GNGT1 is a potential prognostic and immunologic biomarker in gastric cancer by Xuchong Huang, Juan Lin, Jian Wang, Weifeng Yang, Wenquan Ou, Xing Huang, Jiahua Chen, Zixing Zhang, Xiaohua Wu

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GeneRiskCalc: a web-based tool for genetic risk association analysis in case–control studies by Amrit Sudershan, Kuljeet Singh, Parvinder Kumar

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PuMA: PubMed gene/cell type-relation Atlas by Lucas Bickmann, Sarah Sandmann, Carolin Walter, Julian Varghese

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Increasing pathogenic germline variant diagnosis rates in precision medicine: current best practices and future opportunities by Sonam Dukda, Manoharan Kumar, Andrew Calcino, Ulf Schmitz, Matt A. Field

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HIGH-THROUGHPUT SIMULATIONS OF PROKARYOTIC COMMUNITY EVOLUTION WITH HAPLOID EVOLUTIONARY CONSTRUCTOR by Z. S. Mustafin, Yu. G. Matushkin, S. A. Lashin

“…The software is used to simulate the functioning and evolution of prokaryotic communities. …”
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PGBTR: a powerful and general method for inferring bacterial transcriptional regulatory networks by Wei-Cheng Gu, Bin-Guang Ma

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Information and characteristics of EST-SNP loci in grape (Vitis vinifera L.) by LI Meng, GUO Da-long, LIU Chong-huai, ZHANG Guo-hai, HOU Xiao-gai

“…Aiming to mine candidate single nucleotide polymorphism (SNP) loci by aligning homologous expressed sequence tags (EST) using bioinformatics software, 42 493 EST sequences were retrieved from different tissues of nine different grape genotypes in NCBI dbEST database and assembled into 6 126 contigs by CAP3 software, then candidate SNP loci of the contigs were screened by QualitySNP software. …”
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Identification of new diagnostic targets for hepatitis B virus‐induced liver fibrosis by Ying Wang, Shuo Qin, Meng Yang, Xiaoling Wang

“…Transcriptome sequencing technology and bioinformatics analysis are increasingly being used to screen diagnostic targets for liver fibrosis. …”
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UPLC-ESI/MSn metabolic profiling of Cedrela odorata L. and Toona ciliata M. Roem and in vitro investigation of their anti-diabetic activity supported with molecular docking studies by Heba A. S. El-Nashar, Ayman M. Al-Qaaneh, Ayman M. Al-Qaaneh, Md. Shimul Bhuia, Md. Shimul Bhuia, Raihan Chowdhury, Raihan Chowdhury, Mostafa A. Abdel-Maksoud, Hossam Ebaid, Abdul Malik, Muhammad Torequl Islam, Muhammad Torequl Islam, Muhammad Torequl Islam, Mohammed Aufy, Esraa A. Elhawary

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Left ventricular noncompaction associated with titin-truncating variants in the TTN gene by Yu. A. Vakhrushev, T. I. Vershinina, P. A. Fedotov, A. A. Kozyreva, A. M. Kiselev, Yu. V. Fomicheva, E. S. Vasichkina, T. M. Pervunina, A. A. Kostareva

“…Causal role of TTN-truncating variants in development of cardiomyopathies and, in particular, left ventricular noncompaction, requires a comprehensive clinical, segregation and bioinformatic analysis using international databases and the use of bioinformatics software.…”
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MESM: integrating multi-source data for high-accuracy protein-protein interactions prediction through multimodal language models by Feng Wang, Jinming Chu, Liyan Shen, Shan Chang

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Assessment of the new Next Generation Sequencing (NGS) tools to identify genes associated with tolerance to water deficit in sugarcane by John Jaime Riascos Arcos, Héctor Fabio Espitia Navarro, Jershon López Gerena

“…Each library was sequenced using NGS methodologies (Illumina-RNA-Seq) and data were analyzed using specialized bioinformatics software. Among the genes that were observed as differentially expressed it was possible to identify orthologs of those previously associated with tolerance for the traits of interest. …”
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Teaching Analytical Instrumental Analysis to Undergraduates in Specialized Degree Programs with Heterogeneous Prior Knowledge: Reflections on Inquiry Based Lecture Activities by Kirsten A. Tucker, Peter L. Pingerelli

“…Activities included using readily available Internet bioinformatics and database tools for analytical problem-solving; demonstrating principles of electronic hardware and software design and integration; and creating interdisciplinary scientific narratives using biological, environmental, and industrial molecular exemplars. …”
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Discovery of potential ovarian cancer biomarkers using low molecular weight blood plasma proteome profiling by mass spectrometry by V. E. Shevchenko, N. E. Arnotskaya, E. V. Ogorodnikova, N. R. Pogosyan, A. N. Gritsay, K. I. Zhordania

“…The given approach included three basic components: pre-preparation of samples, matrix-assisted laser desorption/ionization time-of-flight mass spectrometry and bioinformatics software for mass spectral data process- ing. …”
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Simultaneous detection of pathogens and antimicrobial resistance genes with the open source, cloud-based, CZ ID platform by Dan Lu, Katrina L. Kalantar, Abigail L. Glascock, Victoria T. Chu, Estella S. Guerrero, Nina Bernick, Xochitl Butcher, Kirsty Ewing, Elizabeth Fahsbender, Olivia Holmes, Erin Hoops, Ann E. Jones, Ryan Lim, Suzette McCanny, Lucia Reynoso, Karyna Rosario, Jennifer Tang, Omar Valenzuela, Peter M. Mourani, Amy J. Pickering, Amogelang R. Raphenya, Brian P. Alcock, Andrew G. McArthur, Charles R. Langelier

“…Metagenomic next-generation sequencing (mNGS) has revolutionized such efforts, but remains challenging due to the lack of open-access bioinformatics tools capable of simultaneously analyzing both microbial and AMR gene sequences. …”
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mbctools: A User-Friendly Metabarcoding and Cross-Platform Pipeline for Analyzing Multiple Amplicon Sequencing Data across a Large Diversity of Organisms by Barnabé, Christian, Sempéré, Guilhem, Manzanilla, Vincent, Millan, Joel Moo, Amblard-Rambert, Antoine, Waleckx, Etienne

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Subcellular localization and expression analysis of MlSOC1 genes during flower bud differentiation period in Magnolia liliflora by XUAN Lingjuan, CHENG Shaoyu, DAI Mengyi, WANG Zhuowei, SHEN Yamei

“…In order to clarify the mechanism of SOC1 in the process of flower formation in Magnolia liliflora, two SOC1 genes were screened out based on the transcriptome data in M. sinostellata, and the complete coding regions of these two SOC1 genes were obtained by homologous gene cloning. The bioinformatics software was used to analyze the information of these two genes, and the expression patterns in different flower bud differentiation periods were verified by real-time fluorescence quantitative polymerase chain reaction (qRT-PCR). …”
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PVT1 affects growth of glioma microvascular endothelial cells by negatively regulating miR-186 by Yawen Ma, Ping Wang, Yixue Xue, Chengbin Qu, Jian Zheng, Xiaobai Liu, Jun Ma, Yunhui Liu

“…We also found that PVT1 overexpression upregulated the expression of the autophagy-related proteins Atg7 and Beclin1, which induced protective autophagy. Bioinformatics software and dual-luciferase system analysis confirmed that PVT1 acts by targeting miR-186. …”
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The role of SLC2A1 in lung adenocarcinoma: From tumorigenesis to patient survival. by Zijun Xiao, Qinqin Long, Jiaxing Liao, Fengdie Huang, Lusheng Liao, Mingyou Dong

“…<h4>Methods</h4>A comprehensive bioinformatics analysis was conducted utilizing online tools and software, including R packages, Gene Set Cancer Analysis (GSCA), cBio Cancer Genomics Portal (cBioPortal), GeneMANIA, STRING, and Xiantao Academic Online databases, to assess the functional implications of the SLC2A gene family in LUAD. …”
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Analysis of the overall development trends and hotspots in the research field of the human gut virome by Yidi Zhang, Ting Mei, Minhui Wang, Chunxia Huang, Hanzhi Yi, Yu Zhan, Sen Yang, Han Wang, Qiulong Yan, Ruochun Guo, Changming Chen

“…Methods A bibliometric analysis was performed on articles retrieved from the Web of Science (WoS) Core Collection database covering the period 2000 to 2024, utilizing VOSviewer, CiteSpace, and the R software environment. Results Over the past 20 years, the number of published papers and citations in the field of enterovirus research has shown a significant growth trend. …”
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