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).

• Differential neuronal survival defines a novel axis of sexual dimorphism in the Drosophila brain.

  PMID 41529688 · PMC7618834 · Cell genomics · 2026 · 8 claims · 7 setups

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  Sex differences in the Drosophila central brain do not result from large-scale transcriptional reprogramming, but from selective modifications within shared developmental lineages mediated by dsx and fru.

  drosophila central dsx+ dsx-gal4>mcd8 single-cell differential scenic

• MUUMI: an R package for statistical and network-based meta-analysis for multi-omics data integration.

  PMID 41634555 · PMC12955011 · BMC bioinformatics · 2026 · 8 claims · 5 setups

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  MUUMI unifies statistical meta-analysis and network-based omics data integration within a single analytical R package framework

  lung integrated ranked thp-1 sequencing microarray statistical

• Large-scale integration of single-cell transcriptomic data captures transitional progenitor states in mouse skeletal muscle regeneration.

  PMID 34773081 · PMC8589952 · Communications biology · 2021 · 8 claims · 7 setups

  Has reproduction · 92

  Large-scale integration of 111 sc/snRNAseq datasets captures rare, transitional myogenic progenitor states (commitment and fusion) that are poorly represented in individual datasets.

  skeletal merged myogenic muscle scrnaseq batch-correction differential

• Bulk RNA-seq datasets analysis integration identifies robust drought-responsive genes and functional networks in Eucalyptus grandis.

  PMID 42038403 · PMC13106539 · Frontiers in bioinformatics · 2026 · 7 claims · 7 setups

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  Meta-analysis integration of three independent RNA-seq drought studies identifies 472 robust differentially expressed genes (274 up, 198 down) that remain significant across the full meta-analysis and all leave-one-out Jackknife iterations

  grandis computational consistently bulk differential leave-one-out

• CanSig Benchmarks Methods for Reproducible Cancer Cell State Discovery from Single-Cell Transcriptomic Data.

  PMID 41231245 · PMC13053056 · Cancer research · 2026 · 7 claims · 7 setups

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  CanSig is a comprehensive benchmarking tool for evaluating computational methods that identify shared transcriptional signatures in cancer from scRNA-seq data

  neftel kim scrna-seq same scrna-seq ground-truth robustness

• GAMMI: graph-guided contrastive and adversarial integration of single-cell and spatial multi-omics data.

  PMID 42108634 · PMC13158126 · Briefings in bioinformatics · 2026 · 6 claims · 5 setups

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  GAMMI consistently outperforms state-of-the-art integration methods (GLUE, Harmony, MIDAS, scMoMaT) in biological conservation and batch correction across five mosaic single-cell multi-omics benchmarks

  pbmc postmortem gse138852 gammi-derived multi-omics scrna-seq differential

• Spatially clustered loci with multiple enhancers are frequent targets of HIV-1 integration.

  PMID 31492853 · PMC6731298 · Nature communications · 2019 · 8 claims · 8 setups

  Has reproduction · 77

  Recurrently targeted HIV-1 integration genes (RIGs) are proximal to super-enhancer (SE) genomic elements

  activated cd4+ cd3 jurkat chip-seq hiv-1 sequencing

• Caloric Restriction Reprograms Adipose Tissues in Rhesus Monkeys.

  PMID 41042069 · PMC12686577 · Aging cell · 2025 · 8 claims · 8 setups

  Has reproduction · 66

  At baseline, SAT and VAT transcriptomes are highly similar, with only ~1% of genes (30 genes, adjusted p<0.05) differentially expressed between depots in Controls

  subcutaneous sat rhesus bulk gsea xcell

• A latent activated olfactory stem cell state revealed by single-cell transcriptomic and epigenomic profiling.

  PMID 41512864 · PMC12903091 · Stem cell reports · 2026 · 7 claims · 8 setups

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  HBC-derived regeneration proceeds via three distinct lineages (rHBC, Sus, mOSN) marked by sequential, lineage-specific transcription factor (TF) expression cascades.

  lineage-traced hbcs* icam1+ scrna-seq trajectory-based seurat

• LazySlide: accessible and interoperable whole-slide image analysis.

  PMID 41862659 · PMC13076205 · Nature methods · 2026 · 8 claims · 8 setups

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  LazySlide is an open-source Python package built on the scverse ecosystem for whole-slide image (WSI) analysis and multimodal integration.

  artery gene wsis breast zero-shot bulk multimodal

• Predicting favorable landing pads for targeted integrations in Chinese hamster ovary cell lines by learning stability characteristics from random transgene integrations.

  PMID 33304461 · PMC7710658 · Computational and structural biotechnology journal · 2020 · 7 claims · 5 setups

  Has reproduction

  Expression stability in CHO cell lines is controlled at three levels: choice of integration site, transgene integrity/concatemerization pattern, and stress-related cellular processes.

  horizon same cho genome rna-seq targeted

• Single-nucleus multiomic profiling of the aging mouse substantia nigra reveals conserved gene alterations linked to Parkinson's disease.

  PMID 41781332 · PMC13138337 · Genome research · 2026 · 8 claims · 7 setups

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  Single-nucleus multiome (RNA+ATAC) sequencing of mouse substantia nigra across four age stages (2, 6, 12, 18 months) yields a 40,125-cell atlas spanning 27 cell subclasses

  substantia allen five oligodendrocyte single-nucleus scrna-seq single-cell

• Genetic alternative splicing regulation mapping of cartilage and synovium reveals tissue-specific mechanisms of joint-related traits.

  PMID 41820402 · PMC13121699 · Nature communications · 2026 · 8 claims · 8 setups

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  Generated a splicing quantitative trait loci (sQTL) resource for human cartilage and synovium from over 200 donors

  degenerated synovium matched paired bulk genotyping differential

• Deep single-cell decoding of human pancreatic islets reveals T2D β-cell gene expression defects.

  PMID 41986506 · PMC13226668 · The EMBO journal · 2026 · 8 claims · 6 setups

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  Single-cell transcriptome profiling of 245,878 islet cells from 48 donors (ND/PD/T2D) identifies 14 distinct, robust islet cell types detected in every donor

  pancreatic aggregated endoc-βh3 subset droplet-based pseudobulk unsupervised

• Development of a pediatric immune cell atlas and characterization of CD4+ T cells in food allergy.

  PMID 42025535 · PMC13105851 · Pediatric allergy and immunology : official publication of the European Society of Pediatric Allergy and Immunology · 2026 · 8 claims · 8 setups

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  A pediatric single-cell PBMC reference atlas was developed from 57 healthy children across 8 public scRNA-seq studies.

  pbmcs cd3+ cd4+ memory scrna-seq pseudobulk bulk

• Expression Atlas update--a database of gene and transcript expression from microarray- and sequencing-based functional genomics experiments.

  PMID 24304889 · PMC3964963 · Nucleic acids research · 2014 · 8 claims · 6 setups

  Has reproduction · 84

  Expression Atlas is a value-added database providing gene, protein and splice variant expression across cell types, organism parts, developmental stages, diseases and other biological/experimental conditions, built from manually curated high-quality microarray and RNA-sequencing experiments from ArrayExpress.

  organisms arrayexpress-derived pride rna-sequencing single-channel two-colour

• Decoding the circRNA-miRNA-mRNA regulatory network in hepatitis B virus-driven hepatocellular carcinoma.

  PMID 41845440 · PMC13107627 · Cell communication and signaling : CCS · 2026 · 8 claims · 8 setups

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  A bioinformatic pipeline combining RNA-seq, circRNA calling, ECDF analysis, PPI, and survival analysis identifies a circRNA-miRNA-mRNA ceRNA network in HBV-integrated HCC cells

  hep3b qpcr dysregulated target bulk circrna rt-qpcr

• Integrating transcriptomic datasets across neurological disease identifies unique myeloid subpopulations driving disease-specific signatures.

  PMID 36527260 · PMC10952672 · Glia · 2023 · 6 claims · 3 setups

  Has reproduction · 26

  The bulk microglial and monocyte transcriptomic program is highly contingent on the disease environment, challenging the notion of a universal microglial disease signature

  acutely microglia c57bl meta-analysis integration spectral

• huSA: a comprehensive database for multi-dimensional resolution of bulk, single cell and spatial transcription profiles in skin diseases.

  PMID 41719583 · PMC12923168 · Database : the journal of biological databases and curation · 2026 · 7 claims · 8 setups

  Has reproduction · 50

  huSA is a comprehensive, publicly accessible database integrating bulk RNA-seq, scRNA-seq, and spatial transcriptomics data across 17 skin diseases and 63 independent datasets

  skin scrna-seq scrna-seq transcription cell-cell

• Heterochronic transcription factor expression drives cone-dominant retina development in 13-lined ground squirrels.

  PMID 41649260 · PMC12880807 · eLife · 2026 · 8 claims · 8 setups

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  13LGS cone photoreceptors arise from both early-stage and late-stage neurogenic progenitors, unlike mice where cones arise only from early-stage progenitors

  13-lined retina 13lgs retinal single-cell scrna-seq chromvar