Loss of Lkb1 cooperates with BrafV600E and ultraviolet radiation, increasing melanoma multiplicity and neural‐like dedifferentiation by Kimberley McGrail, Elena González‐Sánchez, Paula Granado‐Martínez, Roberto Orsenigo, Yuxin Ding, Berta Ferrer, Javier Hernández‐Losa, Iván Ortega, Juan Martín‐Caballero, Eva Muñoz‐Couselo, Vicente García‐Patos, Juan A. Recio

“…Analysis of human melanoma tumors [data from The Cancer Genome Atlas (TCGA)] revealed that 50% or more of the samples expressed no or low amounts of serine/threonine protein kinase STK11 (also known as LKB1) protein. …”
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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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Diet-derived urolithin A is produced by a dehydroxylase encoded by human gut Enterocloster species by Reilly Pidgeon, Sacha Mitchell, Michael Shamash, Layan Suleiman, Lharbi Dridi, Corinne F. Maurice, Bastien Castagner

“…Here, we use a combination of untargeted bacterial transcriptomics, proteomics, and comparative genomics to uncover an inducible uroC dehydroxylase (ucd) operon in Enterocloster species. …”
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Integrated Bioinformatics-Based Identification of Potential Diagnostic Biomarkers Associated with Diabetic Foot Ulcer Development by Long Qian, Zhipeng Xia, Ming Zhang, Qiong Han, Die Hu, Sha Qi, Danmou Xing, Yan Chen, Xin Zhao

“…These DEGs were then arranged into a protein-protein interaction (PPI) network, and Kyoto Encyclopedia of Genes and Genomes (KEGG) pathway and Gene Ontology (GO) term enrichment analyses were performed to explore the functional roles of these genes. …”
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Therapies for Mitochondrial Disorders by Kayli Sousa Smyth, Anne Mulvihill

“…Mitochondria contain their own genome, mitochondrial DNA (mtDNA), which is maternally inherited from the oocyte. …”
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Systematic and Cell Type-Specific Telomere Length Changes in Subsets of Lymphocytes by Jue Lin, Joshua Cheon, Rashida Brown, Michael Coccia, Eli Puterman, Kirstin Aschbacher, Elizabeth Sinclair, Elissa Epel, Elizabeth H. Blackburn

“…Telomeres, the protective DNA-protein complexes at the ends of linear chromosomes, are important for genome stability. Leukocyte or peripheral blood mononuclear cell (PBMC) telomere length is a potential biomarker for human aging that integrates genetic, environmental, and lifestyle factors and is associated with mortality and risks for major diseases. …”
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The Pathogenesis of Nonalcoholic Fatty Liver Disease: Interplay between Diet, Gut Microbiota, and Genetic Background by Jinsheng Yu, Sharon Marsh, Junbo Hu, Wenke Feng, Chaodong Wu

“…Moreover, several genetic variants have been identified through genome-wide association studies, particularly rs738409 (Ile748Met) in PNPLA3 and rs58542926 (Glu167Lys) in TM6SF2, which are critical risk alleles of the disease. …”
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miRNA-328-3p regulates ZO-1 expression and inhibits PEDV proliferation via the PLC-β1-PKC pathway. by Han Zhao, Jiayu Zhang, Dengliang Li, Zhanding Cui, Jiuyuan Liu, Di Bao, Yiming Wei, Xinyue Zhang, Zhimin Wu, Tianqi Zhang, Kai Wang, Shushuai Yi, Wei Lian, Guixue Hu

“…Furthermore, PLC-β1 overexpression increased both viral genome expression and PEDV titers, whereas its silencing had the opposite effect. …”
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Matrix Metalloproteinase-9 is associated with tumor microenvironment remodeling of bladder cancer by Fang Fang, Tiange Wu, Mengxue Wang, Wenchao Li, Zonghao You, Ming Chen, Han Guan

“…We utilized these two algorithms to analyze the immune components of 433 bladder cancer cases from The Cancer Genome Atlas database, aiming to compensate for the current lack of large-sample single-cell information. …”
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Antioxidant and cytotoxic potentials of Streptomyces gilvigriseus MUSC 26T isolated from mangrove soil in Malaysia by Hooi-Leng Ser, Wai-Fong Yin, Kok-Gan Chan, Tahir Mehmood Khan, Bey-Hing Goh, Learn-Han Lee

“…By the same token, the availability of its genome sequence allows further investigation into the biosynthetic gene clusters responsible for the production of these compounds which could essentially accelerate its development as chemopreventive drug(s).…”
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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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Enhancing foundation models for scientific discovery via multimodal knowledge graph representations by Vanessa Lopez, Lam Hoang, Marcos Martinez-Galindo, Raúl Fernández-Díaz, Marco Luca Sbodio, Rodrigo Ordonez-Hurtado, Mykhaylo Zayats, Natasha Mulligan, Joao Bettencourt-Silva

“…Foundation Models (FMs) hold transformative potential to accelerate scientific discovery, yet reaching their full capacity in complex, highly multimodal domains such as genomics, drug discovery, and materials science requires a deeper consideration of the contextual nature of the scientific knowledge. …”
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