Bioinformatics Advances

GitHub - jadedavis5/NanoFLORA Contribute to jadedavis5/NanoFLORA development by creating an account on GitHub.

💻 Benchmarking code and analysis workflows are openly available at https://github.com/jadedavis5/benchmarking_paper, with an associated Nextflow pipeline for direct RNA processing at

Reference-guided StringTie3 and IsoQuant showed >98% sensitivity and identified over 700 previously unannotated transcripts, many supported by Illumina junction evidence and linked to disease response.

This study benchmarks five long-read genome annotation tools using Oxford Nanopore direct RNA sequencing from barley infected with Net Form Net Blotch.

🌾Now published in Bioinformatics Advances: "Benchmarking methods for genome annotation using Nanopore direct RNA in a non-model crop plant"

Full article available: https://doi.org/10.1093/bioadv/vbag030

Authors include: @kgagalova.bsky.social

💻 CytoAnalyst is available open source as a web-based platform at https://cytoanalyst.tinnguyen-lab.com/, with documentation and tutorials at https://cytoanalyst.tinnguyen-lab.com/docs/.

Across four datasets and 28 cell types, LLMs achieved average accuracy up to 0.776, outperforming scCATCH, scType, and SingleR.

This study introduces an LLM-powered workflow for semi-automatic cell type annotation in scRNA-seq data. Marker genes from clustering and differential analysis are passed to Meta’s Llama 3.3 with ontology-constrained prompting.

🧬 Explore the latest from Bioinformatics Advances: "Cell type annotation using large language models (LLMs) and CytoAnalyst"

Full article available: https://doi.org/10.1093/bioadv/vbag001

GitHub - aylz83/inspectorORF: Simplify the analysis and visualization of translated open reading frames (ORFs) using Ribo-Seq data Simplify the analysis and visualization of translated open reading frames (ORFs) using Ribo-Seq data - aylz83/inspectorORF

💻 InspectorORF is available as an open source R package at https://www.github.com/aylz83/inspectorORF, with support for integrating proteomics, long-read sequencing, and custom transcriptomic metadata into reproducible visual analyses.

This paper introduces InspectorORF, an R package for transcript- and ORF-level visualization of Ribo-Seq and RNA-Seq data. It integrates outputs from ORFquant or RiboTaper w/ RNA-Seq coverage, enabling inspection of triplet periodicity, alternative start codons and translated ORFs across conditions.

📊 Explore the latest from Bioinformatics Advances: “InspectorORF: A tool for visualising Ribo-Seq and additional genomic or transcriptomic data”

Read the full paper here: https://doi.org/10.1093/bioadv/vbag031

Authors include: @evol-molly.bsky.social

📊 The authors identified a four-gene prognostic signature (C1R, F2RL2, FBLN1, STC2) that stratified HBV-HCC patient survival and linked Ca2+-signaling dysregulation to EMT, angiogenesis, myogenesis, and coagulation pathways. Data and analyses are fully contained within the article.

Across 112 samples, 432 Ca2+-signaling genes were differentially expressed, with LASSO and Cox models identifying prognostic signatures with C-indices up to 0.725.

This study investigated transcriptional and epigenetic dysregulation of Ca2+-signaling genes in HBV-HCC using bulk RNA-seq, ChIP-seq, and DNA methylation datasets.

🧬 Explore the latest from Bioinformatics Advances: “Transcriptional and epigenetic regulation of Ca2+-signaling genes in hepatitis B-derived hepatocellular carcinoma and their association with the cancer hallmarks” 

Full article available: https://doi.org/10.1093/bioadv/vbaf331

📚 The article emphasizes a human-in-the-loop framework where AI accelerates routine tasks but curators provide critical evaluation. Examples span Global Core BioData and ELIXIR Core Data Resources implementing production systems for literature recommendation, entity recognition, and quality control.

This perspective reviews how LLMs and agentic AI augment literature curation for biological knowledgebases. GOFlowLLM achieved 86.7% curator agreement for miRNA curation; InterPro generated 3,000+ AI summaries; and GNorm2 reached an F1-score of 0.894 for gene recognition.

🤖 Now published in Bioinformatics Advances: "Empowering biological knowledgebases: Advances in human-in-the-loop AI-driven literature curation"

Read the full paper here: https://doi.org/10.1093/bioadv/vbag028

Authors include: @matt.jeffry.es, @matthiasblum.bsky.social, @raulrod.bsky.social

💻 CaRinDB is freely available at https://bioinfo.imd.ufrn.br/CaRinDB/ with an interactive web interface for custom plotting and data exploration.

CaRinDB integrates TCGA cancer mutations with functional predictions, allelic frequencies, and residue interaction network parameters from PDB structures and AlphaFold models. The database includes 26,893 variants mapped to experimental structures and 201,447 to AlphaFold predictions.

🔬 Just out in Bioinformatics Advances: "CaRinDB: An integrated database of common cancer mutations and residue interaction network parameters"

Explore the full study: https://doi.org/10.1093/bioadv/vbaf313

GitHub - dkoptekin/pygenstrat Contribute to dkoptekin/pygenstrat development by creating an account on GitHub.

💻 pygenstrat is open-source and freely available on GitHub at https://github.com/dkoptekin/pygenstrat.

Benchmarked on the Allen Ancient DNA Resource with 17,629 individuals and 1.2 million SNPs, pygenstrat achieved 2–15x speedups and 90-95% memory reduction compared to convertf while producing equivalent outputs.

pygenstrat provides comprehensive EIGENSTRAT format processing for ancient DNA analysis through memory-efficient chunked algorithms. The tool supports extensive filtering, subsetting, format conversion, pseudo-haploidization, and allele polarization operations.

🧬 Now published in Bioinformatics Advances: "pygenstrat: A Python package for EIGENSTRAT data processing" by @dilekopter.bsky.social

Full article available: https://doi.org/10.1093/bioadv/vbag022

💻 HDAnalyzeR is freely available as an open-source R package at https://github.com/kantonopoulos/HDAnalyzeR with a web application at https://hdanalyzer.serve.scilifelab.se.

The package reduced code complexity by 50-80% while maintaining identical runtimes.

HDAnalyzeR provides modular workflows for high-dimensional omics analysis, from quality control to differential expression and enrichment. Applied to blood cancer proteomics, it identified an 8-protein LASSO panel achieving perfect CLL classification (AUC = 1.0).

🔬 Explore the latest from Bioinformatics Advances: "HDAnalyzeR: Streamlining data analysis for biomarker research"

Read the full paper here: https://doi.org/10.1093/bioadv/vbag020 

Authors include: @buenoalvez.bsky.social

GPTBioInsightor — GPTBioInsightor GPTBioInsightor# GPTBioInsightor is a tool designed for single-cell data analysis, particularly beneficial for newcomers to a biological field or those in interdisciplinary areas who may lack sufficient biological background knowledge. GPTBioInsightor utilizes the powerful capabilities of large lang...

💻 GPTBioInsightor is freely available on GitHub at https://github.com/huang-sh/GPTBioInsightor under BSD-3-Clause license, installable via PyPI at https://pypi.org/project/gptbioinsightor with documentation at https://gptbioinsightor.readthedocs.io.