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).

• Enhancing cell subpopulation discovery in cancer by integrating single-cell transcriptome and expressed variants.

  PMID 41647537 · PMC12869734 · Fundamental research · 2026 · 6 claims · 3 setups

  Has reproduction · 68

  scCluster, an end-to-end deep clustering model integrating gene expression and expressed variant (eSNP) features, stratifies cell subpopulations in cancer scRNA-seq data.

  raw real-world expressed gene deep

• Correcting scale distortion in RNA sequencing data.

  PMID 39875825 · PMC11776150 · BMC bioinformatics · 2025 · 8 claims · 8 setups

  Has reproduction · 76

  Local averaging reveals expression-level-dependent biases that differ from sample to sample across all RNA-seq datasets studied, and are not corrected by conventional normalization (TPM/FPKM)

  tcga su2c gse47774 gtex bulk computational d'agostino

• Manually curated transcriptomics data collection for toxicogenomic assessment of engineered nanomaterials.

  PMID 33558569 · PMC7870661 · Scientific data · 2021 · 7 claims · 7 setups

  Has reproduction · 94

  A unified collection of 101 manually curated and homogenized transcriptomics datasets covering human, mouse, and rat ENM exposures in vitro and in vivo was compiled.

  engineered geo gene rna-seq enm

• First step toward gene expression data integration: transcriptomic data acquisition with COMMAND>_.

  PMID 30691411 · PMC6348648 · BMC bioinformatics · 2019 · 7 claims · 3 setups

  Has reproduction · 30

  COMMAND>_ is a flexible multi-user web application that searches, downloads, parses, re-annotates, and imports gene expression experiments into a coherent data model.

  small user-defined microarray affymetrix rna-seq probe-to-gene

• WASP: a versatile, web-accessible single cell RNA-Seq processing platform.

  PMID 33736596 · PMC7977290 · BMC genomics · 2021 · 7 claims · 7 setups

  Has reproduction · 59

  WASP is a software platform for processing Drop-Seq-based scRNA-seq data generated with ddSEQ or 10x protocols, combining a Snakemake pre-processing pipeline with an R Shiny post-processing application.

  specified generic scrna-seq read reference

• 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

• IL-6 trans-Signaling Regulates Neutrophilic Inflammation in Alcohol-Associated Hepatitis.

  PMID 40562277 · PMC13168973 · The American journal of pathology · 2026 · 8 claims · 8 setups

  Has reproduction · 71

  Hepatic IL-6R expression progressively declines with increasing severity of alcohol-related liver disease, from normal to early ASH to nonsevere and severe AH

  liver hepatocytes hepg2 ptpn11 bulk immunohistochemistry single-cell

• A statistical framework for consolidating "sibling" probe sets for Affymetrix GeneChip data.

  PMID 18435860 · PMC2397416 · BMC genomics · 2008 · 7 claims · 4 setups

  Full-text index only

  A two-way ANOVA model with a treatment x probe-set interaction term can automatically determine whether sibling probe sets for a gene behave similarly (non-significant interaction, consolidate) or differently (significant interaction, treat as independent)

  retina thyroid spermatogonial differentially two-way paired anova-based

• ScLRTC: imputation for single-cell RNA-seq data via low-rank tensor completion.

  PMID 34844559 · PMC8628418 · BMC genomics · 2021 · 8 claims · 8 setups

  Has reproduction · 85

  scLRTC imputes dropout entries closest to the original expression values on simulated datasets, outperforming other state-of-the-art methods by SSE and PCC.

  usoskin pollen zeisel yan scrna-seq umap masking

• Different approaches to Imaging Mass Cytometry data analysis.

  PMID 37092034 · PMC10115470 · Bioinformatics advances · 2023 · 8 claims · 5 setups

  Has reproduction

  Imaging Mass Cytometry (IMC) is a high-multiplexing imaging platform capable of simultaneously detecting and visualizing up to 40 different protein targets in tissue sections.

  ffpe imc imaging raw channel

• Fungal metabarcoding data integration framework for the MycoDiversity DataBase (MDDB).

  PMID 32463383 · PMC7734503 · Journal of integrative bioinformatics · 2020 · 6 claims · 5 setups

  Has reproduction · 78

  The MycoDiversity DataBase (MDDB) is a curated repository integrating public fungal metabarcoding data of environmental samples to study fungal biodiversity patterns in space and time.

  fungal pubmed pdf sra metabarcoding acquisition regular-expression

• Blood Transcriptome Analysis of Septic Patients Reveals a Long Non-Coding Alu-RNA in the Complement C5a Receptor 1 Gene.

  PMID 35447887 · PMC9027897 · Non-coding RNA · 2022 · 6 claims · 7 setups

  Has reproduction · 64

  A computational pipeline intersecting immune gene coordinates with Alu element coordinates can identify candidate Alu-lncRNAs

  peripheral genome blood bulk illumina ion

• Transcriptome profiling of Giardia intestinalis using strand-specific RNA-seq.

  PMID 23555231 · PMC3610916 · PLoS computational biology · 2013 · 8 claims · 8 setups

  Has reproduction · 74

  Most of the G. intestinalis genome is transcribed in in vitro-grown trophozoites, but at vastly different expression levels.

  intestinalis same rna-seq strand-specific technical reverse

• SeqBuster, a bioinformatic tool for the processing and analysis of small RNAs datasets, reveals ubiquitous miRNA modifications in human embryonic cells.

  PMID 20008100 · PMC2836562 · Nucleic acids research · 2010 · 8 claims · 6 setups

  Full-text index only

  SeqBuster is a versatile web-based and stand-alone bioinformatic toolkit for processing and analyzing large-scale small RNA deep sequencing datasets.

  embryonic hesc small sequence adapter

• MetaGT: A pipeline for de novo assembly of metatranscriptomes with the aid of metagenomic data.

  PMID 36386613 · PMC9651917 · Frontiers in microbiology · 2022 · 7 claims · 4 setups

  Has reproduction · 83

  MetaGT is a pipeline that combines metatranscriptomic and metagenomic data from the same sample to assemble complete transcript sequences

  simulated mock16 real snailgut novo transcript gene

• 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

• Polyploidy and the petal transcriptome of Gossypium.

  PMID 24393201 · PMC3890615 · BMC plant biology · 2014 · 8 claims · 8 setups

  Has reproduction · 51

  Most homoeologous gene pairs in polyploid cotton petals are expressed at equal levels, indicating a surprising level of expression homeostasis; only ~20% of expressed genes show significant genome bias.

  petal rna-seq commonly polyploid rna-seq read universal

• Optimization of protein solubilization for the analysis of the CD14 human monocyte membrane proteome using LC-MS/MS.

  PMID 19709643 · PMC3159575 · Journal of proteomics · 2009 · 7 claims · 5 setups

  Full-text index only

  Methanol-based solubilization, alone or combined with PPS, yields significantly higher membrane protein identification/enrichment than PPS alone in monocyte membrane proteomics

  bacteriorhodopsin crude immuno-affinity lc-ms sds-page shotgun facs

• GenomeRNAi: a database for cell-based RNAi phenotypes. 2009 update.

  PMID 19910367 · PMC2808900 · Nucleic acids research · 2010 · 7 claims · 7 setups

  Full-text index only

  GenomeRNAi is a database integrating RNAi phenotypes, reagents, and gene annotations from cell-based screens in Drosophila and human cells

  drosophila hela genome-scale image-based rna-seq

• Nucleosome regulatory dynamics in response to TGFβ.

  PMID 24771338 · PMC4066760 · Nucleic acids research · 2014 · 8 claims · 7 setups

  Has reproduction · 59

  SuMMIt, a Bayesian strand-based mixture model requiring support from both ends of sequenced fragments, enables precise nucleosome mid-position calling, fuzziness scoring and between-condition change detection.

  hepatocellular hepg2 130-bp mnase strand-specific taqman