A cross-tissue transcriptome-wide association study identified susceptibility genes for age-related macular degeneration by Hongfan Yang, Haofei Huang, Kunlin Pu

“…Multi-marker Analysis of Genomic Annotation (MAGMA) was employed to validate results and identify reliable susceptibility genes, followed by summary data-based Mendelian randomization (SMR) and colocalization analyses to explore causal associations. …”
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Nuclear Position and Shape Deformation of Chromosome 8 Territories in Pancreatic Ductal Adenocarcinoma by Sylvia Timme, Eberhard Schmitt, Stefan Stein, Jutta Schwarz-Finsterle, Jenny Wagner, Axel Walch, Martin Werner, Michael Hausmann, Thorsten Wiech

“…This decreased roundness of CTs may reflect the genomic and transcriptional alterations in carcinoma.…”
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Subgenome asymmetry of gibberellins-related genes plays important roles in regulating rapid growth of bamboos by Ling Mao, Cen Guo, Liang-Zhong Niu, Yu-Jiao Wang, Guihua Jin, Yi-Zhou Yang, Ke-Cheng Qian, Yang Yang, Xuemei Zhang, Peng-Fei Ma, De-Zhu Li, Zhen-Hua Guo

“…However, the genetic basis and evolution of this trait are poorly understood. Taking advantage of genomic resources of 11 representative bamboos at different ploidal levels, we integrated morphological, physiological, and transcriptomic datasets to investigate rapid growth. …”
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Unlocking precision medicine: clinical applications of integrating health records, genetics, and immunology through artificial intelligence by Yi-Ming Chen, Tzu-Hung Hsiao, Ching-Heng Lin, Yang C. Fann

“…Machine learning models excel at identifying high-risk patients, predicting disease activity, and optimizing therapeutic strategies based on clinical, genomic, and immunological profiles. Deep learning techniques have significantly advanced variant calling, pathogenicity prediction, splicing analysis, and MHC-peptide binding predictions in genetics. …”
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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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CHD6 has poly(ADP-ribose)- and DNA-binding domains and regulates PARP1/2-trapping inhibitor sensitivity via abasic site repair by Luc Provencher, Wilson Nartey, Peter M. Brownlee, Austin W. Atkins, Jean-Philippe Gagné, Lou Baudrier, Nicholas S. Y. Ting, Cortt G. Piett, Shujuan Fang, Dustin D. Pearson, Shaun Moore, Pierre Billon, Zachary D. Nagel, Guy G. Poirier, Gareth J. Williams, Aaron A. Goodarzi

“…DNA repair pathway screening reveals that CHD6 loss elicits insufficiency in apurinic-apyrimidinic endonuclease (APEX1) activity and genomic abasic site accumulation. We reveal APEX1-linked roles for CHD6 important for understanding PARP1/2-trapping inhibitor sensitivity.…”
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SOX5-Null Heterozygous Mutation in a Family with Adult-Onset Hyperkinesia and Behavioral Abnormalities by Michael Zech, Katharina Poustka, Sylvia Boesch, Riccardo Berutti, Tim M. Strom, Wolfgang Grisold, Werner Poewe, Juliane Winkelmann

“…SOX5 haploinsufficiency induced by larger genomic deletions has been linked to a recognizable pediatric syndrome combining developmental delay with intellectual disability, mild dysmorphism, inadequate behavior, and variable additional features including motor disturbances. …”
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In Silico Evolution of Gene Cooption in Pattern-Forming Gene Networks by Alexander V. Spirov, Marat A. Sabirov, David M. Holloway

“…Such re-arrangement of pre-existing networks is likely more common for increasing genomic complexity than the creation of new genes. …”
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Development of animal models to study aggressive thyroid cancers by Shovan Dutta, Jeffrey A Knauf

“…Recent studies exploring the genomic landscape of advanced thyroid cancer have identified several cooperating mutations, which are secondary genetic alterations that work alongside driver mutations to promote thyroid tumor progression. …”
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ChromaFold predicts the 3D contact map from single-cell chromatin accessibility by Vianne R. Gao, Rui Yang, Arnav Das, Renhe Luo, Hanzhi Luo, Dylan R. McNally, Ioannis Karagiannidis, Martin A. Rivas, Zhong-Min Wang, Darko Barisic, Alireza Karbalayghareh, Wilfred Wong, Yingqian A. Zhan, Christopher R. Chin, William S. Noble, Jeff A. Bilmes, Effie Apostolou, Michael G. Kharas, Wendy Béguelin, Aaron D. Viny, Danwei Huangfu, Alexander Y. Rudensky, Ari M. Melnick, Christina S. Leslie

“…However, achieving this resolution with current 3D genomics technologies is often infeasible given limited input cell numbers. …”
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Association between Polymorphisms in Interleukin-17A and -17F Genes and Chronic Periodontal Disease by Jôice Dias Corrêa, Mila Fernandes Moreira Madeira, Renata Gonçalves Resende, Jeane de Fátima Correia-Silva, Ricardo Santiago Gomez, Danielle da Glória de Souza, Mauro Martins Teixeira, Celso Martins Queiroz-Junior, Tarcília Aparecida da Silva

“…Material and Methods. Genomic DNA was obtained from 30 CP patients and 30 healthy controls (HCs). …”
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AutoPVPrimer: A comprehensive AI-Enhanced pipeline for efficient plant virus primer design and assessment. by Abozar Ghorbani, Mahsa Rostami, Elham Ashrafi-Dehkordi, Pietro Hiram Guzzi

“…The pipeline uses Biopython to automatically retrieve different genomic sequences from the NCBI database to increase the robustness of the subsequent primer design. …”
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Transmitted Drug Resistance among People Living with HIV/Aids at Major Cities of Sao Paulo State, Brazil by Joao Leandro Paula Ferreira, Rosangela Rodrigues, Andre Minhoto Lança, Valeria Correia de Almeida, Simone Queiroz Rocha, Taisa Grotta Ragazzo, Denise Lotufo Estevam, Luis Fernando de Macedo Brigido

“…Seventy-six percent of genomes (13/17) with TDR carried a nonnucleoside reverse transcriptase inhibitor (NNRTI) resistance mutation, mostly K103N/S (9/13, 69%), potentially compromising the preferential first-line therapy suggested by the Brazilian HIV Treatment Guideline that recommends efavirenz-based combinations. …”
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Identification of Functional Modules and Key Pathways Associated with Innervation in Graft Bone—CGRP Regulates the Differentiation of Bone Marrow Mesenchymal Stem Cells via p38 MAP... by Ziqian Wu, Xudong Wang, Jingcun Shi, Anand Gupta, Yuhan Zhang, Bingqing Zhang, Yang Cao, Lei Wang

“…We identified differentially expressed genes) from these samples and used the gene ontology and Kyoto Encyclopedia of Genes and Genomes databases for functional enrichment and signaling pathway analysis. …”
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Epigenetic Properties of Compounds Contained in Functional Foods Against Cancer by Giulia Casari, Brenda Romaldi, Andrea Scirè, Cristina Minnelli, Daniela Marzioni, Gianna Ferretti, Tatiana Armeni

“…Epigenetics encompasses reversible and heritable genomic changes in histones, DNA expression, and non-coding RNAs that occur without modifying the nucleotide DNA sequence. …”
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Adeno-associated virus-based gene therapy for hemophilia–addressing the gaps by Wolfgang Miesbach, Paul Batty, Pratima Chowdary, Sylvia Fong, Radoslaw Kaczmarek, Frank W.G. Leebeek, Brian Long, Johnny Mahlangu, Mike Makris, Glenn F. Pierce, Steven W. Pipe, Alok Srivastava, Jan Voorberg, Flora Peyvandi

“…This manuscript follows literature reviews and structured discussions by the International Society on Thrombosis and Haemostasis Scientific and Standardization Committee Working Group on Gene Therapy that identified specific areas requiring standardization of methods, including viral vector production, liver function assessment, quantification of factor (F)VIII and FIX expression levels, assessment of antiadeno-associated viral antibodies, and genomic integration detection methods. Standardization strategies aim to achieve consistent vector quality, effective patient selection, and uniform assessment methods by implementing advanced laboratory techniques and standardized protocols. …”
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Differential pathological changes in colon microenvironments in acute and chronic mouse models of inflammatory bowel disease by NaYeon Ham, Minji Park, Young-An Bae, Eui-Ju Yeo, YunJae Jung

“…RNA-sequencing revealed genetic changes in acute and chronic colitis, marked by the maintenance of genomic integrity in the acute phase and extracellular matrix dynamics in the chronic phase. …”
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A TaqMan Real-Time PCR Assay for Detection and Quantification of Sporisorium scitamineum in Sugarcane by Yachun Su, Shanshan Wang, Jinlong Guo, Bantong Xue, Liping Xu, Youxiong Que

“…This method was more sensitive (a detection limit of 10 ag pbE DNA and 0.8 ng sugarcane genomic DNA) than that of conventional PCR (10 fg and 100 ng, resp.). …”
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Epigenetic Methylation of Parathyroid CaR and VDR Promoters in Experimental Secondary Hyperparathyroidism by Jacob Hofman-Bang, Eva Gravesen, Klaus Olgaard, Ewa Lewin

“…Melting temperature profiling of CaR and VDR PCR products after bisulfite treatment of genomic DNA from rat parathyroids was performed. Real-time PCR measured expression of PTH, CaR, VDR, and klotho genes in vitro. …”
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Insights into the molecular mechanisms and nanoparticle-based therapies for gastric cancer: A review by Smarika Chauhan, Eswar Marcharla, Sneha Hariharan, Saranya Vinayagam, Thanigaivel Sundaram, Priya SD, Swamynathan Ganesan, Maximilian Lackner

“…This review aims to explore the role of nanoparticles in the prognosis and diagnosis of gastric cancer. We have analysed genomic pathways linked with gastric carcinoma and explored the utilisation of nanoparticles for multimodal imaging techniques, precise drug delivery and efficient therapeutic approaches. …”
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