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).
-
Has reproduction · 76
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
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
-
Has reproduction · 50
Exploiting convergent phenotypes to derive a pan-cancer cisplatin response gene expression signature.
PMID 37076665 · PMC10115855 · NPJ precision oncology · 2023 · 8 claims · 8 setups
A convergent-phenotype-based seed gene/co-expression method can extract consensus gene expression signatures predictive of response to chemotherapeutic drugs in the GDSC database
-
Has reproduction · 95
transXpress: a Snakemake pipeline for streamlined de novo transcriptome assembly and annotation.
PMID 37016291 · PMC10074830 · BMC bioinformatics · 2023 · 6 claims · 7 setups
transXpress is a Snakemake pipeline that streamlines de novo transcriptome assembly, quantification, and annotation for non-model organisms
-
Full-text index only
The use of neuroproteomics in drug abuse research.
PMID 19926406 · PMC3947580 · Drug and alcohol dependence · 2010 · 8 claims · 8 setups
Neuroproteomic technologies (2D-DIGE, iTRAQ, ICAT, etc.) enable identification of protein-level changes underlying effects of drugs of abuse such as amphetamine, morphine, cocaine, and alcohol.
-
Has reproduction · 92
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
Large-scale integration of 111 sc/snRNAseq datasets captures rare, transitional myogenic progenitor states (commitment and fusion) that are poorly represented in individual datasets.
-
Full-text index only
A re-annotation pipeline for Illumina BeadArrays: improving the interpretation of gene expression data.
PMID 19923232 · PMC2817484 · Nucleic acids research · 2010 · 8 claims · 7 setups
A Perl-based pipeline that BLASTs/BLATs Illumina probe sequences against genomes and transcript databases (RefSeq, UCSC Known Genes, UniGene/GenBank, Ensembl) can classify probes by quality grade (Perfect/Good/Bad/No match) and is applicable across 8 BeadArray platforms and other array types
-
Has reproduction · 97
Duvernoy's Gland Transcriptomics of the Plains Black-Headed Snake, Tantilla nigriceps (Squamata, Colubridae): Unearthing the Venom of Small Rear-Fanged Snakes.
PMID 34066626 · PMC8148590 · Toxins · 2021 · 8 claims · 5 setups
The T. nigriceps Duvernoy's gland transcriptome is dominated by three toxin families: three-finger toxins (3FTxs), cysteine-rich secretory proteins (CRISPs), and snake venom metalloproteinases (SVMPIIIs)
-
Has reproduction · 33
To Explore the Key Subgroup and Their Immune Microenvironment During the Formation of Coronary Plaque With scRNA-seq.
PMID 40454289 · PMC12126265 · Cardiology research and practice · 2025 · 6 claims · 8 setups
C1 RACK1+ NK cells are a crucial subgroup for understanding coronary plaque formation, exhibiting the highest cell stemness/differentiation potential and positioned at the start of the pseudotime trajectory
-
Has reproduction · 82
SMAGEXP: a galaxy tool suite for transcriptomics data meta-analysis.
PMID 30698691 · PMC6354025 · GigaScience · 2019 · 8 claims · 5 setups
SMAGEXP integrates the metaMA and metaRNASeq R packages into Galaxy to provide a unified tool suite for transcriptomics meta-analysis.
-
Has reproduction · 45
De novo transcriptomic analysis of leaf and fruit tissue of Cornus officinalis using Illumina platform.
PMID 29451882 · PMC5815590 · PloS one · 2018 · 7 claims · 7 setups
This is the first de novo transcriptomic analysis of Cornus officinalis, providing fundamental gene and biosynthetic pathway information.
-
Has reproduction · 67
Unraveling the timeline of gene expression: A pseudotemporal trajectory analysis of single-cell RNA sequencing data.
PMID 37994351 · PMC10663991 · F1000Research · 2023 · 7 claims · 7 setups
A reproducible R-based workflow combines Seurat (QC, clustering, integration), monocle3 (trajectory inference), and edgeR (pseudo-bulk time course analysis) to perform single-cell pseudotemporal time course analysis.
-
Has reproduction · 100
Exploring Gene Expression Patterns in Alzheimer's Disease Using a Human Microarray Data Meta-Analysis.
PMID 41744654 · PMC12938635 · Biology · 2026 · 6 claims · 7 setups
AD brains show a distinct transcriptomic profile with up-regulation of immune/inflammation genes and down-regulation of synapse/neuronal-signaling genes
-
Has reproduction · 84
Genome of the endangered Guatemalan Beaded Lizard, Heloderma charlesbogerti, reveals evolutionary relationships of squamates and declines in effective population sizes.
PMID 36226801 · PMC9713440 · G3 (Bethesda, Md.) · 2022 · 8 claims · 7 setups
The assembled draft genome of H. charlesbogerti totals 2.31 Gb, similar in size to related species
-
Has reproduction · 100
A comprehensive framework for analysis of microRNA sequencing data in metastatic colorectal cancer.
PMID 35047825 · PMC8759566 · NAR cancer · 2022 · 7 claims · 7 setups
Five miRNAs (Mir-210_3p, Mir-191_5p, Mir-8-P1b_3p [miR-141-3p], Mir-1307_5p, Mir-155_5p) are up-regulated at multiple metastatic sites in colorectal cancer.
-
Has reproduction · 93
Extensive transgressive gene expression in testis but not ovary in the homoploid hybrid Italian sparrow.
PMID 35726533 · PMC9542029 · Molecular ecology · 2022 · 7 claims · 8 setups
Italian sparrow testis exhibits extensive transgressive gene expression relative to both parental species
-
Has reproduction · 100
msPIPE: a pipeline for the analysis and visualization of whole-genome bisulfite sequencing data.
PMID 36123620 · PMC9487059 · BMC bioinformatics · 2022 · 6 claims · 8 setups
msPIPE is a new end-to-end pipeline integrating pre-processing, alignment & methylation calling, and downstream DNA methylation analysis (profiling, HMR, DMR, functional enrichment) with publication-quality figure output for WGBS data
-
Has reproduction · 71
Single-Cell Transcriptomic Landscape of Right-Sided Colon Cancer Reveals Cellular and Molecular Features of Metastatic Potential.
PMID 41898210 · PMC13024220 · Biomedicines · 2026 · 8 claims · 8 setups
Liver metastatic potential in RCC is marked by stem-like tumor states, metabolic plasticity, and microenvironmental remodeling.
-
Has reproduction · 53
Blood RNA signature RISK4LEP predicts leprosy years before clinical onset.
PMID 34090257 · PMC8182229 · EBioMedicine · 2021 · 7 claims · 5 setups
A 4-gene blood RNA signature (RISK4LEP: MT-ND2, REX1BD, TPGS1, UBC) predicts leprosy development 4–61 months before clinical diagnosis
-
Has reproduction · 38
RNA-Seq transcriptome profiling of upland cotton (Gossypium hirsutum L.) root tissue under water-deficit stress.
PMID 24324815 · PMC3855774 · PloS one · 2013 · 8 claims · 8 setups
A total of 1,530 transcripts were differentially expressed between well-watered and water-deficit stressed field-grown upland cotton root tissues (913 up-regulated, 617 down-regulated).
-
Has reproduction · 41
RNA-sequence analysis of primary alveolar macrophages after in vitro infection with porcine reproductive and respiratory syndrome virus strains of differing virulence.
PMID 24643046 · PMC3958415 · PloS one · 2014 · 8 claims · 8 setups
Infection of PAMs with either LV or Lena affects signaling pathways directly linked to the innate immune response, including IRF activation, RIG1-like receptors, TLRs and PKR pathways.