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 · 75
Revealing the critical state and identifying individualized dynamic network biomarker for type 2 diabetes through advanced analysis methods on individual basis.
PMID 39890881 · PMC11785715 · Scientific reports · 2025 · 8 claims · 5 setups
sJSD, NIG, and TNFE methods can detect critical states/tipping points before disease deterioration using only a single sample
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Expression profiling of drug response--from genes to pathways.
PMID 17117610 · PMC3181826 · Dialogues in clinical neuroscience · 2006 · 8 claims · 8 setups
Understanding individual response to a drug (efficacy/tolerability) is the major bottleneck in current drug development and clinical trials.
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Optimality driven nearest centroid classification from genomic data.
PMID 17912341 · PMC1991588 · PloS one · 2007 · 7 claims · 5 setups
A theoretical result determines the subset of features of a given size that minimizes the misclassification rate for a nearest-centroid (LDA) classifier, based on equation (4).
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Basic and applied biology of the primate reproductive tract--a symposium in honor of the career of Dr Robert M Brenner: introduction and overview.
PMID 17118166 · PMC1775062 · Reproductive biology and endocrinology : RB&E · 2006 · 8 claims · 6 setups
A critical ~36-hour window exists after progesterone withdrawal in macaques during which menstruation can still be blocked by progesterone add-back, after which it becomes inevitable
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Has reproduction · 55
Identification and verification of diagnostic biomarkers in recurrent pregnancy loss via machine learning algorithm and WGCNA.
PMID 37691920 · PMC10485775 · Frontiers in immunology · 2023 · 8 claims · 8 setups
352 DEGs (198 up-regulated, 154 down-regulated) were identified between RPL and control endometrial samples
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Has reproduction · 97
Metatranscriptomics From a Small Aquatic System: Microeukaryotic Community Functions Through the Diurnal Cycle.
PMID 32523568 · PMC7261829 · Frontiers in microbiology · 2020 · 6 claims · 6 setups
Photosynthesis-related and translational transcripts are upregulated at midday (high light) compared to night/darkness in the pond microeukaryotic community
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Has reproduction · 62
A comparative gene co-expression analysis using self-organizing maps on two congener filmy ferns identifies specific desiccation tolerance mechanisms associated to their microhabitat preference.
PMID 32019526 · PMC7001327 · BMC plant biology · 2020 · 8 claims · 6 setups
H. caudiculatum (lower canopy) exhibits about twice as many differentially expressed genes as H. dentatum (upper canopy), with a higher proportion of both increased and decreased gene abundance during dehydration.
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Genomic and proteomic approaches for studying human cancer: prospects for true patient-tailored therapy.
PMID 15601541 · PMC3525069 · Human genomics · 2004 · 8 claims · 6 setups
DNA microarray gene expression profiling generates robust molecular classifications for many tumour types (brain, breast, colon, gastric, kidney, leukaemia, lymphoma, lung, melanoma, ovary, prostate, etc.)
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Detection of venous thromboembolism by proteomic serum biomarkers.
PMID 17579716 · PMC1891085 · PloS one · 2007 · 5 claims · 8 setups
A neural network-based classifier built from direct MALDI-TOF MS serum protein expression profiles can diagnose VTE with sensitivity/specificity that exceeds D-dimer assays
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Has reproduction · 76
Correcting scale distortion in RNA sequencing data.
PMID 39875825 · PMC11776150 · BMC bioinformatics · 2025 · 8 claims · 8 setups
Local averaging reveals expression-level-dependent biases that differ from sample to sample across all RNA-seq datasets studied, and are not corrected by conventional normalization (TPM/FPKM)
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In vitro and in silico analysis reveals an efficient algorithm to predict the splicing consequences of mutations at the 5' splice sites.
PMID 17726045 · PMC2094079 · Nucleic acids research · 2007 · 8 claims · 6 setups
Two exonic mutations, PINK1 E417G and PARK7 E64D, disrupt binding to U1 snRNA and cause skipping of the mutation-harboring exon
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POCUS: mining genomic sequence annotation to predict disease genes.
PMID 14611661 · PMC329128 · Genome biology · 2003 · 8 claims · 6 setups
Genes predisposing to the same disease tend to share functional annotation IDs (GO/InterPro) more than expected by chance
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Has reproduction · 87
High-resolution mapping of transcriptional dynamics across tissue development reveals a stable mRNA-tRNA interface.
PMID 25122613 · PMC4216921 · Genome research · 2014 · 8 claims · 7 setups
mRNA codon and amino acid pools are highly stable across mouse development and across tissues, simply reflecting the genomic background distribution of any possible transcriptome.
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A golden age of brain exploration.
PMID 15660159 · PMC544547 · PLoS biology · 2005 · 8 claims · 3 setups
Over 99% of neuroscience literature focuses on only 1% of the ~15,000–16,000 genes expressed in the brain, leaving most brain-expressed genes uncharacterized.
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Has reproduction · 65
comBO: A combined human bone and lympho-myeloid bone marrow organoid for preclinical modeling of hematopoietic disorders.
PMID 41734765 · PMC7618947 · Cell stem cell · 2026 · 8 claims · 8 setups
comBO is a single iPSC differentiation generating lymphoid, myeloid, vascular, mesenchymal stromal, and functional osteo/adipogenic lineages within one organoid