochastic Nonlinear Dynamical System of Kannan-Type in New Sequence Space of Soft Functions by Meshayil M. Alsolmi, Awad A. Bakery

“…In this paper, we construct and investigate the space of weighted Gamma matrix of order r in Nakano sequence space of soft functions. The idealization of the mappings has been achieved through the use of extended s-soft functions and this sequence space of soft functions. …”
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The genome sequence of Radford’s Flame Shoulder, Ochropleura leucogaster (Freyer, 1831) [version 1; peer review: 2 approved] by Mark J. Sterling, David C. Lees

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Protocol Sequence-IEEE 802.11p Based Channel Access Mechanism in VANET/LTE-Advanced Heterogeneous Network by Zhexin Xu, Lingling Cai, Xiao Lin, Yi Wu

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Correction: Detection and classification of long terminal repeat sequences in plant LTR-retrotransposons and their analysis using explainable machine learning by Jakub Horvath, Pavel Jedlicka, Marie Kratka, Zdenek Kubat, Eduard Kejnovsky, Matej Lexa

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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

“…Genomic diversity, heterozygosity, DNA recombination, and haplotype network were calculated using AkInt3 sequences. Low polymorphism in the <i>COI</i> sequence divided <i>B. globosus</i> into six haplotypes (C1–C6). …”
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Identification of an Autophagy-Related Signature Based on Whole Bone Marrow Sequencing for the Prognosis and Immune Microenvironment Characterization of Multiple Myeloma by Licheng Li, Ting Chen, Jishi Wang, Mengxing Li, Qinshan Li

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Analysis of KRAS Mutations of Exon 2 Codons 12 and 13 by SNaPshot Analysis in Comparison to Common DNA Sequencing by Rica Zinsky, Servet Bölükbas, Holger Bartsch, Joachim Schirren, Annette Fisseler-Eckhoff

“…Under this aspect, the sensitivity and specificity of the SNaPshot analysis in comparison to the commonly used DNA sequencing was checked. We examined KRAS mutations in exon 2 codons 12 and 13 with DNA sequencing and SNaPshot analysis in 100 formalin-fixed paraffin-embedded tumor tissue samples of pancreatic carcinoma, colorectal carcinoma, and nonsmall cell lung cancer specimens of the primary tumor or metastases. 40% of these samples demonstrated mutated KRAS genes using sequencing and SNaPshot-analysis; additional five samples (45/100) were identified only with the SNaPshot. …”
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Transcriptome, miRNA, and degradome sequencing reveal the leaf stripe (Pyrenophora graminea) resistance genes in Tibetan hulless barley by Yue Wang, Qian Hu, Youhua Yao, Yongmei Cui, Yixiong Bai, Likun An, Xin Li, Baojun Ding, Xiaohua Yao, Kunlun Wu

“…Using RNA-seq, small RNA sequencing (miRNA-seq) combined with degradome sequencing (degradome-seq), four pairs associated with leaf-stripe miRNAs and target genes were obtained, namely Hvu-miR168-5p and Argonaute1 (HvAGO1), Hvu-novel-52 and growth-regulating factor 6 (HvGRF6), Hvu-miR6195 and chemocyanin-like protein (CLP), and Hvu-miR159b and gibberellin-dependent MYB (GAMYB). …”
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Exome sequencing reveals a rare damaging variant in GRIN2C in familial late-onset Alzheimer's disease by Elisa Rubino, Maria Italia, Elisa Giorgio, Silvia Boschi, Paola Dimartino, Tommaso Pippucci, Fausto Roveta, Clara Maria Cambria, Gabriella Elia, Andrea Marcinnò, Salvatore Gallone, Ekaterina Rogaeva, Flavia Antonucci, Alfredo Brusco, Fabrizio Gardoni, Innocenzo Rainero

“…Genomic DNA from family members was extracted and initially screened for pathogenic mutations in APP, PSEN1, and PSEN2, and screened for 77 genes associated with neurodegenerative conditions using NeuroX array assay. Exome sequencing was performed on three affected individuals and two healthy relatives. …”
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Evaluating the droplet digital PCR and direct Sanger sequencing for the detection of the BRAFV600E mutation in papillary thyroid carcinoma by Akankshya Dash, Chinnasamy Ragavendran

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Combined analysis of 16S rRNA gene sequencing data reveals core vaginal bacteria across livestock species by Lucille C. Jonas, Lucille C. Jonas, Curtis R. Youngs, Stephan Schmitz-Esser, Stephan Schmitz-Esser

“…To address this variability, we conducted a combined analysis of publicly available 16S rRNA gene amplicon sequencing datasets to reveal the core vaginal microbiota in cattle, sheep, and pigs. …”
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Application of Sequence-Dependent Electrophoresis Fingerprinting in Exploring Biodiversity and Population Dynamics of Human Intestinal Microbiota: What Can Be Revealed? by Geert Huys, Tom Vanhoutte, Peter Vandamme

“…Sequence-dependent electrophoresis (SDE) fingerprinting techniques such as denaturing gradient gel electrophoresis (DGGE) have become commonplace in the field of molecular microbial ecology. …”
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Uncovering potential causal genes for undiagnosed congenital anomalies using an in-house pipeline for trio-based whole-genome sequencing by Jeong-Min Kim, Hye-Won Cho, Dong Mun Shin, Oc-Hee Kim, Jihyun Kim, Hyeji Lee, Gang-Hee Lee, Joon-Yong An, Misun Yang, Heui Seung Jo, Ja-Hyun Jang, Yun Sil Chang, Hyun-Young Park, Mi-Hyun Park

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Identification of Nontuberculous Mycobacteria in Patients with Pulmonary Diseases in Gyeongnam, Korea, Using Multiplex PCR and Multigene Sequence-Based Analysis by Min-Jeong Kim, Kyu-Min Kim, Jeong-Ih Shin, Jong-Hun Ha, Dong-Hae Lee, Jeong-Gyu Choi, Jin-Sik Park, Jung-Hyun Byun, Jung-Wan Yoo, Seokyong Eum, Myunghwan Jung, Seung Chul Baik, Woo Kon Lee, Hyung Lyun Kang, Min-Kyoung Shin

“…In this study, two-step multiplex PCR (mPCR) and multigene sequence-based analysis were used to accurately identify NTM species in 320 clinical isolates from Gyeongsang National University Hospital (GNUH). …”
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Comparing subsampling strategies for metagenomic analysis in microbial studies using amplicon sequence variants versus operational taxonomic units by Daniel Segura, Divya Sharma, Osvaldo Espin-Garcia

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