Identification of the first case of Penicillium marneffei infection in Shaanxi province by nanopore sequencing by Dongli Liu, Lin Ma, Lingfeng Mao, Yiqun Wang, Long Ding, Anli Wang

“…We performed nanopore genome sequencing on blood samples of the patient and obtained 84,000 reads in 3.5 hours. …”
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Exploring the presence of the GPR126 single nucleotide polymorphism (rs536714306) in periodontal patients of European ancestry by Eirini Chatzopoulou, Galinos Fanourakis, Nikolaos Papanikolaou, Ioulia Chatzistamou, Xanthippi Dereka, Heleni Vastardis

“…The homozygous for the reference allele GG genotype was observed in 100% of participants across all groups examined. …”
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Analysis of Isoniazid, Streptomycin and Ethambutol resistance in Mycobacterium tuberculosis isolates from Morocco by Imane Chaoui, Radia Sabouni, Moussa Kourout, Annemie M. Jordaan, Ouafae Lahlou, Rajae Elouad, Mohammed Akrim, Thomas C. Victor, Mohammed Elmzibri

“…Based on these results, rapid drug resistance genotyping can be used as an adjunct to the traditional culture based methods in reference laboratories.…”
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Sjögren’s syndrome is associated with a reduction in the surface area of the right caudal anterior cingulate gyrus by Ping Wang, Yunpeng Tai, Xiaofang Zhu, Xinyi Wan, An Sun, Jiajia Wang, Hui Cheng, Jingwei Hong, Yi Zhang, Xiaobing Wang

“…We also used CELLECT to leverage genome-wide association study (GWAS) and single-cell RNA sequencing (scRNA-seq) data to identify pathogenic cell types. …”
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Characteristics of CVA16 B1c strains isolated for the first time in the Heilongjiang Province of China by Tingting Yang, Qiang Sun, Qiang Sun, Qiang Sun, Hui Liu, Ming Yang, Shuhong Chen, Wei Sun, Jun Xu, Dongmei Yan, Dongmei Yan, Dongmei Yan, Shuangli Zhu, Shuangli Zhu, Shuangli Zhu, Zhenzhi Han, Jinbo Xiao, Jinbo Xiao, Jinbo Xiao, Huanhuan Lu, Huanhuan Lu, Huanhuan Lu, Ying Liu, Ying Liu, Ying Liu, Qian Yang, Qian Yang, Qian Yang, Yong Zhang, Yong Zhang, Yong Zhang

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Swiftly identifying strongly unique k-mers by Jens Zentgraf, Sven Rahmann

“…An optimized combined approach running with 16 threads on a 16-core workstation yields wall times below 20 seconds on the 2.5 billion distinct 31-mers of the human telomere-to-telomere reference genome. Availability An implementation can be found at https://gitlab.com/rahmannlab/strong-k-mers .…”
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4CMenB vaccine coverage of invasive serogroup B meningococci collected in Belgium between 2016 and 2022 by Nathalie Goeders, Kevin Vanneste, Nancy H.C. Roosens, Bert Bogaerts, Wesley Mattheus

“…In Europe, serogroup B (MenB) is the leading cause of invasive meningococcal disease (IMD), particularly in young children. Genomic surveillance of circulating MenB strains through whole genome sequencing (WGS) provides a powerful tool to assess the potential impact of vaccination strategies, including the 4CMenB vaccine, which is available for infants from 2 months of age. …”
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Influence of allelic polymorphism in the 3’ untranslated region of the <i>StTCP23</i> gene on the tolerance of potato cultivars to the potato spindle tuber viroid by N. V. Mironenko, A. V. Kochetov, O. S. Afanasenko

“…Cultivars with the A allele (‘Gala’, ‘Colomba’, ‘Favorit’, and ‘Fioletovy’) identical to the reference genome or a high dose of the C allele with a deletion of four nucleotides (cv. …”
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Virus versus host plant microRNAs: who determines the outcome of the interaction? by Fatemeh Maghuly, Rose C Ramkat, Margit Laimer

“…In the current study, computational and stem-loop Reverse Transcription - Polymerase Chain Reaction (RT-PCR) approaches were employed to a) predict and validate virus encoded mature miRNAs (miRs) in 39 DNA-A sequences of the bipartite genomes of African cassava mosaic virus (ACMV) and East African cassava mosaic virus-Uganda (EACMV-UG) isolates, b) determine whether virus encoded miRs/miRs* generated from the 5'/3' harpin arms have the capacity to bind to genomic sequences of the host plants Jatropha or cassava and c) investigate whether plant encoded miR/miR* sequences have the potential to bind to the viral genomes. …”
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Insights to the taxonomy and phylogeny of the genus Ptilagrostis worldwide (Poaceae, Stipeae) with a key to species identification, checklist and outlines for further studies by Marta Krzempek, Ewelina Klichowska, Marcin Nobis

“…We analysed all species possessing the characteristic ‘Ptilagrostis pattern’ of the lemma epidermis, with a particular reference to species possessing the terminal segment of the awn (seta) covered by short (up to 1 mm long) hairs that, until now, were treated as representatives of the genus Achnatherum. …”
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Proteome-wide association studies using summary pQTL data of brain, CSF, and plasma identify 30 risk genes of Alzheimer’s disease dementia by Tingyang Hu, Qiang Liu, Qile Dai, Aron S. Buchman, David A. Bennett, Shinya Tasaki, Yanling Wang, Nicholas T. Seyfried, Philip L. De Jager, Michael P. Epstein, Jingjing Yang

“…Existing PWAS analyses of AD often rely on the availability of individual-level proteomic and genetic data of a reference panel. Leveraging summary protein quantitative trait loci (pQTL) reference data of multiple AD-relevant tissues is expected to improve PWAS findings of AD dementia. …”
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Comparative assessment of line probe assays and targeted next-generation sequencing in drug-resistant tuberculosis diagnosisResearch in context by Giovanna Carpi, Marva Seifert, Andres De la Rossa, Swapna Uplekar, Camilla Rodrigues, Nestani Tukvadze, Shaheed V. Omar, Anita Suresh, Timothy C. Rodwell, Rebecca E. Colman

“…Diagnostic performance of the LPAs and previously established tNGS performance were compared, including sensitivity and specificity, for rifampicin, isoniazid, fluoroquinolones (moxifloxacin, levofloxacin), and amikacin, using a composite reference standard of phenotypic drug susceptibility testing and whole-genome sequencing. …”
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Phylogenetic analysis of a 2024 Sheeppox virus isolate from the Almaty region of Kazakhstan and investigation of its pathogenicity in merino sheep by Moldir Azanbekova, Muratbay Mambetaliyev, Aisulu Valiyeva, Nurlan Kozhabergenov, Nurbek Aldayarov, Sanat Kilibayev, Bekbolat Usserbayev, Moldir Tuyskanova, Balziya Kadyrova, Balzhan Myrzakhmetova, Lespek Kutumbetov, Olga Chervyakova, Sergazy Nurabayev, Maxat Berdikulov, Aslan Kerimbayev, Aralbek Rsaliyev, Yergali Abduraimov, Kuandyk Zhugunissov

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The cAMP responsive element modulator (CREM) transcription factor influences susceptibility to undernutrition and infection by Audrey C. Brown, Md. Jashim Uddin, Rebecca M. Munday, Farha Naz, G. Brett Moreau, Girija Ramakrishnan, Stephen S. Rich, Rashidul Haque, Genevieve L. Wojcik, Priya Duggal, Chelsea Marie, William A. Petri

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Comprehensive analysis of SPL gene family and miR156a/SPLs in the regulation of terpenoid indole alkaloid biosynthesis in Catharanthus roseus L by Yaojie Zhang, Xiaofan Ni, Xueqing Fu, Ayat Taheri, Wei Zhang, Pin Liu, Hang Liu, Ling Li, Yuliang Wang, Kexuan Tang

“…Results In this study, genome-wide analysis identified fourteen CrSPL genes. …”
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Identification and Candidate Gene Analysis of qCTS11-TK9, a Novel Major Quantitative Trait Locus Associated with Chilling Tolerance in Rice Seedlings by Sheng-Shan Wang, Yu-Ting Liu, Pei-Hua Tsai, Shu-Fang Cheng, Kai-Yi Chen, Rong-Kuen Chen

“…High-resolution linkage analysis delimited qCTS11-TK9 to a 191-kb genomic region containing 16 annotated putative genes in the rice reference genome. …”
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Linking genetic and phenotypic bedaquiline resistance in Mycobacterium tuberculosis strains from Georgia. by Nino Maghradze, Chloé Loiseau, Galo Adrian Goig, Nino Bablishvili, Levan Jugheli, Sonia Borrell, Nestani Tukvadze, Russell Ryan Kempker, Zaza Avaliani, Sebastien Gagneux

“…<h4>Methods</h4>We used retrospective Mtb isolates (2011-2019) with whole-genome sequencing data, and prospectively collected diagnostic isolates with phenotypic resistance (2019-2022) to bedaquiline at the Georgian National Reference Laboratory. …”
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Transcriptome Analysis Reveals the Putative Polyketide Synthase Gene Involved in Hispidin Biosynthesis in Sanghuangporus sanghuang by Jiansheng Wei, Liangyan Liu, Xiaolong Yuan, Dong Wang, Xinyue Wang, Wei Bi, Yan Yang, Yi Wang

“…Five PKSs were identified using genome annotation. Comparative analysis with the reference transcriptome showed that two PKSs (ShPKS3 and ShPKS4) had low expression levels in four types of media. …”
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Genetic determinants of pOXA-48 plasmid maintenance and propagation in Escherichia coli by Yannick Baffert, Nathan Fraikin, Yasmine Makhloufi, Julie Baltenneck, Marie-Eve Val, Annick Dedieu-Berne, Jonathan Degosserie, Bogdan I. Iorga, Pierre Bogaerts, Erwan Gueguen, Christian Lesterlin, Sarah Bigot

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Multidimensional third-generation sequencing of modified DNA bases allows interrogation of complex biological systems by Serena S. David, Brendan A. Pacheco, Kensei Kishimoto, Sam Vantine, Kai Hu, Haibo Liu, Diana L. Davis, Hoang Tran, Benjamin F. Sallis, Levi Ali, Cole M. Haynes, Beth A. McCormick, Lihua Julie Zhu, William A. Flavahan

“…Here, we present a method based on barcoded split-pool synthesis to generate reference standard oligonucleotides allowing novel base sequencing. …”
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