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).
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Has reproduction · 78
Widespread mono- and oligoadenylation direct small noncoding RNA maturation versus degradation fates.
PMID 41350938 · PMC12811392 · The EMBO journal · 2026 · 8 claims · 2 setups
Post-transcriptional adenylation of newly transcribed sncRNAs is widespread and occurs in two distinct varieties: transient oligoadenylation and stable monoadenylation
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Leveraging two-way probe-level block design for identifying differential gene expression with high-density oligonucleotide arrays.
PMID 15099405 · PMC411067 · BMC bioinformatics · 2004 · 7 claims · 2 setups
Two-way ANOVA and Mack-Skillings tests on probe-level data with FDR control are substantially more powerful than t-test/Wilcoxon on probe-set level data for detecting differential expression
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Decision forest analysis of 61 single nucleotide polymorphisms in a case-control study of esophageal cancer; a novel method.
PMID 16026601 · PMC1637030 · BMC bioinformatics · 2005 · 8 claims · 2 setups
DF-SNPs, a novel adaptation of the Decision Forest method, can classify esophageal cancer cases vs. controls based on SNP genotype data with high concordance, sensitivity, and specificity.
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Has reproduction · 84
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
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.
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Defining the proteome.
PMID 16356278 · PMC1414090 · Genome biology · 2005 · 8 claims · 8 setups
Integration of multi-omics data is an important step toward a systems-biology approach to the proteome
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Has reproduction · 96
A bioinformatic pipeline for simulating viral integration data.
PMID 35496474 · PMC9046613 · Data in brief · 2022 · 7 claims · 3 setups
A snakemake-based pipeline was developed to simulate integration of a viral or vector genome into a host genome, including sub-genomic fragment integration, structural variation, and host-site deletions.
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Has reproduction · 86
Molecular Classification Models for Triple Negative Breast Cancer Subtype Using Machine Learning.
PMID 34575658 · PMC8472680 · Journal of personalized medicine · 2021 · 7 claims · 4 setups
TNBC can be divided into four gene-expression-defined subtypes: BLIA, BLIS, MES, and LAR
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Has reproduction · 70
Bulk and single-cell characterisation of the immune heterogeneity of atherosclerosis identifies novel targets for immunotherapy.
PMID 36855107 · PMC9974063 · BMC biology · 2023 · 8 claims · 8 setups
Integration of scRNA-seq datasets from human atherosclerosis samples identifies 28 distinct immune cell subpopulations with heterogeneity in tissue preference, genetics, function, immune dynamics, transcriptional regulators, metabolism, and cell communication.
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Has reproduction · 75
Identification and analysis of genes associated with epithelial ovarian cancer by integrated bioinformatics methods.
PMID 34143800 · PMC8213194 · PloS one · 2021 · 8 claims · 7 setups
306 overlapping DEGs (265 up-regulated, 41 down-regulated) were identified from three independent GEO microarray datasets comparing EOC and adjacent normal ovarian tissue
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Has reproduction · 94
A Deluge of Complex Repeats: The Solanum Genome.
PMID 26241045 · PMC4524691 · PloS one · 2015 · 8 claims · 8 setups
~50–60% of the genomes of S. tuberosum and S. lycopersicum are composed of repetitive elements
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Has reproduction · 90
Systematic Assessment of Small RNA Profiling in Human Extracellular Vesicles.
PMID 37444556 · PMC10340377 · Cancers · 2023 · 8 claims · 6 setups
EV extraction methods vary in reproducibility for isolating small RNAs, with effects on small RNA composition
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Has reproduction · 71
Comprehensive comparison of gene expression diversity among a variety of human stem cells.
PMID 36458020 · PMC9706419 · NAR genomics and bioinformatics · 2022 · 8 claims · 8 setups
Tissue origin has a stronger influence on gene expression in iPSCs than in other stem cell types
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Has reproduction · 65
comBO: A combined human bone and lympho-myeloid bone marrow organoid for preclinical modeling of hematopoietic disorders.
PMID 41734765 · PMC7618947 · Cell stem cell · 2026 · 8 claims · 8 setups
comBO is a single iPSC-derived organoid differentiation that generates osteolineage, vascular, lymphoid, and myeloid compartments together
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Has reproduction · 73
Expression of neurofibromin 1 in colorectal cancer and cetuximab resistance.
PMID 34779495 · PMC8611403 · Oncology reports · 2022 · 7 claims · 8 setups
NF1 is highly expressed in cetuximab-sensitive colorectal cancer cell lines (NCI-H508, Caco2) but weakly expressed in cetuximab-resistant lines (KM12C, SW480)
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Has reproduction · 74
Identification and validation of a metabolic-related gene risk model predicting the prognosis of lung, colon, and breast cancers.
PMID 39779736 · PMC11711664 · Scientific reports · 2025 · 8 claims · 8 setups
540 DEGs overlap across breast, colorectal, and lung cancers out of 11,384 DEGs analyzed
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Has reproduction · 80
Synthesis of transcriptomic studies reveals a core response to heat stress in abalone (genus Haliotis).
PMID 40361012 · PMC12070547 · BMC genomics · 2025 · 7 claims · 8 setups
A core set of 74 differentially expressed genes (DEGs) responds to heat stress in at least 7 of 9 independent abalone RNA-seq studies
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Has reproduction
miRge3.0: a comprehensive microRNA and tRF sequencing analysis pipeline.
PMID 34308351 · PMC8294687 · NAR genomics and bioinformatics · 2021 · 8 claims · 6 setups
miRge3.0 is a Python 3-based small RNA-seq and tRF analysis pipeline that improves on miRge2.0 (which was Python 2.7-based)
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Has reproduction · 63
Comparative Genomics of Borderline Oxacillin-Resistant Staphylococcus aureus Detected during a Pseudo-outbreak of Methicillin-Resistant S. aureus in a Neonatal Intensive Care Unit.
PMID 35038924 · PMC8764539 · mBio · 2022 · 7 claims · 8 setups
Of 42 isolates flagged as MRSA by screening agar, only 9 were PBP2a- and mecA-positive true MRSA, while the remaining 33 were mecA-negative and largely met criteria for BORSA
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Has reproduction · 20
Expression and Secretion of Circular RNAs in the Parasitic Nematode, Ascaris suum.
PMID 35711944 · PMC9194832 · Frontiers in genetics · 2022 · 8 claims · 7 setups
A. suum expresses 1,997 distinct circRNAs identified via next-generation sequencing in adult female body wall and ovary-enriched tissue
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Has reproduction · 66
Integrative bioinformatics and artificial intelligence analyses of transcriptomics data identified genes associated with major depressive disorders including NRG1.
PMID 37583471 · PMC10423927 · Neurobiology of stress · 2023 · 7 claims · 5 setups
Differentially expressed genes in MDD patients are enriched in immune response, inflammatory response, neurodegeneration, and cerebellar atrophy pathways.