c-Triadem: A constrained, explainable deep learning model to identify novel biomarkers in Alzheimer's disease. by Sherlyn Jemimah, Ferial Abuhantash, Aamna AlShehhi

“…We trained the model with blood genotyping data, microarray, and clinical features from the Alzheimer's Neuroimaging Disease Initiative (ADNI). …”
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Type-2 diabetes epigenetic biomarkers: present status and future directions for global and Indigenous health by Sarah Munns, Sarah Munns, Alex Brown, Alex Brown, Sam Buckberry, Sam Buckberry

“…We critically evaluate previous DNA methylation biomarker studies, particularly those using microarray platforms, and advocate for a shift towards sequencing-based approaches to improve genome-wide coverage. …”
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Comprehensive analysis of intervention and control studies for the computational identification of dengue biomarker genes. by Jibon Kumar Paul, Mahir Azmal, Tasnim Alam, Omar Faruk Talukder, Ajit Ghosh

“…This study conducted a comprehensive analysis of differential gene expression in dengue fever patients using multiple microarray datasets from the NCBI GEO database. Through bioinformatics approaches, 163 potential biomarker genes were identified, with some overlapping previously reported biomarkers and others representing novel candidates. …”
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Cell cycle- and cancer-associated gene networks activated by Dsg2: evidence of cystatin A deregulation and a potential role in cell-cell adhesion. by Abhilasha Gupta, Daniela Nitoiu, Donna Brennan-Crispi, Sankar Addya, Natalia A Riobo, David P Kelsell, Mỹ G Mahoney

“…CSTA is deregulated in several skin cancers, including squamous cell carcinomas (SCC) and loss of function mutations lead to recessive skin fragility disorders. The microarray results were confirmed by qPCR, immunoblotting, and immunohistochemistry. …”
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Unravelling the Impact of an Additional Sex Chromosome in an Adult Female by Sigin George, Vikas Dagar, Barun Kumar Chakrabarty, N. Nagaraja

“…Interphase fluorescence in situ hybridisation was performed to confirm the diagnosis. Chromosomal microarray, which is a more expensive test, substantiated the presence of additional X chromosomes but failed to detect the presence of low level of mosaicism. …”
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miRNA-REGULATED PATHWAYS OF CD8+ T CELLS IN TNBC MOUSE MODEL by Müge Öçal Demirtaş, Bala Gür Dedeoğlu

“…Following RNA isolation, miRNA microarray analysis was performed. Differentially expressed miRNAs between the groups were detected. …”
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Clustering, Pathway Enrichment, and Protein-Protein Interaction Analysis of Gene Expression in Neurodevelopmental Disorders by Ruchi Yadav, Prachi Srivastava

“…In this study, we have used four samples of microarray neuronal developmental data: control, RV (resveratrol), NGF (nerve growth factor), and RV + NGF. …”
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The impact of the nucleosome code on protein-coding sequence evolution in yeast. by Tobias Warnecke, Nizar N Batada, Laurence D Hurst

“…We identify nucleosome positioning as a likely candidate to set up such a DNA-level selective regime and use high-resolution microarray data in yeast to compare the evolution of coding sequence bound to or free from nucleosomes. …”
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Inhibition of ATG5-mediated autophagy maintains PMAIP1 stability to promote cell apoptosis and suppress triple-negative breast cancer progression by Fangjian Shang, Hongfeng Nie, Liyan Du, Jin Shang, Xiangquan Song, Ya Chen, Hui Li, Zhuo Wang, Yixin Qi, Liyan Zhao

“…Methods TNBC-related datasets were retrieved from The Cancer Genome Atlas and selected by Prediction Analysis of Microarray 50 analysis to assess the expression of PMAIP1 in the samples. …”
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The expression levels of CYP3A4 and CYP3A5 serve as potential prognostic biomarkers in lung adenocarcinoma by Mao Qixing, Xu Juqing, Wang Yajing, Dong Gaochao, Xia Wenjie, Shi Run, Wang Anpeng, Xu Lin, Jiang Feng, Wang Jun

“…The expression of CYP3A4, together with CYP3A5, was detected by the chip data from Gene Expression Omnibus datasets and immunohistochemistry staining of the tissue microarray. …”
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Profiling of Circulating Cell-free DNA Methylation Patterns Identifies Aberrant Methylated CTBP1 Promotor Sites for Prediction of Alzheimer’s Disease by Zhiwu Dong, Kewen Zhao, Hongjun Gu, Wenwei Yang, Xin Zhang

“…The R Bioconductor Linear Models for Microarray Data (LIMMA) package was employed to identify methylation variable positions (MVPs), and Probe Lasso was used to pinpoint differentially methylated regions (DMRs) linked to AD. …”
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Host genome drives the microbiota enrichment of beneficial microbes in shrimp: exploring the hologenome perspective by Fernanda Cornejo-Granados, Luigui Gallardo-Becerra, Sandra Romero-Hidalgo, Alonso A. Lopez-Zavala, Andrés Cota-Huízar, Melany Cervantes-Echeverría, Rogerio R. Sotelo-Mundo, Adrian Ochoa-Leyva

“…Results Using genome-wide SNP microarray analysis, we confirmed that Gen1 and Gen2 represented distinct genetic populations. …”
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An Ensemble Classification Method for High-Dimensional Data Using Neighborhood Rough Set by Jing Zhang, Guang Lu, Jiaquan Li, Chuanwen Li

“…Mining useful knowledge from high-dimensional data is a hot research topic. Efficient and effective sample classification and feature selection are challenging tasks due to high dimensionality and small sample size of microarray data. …”
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The transcription factors Snail and Slug activate the transforming growth factor-beta signaling pathway in breast cancer. by Archana Dhasarathy, Dhiral Phadke, Deepak Mav, Ruchir R Shah, Paul A Wade

“…In order to obtain a global view of the impact of Snail and Slug expression, we performed a microarray experiment using the MCF-7 breast cancer cell line, which does not express detectable levels of Snail or Slug. …”
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Decrease in pneumococcal co-colonization following vaccination with the seven-valent pneumococcal conjugate vaccine. by Carina Valente, Jason Hinds, Francisco Pinto, Silvio D Brugger, Katherine Gould, Kathrin Mühlemann, Hermínia de Lencastre, Raquel Sá-Leão

“…Co-colonization, serotype identification, and relative serotype abundance were detected by analysis of DNA of the total bacterial growth of the primary culture plate using the plyNCR-RFLP method and a molecular serotyping microarray-based strategy. …”
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Long Noncoding RNAs and mRNA Regulation in Peripheral Blood Mononuclear Cells of Patients with Chronic Obstructive Pulmonary Disease by Xiaoyan Qu, Xiaomin Dang, Weijia Wang, Ying Li, Dan Xu, Dong Shang, Ying Chang

“…Methods. lncRNA and mRNA profiling of PBMCs from 17 smokers and 14 COPD subjects was detected by high-throughput microarray. The expression of dysregulated lncRNAs was validated by qPCR. …”
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Gene co-expression module study identifies key genes and pathways underpinning hypercholesterolemia-induced atherosclerosis development by Muhammad-Redha Abdullah-Zawawi, Muhammad Irfan Abdul Jalal, Siti Aishah Sulaiman, Nur Alyaa Afifah Md Shahri, Rahman Jamal, Nor Azian Abdul Murad

“…Methods The Affymetrix microarray dataset (GSE13985), which includes samples from five healthy controls and five FH patients, was obtained from the Gene Expression Omnibus (GEO) database. …”
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Identification of Key Genes and Potential Therapeutic Targets in Sepsis-Associated Acute Kidney Injury Using Transformer and Machine Learning Approaches by Zhendong Zhai, JunZhe Peng, Wenjun Zhong, Jun Tao, Yaqi Ao, Bailin Niu, Li Zhu

“…Early diagnosis and effective therapy remain difficult despite extensive investigation. …”
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Mapping autoantibody targets of full-length C-reactive protein in systemic lupus erythematosus: importance for neutrophil function and classical complement activation by Jesper Karlsson, Lina Wirestam, Hanna Duàn, Suhana Ahmad, Daniel Appelgren, Helena Enocsson, Jonas Wetterö, Christopher Sjöwall

“…The levels of anti-CRP and SLE-associated antibodies were assessed, and a microarray-based linear epitope mapping was performed to detect binding sites on the full CRP monomer. …”
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Genetic test results and one-year developmental outcomes of fetuses with congenital heart disease by Hui Hu, Bo Zhou, Qunda Shan, Shuangshuang Shen, Xiangdong Zhang, Penglong Chen, Jiao Liu, Xiaofang Lan

“…ObjectiveThis study evaluated the utility of single nucleotide polymorphism (SNP) microarray analysis in prenatal genetic assessment of fetuses diagnosed with congenital heart disease (CHD), retrospectively analyzing pregnancy outcomes and their association with physical and intellectual development within the first year of life.Patients and methodsIt included 105 fetuses diagnosed with CHD via prenatal echocardiography from January 2016 to June 2020, categorized into two groups: isolated cardiac structural abnormalities (76 cases) and additional extracardiac structural abnormalities (29 cases). …”
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