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 · 53
Blood RNA signature RISK4LEP predicts leprosy years before clinical onset.
PMID 34090257 · PMC8182229 · EBioMedicine · 2021 · 8 claims · 6 setups
1,613 genes were differentially expressed in leprosy progressors before diagnosis (t=1) compared to household contacts.
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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.
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Has reproduction · 54
EpiDiverse Toolkit: a pipeline suite for the analysis of bisulfite sequencing data in ecological plant epigenetics.
PMID 34805989 · PMC8598301 · NAR genomics and bioinformatics · 2021 · 8 claims · 5 setups
EpiDiverse Toolkit provides Nextflow-based pipelines for WGBS mapping, methylation calling, variant calling, differential methylation, and EWAS tailored to non-model plant ecology
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Has reproduction · 50
Implementing the reuse of public DIA proteomics datasets: from the PRIDE database to Expression Atlas.
PMID 35701420 · PMC9197839 · Scientific data · 2022 · 8 claims · 5 setups
An open, containerised, Nextflow-orchestrated reanalysis pipeline combining metadata annotation, SWATH-MS analysis, statistical analysis, and Expression Atlas integration was developed for public DIA data.
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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
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Has reproduction · 46
De novo transcriptome assembly and comprehensive assessment provide insight into fruiting body formation of Sparassis latifolia.
PMID 35773379 · PMC9247108 · Scientific reports · 2022 · 6 claims · 7 setups
De novo transcriptome assembly of S. latifolia produced 48,549 unigenes, 71.53% (34,728) of which were annotated against KEGG, GO, and/or KOG databases
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Has reproduction · 68
Genome-wide DNA hypermethylation opposes healing in patients with chronic wounds by impairing epithelial-mesenchymal transition.
PMID 35819852 · PMC9433101 · The Journal of clinical investigation · 2022 · 8 claims · 8 setups
Chronic wound-edge tissue exhibits genome-wide DNA hypermethylation, with hypermethylation more prominent than hypomethylation across differentially methylated regions.
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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 · 93
Global and precise identification of functional miRNA targets in mESCs by integrative analysis.
PMID 35899551 · PMC9442311 · EMBO reports · 2022 · 8 claims · 8 setups
Fewer than 10% of expressed genes are directly and functionally regulated by miRNAs in mESCs
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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
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Has reproduction · 100
Lipopolysaccharide distinctively alters human microglia transcriptomes to resemble microglia from Alzheimer's disease mouse models.
PMID 36254682 · PMC9612871 · Disease models & mechanisms · 2022 · 8 claims · 8 setups
iPSC-microglia show a shared core transcriptional response to ATPγS and to LPS+IFN-γ, suggesting a convergent mechanism of action
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Has reproduction · 64
A novel and dual digestive symbiosis scales up the nutrition and immune system of the holobiont Rimicaris exoculata.
PMID 36333777 · PMC9636832 · Microbiome · 2022 · 7 claims · 6 setups
Genome-resolved metagenomics of separated foregut and midgut reconstructed 20 MAGs including novel lineages of Hepatoplasmataceae (foregut) and Deferribacteres (midgut).
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Has reproduction · 84
The seeker R package: simplified fetching and processing of transcriptome data.
PMID 36389425 · PMC9648347 · PeerJ · 2022 · 8 claims · 4 setups
seeker is an R package that wraps existing tools to fetch and process RNA-seq and microarray data, providing a standard interface, simple parallelization, and detailed logging
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Has reproduction · 56
Modulation of HERV Expression by Four Different Encephalitic Arboviruses during Infection of Human Primary Astrocytes.
PMID 36423114 · PMC9694637 · Viruses · 2022 · 6 claims · 7 setups
The four arboviruses commonly induce upregulation of HERVs in human primary astrocytes, with 15 HERVs co-modulated by all four viruses, including highly upregulated HERV4_4q22.1
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Has reproduction · 59
The rates of adult neurogenesis and oligodendrogenesis are linked to cell cycle regulation through p27-dependent gene repression of SOX2.
PMID 36627412 · PMC9832098 · Cellular and molecular life sciences : CMLS · 2023 · 8 claims · 8 setups
p27 restricts residual CDK activity after mitogen withdrawal to antagonize cell cycling, but is not essential for cell cycle exit per se
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Has reproduction · 52
Social complexity, life-history and lineage influence the molecular basis of castes in vespid wasps.
PMID 36828829 · PMC9958023 · Nature communications · 2023 · 8 claims · 7 setups
A shared genetic toolkit of caste-associated genes exists across vespid wasp species spanning different levels of social complexity
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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
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Has reproduction · 76
Analysis of the Hypoxic Response in a Mouse Cortical Collecting Duct-Derived Cell Line Suggests That Esrra Is Partially Involved in Hif1α-Mediated Hypoxia-Inducible Gene Expression in mCCD(cl1) Cells.
PMID 35806266 · PMC9267015 · International journal of molecular sciences · 2022 · 8 claims · 7 setups
mCCD cl1 cells mount a broad transcriptional response to 24 h hypoxia (0.2% O2), with 3086 genes differentially expressed
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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.