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The genome of Comamonas sediminis FS4_11, a bacterial strain with mycotoxin fumonisin B1 (FB1) transformation capability, was sequenced using Oxford Nanopore Technologies (ONT) and Illumina platforms. The final assembly generated a circular chromosome of 5,148,490 …
Read PDFThe placenta is a temporary organ present during pregnancy that is responsible for coordinating all aspects of pregnancy between the mother and fetus. It has a distinct epigenetic, transcriptomic, and mutational landscape with low levels …
Read PDFThe life cycle of <i>Plasmodium falciparum</i> is characterized by complex regulatory changes that allow adaptation of the parasites to different environmental conditions, which are especially pronounced during transmission between the mammalian host and the insect …
Read PDFWith the advent of long-read DNA sequencing technologies, assembling eukaryotic genomes has become routine; however, properly phasing the maternal and paternal contributions, which is of great value for breeding programs, remains technically challenging. Here, we …
Read PDFThe protocol for Extraction and Analysis of Small Yeast-Chromosomes (EASY-C) is a transformative, rapid, cost-effective, and user-friendly method designed for the efficient isolation of artificial synthetic mini-chromosomes (~42-52 kb) and large plasmids (~12 kb) from …
Read PDFWe report the complete circular genome sequence (2,316,546 bp; 37.0% G + C) of <i>Solobacterium moorei</i> 10714-02, a gram-positive obligate anaerobe isolated from stool samples of a human colorectal cancer patient, differing from the typically …
Read PDF<b>Introduction.</b> Cholera, caused by <i>Vibrio cholerae</i>, remains a priority public health concern, particularly in developing countries. The first cholera outbreak in Zambia was documented in the 1970s, with recurring epidemics reported since then. In 2023, …
Read PDFEnvironmental DNA (eDNA) metabarcoding is a key tool in biodiversity monitoring due to its high-throughput, non-destructive nature. While short-read (SR) sequencing platforms such as Illumina Miseq have been routinely used in environmental monitoring, their limited …
Read PDFNanopore sequencing is an increasingly central tool for genomics. Despite rapid advances in the field, large data volumes and computational bottlenecks continue to pose major challenges. Here, we introduce ex-zd, a new data compression strategy …
Read PDFAnsell's mole-rat (Fukomys anselli) is an African rodent known for its subterranean lifestyle and unique phenotypic traits, including extreme longevity, magnetoreception, and a cooperative breeding social structure. Efforts to dissect the genetic architecture of these …
Read PDF<i>Klebsiella pneumoniae</i> is a leading cause of healthcare-associated infections worldwide, yet its population structure and transmission dynamics remain largely uncharacterized in New Zealand hospitals. We conducted a 15-month prospective genomic surveillance pilot at Wellington Regional …
Read PDF<h4>Introduction</h4>Thyroblastoma is a rare and highly aggressive embryonal thyroid malignancy typically associated with DICER1 alterations. However, DICER1-wildtype cases remain poorly characterized at the molecular level.<h4>Methods</h4>We report a case of aggressive thyroblastoma in a 62-year-old male, …
Read PDFDNA methylation is a key regulator of eukaryotic genomes, most commonly through 5-methylcytosine (5mC). In contrast, the existence and function of N<sup>6</sup>-methyladenine (6mA) in eukaryotes have been controversial, with conflicting reports resulting from methodological artifacts. …
Read PDFThe Yarkand hare (Lepus yarkandensis) is endemic to the Tarim Basin in Xinjiang, China. It is a key species and a critical component of the Tarim Basin ecosystems. However, the lack of a reference genome …
Read PDFLong-read sequencing data is useful for detecting large and complex structural variations; however, technical artifacts can lead to false structural variant calls. In our analyses, we became aware of a foldback artifact in long-read data. …
Read PDFBACKGROUND: Imported malaria cases, driven by human migration and travel, pose a significant challenge to malaria elimination efforts. Genomic approaches have become essential for distinguishing between local transmission and imported infections. The state of Sarawak, …
Read PDFBACKGROUND: A highly complex karyotype (high-CK) is a key biomarker of poor prognosis in chronic lymphocytic leukemia (CLL). While conventional methods lack the resolution to fully characterize complex structural variants (SVs), emerging technologies such as …
Read PDFTropaeolum tuberosum is a tuber-forming crop native to the Andes, valued for its nutritional content, pest resistance, and adaptation to high-altitude environments. Despite its contribution to food security and sustainable agriculture, it remains an underutilized …
Read PDF<h4>Motivation</h4>Nanopores are cutting-edge interdisciplinary tools that can analyze biomolecules at the single-molecule level for many applications, e.g. DNA sequencing. Efforts are underway to extend nanopores to proteomics, including the development of machine learning algorithms for …
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