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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Incorporating genetics and genomics in risk assessment for inhaled manganese: from data to policy.
PMID 19646473 · PMC2765692 · Neurotoxicology · 2009 · 8 claims · 7 setups
Inhaled manganese bypasses normal homeostatic regulation and can accumulate in the brain, unlike dietary manganese which is readily excreted
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Optimized mixed Markov models for motif identification.
PMID 16749929 · PMC1534070 · BMC bioinformatics · 2006 · 8 claims · 4 setups
OMiMa can incorporate more than NNSplice's pairwise dependencies
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BABELOMICS: a systems biology perspective in the functional annotation of genome-scale experiments.
PMID 16845052 · PMC1538844 · Nucleic acids research · 2006 · 8 claims · 8 setups
Babelomics is presented as an updated, complete suite of web tools for functional analysis of genome-scale experiments with new and improved modules
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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.
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High mitochondrial DNA stability in B-cell chronic lymphocytic leukemia.
PMID 19924307 · PMC2775629 · PloS one · 2009 · 7 claims · 5 setups
mtDNA control-region instability is not the primary causal factor in B-CLL
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Has reproduction · 83
Functional module detection through integration of single-cell RNA sequencing data with protein-protein interaction networks.
PMID 33138772 · PMC7607865 · BMC genomics · 2020 · 8 claims · 6 setups
scPPIN integrates scRNA-seq-derived p-values with PPINs to detect maximum-weight connected subgraphs (active/functional modules) via an exact Steiner-tree approach
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Has reproduction · 48
Rbfox2 controls autoregulation in RNA-binding protein networks.
PMID 24637117 · PMC3967051 · Genes & development · 2014 · 8 claims · 8 setups
Rbfox2 cross-regulates AS-NMD events within RNA-binding protein genes to alter their expression, tuning autoregulatory splicing networks and placing Rbfox2 at a critical node of a multilayer regulatory network.
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A novel de novo PAX6 mutation in an Ashkenazi-Jewish family with aniridia.
PMID 18334930 · PMC2255027 · Molecular vision · 2008 · 7 claims · 5 setups
A novel heterozygous de novo PAX6 frameshift mutation (c.577_578insG, insG@Gly72) in exon 6 causes autosomal dominant aniridia with congenital cataract, nystagmus, and glaucoma in this family.
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Proteomic characterization of HIV-modulated membrane receptors, kinases and signaling proteins involved in novel angiogenic pathways.
PMID 19712456 · PMC2754444 · Journal of translational medicine · 2009 · 7 claims · 5 setups
31 HIV-modulated cellular proteins were identified as functionally associated with signaling events involved in angiogenesis
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Has reproduction · 71
Machine Learning-Based Integrated Analysis of PANoptosis Patterns in Acute Myeloid Leukemia Reveals a Signature Predicting Survival and Immunotherapy.
PMID 38322112 · PMC10846924 · International journal of clinical practice · 2024 · 7 claims · 7 setups
AML patients can be categorized into two distinct PANRG-based clusters with differing prognosis and immune characteristics
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Has reproduction · 100
Recurrent RNA edits in human preimplantation potentially enhance maternal mRNA clearance.
PMID 36543858 · PMC9772385 · Communications biology · 2022 · 8 claims · 7 setups
Compiled the largest human embryonic A-to-I editome to date from 2071 RNA-seq transcriptomes and identified thousands of per-stage Recurrent Embryonic Edits (REEs, present in ≥50% of samples per stage)
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Linking disease-associated genes to regulatory networks via promoter organization.
PMID 15701758 · PMC549397 · Nucleic acids research · 2005 · 8 claims · 7 setups
Pairs of TFBSs conserved both vertically (orthologous genes) and horizontally (co-regulated genes) can serve as seeds to build promoter models representing potential co-regulation networks
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Has reproduction · 58
Revised annotations, sex-biased expression, and lineage-specific genes in the Drosophila melanogaster group.
PMID 25273863 · PMC4267930 · G3 (Bethesda, Md.) · 2014 · 8 claims · 6 setups
Revised RNA-seq-based gene models for D. ananassae, D. yakuba, and D. simulans include UTRs, empirically verified intron-exon boundaries, and previously unannotated novel exons, improving on r1.3 comparative-genomics annotations that lack UTRs.
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Has reproduction · 58
Investigating epigenetic biomarkers of age, sex, and disease in captive South African cheetahs (Acinonyx jubatus jubatus).
PMID 41528985 · PMC12798976 · PloS one · 2026 · 8 claims · 7 setups
A cheetah-specific epigenetic age clock using 52 CpG sites predicts chronological age across blood and liver with r=0.97 and MAE=0.86 years
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Has reproduction · 98
Systems spatiotemporal dynamics of traumatic brain injury at single-cell resolution reveals humanin as a therapeutic target.
PMID 35951114 · PMC9372016 · Cellular and molecular life sciences : CMLS · 2022 · 8 claims · 8 setups
Coordinated gene expression patterns across cell types are disrupted and re-organized by mTBI with distinct regional, cellular, and temporal (24-h vs 7-day) specificity.