Gene-specific machine learning model to predict the pathogenicity of BRCA2 variants by Mohannad N. Khandakji (13885434)

“…<h3>Background</h3><p dir="ltr">Existing BRCA2-specific variant pathogenicity prediction algorithms focus on the prediction of the functional impact of a subtype of variants alone. …”

Single-Cell Transcriptome Analysis Highlights a Role for Neutrophils and Inflammatory Macrophages in the Pathogenesis of Severe COVID-19 by Hibah Shaath (5599658)

“…Further analyses revealed genes associated with the inflammatory response and chemotaxis of myeloid cells, phagocytes, and granulocytes, among the top activated functional categories in BAL from severe COVID-19-affected patients. …”

Kernel-Ridge-Regression-Based Randomized Network for Brain Age Classification and Estimation by Raveendra Pilli (21633287)

“…Features from MRI images are extracted using 3-D-CNN and fed into the wavelet KRR-RVFL network for brain age classification and prediction. The proposed algorithm achieved high classification accuracy, 97.22%, 99.31%, and 95.83% for GM, WM, and CSF regions, respectively. …”

Optimizing clopidogrel dose response by Saab, Yolande B.

“…Purpose Response to clopidogrel varies widely with nonresponse rates ranging from 4% to 30%. A reduced function of the gene variant of the CYP2C19 has been associated with lower drug metabolite levels, and hence diminished platelet inhibition. …”
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Detecting protein complexes in protein interaction networks using Mapper and Graph Convolution Networks by Daou, Leonardo

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Blood-Based Proteomic Profiling Identifies Potential Biomarker Candidates and Pathogenic Pathways in Dementia by Hanan Ehtewish (17149825)

“…We used a high-throughput proximity extension immunoassay to quantify 1090 proteins in 122 participants (22 with dementia, 64 with mild cognitive impairment (MCI), and 36 controls with normal cognitive function). Limma-based differential expression analysis reported the dysregulation of 61 proteins in the plasma of those with dementia compared with controls, and machine learning algorithms identified 17 stable diagnostic biomarkers that differentiated individuals with AUC = 0.98 ± 0.02. …”

Single-Cell Transcriptome Analysis Revealed Heterogeneity and Identified Novel Therapeutic Targets for Breast Cancer Subtypes by Radhakrishnan Vishnubalaji (3563306)

“…Differential expression and gene set enrichment analysis in TNBC revealed enrichment in the cycle and mitosis functional categories in FDPShigh, while ENO1high was associated with numerous functional categories, including cell cycle, glycolysis, and ATP metabolic processes. …”

Autism Detection of MRI Brain Images Using Hybrid Deep CNN With DM-Resnet Classifier by JAIN, SWETA

“…The hyper parameters are optimized with DM optimization algorithm which improves the accuracy of classifier. …”
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Cohen syndrome and early-onset epileptic encephalopathy in male triplets: two disease-causing mutations in VPS13B and NAPB by Alice AbdelAleem (17753799)

“…Homozygosity mapping of ES data of this consanguineous family revealed multiple chromosomal regions of homozygosity stretches with the residing of VPS13B (chr8: 100830758G > A) and NAPB (Chr20: 23,375,774 A > C) variants within the largest homozygous blocks further supporting the disease-genes causal role. Interestingly, the functions of the two proteins; VPS13B, a transmembrane protein involved in intracellular protein transport, and SNAP-beta involved in neurotransmitters release at the neuronal synaptic complexes, have been associated with Golgi-mediated vesicular trafficking. …”

Exploring the Dynamic Interplay of Deleterious Variants on the RAF1–RAP1A Binding in Cancer: Conformational Analysis, Binding Free Energy, and Essential Dynamics by Abbas Khan (5141000)

“…Hence, the current study focuses on the screening of clinically reported substitutions in the <i>RAF1</i> and <i>RAP1A</i> genes using predictive algorithms integrated with all‐atoms simulation, essential dynamics, and binding free energy methods. …”

Copy number variations in the genome of the Qatari population by Khalid A. Fakhro (3158862)

“…Up to 40 % of all CNVs affected genes, including novel CNVs affecting Mendelian disease genes, segregating at different frequencies in the 3 major Qatari subpopulations, including those with Bedouin, Persian/South Asian, and African ancestry. …”

Integrated whole transcriptome and small RNA analysis revealed multiple regulatory networks in colorectal cancer by Hibah Shaath (5599658)

“…IPA in combination with in silico prediction algorithms and experimentally validated databases gave insight into the complex associations and interactions between downregulated miRNAs and upregulated mRNAs in CRC and vice versa. …”