Genomic evolution of SARS-CoV-2 in Morocco: Insights from whole genome sequences collected from 2020 to 2024 by Hamza GHAMMAZ, Marouane MELLOUL, Ahlam MBARKI, Mouhssine HEMLALI, Taha CHOUATI, Hicham EL ANNAZ, Nadia TOUIL, Mostafa ELOUENNASS, Khalid ENNIBI, Elmostafa EL FAHIME

“…A total of 2630 SARS-CoV-2 genome sequences were analyzed using bioinformatic tools such as Nextclade, followed by phylogenetic and statistical analyses. …”
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approach to calculate the transcript capacity by Young-Sup Lee, Kyung-Hye Won, Jae-Don Oh, Donghyun Shin

“…We expect that our analysis contributes to estimating TC in the diverse species and playing a benevolent role to the new bioinformatic analysis.…”
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Accelerating next generation sequencing data analysis: an evaluation of optimized best practices for Genome Analysis Toolkit algorithms by Karl R. Franke, Erin L. Crowgey

“…Additionally, the IBM POWER9 CPU performed well on bioinformatic workloads when tested with 10 different tools for alignment/mapping.…”
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Anticancer Ribosomally Synthesized and Post-Translationally Modified Peptides from Plants: Structures, Therapeutic Potential, and Future Directions by Hyeon-Jeong Hwang, Youngsang Nam, Chanhee Jang, Eun La Kim, Eun Seo Jang, Yeo Jin Lee, Seoung Rak Lee

“…By integrating traditional ethnobotanical knowledge with modern genomic and bioinformatic approaches, this study underscores the importance of plant RiPPs as a resource for developing innovative cancer treatments. …”
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Deciphering the Differences Between Epstein–Barr Virus‐Associated and Negative Gastric Cancer in the Prospect of CDKN2A Genomic Alterations and Lymphoid Infiltration by Fuda Xie, Bonan Chen, Yang Lyu, Peiyao Yu, Canbin Fang, Kam Tong Leung, Shouyu Wang, Dazhi Xu, Jun Yu, Kwok Wai Lo, Ka Fai To, Wei Kang

“…Functional potentials of EBV infection were predicted by bioinformatic enrichment analysis. Results CDKN2A genestayed intact in all EBV‐associated GC cases. …”
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THEORETICAL AND INSILCO PHARMACOKINETIC INVESTIGATIONS ON SOME PHENYL PIPERIDINE DERIVATIVES AS NOVEL ANTIDEPRESSANT AGENTS by Olasupo Sabitu Babatunde Babatunde, Adamu Uzairu, Gideon Adamu Shallangwa, Sani Uba

“… A theoretical bioinformatic investigation was carried out on some Inhibitors of serotonin transporter (SERT) of Phenyl piperidine derivatives using Density Functional Theory (DFT/B3LYP/6-31G*) at ground state with Spartan 14 V1.1.4 software in modeling the antipsychotic activity of the compounds. …”
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A single-cell RNA sequencing dataset of peripheral blood cells in long COVID patients on herbal therapy by Karolina Hanna Prazanowska, Tae-Hun Kim, Jung Won Kang, Young-Hee Jin, Sunoh Kwon, Su Bin Lim

“…To ensure the technical validity of our dataset, we implemented rigorous quality checks throughout stages of the study, including sample preparation, sequencing, and bioinformatic data analysis levels. This transcriptomic data may serve as a resource to deepen our insights into the role of herbal medicines in management of long COVID.…”
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The Impact of PPARγ Genetic Variants on IBD Susceptibility and IBD Disease Course by Jessica Mwinyi, Christa Grete-Wenger, Jyrki J. Eloranta, Gerd A. Kullak-Ublick

“…We determined genetic variants in the coding exons and flanking intronic sequences of the NR1C3 gene in 284 IBD patients and 194 controls and predicted NR1C3 haplotypes via bioinformatic analysis. We investigated whether certain NR1C3 variants are associated with susceptibility to IBD or its disease course. …”
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PathoGD: an integrative genomics approach to primer and guide RNA design for CRISPR-based diagnostics by Soo Jen Low, Matthew O’Neill, William J. Kerry, Natasha Wild, Marcelina Krysiak, Yi Nong, Francesca Azzato, Eileen Hor, Lewis Williams, George Taiaroa, Eike Steinig, Shivani Pasricha, Deborah A. Williamson

“…Here we present PathoGD, a bioinformatic pipeline for rapid and high-throughput design of RPA primers and gRNAs for CRISPR-Cas12a-based pathogen detection. …”
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Rare Somatic MEN1 Gene Pathogenic Variant in a Patient Affected by Atypical Parathyroid Adenoma by Luigia Cinque, Flavia Pugliese, Celeste Clemente, Stefano Castellana, Maria Pia Leone, Danilo de Martino, Teresa Balsamo, Claudia Battista, Tommaso Biagini, Paolo Graziano, Marco Castori, Alfredo Scillitani, Vito Guarnieri

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Genomic and Drug Resistance Profile of Bovine Multidrug-Resistant <i>Escherichia coli</i> Isolated in Kazakhstan by Pavel G. Alexyuk, Andrey P. Bogoyavlenskiy, Yergali S. Moldakhanov, Kuralay S. Akanova, Adolat N. Manakbayeva, Timur Kerimov, Vladimir E. Berezin, Madina S. Alexyuk

“…Whole-genome sequencing, followed by bioinformatic processing and the annotation of genes of this strain, showed that the genome has a total length of 4,803,482 bp and contains 4986 genes, including 122 RNA genes. …”
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RKIP Suppresses Breast Cancer Metastasis to the Bone by Regulating Stroma-Associated Genes by Elena Bevilacqua, Casey A. Frankenberger, Marsha Rich Rosner

“…Experimental validation is followed by further bioinformatic analysis to establish the clinical significance of discoveries. …”
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The effects of the ketone body ?-hydroxybutyrate on the neuronal transcriptome by Zayn Cheema, Megan Chen, Dana Poon, Taara Reddy, John Vergis, Sinead O'Donovan

“…To assess the effect of BHB administration on the neuronal transcriptome, we reanalyzed a publicly available RNAseq dataset (GSE252513) using a bioinformatic “3-pod” approach. We conducted pathway analysis and identified leading edge genes using Gene Set Enrichment Analysis (GSEA) and conducted chemical perturbagen analysis using the iLINCS repository to identify drugs that are concordant and discordant with BHB administration. …”
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The Polymorphisms with Cataract Susceptibility Impair the EPHA2 Receptor Stability and Its Cytoprotective Function by Jin Yang, Dan Li, Qi Fan, Lei Cai, Xiaodi Qiu, Peng Zhou, Yi Lu

“…Despite accumulating evidence revealing susceptibility genes for age-related cataract, its pathophysiology leading to visual impairment at the cellular and molecular level remains poorly understood. Recent bioinformatic studies uncovered the association of two single nucleotide polymorphisms in human EPHA2, rs2291806 and rs1058371, with age-related cataract. …”
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Antibody Responses and the Vaccine Efficacy of Recombinant Glycosyltransferase and Nicastrin Against <i>Schistosoma japonicum</i> by Bowen Dong, Haoran Zhong, Danlin Zhu, Luobin Wu, Jinming Wang, Hao Li, Yamei Jin

“…Previous proteomic studies from our group revealed that the expression of <i>Schistosoma japonicum</i> glycosyltransferase and nicastrin as proteins was higher in single-sex males than mated males, suggesting their critical roles in parasite reproduction and their potential as vaccine candidates. In this study, bioinformatic tools were employed to analyze the structural and functional properties of these proteins, including their signal peptide regions, transmembrane domains, tertiary structures, and protein interaction networks. …”
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Phylogeography of the woolly mammoth (<i>Mammuthus primigenius</i>) in the Minusinsk Depression of southern Siberia in the Late Pleistocene by S. A. Modina, M. A. Kusliy, D. G. Malikov, A. S. Molodtseva

“…Within the framework of this effort, libraries for high-throughput sequencing of seven bone samples of woolly mammoths were obtained, two-round enrichment using biotinylated probes of modern mtDNA of Elephas maximus immobilised on magnetic microspheres and sequencing with subsequent bioinformatic analysis were carried out. Phylogenetic reconstructions showed the presence of all studied mammoths in clade I, which expanded its range. …”
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LPCAT3 regulates the proliferation and metastasis of serous ovarian cancer by modulating arachidonic acid by Fang Wen, Hongjian Ling, Rui Ran, Xinya Li, Houmei Wang, Qianfen Liu, Min Li, Tinghe Yu

“…Methods: LPCAT3 protein in ovarian cancer tissues was detected using bioinformatic and immunohistoche mical assays. Cell behaviors were observed after up- or down-regulating LPCAT3. …”
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Metabolic Blockade-Based Genome Mining of <i>Malbranchea circinata</i> SDU050: Discovery of Diverse Secondary Metabolites by Hu Yang, Xiaowei Luo, Zhuo Shang, Kunlong Li, Jian Cai, Yingying Chen, Longchao Xin, Jianhua Ju

“…This study reports the isolation and identification of four classes of secondary metabolites from wild-type <i>M. circinata</i> SDU050, alongside five additional metabolite classes, including three novel cytochalasins (<b>7</b>–<b>9</b>), obtained from a mutant strain through the metabolic blockade strategy. Furthermore, bioinformatic analysis of the BGC associated with the isocoumarin sclerin (<b>1</b>) enabled the deduction of its biosynthetic pathway based on gene function predictions. …”
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N-trans-Feruloyloctopamine Wakes Up BBC3, DDIT3, CDKN1A, and NOXA Signals to Accelerate HCC Cell Apoptosis by Bin Ma, Jing Li, Wen-Ke Yang, Mei-Gui Zhang, Xiao-Dong Xie, Zhong-Tian Bai

“…Real-time cell analyzer and flow cytometry data reveal that tumor cell proliferation and apoptosis were impacted by FO. DAVID bioinformatic data showed that most of the biological process GO terms are related to proliferation and apoptosis. …”
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Gut microbial profiles of patients with optic neuritis or myasthenia gravis by Tao Wu, Hanqiu Jiang, Chen Lin, Jingting Peng, Xiuyun Kong, Jie Yu, Jiawei Wang, Shilei Cui

“…Microbial genomic DNA was extracted, and the V3–V4 regions of bacterial 16S rRNA genes were amplified and sequenced. Bioinformatic analyses was performed to compare the alpha-diversity, beta-diversity, taxonomic assignments, and bacterial richness of the groups. …”
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