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 · 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 · 83
Multiomic machine learning on lactylation for molecular typing and prognosis of lung adenocarcinoma.
PMID 39856156 · PMC11760357 · Scientific reports · 2025 · 8 claims · 8 setups
Ten multiomics clustering algorithms identify two distinct lactylation cancer subtypes (CS1 and CS2) in LUAD
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Has reproduction
Comprehensive analysis of m(6)A methylome alterations after azacytidine plus venetoclax treatment for acute myeloid leukemia by nanopore sequencing.
PMID 38510975 · PMC10950754 · Computational and structural biotechnology journal · 2024 · 8 claims · 6 setups
m6A site number and m6A levels are significantly lower in post-treatment complete remission (CR) bone marrow than in pre-treatment AML bone marrow
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Has reproduction · 44
Dynamic Gene Attention Focus (DyGAF): Enhancing Biomarker Identification Through Dual-Model Attention Networks.
PMID 40160891 · PMC11951896 · Bioinformatics and biology insights · 2025 · 6 claims · 5 setups
DyGAF, a dual-model attention neural network (independent Model A + dependent Model B), identifies and ranks genes by significance for COVID-19 biomarker discovery more effectively than differential expression analysis (DEA) and random forest (RF) feature selection
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Has reproduction · 78
A network-based model of Aspergillus fumigatus elucidates regulators of development and defensive natural products of an opportunistic pathogen.
PMID 41505094 · PMC12781895 · Nucleic acids research · 2026 · 7 claims · 6 setups
MERLIN-P-TFA network inference on 18 curated public RNA-seq datasets produced a genome-wide GRN resource for A. fumigatus called GRAsp.
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Has reproduction · 77
Representing and querying disease networks using graph databases.
PMID 27462371 · PMC4960687 · BioData mining · 2016 · 7 claims · 8 setups
Graph databases are well suited for representing biological information because it is typically highly connected, semi-structured and unpredictable, unlike relational databases which require rigid schemas.
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Has reproduction · 80
DMN-seq enriches DNA hypomethylated regions for biomarker discovery using 5-methylcytosine glycosylase.
PMID 41673887 · PMC13097799 · Genome biology · 2026 · 8 claims · 9 setups
DMN-seq (DMN+) uses DME to nick DNA specifically at 5mC sites, enabling 5mC detection at single-base resolution via selective adaptor ligation
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Has reproduction · 86
Prediction, syntax and semantic grounding in the brain and large language models.
PMID 41807493 · PMC12979642 · Scientific reports · 2026 · 7 claims · 8 setups
Nouns show significant pre-onset (anticipatory) neural activity in ERPs/ERFs, suggesting enhanced anticipatory processing for this word class.
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Has reproduction · 78
Long-read nanopore shotgun metagenomic DNA sequencing for river biodiversity, wildlife, pollution, and environmental health monitoring.
PMID 42038409 · PMC13107125 · NAR genomics and bioinformatics · 2026 · 7 claims · 7 setups
Long-read shotgun metagenomic sequencing of eDNA can simultaneously detect and quantify organismal DNA from viruses to mammals in a single assay
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Has reproduction · 74
SpaGene: A Deep Adversarial Framework for Spatial Gene Imputation.
PMID 42146899 · PMC13176606 · Computational and structural biotechnology journal · 2026 · 8 claims · 6 setups
SpaGene improves average PCC and SSIM and reduces RMSE compared to 6 baseline methods (SpaGE, gimVI, Tangram, VISTA, spRefine, stDiff) across 8 diverse ST-SC dataset pairs under gene-holdout evaluation.
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Has reproduction · 57
KARAJ: An Efficient Adaptive Multi-Processor Tool to Streamline Genomic and Transcriptomic Sequence Data Acquisition.
PMID 36430895 · PMC9694301 · International journal of molecular sciences · 2022 · 8 claims · 6 setups
KARAJ automates end-to-end querying and downloading of genomic/transcriptomic sequence data from a list of PMCIDs, URLs, or accession numbers
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Has reproduction · 75
Transcriptomic analysis unravels the molecular response of Lonicera japonica leaves to chilling stress.
PMID 36618608 · PMC9815118 · Frontiers in plant science · 2022 · 8 claims · 8 setups
Chilling stress significantly alters the ratio of anthocyanins, chlorophylls, and carotenoids, causing leaf color to change from green to purple
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Has reproduction · 60
TRAPID 2.0: a web application for taxonomic and functional analysis of de novo transcriptomes.
PMID 34197621 · PMC8464036 · Nucleic acids research · 2021 · 8 claims · 8 setups
TRAPID 2.0 is a web application performing global characterization of de novo transcriptomes via structural, functional, and taxonomic annotation in an initial processing phase, followed by an exploratory phase of downstream analyses.
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Has reproduction
Human Retrotransposons and Effective Computational Detection Methods for Next-Generation Sequencing Data.
PMID 36295018 · PMC9605557 · Life (Basel, Switzerland) · 2022 · 8 claims · 7 setups
Transposable elements make up nearly 45% of the human genome, vastly exceeding the ~1.5% that is protein-coding.
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Has reproduction · 74
Genetic architecture of natural variation of cardiac performance from flies to humans.
PMID 36383075 · PMC9668334 · eLife · 2022 · 8 claims · 7 setups
Natural genetic variation significantly influences cardiac performance traits (rhythmicity and contractility) across 167 DGRP lines
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Has reproduction · 76
What the Phage: a scalable workflow for the identification and analysis of phage sequences.
PMID 36399058 · PMC9673492 · GigaScience · 2022 · 8 claims · 7 setups
WtP combines 11 tools (14 approaches) for phage prediction in a parallel, containerized Nextflow workflow
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Has reproduction · 80
Multiomic analysis of malignant pleural mesothelioma identifies molecular axes and specialized tumor profiles driving intertumor heterogeneity.
PMID 36928603 · PMC10101853 · Nature genetics · 2023 · 8 claims · 6 setups
The WHO histopathological classification of MPM accounts for only up to ~10% of interpatient molecular differences
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Has reproduction · 89
Comparative genomics of dairy-associated Staphylococcus aureus from selected sub-Saharan African regions reveals milk as reservoir for human-and animal-derived strains and identifies a putative animal-related clade with presumptive novel siderophore.
PMID 36046020 · PMC9421002 · Frontiers in microbiology · 2022 · 7 claims · 8 setups
Milk serves as a reservoir for both human- and animal-derived S. aureus strains in sub-Saharan Africa
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Has reproduction · 84
Towards reliable whole genome sequencing for outbreak preparedness and response.
PMID 35945497 · PMC9361258 · BMC genomics · 2022 · 7 claims · 4 setups
Amplicon-based Nanopore sequencing can rapidly generate whole genome sequences in samples with viral load up to Ct 33.
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Has reproduction · 85
Evolution and codon usage bias of mitochondrial and nuclear genomes in Aspergillus section Flavi.
PMID 36305682 · PMC9836360 · G3 (Bethesda, Md.) · 2023 · 8 claims · 8 setups
18 new mitochondrial genomes were assembled for Aspergillus section Flavi species, complementing 3 existing reference mitogenomes, for a total of 20 species analyzed.