Optimized convolutional neural network using African vulture optimization algorithm for the detection of exons by K. Jayasree, Malaya Kumar Hota

“…Abstract The detection of exons is an important area of research in genomic sequence analysis. Many signal-processing methods have been established successfully for detecting the exons based on their periodicity property. …”
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Accelerating next generation sequencing data analysis: an evaluation of optimized best practices for Genome Analysis Toolkit algorithms by Karl R. Franke, Erin L. Crowgey

“…Parabricks was able to process a 50× whole-genome sequencing library in under 3 h and Sentieon finished in under 8 h, whereas GATK v4.1.0 needed nearly 24 h. …”
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Role of plasmids in antibiotic resistance in clinical infections and implications for epidemiological surveillance: a review by Ayodele Oluwaseun Ajayi, Olajide Joseph Akinjogunla, Adebowale Toba Odeyemi, Akinyomade Oladipo Owolabi

“…Recent technologies like replicon typing and whole genome sequencing (WGS) have become the gold standard for molecular epidemiology of plasmids for the detection and control of epidemics in clinical settings. …”
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Long journey of 16S rRNA‐amplicon sequencing toward cell‐based functional bacterial microbiota characterization by Jianshi Jin, Xiongduo Liu, Katsuyuki Shiroguchi

“…Furthermore, we present the prospects for further technical development, including the combined use of high‐throughput methods and other informative analyses, such as whole‐genome sequencing in the common unit of the cell, which enables bacterial microbiota characterization based on both the number of cells and their functions.…”
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COVID-19 Whole-Genome Resequencing with Redundant Tiling PCR and Subtract-Based Amplicon Normalization Successfully Characterized SARS-CoV-2 Variants in Clinical Specimens by Tatsuki Sugi, Mizanur Rahman, Rummana Rahim, Abu Hasan, Naoko Kawai, Kyoko Hayashida, Junya Yamagishi

“…With an increasing number of severe acute respiratory syndrome coronavirus-2 (SARS-CoV-2) sequences gathered worldwide, we recognize that deletion mutants and nucleotide substitutions that may affect whole-genome sequencing are accumulating. Here, we propose an additional strategy for tiling PCR for whole-genome resequencing, which can make the pipeline robust for mutations at the primer annealing site by a redundant amplicon scheme. …”
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A sequencing-based method for quantifying gene-deletion mutants of bacteria in the intracellular environment by Xiao Fei, Xiao Fei, Zengzhi Yuan, Zengzhi Yuan, Sandra Marina Wellner, Yibing Ma, John Elmerdahl Olsen

“…Notably, the simplicity and standardization of the method, rooted in standard whole-genome sequencing protocols, make it easily implementable across various laboratories.…”
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Intratumor heterogeneity of HPV integration in HPV-associated head and neck cancer by Noah Sasa, Toshihiro Kishikawa, Masashi Mori, Rie Ito, Yumie Mizoro, Masami Suzuki, Hirotaka Eguchi, Hidenori Tanaka, Takahito Fukusumi, Motoyuki Suzuki, Yukinori Takenaka, Keisuke Nimura, Yukinori Okada, Hidenori Inohara

“…Abstract Integration of human papillomavirus (HPV) into the host genome drives HPV-positive head and neck squamous cell carcinoma (HPV+ HNSCC). Whole-genome sequencing of 51 tumors revealed intratumor heterogeneity of HPV integration, with 44% of breakpoints subclonal, and a biased distribution of integration breakpoints across the HPV genome. …”
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Reverse Genetic Strategies in Caenorhabditis elegans: Towards Controlled Manipulation of the Genome by Howard A. Baylis, Rafael P. Vázquez-Manrique

“…Caenorhabditis elegans has a complete annotated genome sequence that is augmented by increasing quantities of data from high-throughput postgenomic analyses. …”
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Emergence and clonal dissemination of KPC-2- and NDM-1-coharboring Citrobacter freundii in China with an IncR plasmid by Juanjuan Zhou, Minghui Zhen, Kaijie Gao, Lu Xu, Dongyu Zhang, Junmei Yang

“…Comprehensive characterization, including antimicrobial susceptibility testing, plasmid conjugation, whole-genome sequencing, and comparative genomics, was conducted for these clinical strains. …”
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Genomic detection of Panton-Valentine Leucocidins encoding genes, virulence factors and distribution of antiseptic resistance determinants among Methicillin-resistant S. aureus iso... by Masoud A. Juma, Tolbert Sonda, Boaz Wadugu, Davis Kuchaka, Mariana Shayo, Petro Paulo, Patrick Kimu, Livin E. Kanje, Melkiory Beti, Marco Van Zwetselaar, Blandina Mmbaga, Happiness Kumburu

“…Bacterial analysis was carried out using classical microbiological techniques and whole genome sequencing (WGS) using the Illumina Nextseq 550 sequencer platform. …”
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Single‐egg comet assay: A protocol to quantify DNA damage in natural bioarchives by Rejin Salimraj, Alessio Perotti, Marcin W. Wojewodzic, Dagmar Frisch

“…More generally, the SE‐CA is applicable to testing DNA integrity in individual propagules prior to genome sequencing or to quantify environmental impacts on natural sedimentary biobanks.…”
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Improved 11α-hydroxycanrenone production by modification of cytochrome P450 monooxygenase gene in Aspergillus ochraceus by Li Qianqian, Shi Li, Liu Yingying, Guan Shimin, Zhang Shuo, Cai Baoguo, Rong Shaofeng

“…To improve the efficiency of 11α-hydroxycanrenone production, the CYP monooxygenase-coding gene of MF018 was predicted and cloned based on whole-genome sequencing results. A recombinant A. ochraceus strain MF010 with the high expression of CYP monooxygenase was then obtained through homologous recombination. …”
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Chromosome-level genome assembly of the pine wood nematode carrier Arhopalus unicolor by Xiangying Zou, Liqiong Zeng, Xingzao You, Jinghui Zhong, Chensheng Tang, Zhaofei Zheng, Xiaochun Lin, Biaoqiang Zhang, Xinliang Zhang, Yu Fang, Yanli Sun, Shouping Cai, Jun Su

“…Furthermore, the genome contains 71.74% repeat elements and encompasses 16,450 predicted protein-coding genes. This genome sequence of A. unicolor will be a valuable resource for understanding the genetics and evolutionary history of this species and for developing effective management strategies for this PWN carrier.…”
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Resolving Rapid Radiation of Voles and Lemmings (Arvicolinae: Cricetinae, Rodentia) with QuaddRAD Sequencing and Transcriptome Analysis by Natalia Abramson, Elizaveta Skalon, Olga Bondareva, Semen Bodrov, Tatyana Petrova, Ivan Dvoyashov

“…For the first time, whole-genome sequencing data resolved relations within the third radiation wave of the subfamily’s taxa, namely the tribes Arvicolini, Lagurini, and Ellobiusini, which have formed polytomy in mitochondrial trees in earlier articles. …”
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MethylBERT enables read-level DNA methylation pattern identification and tumour deconvolution using a Transformer-based model by Yunhee Jeong, Clarissa Gerhäuser, Guido Sauter, Thorsten Schlomm, Karl Rohr, Pavlo Lutsik

“…MethylBERT identifies tumour-derived sequence reads based on their methylation patterns and local genomic sequence, and estimates tumour cell fractions within bulk samples. …”
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Identification of DLEC1 D215N Somatic Mutation in Formalin Fixed Paraffin Embedded Melanoma and Melanocytic Nevi Specimens by Ricardo Vieira, Maria José Simões, Susana Carmona, Conceição Egas, Carlos Faro, Américo Figueiredo

“…DLEC1 D215N somatic mutation (COSM36702) was identified in a melanoma cell line through whole genome sequencing. However, little is known about the implication and prevalence of this mutation in primary melanomas or in melanocytic nevi. …”
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Crown Gall Induced by a Natural Isolate of <i>Brucella</i> (<i>Ochrobactrum</i>) <i>pseudogrignonense</i> Containing a Tumor-Inducing Plasmid by Marjolein J. G. Hooykaas, Paul J. J. Hooykaas

“…Unexpectedly, we found evidence that a natural isolate from a rose crown gall, called NBC51/LBA8980, was a bacterium that did not belong to the <i>Rhizobiaceae</i> family. Whole-genome sequencing revealed that this bacterium contained three large DNA circles with rRNA and tRNA genes, representing one chromosome and two chromids, respectively, and two megaplasmids, including a Ti plasmid. …”
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Neuromuscular diseases: genomics-driven advances by Anna Cho

“…While fewer than 30 NMDs had known genetic causes before the 1990s, more than 600 have now been identified, largely due to the adoption of next-generation sequencing (NGS) technologies such as whole-exome sequencing (WES) and whole-genome sequencing (WGS). These technologies have enabled more precise and earlier diagnoses, although the genetic complexity of many NMDs continues to pose challenges. …”
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Unraveling the metabolic landscape of Exophiala spinifera strain FM: Model reconstruction, insights into biodesulfurization and beyond. by Hamta Babaei Naeij, Zahra Etemadifar, John Kilbane, Mohammad Hossein Karimi-Jafari, Sepideh Mofidifar

“…However, the specific pathway and enzymes involved in this process remain unclear due to limited genome sequencing and metabolic understanding of E. spinifera. …”
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Next-Generation Sequencing and Epigenomics Research: A Hammer in Search of Nails by Shrutii Sarda, Sridhar Hannenhalli

“…., how the genome is marked at specific developmental periods, in different tissues, as well as across individuals and species-the promise of the genome sequencing project in understanding biology cannot be fulfilled. …”
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