Fast and accurate imputation of genotypes from noisy low-coverage sequencing data in bi-parental populations. by Cécile Triay, Alice Boizet, Christopher Fragoso, Anestis Gkanogiannis, Jean-François Rami, Mathias Lorieux

“…The main issues with these low-coverage genotyping methods are (1) poor performance at heterozygous loci, (2) high percentage of missing data, (3) local errors due to erroneous mapping of sequencing reads and reference genome mistakes, and (4) global, technical errors inherent to NGS itself. …”
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Phylogenetic and pangenomic analyses of members of the family <i>Micrococcaceae</i> related to a plant-growth-promoting rhizobacterium isolated from the rhizosphere of potato (<i>S... by S. Yu. Shchyogolev, G. L. Burygin, L. A. Dykman, L. Yu. Matora

“…In these studies, we used whole-genome phylogenetic tests and pangenomic analysis. …”
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Molecular and Biochemical Mechanisms of Scutellum Color Variation in <i>Bactrocera dorsalis</i> Adults (Diptera: Tephritidae) by Guangli Wang, Weijun Li, Jiazhan Wu, Ye Xu, Zhaohuan Xu, Qingxiu Xie, Yugui Ge, Haiyan Yang, Xiaozhen Li

“…To reveal genetic correlates among the three races, the genomes of 22 samples (8 with YS, 7 with LYS, and 7 with WS) were sequenced by high-throughput sequencing technology. …”
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Myeloid dendritic cells and periodontal disease association: integrated study of single-cell sequencing and Mendelian randomization analysis by ChengJi Shi, XinYi Ou, XiaoXu Lei, LiJuan Huang, ShuHao Xu, Wei Li, Xi Zhao

“…Gene ontology and Kyoto Encyclopedia of Genes and Genomes analyses highlighted crucial pathways involved in periodontal inflammation and tissue destruction. …”
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Elevated LIF and JAK-STAT activation drive severe COVID-19 in myeloma patients receiving the BCMA-CD3 bispecific antibody Elranatamab by Ziping Li, Fujing Zhang, Xianghong Jin, Junling Zhuang

“…Kyoto Encyclopedia of Genes and Genomes (KEGG) analysis showed that these DEPs were enriched in cytokine-cytokine receptor interaction and JAK-STAT signaling pathways. …”
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Two-Step Transfer Learning Improves Deep Learning–Based Drug Response Prediction in Small Datasets: A Case Study of Glioblastoma by Jie Ju, Ioannis Ntafoulis, Michelle Klein, Marcel JT Reinders, Martine Lamfers, Andrew P Stubbs, Yunlei Li

“…The 2-step TL framework was built on 3 datasets: (1) the subset of the Genomics of Drug Sensitivity in Cancer (GDSC) dataset, including miscellaneous cell cultures treated by TMZ, cyclophosphamide, bortezomib, and oxaliplatin, as the source dataset; (2) the Human Glioblastoma Cell Culture (HGCC) dataset, for fine-tuning; and (3) a small target dataset GSE232173, for validation. …”
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Ki-67 and CDK1 control the dynamic association of nuclear lipids with mitotic chromosomes by Hsiao-Tang Hu, Ueh-Ting Tim Wang, Bi-Chang Chen, Yi-Ping Hsueh, Ting-Fang Wang

“…Given that Ki-67 has been proposed to promote chromosome individualization and establish chromosome-cytoplasmic compartmentalization during open mitosis in vertebrates, our results reveal that nuclear lipid enrichment at the perichromosomal layer enhances the ability of Ki-67 to form a protective perichromosomal barrier (chromosome envelope), which is critical for correct chromosome segregation and maintenance of genome integrity during mitosis.…”
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Developing a novel model for predicting overall survival in late-onset colon adenocarcinoma patients based on LODDS: a study based on the SEER database and external validation by Chen Chen, Heng-Bo Xia, Wei-Wei Yuan, Meng-Ci Zhou, Xue Zhang, A.-Man Xu

“…Results A total of 103,291 and 100 patients with late-onset colon adenocarcinoma (50–80 years old) were screened from the Surveillance, Epidemiology, and End Results (SEER) and The Cancer Genome Atlas (TCGA) databases, respectively. Cox regression analysis revealed independent risk factors for OS and CSS, including age, gender, race, size, LODDS stage, PLN stage, LNR stage, and TNM stage. …”
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Fodder qualities of heterotic hybrids from intergeneric crosses between maize and eastern gamagrass by P. A. Panikhin, V. A. Sokolov

“…This paper presents the results obtained in the process of assessing fodder qualities of apomictic maize × Tripsacum hybrids, where two maize genomes from the lines participating in hybrid selection for F1 seeds were added to the 36 chromosomes of eastern gamagrass. …”
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Serial Paediatrics Omics Tracking in Myalgic Encephalomyelitis (SPOT-ME): protocol paper for a multidisciplinary, observational study of clinical and biological markers of paediatr... by Adam Scheinberg, Natalie Thomas, Katherine Huang, Paul R Gooley, Elisha K Josev, Tracey Chau, Darcy Tantanis, Sarah J Knight, Christopher W Armstrong

“…ME/CFS patients aged 12–19 years and controls will donate biosamples of urine, blood, and peripheral blood mononuclear cells for an in-depth omics profiling analysis (whole-genome sequencing, metabolomics and quantitative proteomics) while being assessed by gold-standard clinical and neuropsychological measures. …”
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Epigenome-wide DNA methylation profiling in septic and non-septic patients with similar infections: potential use as sepsis biomarkers by Ian López-Cruz, Ian López-Cruz, José Luis García-Giménez, José Luis García-Giménez, José Luis García-Giménez, Manuel Madrazo, Manuel Madrazo, Judit García-Guallarte, Laura Piles, Federico V. Pallardó, Federico V. Pallardó, Federico V. Pallardó, Arturo Artero, Arturo Artero

“…Whole blood samples from these patients were analyzed using the Infinium MethylationEPIC v2.0 kit, enabling genome-wide methylation analysis. Selected genes with differential methylation were validated by pyrosequencing.ResultsSignificant differential DNA methylation patterns were identified between septic and non-septic individuals uising. …”
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Aberrant DNA Methylation of FTH-1 and SHOX2 Contributes to Lung Cancer Progression by Salar Tahmasbi, Armin Sadeghi, Habib Zarredar, Milad Asadi, Shahryar Hashemzadeh, Venus Zafari, Hamed Sabbagh-Jadid, Mortaza Raeisi

“…Ferritin heavy chain 1 (FTH-1) and SHOX homeobox 2 (SHOX2) DNA methylation were investigated in non-small cell lung cancer (NSCLC) as novel epigenetic biomarkers.Method: In this case-control study, we initially evaluated the diagnostic value of FTH-1 and SHOX2 DNA methylation, and the Cancer Genome Atlas (TCGA) data on the methylation profile of NSCLC was analyzed. …”
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Characterization of <i>Streptococcus pyogenes</i> Strains from Tonsillopharyngitis and Scarlet Fever Resurgence, 2023—FIRST Detection of M1_UK in Bulgaria by Emma Keuleyan, Theodor Todorov, Deyan Donchev, Ani Kevorkyan, Radoslava Vazharova, Alexander Kukov, Georgi Todorov, Boriana Georgieva, Iskra Altankova, Yordanka Uzunova

“…Virulence factors were identified using multiplex PCR and whole genome sequencing (WGS). Immune responses were measured through detection of serum complement levels, lymphocyte subsets, and cytokine profiling. …”
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Carbon monoxide-oxidising Pseudomonadota on volcanic deposits by Robin A. Dawson, Nicola Fantom, Tamara Martin-Pozas, Patricia Aguila, Gary M. King, Marcela Hernández

“…Both strains oxidise CO across a broad range of concentrations (< 100 ppmv – 10,000 ppmv), and genome sequence analysis revealed a candidate form-I carbon monoxide dehydrogenase (CODH), which is likely to catalyse this process. …”
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Isolation and Identification of Lipase-producing Actinobacteria from the Lut Desert of Iran by Samira Abedi-Dolatabadi, Moj Khaleghi, Sedigheh Ghasemzadeh, Azadeh Lohrasbi-Nejad, Arastoo Badoei Delfard

“…Actinobacteria, which are Gram-positive bacteria, have the largest genome size among bacteria and produce various secondary metabolites, including enzymes. …”
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Dysfunction in mitochondrial electron transport chain drives the pathogenesis of pulmonary arterial hypertension: insights from a multi-omics investigation by Xin Zhang, Jieling Li, Minyi Fu, Xijie Geng, Junjie Hu, Ke-Jing Tang, Pan Chen, Jianyong Zou, Xiaoman Liu, Bo Zeng

“…Kyoto Encyclopedia of Genes and Genomes (KEGG) analysis investigated shared pathways, and canonical correlation analysis assessed gene-metabolite relationships. …”
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Dicoumarol sensitizes hepatocellular carcinoma cells to ferroptosis induced by imidazole ketone erastin by Ziwei Yang, Ziwei Yang, Tixin Han, Ruibin Yang, Ruibin Yang, Yinuo Zhang, Yinuo Zhang, Yifei Qin, Yifei Qin, Yifei Qin, Jialu Hou, Jialu Hou, Fei Huo, Fei Huo, Zhuan Feng, Zhuan Feng, Yaxin Ding, Yaxin Ding, Jiali Yang, Jiali Yang, Gang Zhou, Gang Zhou, Shijie Wang, Shijie Wang, Xiaohang Xie, Xiaohang Xie, Peng Lin, Peng Lin, Zhi-Nan Chen, Zhi-Nan Chen, Jiao Wu, Jiao Wu

“…The intrinsic factors determining sensitivity to IKE-induced ferroptosis remain to be explored to improve its efficacy.MethodsBulk RNA-sequencing data from hepatocellular carcinoma (HCC) and normal liver tissues were collected from The Cancer Genome Atlas (TCGA) and the Genotype-Tissue Expression (GTEx) databases. …”
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Killer-Cell Immunoglobulin-Like Receptors (KIR) in HIV-Exposed Infants in Cameroon by Kagoué Simeni Luc-Aimé, Yindom Louis-Marie, Loni Ekali Gabriel, Clauvis Kunkeng Yengo, F. Esemu Livo, Nguedia Jules Clement Assob

“…This may be partly due to differences in host immunogenetic factors in highly polymorphic regions of the human genome such as those encoding the killer-cell immunoglobulin-like receptor (KIR) molecules which modulate the activities of natural killer cells. …”
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RETRACTED ARTICLE: Single-cell omics and machine learning integration to develop a polyamine metabolism-based risk score model in breast cancer patients by Xiliang Zhang, Hanjie Guo, Xiaolong Li, Wei Tao, Xiaoqing Ma, Yuxing Zhang, Weidong Xiao

“…Data from The Cancer Genome Atlas, Gene Expression Omnibus, and Genotype-Tissue Expression identified 286 differentially expressed genes linked to polyamine pathways in breast cancer. …”
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Advances in Molecular Genetics of Reproductive Isolation in Rice by Shunmei LI, Zihan ZHENG, Ruiying LIU, Hongze GUO, Lin ZHENG, Yongyao XIE

“…According to these findings, several strategies and methods such as developing wide compatibility lines, breeding intersubspecific introgression rice and establishing artificial hybrid compatible lines by genome editing have been proposed to overcome RI in rice. …”
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