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 · 35
Transcriptional firing represses bactericidal activity in cystic fibrosis airway neutrophils.
PMID 33948572 · PMC8080108 · Cell reports. Medicine · 2021 · 8 claims · 8 setups
Neutrophils recruited to CF airways undergo rapid, broad transcriptional firing that upregulates anabolic genes and downregulates antimicrobial genes
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Has reproduction · 74
MicroPIPE: validating an end-to-end workflow for high-quality complete bacterial genome construction.
PMID 34172000 · PMC8235852 · BMC genomics · 2021 · 8 claims · 8 setups
MicroPIPE, an end-to-end Nextflow/Singularity-based pipeline built from systematically validated tool choices, produces high-quality complete bacterial genome assemblies without manual intervention.
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Has reproduction · 75
Frequency and patterns of ribonucleotide incorporation around autonomously replicating sequences in yeast reveal the division of labor of replicative DNA polymerases.
PMID 34551434 · PMC8501979 · Nucleic acids research · 2021 · 6 claims · 4 setups
rNTP incorporation is preferentially found on the leading strand in yeast cells expressing wild-type replicative DNA polymerases
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Has reproduction · 57
Environmental selection overturns the decay relationship of soil prokaryotic community over geographic distance across grassland biotas.
PMID 35073255 · PMC8828049 · eLife · 2022 · 8 claims · 7 setups
Prokaryotic community similarity follows a significant U-shape relationship over geographic distance up to 4000 km, decreasing within biotas but increasing across biotas after a tipping point of 1760-1920 km
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Has reproduction · 64
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
A computational pipeline intersecting immune gene coordinates with Alu element coordinates can identify candidate Alu-lncRNAs
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Has reproduction · 94
BaRTv2: a highly resolved barley reference transcriptome for accurate transcript-specific RNA-seq quantification.
PMID 35704392 · PMC9546494 · The Plant journal : for cell and molecular biology · 2022 · 8 claims · 6 setups
BaRTv2.18 is the most comprehensive and resolved reference transcriptome in barley to date, containing 39,434 genes and 148,260 transcripts
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Has reproduction · 58
iCOMIC: a graphical interface-driven bioinformatics pipeline for analyzing cancer omics data.
PMID 35899080 · PMC9310080 · NAR genomics and bioinformatics · 2022 · 8 claims · 4 setups
iCOMIC provides a GUI-driven, Snakemake-based pipeline integrating multiple tools for DNA-Seq and RNA-Seq analysis with minimal command-line interaction.
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Has reproduction · 85
Systematic Analysis of Long Non-Coding RNA Genes in Nonalcoholic Fatty Liver Disease.
PMID 35893239 · PMC9332188 · Non-coding RNA · 2022 · 6 claims · 5 setups
Many lncRNAs, like protein-coding genes, are differentially expressed in NAFLD patients compared to healthy normal-weight and obese individuals.
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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 · 71
Transcriptomic Study on the Lungs of Broilers with Ascites Syndrome.
PMID 36611783 · PMC9817706 · Animals : an open access journal from MDPI · 2023 · 8 claims · 6 setups
1442 genes were differentially expressed in AS broiler lung vs normal lung (614 up-regulated, 828 down-regulated)
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Has reproduction · 99
A chromosome-level genome assembly of Plantago ovata.
PMID 36707685 · PMC9883528 · Scientific reports · 2023 · 8 claims · 8 setups
A chromosome-level reference genome assembly of P. ovata was constructed using PacBio long reads and Hi-C scaffolding.
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Has reproduction · 67
Evaluating native-like structures of RNA-protein complexes through the deep learning method.
PMID 36828844 · PMC9958188 · Nature communications · 2023 · 8 claims · 7 setups
DRPScore identifies native-like RNA-protein structures with higher success rates than ITScore-PR, DARS-RNP, and 3dRPC across bound and unbound testing sets.
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Has reproduction · 85
Predicting the pathogenicity of missense variants using features derived from AlphaFold2.
PMID 37084271 · PMC10203375 · Bioinformatics (Oxford, England) · 2023 · 6 claims · 8 setups
AlphaFold2-derived structural features (solvent accessibility, amino acid network features, physicochemical environment, pLDDT) can be used to train a random forest classifier (AlphScore) that distinguishes proxy-benign from proxy-pathogenic missense variants.
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Has reproduction · 75
An informatics research platform to make public gene expression time-course datasets reusable for more scientific discoveries.
PMID 33247935 · PMC7698665 · Database : the journal of biological databases and curation · 2020 · 8 claims · 6 setups
GETc enables discovery and visualization of time-course gene expression data and analytical results from GEO
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Has reproduction · 69
Machine learning-based identification of an immunotherapy-related signature to enhance outcomes and immunotherapy responses in melanoma.
PMID 39355255 · PMC11442245 · Frontiers in immunology · 2024 · 8 claims · 8 setups
66 consensus immunotherapy prognostic genes (CITPGs) were identified from the intersection of WGCNA modules, immunotherapy responder-vs-non-responder DEGs, and tumor-vs-normal DEGs
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Has reproduction · 70
MACanalyzeR scRNAseq analysis tool reveals PPARγ(HIGH)/GDF15(HIGH) lipid-associated macrophages facilitate thermogenic expansion in BAT.
PMID 40450001 · PMC12126529 · Nature communications · 2025 · 8 claims · 8 setups
MACanalyzeR is a novel computational scRNAseq framework (with FoamSpotteR, MacPolarizeR, and PathAnalyzeR modules) for comprehensive monocyte/macrophage metabolic and phenotypic profiling
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Has reproduction · 78
GenTB: A user-friendly genome-based predictor for tuberculosis resistance powered by machine learning.
PMID 34461978 · PMC8407037 · Genome medicine · 2021 · 8 claims · 6 setups
GenTB is a free, open, web-based application offering two ML predictors (Random Forest and WDNN) that predict resistance to 13 and 10 anti-TB drugs, respectively.
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Prognostic significance of p53 and ras gene abnormalities in lung adenocarcinoma patients with stage I disease after curative resection.
PMID 7852188 · PMC5919395 · Japanese journal of cancer research : Gann · 1994 · 6 claims · 5 setups
Presence of p53 gene abnormalities is associated with shorter disease-free survival in stage I lung adenocarcinoma
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A cell biological perspective on genome research.
PMID 8522596 · PMC2120688 · The Journal of cell biology · 1995 · 7 claims · 7 setups
Genome sequencing represents a sixth stage in the historical progression of structural biology (comparative anatomy through crystallography), and will be similarly valuable once related to function.
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Toxicogenomics research consortium sails into uncharted waters.
PMID 12460811 · PMC1241122 · Environmental health perspectives · 2002 · 8 claims · 8 setups
The NIEHS-funded $37 million Toxicogenomics Research Consortium (TRC) combines the NIEHS Microarray Center with five academic institutions (UNC, Duke, Fred Hutchinson/UW, MIT, OHSU) to define genetic variability, set gene expression standards, and study environmental stress responses.