Applying the Concept of Peptide Uniqueness to Anti-Polio Vaccination by Darja Kanduc, Candida Fasano, Giovanni Capone, Antonella Pesce Delfino, Michele Calabrò, Lorenzo Polimeno

“…To design peptide-based anti-polio vaccines exempt from potential cross-reactivity risks and possibly able to reduce rare potential adverse events such as the postvaccine paralytic poliomyelitis due to the tendency of the poliovirus genome to mutate. Methods. Proteins from poliovirus type 1, strain Mahoney, were analyzed for amino acid sequence identity to the human proteome at the pentapeptide level, searching for sequences that (1) have zero percent of identity to human proteins, (2) are potentially endowed with an immunologic potential, and (3) are highly conserved among poliovirus strains. …”
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A Comprehensive Methodological Review of Major Developments in Bioinformatics Pipelines for Transcriptomic Data Analysis by Awais ALi, Syed Luqman Ali, Abdelkarem Omneya

“…Materials and Methods: This review highlights recent software and database improvements for processing RNA-Seq data, including steps like matching sequences to the genome, reconstructing RNA molecules, and measuring RNA abundance. …”
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GAMG alleviates liver fibrosis through inducing ferroptosis in inflammatory macrophages via the IRF1/SLC7A11 signaling pathway by Qing Pang, Shuai Zhou, Yong Wang, Hongtao Pan, Zhixin Wang, Xilaing Qin, Chao Zhu, Shilei Chen, Huichun Liu, Xiaosi Hu, Hao Jin

“…Single-cell RNA sequencing revealed that GAMG significantly affected the changes of macrophage subsets in LF, and Funrich analysis identified IRF1 as a key transcription factor regulating the macrophage genome. IRF1 was significantly increased while ferroptosis related SLC7A11 was significantly down-regulated in GAMG treated inflammatory macrophages. …”
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Polygenic diseases by Sergey Dolomatov, Walery Zukow, Anna Zhukova, Svetlana Smirnova

“…The review encompasses nutrigenetics, sports genomics, and genetic markers associated with athletic performance and injury risk. …”
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Comparative analysis of regression algorithms for drug response prediction using GDSC dataset by Soojung Ha, Juho Park, Kyuri Jo

“…Methods We compared and evaluated the performance of 13 representative regression algorithms using Genomics of Drug Sensitivity in Cancer (GDSC) dataset. …”
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A sedimentary ancient DNA perspective on human and carnivore persistence through the Late Pleistocene in El Mirón Cave, Spain by Pere Gelabert, Victoria Oberreiter, Lawrence Guy Straus, Manuel Ramón González Morales, Susanna Sawyer, Ana B. Marín-Arroyo, Jeanne Marie Geiling, Florian Exler, Florian Brueck, Stefan Franz, Fernanda Tenorio Cano, Sophie Szedlacsek, Evelyn Zelger, Michelle Hämmerle, Brina Zagorc, Alejandro Llanos-Lizcano, Olivia Cheronet, José-Miguel Tejero, Thomas Rattei, Stephan M. Kraemer, Ron Pinhasi

“…Additionally, we provide phylogenetic analyses on 70 sedaDNA mtDNA genomes of fauna including the densest Iberian Pleistocene sampling of C. lupus. …”
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Peripheral Blood DNA Methylation Changes in Response to <i>Centella asiatica</i> Treatment in Aged Mice by Olivia Monestime, Brett A. Davis, Cora Layman, Kandace J. Wheeler, Wyatt Hack, Jonathan A. Zweig, Amala Soumyanath, Lucia Carbone, Nora E. Gray

“…Reduced representation bisulfite sequencing (RRBS) was used to identify genome-wide differential methylation in the blood of CAW-treated aged mice compared to vehicle-treated aged mice. …”
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Post-mortem and histological lesions in the European minks (Mustela lutreola) induced by spontaneous infection with coronavirus SARS-CoV-2 by I. A. Subbotina, I. N. Gromov

“…Profound and detailed studies of the virus circulation in the European mink population and the clinical manifestations of the disease, comprehensive approaches to the disease diagnosis, including epidemiological studies, clinical and post-mortem examinations, molecular genetic laboratory diagnostics (polymerase chain reaction and full-genome sequencing) contributed to better understanding of the disease features. …”
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Brain gliomas new transcriptomic discoveries from differentially expressed genes to therapeutic targets by Shiwen Pei, Zhiquan Jiang, Hongwei Cheng

“…Gene set enrichment analysis and immunocytometric analysis further explored the biological functions and pathways of identified genes, which were validated using The Cancer Genome Atlas and Genotype-Tissue Expression datasets. …”
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A Novel 8-Gene Prognostic Signature for Survival Prediction of Uveal Melanoma by Zhongjun Tang, Kebo Cai

“…In the validation phase, the signature was validated in The Cancer Genome Atlas database. Results. Forty-one genes were identified as hub genes of metastasis by WGCNA. …”
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Liquid Chromatography-Mass Spectrometry-Based Untargeted Metabolomics Analysis of Differential Metabolites in Three Types of Boza Made from Different Raw Materials by WANG Qi, GAO Yan, XUE Juanjuan, ZENG Jun, HUO Xiangdong, ZHAO Zhongkai

“…According to Kyoto Encyclopedia of Genes and Genomes (KEGG) metabolic pathway enrichment analysis, these differential metabolites mainly participated in the biosynthesis of various secondary metabolites in plants, the biosynthesis of phenylpropanoids, the biosynthesis and degradation of flavonoids, and other metabolic pathways. …”
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Characterization of tumor evolution by functional clonality and phylogenetics in hepatocellular carcinoma by Zeynep Kacar, Eric Slud, Doron Levy, Julián Candia, Anuradha Budhu, Marshonna Forgues, Xiaolin Wu, Arati Raziuddin, Bao Tran, Jyoti Shetty, Yotsawat Pomyen, Jittiporn Chaisaingmongkol, Siritida Rabibhadana, Benjarath Pupacdi, Vajarabhongsa Bhudhisawasdi, Nirush Lertprasertsuke, Chirayu Auewarakul, Suleeporn Sangrajrang, Chulabhorn Mahidol, Mathuros Ruchirawat, Xin Wei Wang

“…Furthermore, we observe significant B cell enrichment in linear trees compared to non-linear trees suggesting the need for further research to uncover potential variations in immune cell types within genomically determined phylogeny types. These results hint at the possibility that tumor cells and their microenvironment may collectively influence the tumor evolution process.…”
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The association between type 2 diabetes and asthma incidence: a longitudinal analysis considering genetic susceptibility by Fei Chen, Ying Yang, Liping Yu, Lulu Song, Cong Zhang, Yifan He, Lili Wu, Wanlu Ma, Bo Zhang

“…A polygenic risk score (PRS) for asthma was derived from genome-wide association studies summary. Cox regression models were used to assess the association between T2D and asthma, incorporating the asthma PRS. …”
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<i>Thermithiobacillus plumbiphilus</i> AAFK—Arsenic-Resistant Bacteria Isolated from Arsenopyrite Material by Artem Shaikin, Anton Zvonarev, Mikhail Vainshtein, Tatiana Abashina

“…The first description of complete genome for the species <i>T. plumbiphilus</i> was also carried out and discovered genes providing the As resistance. …”
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Association between Genetic Instability and Helicobacter pylori Infection in Gastric Epithelial Dysplasia by Jin Su Kim, Woo Chul Chung, Kang-Moon Lee, Chang Nyol Paik, Kyeong Soo Lee, Hye Ji Kim, Young Wook Kim, Ji Han Jung, Seung June Noh, Yun Kyung Lee

“…In gastric carcinogenesis, changes of DNA methylation appear to be an early molecular event, and the genome-wide methylation state is closely correlated with the level of long interspersed nucleotide element-1 (LINE-1) methylation. …”
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Nonylphenol promotes epithelial-mesenchymal transition in colorectal cancer cells by upregulating miR-151a-3p by Biao Wang, Nianjie Zhang, Lin Dai, Yuanwei Zhang, Shuo Yin, Xuefeng Yang

“…Analysis of The Cancer Genome Atlas (TCGA) data revealed increased expression levels of miR-151a-3p in CRC tissues. …”
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Molecular Characterization of Wild and Cultivated Strawberry (Fragaria × ananassa) through DNA Barcode Markers by Awais Qarni, Khushi Muhammad, Abdul Wahab, Amir Ali, Chandni Khizar, Izhar Ullah, Abeer Kazmi, Tahira Sultana, Asma Hameed, Muhammad Younas, Mehdi Rahimi

“…Initially, the efficacy of eight DNA barcode markers was analyzed based on the amplification and sequencing of the genome of selected Fragaria species. The resultant sequences were analyzed using BLAST, MEGA 7.0, and Bio Edit software. …”
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The Genetic Diversity, Population Structure, and Historical Dynamics of Wild <i>Pyrus</i> Species on the Yunnan–Kweichow Plateau by Xiang Yang, Xingguang Dong, Kunming Li, Ying Zhang, Chenxi Xu, Hongliang Huo, Luming Tian, Jiayu Xu, Chao Liu, Dan Qi, Yufen Cao

“…These analyses entailed the collection of 80 accessions, whole-genome resequencing, and the detection of variants including SNPs, InDels, SVs, and CNVs. …”
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Microscopic and molecular detection of Cytauxzoon spp. in cats in Mosul city, Iraq by Sura S. Aghwan, Enas S. Hussein, Salam A Esmaeel

“…The results indicate that some of the tested samples contain DNA from the Cytauxzoon genus, based on the presence of bands at the expected 1600 bp size. The local genome sequence of Cytauxzoon felis Sesa LC775709.1 is highly similar to sequences found in geographically diverse regions such as Switzerland, Italy, France, and the USA. …”
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Bioinformatics approach reveals the critical role of inflammation-related genes in age-related hearing loss by Xi Gu, Chenyu Chen, Yuqing Chen, Chaojun Zeng, Yanchun Lin, Ruosi Guo, Shujin Xu, Chang Lin

“…The IRDEGs were mainly enriched in MAPK, PI3K-Akt, Hippo and JAK-STAT pathways by analysis of Gene Ontology and Kyoto Encyclopedia of Genes and Genomes. We then identified 10 key IRDEGs including Alox5ap, Chil1, Clec7a, Dysf, Fcgr3, etc. using Least absolute shrinkage and selection operator regression analysis and converted them into human genes. …”
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