Bioinformatics Advances

@zhizhid @ShaojieZhang_ 🛠️ RaPID2 software and source code available at github.com/ucfcbb/RaPID2

RaPID2 is a redesigned framework for scalable identity-by-descent detection in biobank-scale genomic data. It combines parallel PBWT, randomized projections, and region-aware partitioning with memory-aware execution modes. This enables efficient large-cohort analysis while eliminating disk I/O bottlenecks.

⚙️ New in Bioinformatics Advances: "Rapid2: A parallel scalable framework for identity-by-descent segment detection via parallel pbwt"  Explore the study: doi.org/10.1093/bioadv…  Authors include: @zhizhid, @ShaojieZhang_

🧰 SIREN is available at under an open-source license. Find it here: github.com/pablovargasmej…

SIREN is a Python pipeline for designing RNA interference constructs while minimizing off-target gene silencing. It generates siRNAs from target sequences, evaluates thermodynamically informed off-target interactions, and ranks dsRNA candidates based on cumulative off-target risk.

🧬 Recently published in Bioinformatics Advances:"Siren: Suite for intelligent RNAi design and evaluation of nucleotide sequences"  Explore the study: doi.org/10.1093/bioadv…

@javiMolinaEspel That's very exciting!

@BioinfoAdv My very first article colab :)

🧬 New in Bioinformatics Advances: "Mirinter-Trans: A transformer-based framework for microRNA interaction prediction"  Read the article: doi.org/10.1093/bioadv…

📦 scTrimClust is available at cran.r-project.org/web/packages/R…

Researchers developed scTrimClust, a method to identify extreme or border cells within scRNA-seq clusters using nearest-neighbour distances in high-dimensional gene expression space. The approach evaluates how removing such cells affects marker gene detection and overall analysis robustness.

🧪 Just published in Bioinformatics Advances: "sctrimclust: A fast approach to robust scRNA-seq analysis using trimmed cell clusters"  Find the paper here: doi.org/10.1093/bioadv…

💾 EGSP is available at github.com/weiliu123/EGSP. Source code at github.com/weiliu123/EGSP

Researchers evaluated single-cell foundation model embeddings for cancer survival prediction across 25 TCGA cancer types. They developed EGSP, integrating embeddings, gene expression, and clinical data. The model improved prognostic accuracy, achieving a mean C-index of 0.724 across cancers.

🧬 New in Bioinformatics Advances: "Leveraging single-cell foundation models for accurate survival outcome prediction"  Read the paper: doi.org/10.1093/bioadv…

💻 Panalyze is available at github.com/downingtim/Pan…

Panalyze is a workflow for constructing and analyzing viral pangenome variation graphs to better capture genomic diversity without reference bias. The tool automates graph construction, exploration, and annotation to support scalable analysis of viral genome variation in lightweight computing environments.

🧬 New in Bioinformatics Advances: "Panalyze: Automated virus pangenome variation graph construction, analysis and annotation"  Read the paper:  doi.org/10.1093/bioadv…

@JaimeMUrtaza 🧪 The memod-s workflow is available at github.com/AlessiaMarotta…

memod-s is a Snakemake-based workflow that streamlines analysis of prokaryotic DNA methylation from Nanopore sequencing data. The pipeline integrates basecalling, quality control, genome assembly, annotation, and methylation profiling to generate genome-wide methylation statistics and visualisations.

🧬 New in Bioinformatics Advances: "Memod-s: A standardised workflow to explore and analyse prokaryotic methylation patterns for Nanopore sequencing data"  Explore the study: doi.org/10.1093/bioadv…  Authors include: @JaimeMUrtaza

🤖 miRInter-Trans is available at github.com/AnacletoLAB/mi….

miRInter-Trans is a transformer-based framework for predicting microRNA interactions directly from RNA sequences. It combines embeddings from the RNA-FM foundation model with a feed-forward neural network to detect interactions across miRNA–lncRNA, miRNA–miRNA, and miRNA–snoRNA datasets.