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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Applying proteomics to the diagnosis and treatment of ALS and related diseases.
PMID 19670321 · PMC2836583 · Muscle & nerve · 2009 · 8 claims · 8 setups
Protein-based biomarkers for ALS/MND require further verification and large-scale validation/qualification studies, including disease mimics, before clinical use
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Has reproduction · 52
Transcriptomic profiling of skeletal muscle adaptations to exercise and inactivity.
PMID 31980607 · PMC6981202 · Nature communications · 2020 · 6 claims · 4 setups
A meta-analysis (MetaMEx) of 66 published human skeletal muscle datasets reveals pathways selectively activated by inactivity, aerobic versus resistance, and acute versus chronic exercise training.
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Has reproduction · 93
A comparison of the large-scale gene expression patterns in summer and fall migratory Pantala flavescens (Fabricius) in northern China.
PMID 39108562 · PMC11301579 · Ecology and evolution · 2024 · 7 claims · 2 setups
624 DEGs were identified between summer (M7) and fall (M10) migratory P. flavescens, with 352 upregulated and 272 downregulated in M7 versus M10
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Has reproduction · 90
Gap-free telomere-to-telomere haplotype assembly of the tomato hind (Cephalopholis sonnerati).
PMID 39578472 · PMC11584678 · Scientific data · 2024 · 8 claims · 8 setups
Two T2T gap-free haplotype assemblies of C. sonnerati (YSFRI_Csonn_HA_1.0 and YSFRI_Csonn_HB_1.0) were successfully generated, each spanning 24 chromosomes with no gaps.
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GENCODE: producing a reference annotation for ENCODE.
PMID 16925838 · PMC1810553 · Genome biology · 2006 · 8 claims · 8 setups
GENCODE annotation combines initial manual annotation by HAVANA, experimental validation, and refinement based on results to identify protein-coding genes in ENCODE regions
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Discovery of molecular subtypes in leiomyosarcoma through integrative molecular profiling.
PMID 19901961 · PMC2820592 · Oncogene · 2010 · 8 claims · 6 setups
Unsupervised gene expression clustering identifies 3 reproducible molecular subtypes of LMS (Group I/muscle-enriched, Group II, Group III)
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Has reproduction · 81
Macrophages on the run: Exercise balances macrophage polarization for improved health.
PMID 39476967 · PMC11585839 · Molecular metabolism · 2024 · 8 claims · 7 setups
Immediate/acute exercise triggers an M1 (pro-inflammatory) macrophage polarization surge.
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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 · 89
miRge 2.0 for comprehensive analysis of microRNA sequencing data.
PMID 30153801 · PMC6112139 · BMC bioinformatics · 2018 · 8 claims · 6 setups
miRge 2.0 introduces a novel SVM-based miRNA detection method using both hairpin structure and isomiR composition, yielding higher specificity for miRNA identification
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Has reproduction · 91
A reference profile-free deconvolution method to infer cancer cell-intrinsic subtypes and tumor-type-specific stromal profiles.
PMID 32111252 · PMC7049190 · Genome medicine · 2020 · 8 claims · 8 setups
DeClust is a reference profile-free deconvolution method that simultaneously deconvolves bulk tumor expression into cancer, immune, and stromal compartments and clusters samples into cancer cell-intrinsic molecular subtypes, outputting subtype-specific reference profiles for the cohort rather than for individuals.
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Has reproduction
Association between Arsenic Level, Gene Expression in Asian Population, and In Vitro Carcinogenic Bladder Tumor.
PMID 35039759 · PMC8760535 · Oxidative medicine and cellular longevity · 2022 · 8 claims · 5 setups
A unique set of 147 genes is associated with arsenic exposure and linked to molecular mechanisms of cancer.
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In silico promoters: modelling of cis-regulatory context facilitates target predictio.
PMID 18505473 · PMC3823354 · Journal of cellular and molecular medicine · 2009 · 8 claims · 8 setups
An integrated 'profiling of transcriptional targets' (PTT) strategy by Freebern et al. identified IGF-1 as a co-modulator of immune cell function genes in mitogen/drug-activated T cells.
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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
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Has reproduction · 97
Identification of immune-related signatures and pathogenesis differences between thoracic aortic aneurysm patients with bicuspid versus tricuspid valves via weighted gene co-expression network analysis.
PMID 37883426 · PMC10602290 · PloS one · 2023 · 6 claims · 7 setups
TAA/TAV pathogenesis is more associated with immune-related gene expression than TAA/BAV, with two WGCNA gene modules (brown and blue) enriched for immune functions.