Table1_A depth-first search algorithm for oligonucleotide design in gene assembly.DOCX by Hanjie Liang (12253847)

“…Based on these fragments, a set of oligonucleotides for gene assembly is produced. …”

Data_Sheet_1_Transcriptome-Based Selection and Validation of Reference Genes for Gene Expression Analysis of Alicyclobacillus acidoterrestris Under Acid Stress.PDF by Ning Zhao (84707)

“…The expression stability of eight new RGs and commonly used RG 16s rRNA was assessed using geNorm, NormFinder, and BestKeeper algorithms. Moreover, the comprehensive analysis using the RefFinder program and the validation using target gene ctsR showed that dnaG and dnaN were the optimal multiple RGs for normalization at pH 4.0; ytvI, dnaG, and 16s rRNA at pH 3.5; icd and dnaG at pH 3.0; and ytvI, dnaG, and spoVE at pH 2.5. …”

Data_Sheet_2_Transcriptome-Based Selection and Validation of Reference Genes for Gene Expression Analysis of Alicyclobacillus acidoterrestris Under Acid Stress.xls by Ning Zhao (84707)

“…The expression stability of eight new RGs and commonly used RG 16s rRNA was assessed using geNorm, NormFinder, and BestKeeper algorithms. Moreover, the comprehensive analysis using the RefFinder program and the validation using target gene ctsR showed that dnaG and dnaN were the optimal multiple RGs for normalization at pH 4.0; ytvI, dnaG, and 16s rRNA at pH 3.5; icd and dnaG at pH 3.0; and ytvI, dnaG, and spoVE at pH 2.5. …”

Table1_Computational prediction of allergenic proteins based on multi-feature fusion.DOCX by Bin Liu (5899)

Data Sheet 1_Clinical potential and experimental validation of prognostic genes in hepatocellular carcinoma revealed by risk modeling utilizing single cell and transcriptome constr... by Hang Deng (1664668)

“…</p>Methods<p>The HCC datasets were obtained from public databases and then differential expression analysis were used to obtain significant gene expression profiles. Subsequently, univariate Cox regression analysis and PH assumption test were performed, and a risk model was developed using an optimal algorithm from 101 combinations on the TCGA-LIHC dataset to pinpoint prognostic genes. …”

Comprehensive analysis of CSR transcription in breast cancer and normal tissues. by Musalula Sinkala (6873695)

DataSheet_1_A novel prognostic model based on three integrin subunit genes-related signature for bladder cancer.docx by Hongtao Tu (11898503)

“…This study endeavored to thoroughly analyze the utility of ITGs in BLCA through computer algorithm-based bioinformatics.</p>Methods<p>BLCA-related materials were sourced from reputable databases, The Cancer Genome Atlas (TCGA) and Gene Expression Omnibus (GEO). …”

Workflow overview to reconstruct integrated host-virus genome-scale models and detect promising compounds with an antiviral activity. by Nantia Leonidou (14833068)

BOFdat Step 3: Identifying species-specific metabolic end goals. by Jean-Christophe Lachance (6619307)

DataSheet2_Prognostic N6-methyladenosine (m6A)-related lncRNA patterns to aid therapy in pancreatic ductal adenocarcinoma.pdf by Yuxin Wang (414197)

“…Gene set variation analysis (GSVA) was employed to assign pathway activity estimates to individual samples. …”

DataSheet1_Prognostic N6-methyladenosine (m6A)-related lncRNA patterns to aid therapy in pancreatic ductal adenocarcinoma.xlsx by Yuxin Wang (414197)

“…Gene set variation analysis (GSVA) was employed to assign pathway activity estimates to individual samples. …”

Supplementary file 1_Development and validation of machine learning-based diagnostic models using blood transcriptomics for early childhood diabetes prediction.xlsx by Xin Huang (11077)

“…Five feature selection methods (Lasso, Elastic Net, Random Forest, Support Vector Machine, and Gradient Boosting Machine) were employed to optimize gene sets. Nine machine learning algorithms (Decision Tree, Gradient Boosting Machine, K-Nearest Neighbors, Linear Discriminant Analysis, Logistic Regression, Multilayer Perceptron, Naive Bayes, Random Forest, and Support Vector Machine) were combined with selected features, generating 45 unique model combinations. …”

Table1_Analytical validation and clinical utilization of K-4CARE™: a comprehensive genomic profiling assay with personalized MRD detection.XLSX by Thien-Phuc Nguyen Hoang (17940656)

“…<p>Background: Biomarker testing has gradually become standard of care in precision oncology to help physicians select optimal treatment for patients. Compared to single-gene or small gene panel testing, comprehensive genomic profiling (CGP) has emerged as a more time- and tissue-efficient method. …”

Image_2_Construction of a novel choline metabolism-related signature to predict prognosis, immune landscape, and chemotherapy response in colon adenocarcinoma.tif by Cong Liu (66219)

“…</p>Methods<p>Choline metabolism-related differentially expressed genes (DEGs) between normal and COAD tissues were screened using datasets from The Cancer Genome Atlas (TCGA), Kyoto Encyclopedia of Genes and Genomes (KEGG), AmiGO2 and Reactome Pathway databases. …”

DataSheet_2_Construction of a novel choline metabolism-related signature to predict prognosis, immune landscape, and chemotherapy response in colon adenocarcinoma.csv by Cong Liu (66219)

“…</p>Methods<p>Choline metabolism-related differentially expressed genes (DEGs) between normal and COAD tissues were screened using datasets from The Cancer Genome Atlas (TCGA), Kyoto Encyclopedia of Genes and Genomes (KEGG), AmiGO2 and Reactome Pathway databases. …”

Image_1_Construction of a novel choline metabolism-related signature to predict prognosis, immune landscape, and chemotherapy response in colon adenocarcinoma.tiff by Cong Liu (66219)

“…</p>Methods<p>Choline metabolism-related differentially expressed genes (DEGs) between normal and COAD tissues were screened using datasets from The Cancer Genome Atlas (TCGA), Kyoto Encyclopedia of Genes and Genomes (KEGG), AmiGO2 and Reactome Pathway databases. …”

DataSheet_3_Construction of a novel choline metabolism-related signature to predict prognosis, immune landscape, and chemotherapy response in colon adenocarcinoma.csv by Cong Liu (66219)

“…</p>Methods<p>Choline metabolism-related differentially expressed genes (DEGs) between normal and COAD tissues were screened using datasets from The Cancer Genome Atlas (TCGA), Kyoto Encyclopedia of Genes and Genomes (KEGG), AmiGO2 and Reactome Pathway databases. …”

DataSheet_4_Construction of a novel choline metabolism-related signature to predict prognosis, immune landscape, and chemotherapy response in colon adenocarcinoma.csv by Cong Liu (66219)

“…</p>Methods<p>Choline metabolism-related differentially expressed genes (DEGs) between normal and COAD tissues were screened using datasets from The Cancer Genome Atlas (TCGA), Kyoto Encyclopedia of Genes and Genomes (KEGG), AmiGO2 and Reactome Pathway databases. …”

Table_2_Construction of a novel choline metabolism-related signature to predict prognosis, immune landscape, and chemotherapy response in colon adenocarcinoma.xlsx by Cong Liu (66219)

“…</p>Methods<p>Choline metabolism-related differentially expressed genes (DEGs) between normal and COAD tissues were screened using datasets from The Cancer Genome Atlas (TCGA), Kyoto Encyclopedia of Genes and Genomes (KEGG), AmiGO2 and Reactome Pathway databases. …”

Table_1_Construction of a novel choline metabolism-related signature to predict prognosis, immune landscape, and chemotherapy response in colon adenocarcinoma.docx by Cong Liu (66219)

“…</p>Methods<p>Choline metabolism-related differentially expressed genes (DEGs) between normal and COAD tissues were screened using datasets from The Cancer Genome Atlas (TCGA), Kyoto Encyclopedia of Genes and Genomes (KEGG), AmiGO2 and Reactome Pathway databases. …”