HAVCR1 Affects the MEK/ERK Pathway in Gastric Adenocarcinomas and Influences Tumor Progression and Patient Outcome by Ji Xue, Ying Li, Jianfeng Yi, Hong Jiang

“…We first determined the expression of HAVCR1 in GAC tissues compared with normal gastric tissues based on the Cancer Genome Atlas (TCGA) database using bioinformatics analysis methods. Then, we assessed the biological function of HAVCR1 in GAC cells using quantitative real-time reverse transcription-PCR (qRT-PCR), western blot, cell counting kit-8- (CCK-) 8, colony formation assay, wound healing assay, and transwell assay. …”
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lncRNA PAPPA-AS1 Induces the Development of Hypertrophic Scar by Upregulating TLR4 through Interacting with TAF15 by Pengju Fan, Yongjie Wang, Jingjing Li, Man Fang

“…In the present study, the regulatory effect of lncRNA PAPPA-AS1 on the Toll-like receptor 4 (TLR4) signal pathway, as well as the molecular mechanism, was investigated. Bioinformatics analysis was utilized to screen the differentially expressed lncRNAs in HTS tissues. …”
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Clustering Pattern and Functional Effect of SNPs in Human miRNA Seed Regions by Sha He, Haiyan Ou, Cunyou Zhao, Jian Zhang

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Advances in antiviral strategies targeting mosquito-borne viruses: cellular, viral, and immune-related approaches by Ayyaz Khan, Zakirullah, Shahid Wahab, Seong-Tshool Hong

“…Additionally, it explores immunomodulatory therapies to enhance antiviral responses and emphasizes the potential of drug repurposing, bioinformatics, artificial intelligence, and deep learning in identifying novel antiviral candidates. …”
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Inferring causal protein signalling networks from single‐cell data based on parallel discrete artificial bee colony algorithm by Jinduo Liu, Jihao Zhai, Junzhong Ji

“…Abstract Inferring causal protein signalling networks from human immune system cell data is a promising approach to unravel the underlying tissue signalling biology and dysfunction in diseased cells, which has attracted considerable attention within the bioinformatics field. Recently, Bayesian network (BN) techniques have gained significant popularity in inferring causal protein signalling networks from multiparameter single‐cell data. …”
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Exploring the Genetic Landscape of Mycobacterium tuberculosis: Unlocking the Differences in Between Latent and Active Tuberculosis by Ali Akbar Velayati, Satoshi Mitaria, Parissa Farnia, Poopak Farnia, Jaladein Ghanavi, Mohsan Maleknia, Yoshiro Murase, Sven Hoffner

“…Whole-genome sequencing and protein structure analysis using bioinformatics tools were performed to characterize and compare mutations in isolates at each phase. …”
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The Potential Diagnostic Value of Immune-Related Genes in Interstitial Fibrosis and Tubular Atrophy after Kidney Transplantation by Bin Yang, Dike Shi, Yahong Chen, Yi Zhu

“…The aim of this study was to reveal new diagnostic markers of IF/TA based on bioinformatics analysis. Methods. Raw data of IF/TA samples after kidney transplantation and control samples after kidney transplantation were extracted from the Gene Expression Omnibus (GEO) database (GSE76882 and GSE120495 datasets), and genes that were differentially expressed between the two groups (DEGs) were screened. …”
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Transcription Factor FXR Activates DHRS9 to Inhibit the Cell Oxidative Phosphorylation and Suppress Colon Cancer Progression by Jinlai Zhao, Yigang Wang, Yang Wang, Jianchao Gao, Haichao Yang, Xiaotang Wu, Hua Li

“…The downstream target gene of FXR was predicted by bioinformatics analysis and found to be associated with cellular oxidative phosphorylation. …”
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A pan-cancer analysis of MARCH8: molecular characteristics, clinical relevance, and immuno-oncology features by Zihan Quan, Songqing Fan, Hongmei Zheng, Yue Ning, Yang Yang

“…We investigated the role of MARCH8 expression in clinical relevance, prognosis, tumor immune microenvironment, immune checkpoint (ICP) with a series of bioinformatics tools and methods, such as TISIDB database, ESTIMATE, and CIBERSORT method. …”
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Upregulation of PGC-1α Attenuates Oxygen-Glucose Deprivation-Induced Hippocampal Neuronal Injury by Bin Han, Hui Zhao, Xingji Gong, Jinping Sun, Song Chi, Tao Liu, Anmu Xie

“…Our results showed that mitochondrial membrane potentials were increased and ROS production was decreased in PGC-1α overexpressing cells, which increased cell viability. The further bioinformatics analysis from ChIP-Seq data indicated that PGC-1α may participate in the regulation of apoptosis, autophagy, and mitophagy pathways in HT-22 cells. …”
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Genomic Analysis of miR-21-3p and Expression Pattern with Target Gene in Olive Flounder by Ara Jo, Hee-Eun Lee, Heui-Soo Kim

“…Using genomic and bioinformatic tools, evolutionary conservation of miR-21-3p was examined in various species, and expression pattern was analyzed in olive flounder. …”
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Nf-Root: A Best-Practice Pipeline for Deep-Learning-Based Analysis of Apoplastic pH in Microscopy Images of Developmental Zones in Plant Root Tissue by Julian Wanner, Luis Kuhn Cuellar, Luiselotte Rausch, Kenneth W. Berendzen, Friederike Wanke, Gisela Gabernet, Klaus Harter, Sven Nahnsen

“…Here, we report Nextflow-root (nf-root), a novel best-practice pipeline for deep-learning-based analysis of fluorescence microscopy images of plant root tissue from A. thaliana. This bioinformatics pipeline performs automatic identification of developmental zones in root tissue images. …”
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CD21low B cells reveal a unique glycosylation pattern with hypersialylation and hyperfucosylation by Peter Tobias Felixberger, Peter Tobias Felixberger, Geoffroy Andrieux, Andrea Maul-Pavicic, Andrea Maul-Pavicic, Sigune Goldacker, Sigune Goldacker, Ina Harder, Ina Harder, Sylvia Gutenberger, Sylvia Gutenberger, Jonathan J. M. Landry, Vladimir Benes, Till Fabian Jakob, Melanie Boerries, Melanie Boerries, Lars Nitschke, Reinhard Edmund Voll, Reinhard Edmund Voll, Klaus Warnatz, Klaus Warnatz, Baerbel Keller, Baerbel Keller

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Evaluation of the resistome and gut microbiome composition of hospitalized patients in a health unit of southern Brazil coming from a high animal husbandry production region by Elisa Pires Coltro, Elisa Pires Coltro, Lucas Cafferati Beltrame, Lucas Cafferati Beltrame, Lucas Cafferati Beltrame, Caroline Ribeiro da Cunha, Caetana Paes Zamparette, Clarissa Feltrin, Vilmar Benetti Filho, Patrícia de Almeida Vanny, Sérgio Beduschi Filho, Taíse Costa Ribeiro Klein, Mara Cristina Scheffer, Jussara Kasuko Palmeiro, Jussara Kasuko Palmeiro, Glauber Wagner, Thaís Cristine Marques Sincero, Thaís Cristine Marques Sincero, Carlos Rodrigo Zárate-Bladés, Carlos Rodrigo Zárate-Bladés

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The Utility of Perirenal Fat in Determining the Risk of Onset and Progression of Diabetic Kidney Disease by Hongtu Hu, Wei Liang, Zongwei Zhang, Zikang Liu, Fan Chu, Yan Bao, Jialu Ran, Guohua Ding

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Sequence Analysis of Hypothetical Proteins from 26695 to Identify Potential Virulence Factors by Ahmad Abu Turab Naqvi, Farah Anjum, Faez Iqbal Khan, Asimul Islam, Faizan Ahmad, Md. Imtaiyaz Hassan

“…This study involves extensive analysis of the HPs using an established pipeline which comprises various bioinformatics tools and databases to find out probable functions of the HPs and identification of virulence factors. …”
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Post-processing enhances protein secondary structure prediction with second order deep learning and embeddings by Sotiris Chatzimiltis, Michalis Agathocleous, Vasilis J. Promponas, Chris Christodoulou

“…Protein Secondary Structure Prediction (PSSP) is regarded as a challenging task in bioinformatics, and numerous approaches to achieve a more accurate prediction have been proposed. …”
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Bioactive molecules from soybeans (Glycine max) with anti-type 2 diabetes activity: a systematic review by Adekunle Babajide Rowaiye, Lorretha Chinonye Emenyonu, Ezinne Janefrances Nwonu, Okiemute Ajiroghene Okpalefe, Joseph Akwoba Ogugua, Victor Oluwatoyin Akinseye, Gordon Chukwuma Ibeanu

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Design of a Multiepitope Pan-Proteomic mRNA Vaccine Construct Against African Swine Fever Virus: A Reverse Vaccinology Approach by Ella Mae Joy S. Sira, Lauren Emily Fajardo, Edward C. Banico, Nyzar Mabeth O. Odchimar, Fredmoore L. Orosco

“…In this study, a reverse vaccinology approach was used to design a multiepitope pan-proteomic mRNA vaccine against ASFV. Various bioinformatics tools were employed to predict epitopes for cytotoxic T lymphocytes, helper T lymphocytes, and B lymphocytes. …”
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Mapping genomic regions affecting sensitivity to bovine respiratory disease on chromosome X using selective DNA pooling by Ehud Lipkin, Maria Giuseppina Strillacci, Miri Cohen-Zinder, Harel Eitam, Moran Yishay, Morris Soller, Carlotta Ferrari, Alessandro Bagnato, Ariel Shabtay

“…All regions overlapped or were very close to previously reported regions. Bioinformatics survey found candidate-by-location genes in these regions. …”
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