Re-annotation of SARS-CoV-2 proteins using an HHpred-based approach opens new opportunities for a better understanding of this virus by Brézellec, Pierre

“…Since the publication of the genome of SARS-CoV-2 – the causative agent of COVID-19 – in January 2020, many bioinformatic tools have been applied to annotate its proteins. …”
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TESTING POTATO COLLECTION SAMPLES FOR THE PRESENCE OF GENES FOR RESISTANCE TO PHYTOPATHOGENS BY MEANS OF DNA MARKERS by A. B. Saynakova, M. S. Romanova, S. N. Krasnikov, O. V. Litvinchuk, Ya. I. Alekseev, A. V. Nikulin, E. V. Terentjeva

“…This study is aimed at screening samples from the collection of the Narym Department of  Breeding and Seed Production of the Siberian Research Institute of Agriculture and Peat (the Branch of the Siberian Federal Agrobiotechnology Research Center, the Russian Academy of Sciences) using the multiplex PCR technique, for genes for resistance to Globodera rostochiensis and Globodera pallidas, potato wart disease, viruses X and Y. 40 samples were tested by means of genetic markers to identify genes for resistance to potato wart disease (Sen1), virus X (Rx), virus Y (Ryadg, Rychc, Rysto), Globodera rostochiensis (H1, Gro1-4) and Globodera pallida (Gpa2), in the genome. The sample included two varieties, three populations produced by self-pollination of the Ideal variety, and 35 individually selected potato hybrids. …”
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Minerals, Toxic Heavy Metals, and Antioxidant Properties of Honeys from Bangladesh by Sudip Paul, Md. Sakib Hossen, E. M. Tanvir, Rizwana Afroz, Delwar Hossen, Sagarika Das, Nikhil Chandra Bhoumik, Nurul Karim, Farha Matin Juliana, Siew Hua Gan, Md. Ibrahim Khalil

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UBE2J1 is identified as a novel plasma cell-related gene involved in the prognosis of high-grade serous ovarian cancer by Yunjie Tian, Ruoyu Dong, Yingxia Guan, Ying Wang, Wei Zhao, Jun Zhang, Shan Kang

“…The effects of immune cell markers on prognosis were analyzed via univariate Cox regression, least absolute shrinkage and selection operator (LASSO) and gene set variation analysis (GSVA) of bulk sequencing data from The Cancer Genome Atlas (TCGA)-HGSOC cohort. Finally, the effects of key markers on HGSOC cells were evaluated via Cell Counting Kit-8 (CCK-8), Transwell, colony formation, wound healing, immunofluorescence and in vivo tumor growth assays. …”
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Screening and validation of tsRNAs associated with lung adenocarcinoma by LU Chunli, SHAN Yifan, XIE Weijia

“…Gene ontology （GO） enrichment analysis and Kyoto Encyclopedia of Genes and Genomes （KEGG） pathway analysis were performed based on DAVID and KOBA KEGG online websites. …”
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Analysing DNA methylation and transcriptomic signatures to predict prostate cancer recurrence risk by Fahad M. Aldakheel, Hadeel Alnajran, Shatha A. Alduraywish, Ayesha Mateen, Mohammed S. Alqahtani, Rabbani Syed

“…This study employs a machine learning approach to identify DNA methylation and RNA expression biomarkers predictive of PCa recurrence using datasets from The Cancer Genome Atlas (TCGA). We analyzed 49,133 genes, identifying 684 differentially methylated genes (DMGs) and 691 differentially expressed genes (DEGs) between recurrence and non-recurrence groups. …”
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Cell-free fat extract improves embryo development and clinical outcomes in older women with previous in-vitro fertilization failure by Xiaowei Zhou, Hanfei Zhu, Jingru Duan, Lan Xia, Shen Zhao, Huihui Xu, Xian Wu, Xiaoling Wang, Bufang Xu, Yi Cao, Aijun Zhang

“…In addition, we performed immunofluorescence staining, multiplex immunoassay, whole-genome amplification and DNA sequencing, time-lapse embryo monitoring, and in vitro experiments. …”
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Mosaic loss of the Y chromosome in human neurodegenerative and oncological diseases by I. L. Kuznetsova, L. I. Uralsky, T. V. Tyazhelova, T. V. Andreeva, E. I. Rogaev

“…Thanks to occurance of large databases of the genome-wide association study (GWAS), there has been a transition to the use of large samples for analyzing genetic changes in both normal and pathological conditions. …”
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Causal Association Between Obstructive Sleep Apnea and Migraine: A Bidirectional Mendelian Randomization Study by Wang YP, Wei HX, Hu YY, Zhang C, Niu YM

“…Investigating the causation will assist in understanding the etiology of OSA and migraine.Methods: Bidirectional two-sample Mendelian randomization (MR) and multivariable MR (MVMR) approaches were carried out to investigate the causal link between OSA and migraine. The public genome-wide association study (GWAS) data for OSA, migraine, and subtypes were obtained from the IUE open GWAS project and the FinnGen consortium. …”
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Epigallocatechin gallate (EGCG) modulates senescent endothelial cell-monocyte communication in age-related vascular inflammation by Sarvatit Patel, Kai Ellis, Kai Ellis, Corey A. Scipione, Jason E. Fish, Jason E. Fish, Jason E. Fish, Jason E. Fish, Kathryn L. Howe, Kathryn L. Howe, Kathryn L. Howe, Kathryn L. Howe, Kathryn L. Howe

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Expression Profile of Genes Potentially Associated with Adequate Glycemic Control in Patients with Type 2 Diabetes Mellitus by Sâmia Cruz Tfaile Corbi, Alliny Souza Bastos, Rafael Nepomuceno, Thamiris Cirelli, Raquel Alves dos Santos, Catarina Satie Takahashi, Cristiane S. Rocha, Silvana Regina Perez Orrico, Claudia V. Maurer-Morelli, Raquel Mantuaneli Scarel-Caminaga

“…In order to identify potential genes related to poorly/well-controlled patients with T2D, our strategy of investigation included a primary screen by microarray (Human Genome U133) in a small group of individuals followed by an independent validation in a greater group using RT-qPCR. …”
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Dual role of Cathepsin S in cutaneous melanoma: insights from mendelian randomization and bioinformatics analysis by Linsa Zhou, Qiang Zhou, Qian Guo, Peng Lai, Chen Rui, Wanqing Li, Xuemei Chen, Yue Zhuo, Xiaoping Zhong, Sen Lin

“…Methods The Gene Expression Omnibus (GEO) database was used to obtain differential genes for CM and normal skin, and the Genome-Wide Association Studies (GWAS) analysis offered summary-level melanoma data for CM. …”
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Effect of trace elements and nutrients on 21 autoimmune diseases: a Mendelian randomization study by Ming-Jie Jia, Hua-Fang Yin, Ying-Chao Liang, Feng Jiang, Hui-Lin Li, Hui-Lin Li

“…However, whether there is a genetic causal effect between serum trace elements, nutrients, and autoimmune diseases remains unclear.ObjectiveThis study aims to investigate the causal effects of serum trace elements and nutrients on 21 autoimmune diseases using Mendelian randomization (MR).MethodsSingle nucleotide polymorphisms for the exposure factors (serum trace elements and vitamins) were obtained from the published UK Biobank database and genome-wide association study (GWAS) public databases. …”
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Metabolic redundancy and specialisation of novel sulfide-oxidizing Sulfurimonas and Sulfurovum along the brine-seawater interface of the Kebrit Deep by Rayyan Alamoudi, Alan Barozzi, Grégoire Michoud, Marc W. Van Goethem, Charlene Odobel, Yue Chen, Ramona Marasco, Daniele Daffonchio

“…Fifty-four Campylobacterota MAGs were assembled and dereplicated into three distinct groups, with the highest-quality genome retained as representative. These genomes represent novel sulfide-oxidizing species within the Sulfurimonas and Sulfurovum genera, which differ from those found in mildly saline deep-sea sulfidic pools. …”
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Nerve Enlargement in Patients with INF2 Variants Causing Peripheral Neuropathy and Focal Segmental Glomerulosclerosis by Quynh Tran Thuy Huong, Linh Tran Nguyen Truc, Hiroko Ueda, Kenji Fukui, Koichiro Higasa, Yoshinori Sato, Shinichi Takeda, Motoshi Hattori, Hiroyasu Tsukaguchi

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Comprehensive identification, characterization and expression analyses of the class III POD gene family in water lily (Nymphaea colorata) by Wasi Ullah Khan, Wasi Ullah Khan, Latif Ullah Khan, Noor Muhammad Khan, Ji Zhang, Wang Wenquan, Wang Wenquan, Fei Chen, Fei Chen

“…These findings provide valuable insights for future exploration of NcPOD functions in water lily growth and stress tolerance, laying a foundation for further comparative genomics and functional studies of this important class of antioxidant genes.…”
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Deciphering the heterogeneity and plasticity of the tumor microenvironment in liver cancer provides insights for prognosis by Yihao Sun, Yihao Sun, Guojuan Shi, Jian Yang, Chun-Zhong Zhou, Chuhan Peng, Yu-Hong Luo, Ying Pan, Rui-Qi Wang

“…Our investigation of liver metastases from intestinal cancer uncovered a group of mast cells that might promote metastasis through pathways like inositol phosphate metabolism. Using genomic and clinical data from The Cancer Genome Atlas, we identified specific cell components linked to tumor characteristics and genetics. …”
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Characterization and comparison of gut microbiota in patients with acute pancreatitis by metagenomics and culturomics by Liang Gong, Xue Li, Li Ji, Guorong Chen, Ziying Han, Lei Su, Dong Wu

“…Our research has contributed to the expanded understanding of the genome, diversity, and function of the intestinal microbiota in patients with AP and provided some reference for selecting culture medium and sample processing methods.…”
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Comparative cytogenetics of anembryonic pregnancies and missed abortions in human by T. V. Nikitina, E. A. Sazhenova, E. N. Tolmacheva, N. N. Sukhanova, S. A. Vasilyev, I. N. Lebedev

“…Thus, although the frequencies of some types of chromosomal pathology differ between AP and MA, the total frequency of chromosomal abnormalities in AP is not increased compared to MA, which indicates the need to search for the causes of AP at other levels of the genome organization, including microstructural chromosomal rearrangements, monogenic mutations, imprinting disorders, and epigenetic abnormalities.…”
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GnIH secreted by green light exposure, regulates bone mass through the activation of Gpr147 by Yu You, Konglin Huo, Liang He, Tongyue Wang, Lei Zhao, Rong Li, Xiaoqing Cheng, Xuebin Ma, Zhiying Yue, Stefan Siwko, Ning Wang, Lujian Liao, Mingyao Liu, Jian Luo

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