Experiments

Searchable full-text extractions: founding hypothesis, core claims, experimental setups, key results and statistics — pulled out of each paper as structure. Search a cell line, an assay or an entity (e.g. HUH7) and find every paper that worked with it. This corpus stands on its own: most entries carry no reproduction assessment (yet).

• Betacoronavirus-specific alternate splicing.

  PMID 35074468 · PMC8782732 · Genomics · 2022 · 8 claims · 8 setups

  Has reproduction · 100

  Genes differentially spliced during SARS-CoV-2 infection show a similar functional (GO) profile to those differentially spliced in SARS-CoV and MERS infection, affecting a diverse set of genes tied to virus biology.

  mrc5 calu-3 nasal lung bulk

• Decoding the interconnected splicing patterns of hepatitis B virus and host using large language and deep learning models.

  PMID 41543530 · PMC12811152 · Microbial genomics · 2026 · 8 claims · 8 setups

  Full-text index only

  HBV splicing efficiency (coSI) correlates more strongly with disease progression than the overall proportion of spliced HBV RNA.

  hbv same host bulk splicing splicebert

• Transcriptome analysis provides insights into the regulatory function of alternative splicing in antiviral immunity in grass carp (Ctenopharyngodon idella).

  PMID 26248502 · PMC4528194 · Scientific reports · 2015 · 8 claims · 8 setups

  Has reproduction · 70

  AS events, including differentially-expressed-transcript-containing genes (DETs), are ubiquitous in head-kidney and spleen transcriptomes of C. idella

  head-kidney idella assembled il-12p40α rna-seq rt-qpcr pcr

• Time course profiling of host cell response to herpesvirus infection using nanopore and synthetic long-read transcriptome sequencing.

  PMID 34244540 · PMC8270970 · Scientific reports · 2021 · 8 claims · 5 setups

  Has reproduction · 50

  BoHV-1 infection causes substantial up- and down-regulation of host gene networks, including antiviral response and viral transcription/translation-associated genes

  bovine direct amplified synthetic

• CRESCENT, a comprehensive RNA-Seq expression, splicing, and coding/non-coding element network tool.

  PMID 41566196 · PMC12895761 · BMC bioinformatics · 2026 · 6 claims · 6 setups

  Full-text index only

  CRESCENT is a Snakemake workflow performing fully automated, comprehensive RNA-Seq analysis integrating differential expression, differential alternative splicing (DAS), differential transcript usage (DTU), and GO enrichment

  arabidopsis bulk rna-seq-based rna-seq

• Benchmarking methods for genome annotation using nanopore direct RNA in a non-model crop plant.

  PMID 41800382 · PMC12967217 · Bioinformatics advances · 2026 · 6 claims · 8 setups

  Full-text index only

  Annotation tools show substantial variation in isoform detection, structural completeness, splicing classification, and handling of 5' read truncation when applied to plant dRNA-seq data.

  barley extracted tool novel nanopore illumina transcriptome