The genetic architecture of local adaptation in a cline by Laroche, Fabien, Lenormand, Thomas

“…It has been repeatedly proposed that the localization of these genes in the genome may not be random, but could be an evolved feature. …”
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Identification and quantification of transposable element transcripts using Long-Read RNA-seq in Drosophila germline tissues by Rebollo, Rita, Gerenton, Pierre, Cumunel, Eric, Mary, Arnaud, Sabot, François, Burlet, Nelly, Gillet, Benjamin, Hughes, Sandrine, S. Oliveira, Daniel, Goubert, Clément, Fablet, Marie, Vieira, Cristina, Lacroix, Vincent

“…However, assigning short reads to their correct genomic location, and genomic feature is not trivial. …”
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Immunogenicity and safety of a live-attenuated SARS-CoV-2 vaccine candidate based on multiple attenuation mechanisms by Mie Suzuki Okutani, Shinya Okamura, Tang Gis, Hitomi Sasaki, Suni Lee, Akiho Kashiwabara, Simon Goto, Mai Matsumoto, Mayuko Yamawaki, Toshiaki Miyazaki, Tatsuya Nakagawa, Masahito Ikawa, Wataru Kamitani, Shiro Takekawa, Koichi Yamanishi, Hirotaka Ebina

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NOS2 as a prognostic biomarker for early-onset colorectal cancer based on public data and clinical validation analysis by Chaoqun Xing, Lipeng Zhao, Weiwei Zou, Xie Peng, Xiao-Liang Xing, Jie Li

“…EOCRC from The Cancer Genome Atlas Program (TCGA) database and Gene Expression Mapping (GEO) database were used to screen biomarkers for prognosis and treatment guidance. …”
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Faster model-based estimation of ancestry proportions by Santander, Cindy G., Refoyo Martinez, Alba, Meisner, Jonas

“…We further show that fastmixture runs approximately 30$\times$ faster than ADMIXTURE on both simulated and empirical data from the 1000 Genomes Project such that our model-based approach scales to much larger sample sizes than previously possible.…”
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A user-friendly software to accurately count and measure cysts from the parasitic nematode Heterodera glycines by Joffrey Mejias, Djampa K. L. Kozlowski, Jackson Goshon, Thomas R. Maier, Thomas J. Baum

“…Researchers and breeders typically employ exploratory methods such as Genome-Wide Association Studies or Quantitative Trait Loci mapping to identify genes linked to resistance. …”
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Beyond the Comfort Zone: Strenuous Sports as a Preventive Tactic Against Benign Prostatic Hyperplasia by Wei Zhang, Gang Li, Chengya Hao, Aijun Cheng

“…The study utilizes single nucleotide polymorphisms (SNPs) associated with strenuous sports obtained from published genome-wide association studies (GWAS), alongside summarized genetic data related to benign prostatic hyperplasia (BPH) from published GWAS. …”
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Microbial methane production from calcium carbonate at moderately alkaline pH by Nicole A. Fiore, Anthony J. Kohtz, Daniel N. Miller, Sanjay Antony-Babu, Donald Pan, Caitlin Lahey, Xi Huang, Yongfeng Lu, Nicole R. Buan, Karrie A. Weber

“…Cells were observed in association with the carbonate mineral matrix via coherent anti-Stokes Raman scattering and two-photon excitation fluorescence microscopy. Genome-resolved metagenomics of the enrichment community confirmed the presence of a methanogen (Methanobacterium sp.) with the metabolic potential for hydrogenotrophic methanogenesis in addition to five bacterial community members. …”
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SCO6564, a novel 3-ketoacyl acyl carrier protein synthase III, contributes in fatty acid synthesis in Streptomyces coelicolor. by Jian-Rong Ma, Jia-Ying Lin, Yuan-Yin Zhang, Yun Chen, Wen-Bing Zhang, Xian-Pu Ni, Yong-Hong Yu

“…In this study, the FabH homolog SCO6564 (named FabH2) was identified in the S. coelicolor genome by BLAST analysis. The expression of fabH2 restored the growth of Ralstonia solanacearum fabH mutant and made the mutant produce small amounts of branched-chain fatty acids. …”
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Gemcitabine combined with baicalein exerts antiviral activity against PEDV by inhibiting the entry and replication phases by Yingge Zheng, Yanfei Zhang, Fangying Xiong, Dehua Luo, Yuxiang Wang, Yijia Zhang, Dengguo Wei

“…Porcine epidemic diarrhea virus (PEDV) is a member of the Coronaviridae family, whose genome consists of a single strand of positive-sense RNA and has evolved into multiple epidemic lineages with no available drugs in clinical practice. …”
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RECQ4-MUS81 interaction contributes to telomere maintenance with implications to Rothmund-Thomson syndrome by Raghib Ashraf, Hana Polasek-Sedlackova, Victoria Marini, Jana Prochazkova, Zdenka Hasanova, Magdalena Zacpalova, Michala Boudova, Lumir Krejci

“…This underscores the importance of RECQ4-MUS81 in safeguarding genome integrity and suggests potential implications for human disease. …”
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Integration of single-cell and bulk RNA-sequencing data to construct and validate a signature based on NK cell marker genes to predict immunotherapy response and prognosis in color... by Xiaoyu Qin, Wenjuan Xu, Jinxiu Wu, Ming Li

“…We integrated scRNA-seq data from four Gene Expression Omnibus (GEO) samples and performed Weighted gene correlation network analysis (WGCNA) based on 587 the Cancer Genome Atlas (TCGA) colorectal cancer samples to uncover NK cell-related genes. …”
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D-2-hydroxyglutarate impairs DNA repair through epigenetic reprogramming by Fengchao Lang, Karambir Kaur, Haiqing Fu, Javeria Zaheer, Diego Luis Ribeiro, Mirit I. Aladjem, Chunzhang Yang

“…Oncometabolites jeopardize genome stability and DNA repair by affecting high-order chromatin structure.…”
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Potential links between human bloodstream infection by Salmonella enterica serovar Typhimurium and international transmission to Colombia. by Yan Li, Caisey V Pulford, Paula Díaz, Blanca M Perez-Sepulveda, Carolina Duarte, Alexander V Predeus, Magdalena Wiesner, Darren Heavens, Ross Low, Christian Schudoma, Angeline Montaño, Neil Hall, Jaime Moreno, Jay C D Hinton

“…We used whole-genome sequencing to analyse multidrug-resistant (MDR) profiles, plasmid distribution, and to define phylogenetic relationships. …”
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Emergence of a novel porcine pestivirus with potential for cross-species transmission in China, 2023 by Li-shuang Deng, Tong Xu, Zhi-wen Xu, Ling Zhu

“…Viremia has been detected in both piglets and mice, with high viral genome loads found in various organs. In vitro results revealed that PAAPeV replicates in ST cells and, to a lesser extent, in human (A549 and HepG2) and monkey (Vero) cells. …”
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Investigating the role of iron status in the development of coeliac disease: a Mendelian randomisation study by Isabel A Hujoel, Margaux Louise Anna Hujoel

“…The SNPs were drawn from a meta-analysis of three genome-wide association studies (GWAS). The association between these SNPs and coeliac disease was assessed using GWAS summary statistics from the UK Biobank. …”
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Unraveling the genetic connections for mitochondrial DNA control region and breast cancer susceptibility by Namra Khalid, Muhammad Umer Khan, Raima Rehman, Shamsa Kanwal, Tazeen Zahid, Muhammad Usman Ghani, Ayesha Iftikhar, Qurban Ali, Muhammad Arshad Javed

“…The study reveals a significant abundance of haplogroup M in breast cancer cases by analyzing breast cancer patients and healthy controls through mitochondrial control region genome sequencing (p < 0.001). Increased frequencies of haplogroups M, H, and R in patients compared to controls suggest their potential role in breast cancer susceptibility. …”
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Research Note: Novel reassortant avian influenza A(H9N2) Viruses in Wild Birds in Shanghai, China, 2020–2023 by Jie Hu, Yuting Xu, Min Ma, Chenyao Zhao, Yue Yuan, Guimei He

“…To better understand the genetic characteristics of these H9N2 viruses in Shanghai, the whole genome sequences were analyzed. Phylogenetical analysis showed that the nine H9N2 viruses have undergone complicated reassortment with waterfowl viruses along the East Asian-Australasian flyways. …”
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Mapping chromatin remodelling in glioblastoma identifies epigenetic regulation of key molecular pathways and novel druggable targets by Claire Vinel, James Boot, Weiwei Jin, Nicola Pomella, Alexandra Hadaway, Charles Mein, Nicolae Radu Zabet, Silvia Marino

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Isolation and characterization of a highly pathogenic strain of Vibrio harveyi EFL-2201 from pearl gentian grouper by Biao Yuan, Zhixia Zhuang, Xiaoru Wang, Huabin Huang, Qingpi Yan

“…In vitro assays indicated that the conditions during the outbreak were conducive to the proliferation, motility, biofilm formation, and chemotaxis of EFL-2201. Whole-genome sequencing of the strain revealed that mechanisms related to adhesion, secretion, toxins, and invasion significantly contributed to its pathogenicity. …”
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