New isoform quantification methods reduce mapping ambiguity and are benchmarked against…

Published papers

• LRP2: a proteogenomics pipeline for long-read informed protein isoform analysis and discovery.

  Bioinformatics (Oxford, England)2026-11-02Megan D Schertzer et al.

  LRP2 is a modular Nextflow pipeline integrating long-read isoform discovery, ORF prediction, differential isoform usage, and DDA/DIA mass-spec evidence for…

• tModBase v2.0: an expanded database of tRNA modifications with an AI-powered assistant.

  Nucleic acids research2026-11-02Yi Tan et al.

  tModBase v2.0 expands a tRNA modification database to 528 datasets across 23 species, adding direct-RNA and modification-specific sequencing data plus an…

• DirectClean: artifact-aware preprocessing and read rescue for Oxford Nanopore direct-cDNA transcriptome sequencing.

  NAR genomics and bioinformatics2026-10-31Qingxiang Guo et al.

  DirectClean: an artifact-aware preprocessing and read-rescue tool for ONT direct-cDNA reads that handles chimeras and splits recoverable reads; retains more…

Preprints

• IG-28 enables identification and quantification of high-confidence isoforms from large bulk and single-cell full-length cDNA datasets

  bioRxiv2026-10-29Calicchio, A. et al.

  IG-28 is a lightweight isoform identification tool for large bulk and single-cell full-length cDNA datasets, outperforming other tools in benchmarks.

• Transcript quantification using context-aware MAPQ modeling

  bioRxiv2026-10-31Hicks, S. C. et al.

  CALMeR conditions long-read MAPQ filtering on transcript context using zero-one inflated beta regression, improving spike-in transcript recovery versus fixed…

• tWhEEL: a transcript-aware workflow for quantifying CRISPR knockout feasibility using transcriptome assembly

  bioRxiv2026-10-31Nakamae, K. et al.

  tWhEEL is a transcript-aware pipeline that infers gene redundancy from transcripts, pairs it with CRISPR guide designs, and scores knockout feasibility across…

• GaussF: An Unbiased Gaussian Framework for High-Precision Transcript Quantification with a Programmable Self-Benchmark Model

  bioRxiv2026-10-30Su, Q.

  GaussF is an alignment-free isoform quantification method using GC-stratified k-mer Gaussian CDF self-benchmarking, benchmarked against Kallisto, Salmon,…

• Refining RNA-Seq Transcriptome Profiles with Transcript-Specific Minimal-Shared Regions

  bioRxiv2026-11-02Su, Q.

  Proposes a minimal-sharing k-mer strategy that isolates transcript-specific regions to reduce mapping ambiguity in RNA-seq isoform quantification,…

• A new tool for quantifying mitochondrial RNA processing intermediates reveals increased levels of immature mRNA species under oxidative stress

  bioRxiv2026-11-02Ozkurede, U. et al.

  New tool quantifies immature mitochondrial mRNAs in short-read RNA-seq; 5' tRNA-extended forms rise under oxidative stress.

• SQANTI-evidence: isoform-resolved, evidence-tiered structural annotation of unannotated genomes from long-read RNA-seq

  bioRxiv2026-11-04Atienza Lopez, P. et al.

  SQANTI-evidence annotates unannotated genomes from long-read RNA-seq alone, using SQANTI3-curated isoforms plus AUGUSTUS predictions; benchmarks show higher…

• Edi-Set-Flow: detecting differential RNA-editing at scale

  bioRxiv2026-11-03Munro, J. E. et al.

  Edi-Set-Flow is a Nextflow pipeline with an R package for transcriptome-wide A-to-I RNA editing detection and differential analysis from bulk RNA-seq, applied…

Related topics

• Scalable Genomic Data Processing Tools
• Nmd Sensitivity And Splicing Estimation
• Rna Regulation Mapping Methods

Topic history