Bioinformatics Advances

📊 Supervised centroid classification using the optimized pipeline achieved 81% accuracy in distinguishing carcinoma from sarcoma in a test set of challenging tumors.

Comparing five read-counting tools and six normalization strategies with DESeq2, featureCounts and a five-gene stable normalization approach (I-HK5) gave the best tumor clustering and matched results from full RNA-seq.

🔬 New research in Bioinformatics Advances: "Optimizing bioinformatic workflows to extract clinically usable gene expression data from targeted tumor RNA sequencing panels: Comparison with total RNA-seq in cancer samples"  Access it here: doi.org/10.1093/bioadv…

🧰 NitroGene is available at github.com/zakkaz1/NitroG…

The framework was validated across collaborative PCA, cross-cohort kinship estimation, and GWAS, producing results concordant with centrally pooled analyses while keeping raw data encrypted throughout.

🔒 New in Bioinformatics Advances: "NitroGene: Privacy-preserving collaborative genomic analysis using AWS Nitro Enclaves"  Read it here: doi.org/10.1093/bioadv…

⚙️ Code for arity maps and abstraqt is available within the Structural Bioinformatics Library at sbl.inria.fr.

The per-residue scorer abstraqt extends this framework to flag hallucinated helices and distorted beta strands that pLDDT assigns high confidence.

🗺️ New paper in Bioinformatics Advances: "Fold or flop: quality assessment of AlphaFold predictions on whole proteomes"  Find it here: doi.org/10.1093/bioadv…

⚙️ Gene expression datasets are publicly available via the Gene Expression Omnibus (GEO) database under accession numbers GSE63514 and GSE9750.

Molecular docking and 200 ns dynamics simulations confirmed stable binding of ginsenoside Re, panaxadiol, daucosterol, and stigmasterol to hub targets TNF, IL6, and SRC.

🌿 New paper: "Exploring the molecular basis of Panax-notoginseng mediated inhibition of cervical cancer through machine learning, transcriptomics analysis, network pharmacology, molecular docking, and in-silico simulation approaches"  Read it here: doi.org/10.1093/bioadv…

🖥️ CasPINS is available at github.com/InnovationLine…, with an archived release on Zenodo at doi.org/10.5281/zenodo…

It supports 90+ species and reduces the discrete user actions required for a standard genome editing computational workflow from 25 to 8 steps.

✂️ New in Bioinformatics Advances: "CasPINS: an integrated web-based platform for CRISPR/TALEN gRNA design, primer generation, and indel decomposition analysis"  Find the full paper at: doi.org/10.1093/bioadv…