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).

• Forseti: a mechanistic and predictive model of the splicing status of scRNA-seq reads.

  PMID 38940130 · PMC11256924 · Bioinformatics (Oxford, England) · 2024 · 7 claims · 5 setups

  Has reproduction · 87

  Forseti is the first probabilistic model for resolving the splicing status of exonic scRNA-seq reads by scoring putative fragments linking read alignments to proximate priming sites

  training simulated held-out paired-end cubic mlp

• Deep-learning prediction of gene expression from personal genomes.

  PMID 41495833 · PMC12869966 · Genome biology · 2026 · 8 claims · 8 setups

  Full-text index only

  Fine-tuning Enformer on paired personal WGS and RNA-seq data (Variformer) corrects Enformer's failure to predict inter-individual gene expression differences across held-out people.

  gtex rosmap same monocyte paired mutagenesis chromhmm

• SVNeoPP: A Workflow for Structural-Variant-Derived Neoantigen Prediction and Prioritization Using Multi-Omics Data.

  PMID 41892252 · PMC13024079 · Biology · 2026 · 8 claims · 7 setups

  Full-text index only

  SVNeoPP is an end-to-end Snakemake workflow that takes WGS and RNA-seq as input to call/annotate SVs, reconstruct altered transcripts and coding sequences in an isoform-aware, traceable manner, and generate candidate peptides.

  tumor hcc sv-derived candidate whole-genome rna-seq peptide

• Identification and Validation of an Autophagy-Related Gene Signature for Prognostic Prediction and Immunotherapy Response in Esophageal Squamous Cell Carcinoma.

  PMID 41681864 · PMC12897147 · Cancers · 2026 · 8 claims · 8 setups

  Full-text index only

  A 4-ARG prognostic model (NBEA, CLOCK, NLRX1, MAGEA3) built via stepwise multivariate Cox regression stratifies ESCC patients into high- and low-risk groups with significantly different survival.

  escc gse53625 gse160269 imvigor210 microarray univariate single-cell

• Systematic and computational identification of Androctonus crassicauda long non-coding RNAs.

  PMID 33633149 · PMC7907363 · Scientific reports · 2021 · 8 claims · 6 setups

  Has reproduction · 71

  13,401 lncRNAs were identified in the A. crassicauda transcriptome using the ECF pipeline

  crassicauda rna-seq coding sequence

• CellPolaris: Transfer Learning for Gene Regulatory Network Construction to Guide Cell State Transitions.

  PMID 41498638 · PMC12948241 · Advanced science (Weinheim, Baden-Wurttemberg, Germany) · 2026 · 8 claims · 8 setups

  Full-text index only

  CellPolaris is a unified computational framework performing TF-centered GRN construction, master TF identification, and TF perturbation simulation

  bulk previously round paired transfer-learning cross-species

• nf-core/circrna: a portable workflow for the quantification, miRNA target prediction and differential expression analysis of circular RNAs.

  PMID 36694127 · PMC9875403 · BMC bioinformatics · 2023 · 8 claims · 4 setups

  Has reproduction · 76

  Existing circRNA workflows are limited: none delineate circRNA-miRNA interactions and only one performs differential expression analysis, requiring users to supplement missing analysis types with in-house expertise

  paired-end rna-seq mature circrna read circrna mirna

• The SARS-CoV-2 subgenome landscape and its novel regulatory features.

  PMID 33713597 · PMC7927579 · Molecular cell · 2021 · 8 claims · 6 setups

  Has reproduction · 84

  Template switching in SARS-CoV-2 can occur bidirectionally, generating diverse subgenomes through successive template-switching events

  vero caco-2 sars-cov-2 ngs nanopore northern

• SiCmiR Atlas: Single-Cell miRNA Landscape Reveals Hub-miRNA and Network Signatures in Human Cancers.

  PMID 41691474 · PMC13042402 · Advanced science (Weinheim, Baden-Wurttemberg, Germany) · 2026 · 8 claims · 8 setups

  Full-text index only

  SiCmiR, a two-layer neural network, predicts mature miRNA expression profiles from only 977 LINCS L1000 landmark genes

  tcga k562 pancreatic acth-secreting paired bulk scrna-seq-based

• An Improved Chromosome-Level Genome Assembly and Comprehensive Annotation of the Model Ascidian Ciona savignyi.

  PMID 41792167 · PMC13087180 · Scientific data · 2026 · 8 claims · 8 setups

  Full-text index only

  An improved chromosome-level genome assembly of C. savignyi was generated using Illumina short reads, ONT long reads, and Hi-C data.

  savignyi illumina oxford hi-c

• Multimodal framework for the joint analysis of single-cell RNA and T cell receptor sequencing data predicts T cell response to cancer immunotherapy.

  PMID 41820396 · PMC13121706 · Nature communications · 2026 · 8 claims · 7 setups

  Full-text index only

  TRIM, a conditional multi-modal variational autoencoder integrating paired scRNAseq and scTCRseq data, predicts T cell clonality and transcriptional states at unmeasured tissue sites/timepoints.

  hnscc colorectal pan-cancer tcr paired umap convolutional

• Identification and Characterization of Small Noncoding RNAs in Genome Sequences of the Edible Fungus Pleurotus ostreatus.

  PMID 27703969 · PMC5040776 · BioMed research international · 2016 · 7 claims · 8 setups

  Has reproduction · 95

  Genome-scale identification detected 254 small noncoding RNAs (snRNAs, snoRNAs, tRNAs, miRNAs, and other Rfam-classified sncRNAs) in the P. ostreatus CCEF00389 genome assembly

  pleurotus ostreatus ccef00389 sncrnas whole-genome rna-seq rfam

• Identification of succinylation-related genes in bladder cancer: integration of single-cell and transcriptomic data.

  PMID 42220482 · PMC13218921 · Frontiers in immunology · 2026 · 8 claims · 8 setups

  Has reproduction · 78

  KCTD16, CD3D, and GSDMB were identified as prognostic succinylation-related genes in BLCA

  soochow-blca tcga-blca gse13507 gse135337 bulk scrna-seq somatic

• Genome-wide signatures of convergent evolution in echolocating mammals.

  PMID 24005325 · PMC3836225 · Nature · 2013 · 8 claims · 8 setups

  Has reproduction

  Genome-wide convergent sequence evolution between echolocating lineages is not rare but widespread and continuously distributed, with signatures consistent with convergence in nearly 200 loci out of 2,326 examined.

  four raw orthologous mammalian whole-genome novo homology-based

• Evidence for limited genetic compartmentalization of HIV-1 between lung and blood.

  PMID 19759830 · PMC2736399 · PloS one · 2009 · 8 claims · 7 setups

  Full-text index only

  Statistical evidence of genetic compartmentalization between lung and blood HIV-1 env sequences was found in 10 of 18 subjects.

  paired lung tissue-pair pooled hiv-1 maximum statistical

• Repurposing public sarcoma multi-omics for neoantigen discovery.

  PMID 42012689 · PMC13100081 · Cancer immunology, immunotherapy : CII · 2026 · 8 claims · 7 setups

  Full-text index only

  Reanalysis of legacy CKS multi-omic data shows that standard genome-wide metrics frequently underestimate the true immunogenic potential of these tumors.

  paired cks peptides whole-exome rna-seq hla

• MirDIP 5.2: tissue context annotation and novel microRNA curation.

  PMID 36453996 · PMC9825511 · Nucleic acids research · 2023 · 7 claims · 6 setups

  Has reproduction · 89

  mirDIP 5.2 removed eight outdated resources, added miRNATIP, and ran five prediction algorithms against miRBase and mirGeneDB miRNAs to expand and improve interaction coverage

  mirnas disease novel type mirna small bulk

• Comparative transcriptome analysis of tomato (Solanum lycopersicum) in response to exogenous abscisic acid.

  PMID 24289302 · PMC4046761 · BMC genomics · 2013 · 8 claims · 7 setups

  Has reproduction · 63

  Exogenous ABA alters the expression of a majority (54.73%) of expressed tomato leaf transcripts, with 2,787 significantly differentially expressed genes, predominantly up-regulated.

  tomato assembled illumina read functional

• OptiType: precision HLA typing from next-generation sequencing data.

  PMID 25143287 · PMC4441069 · Bioinformatics (Oxford, England) · 2014 · 8 claims · 8 setups

  Has reproduction · 95

  OptiType, an ILP-based HLA genotyping algorithm, produces accurate four-digit HLA-I predictions from NGS data not enriched for the HLA cluster.

  colorectal lymphoblastic hapmap genomes rna-seq low-coverage exome

• The sequence and de novo assembly of the giant panda genome.

  PMID 20010809 · PMC3951497 · Nature · 2010 · 8 claims · 8 setups

  Full-text index only

  A draft giant panda genome was successfully generated and assembled de novo using only Illumina Genome Analyser short-read sequencing

  giant panda whole-genome novo read