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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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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Sequence analysis of p53 response-elements suggests multiple binding modes of the p53 tetramer to DNA targets.
PMID 17439973 · PMC1888811 · Nucleic acids research · 2007 · 8 claims · 5 setups
p53REs are not simple direct repeats of half-sites; the two half-sites couple to form a higher-order 20-bp full-site palindrome
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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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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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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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Improved tagging strategy for protein identification in mammalian cells.
PMID 16138932 · PMC1250225 · BMC genomics · 2005 · 7 claims · 7 setups
EGFP tagging via the artificial exon did not affect the subcellular localization of the tagged endogenous proteins
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FeatureScan: revealing property-dependent similarity of nucleotide sequences.
PMID 16845077 · PMC1538849 · Nucleic acids research · 2006 · 6 claims · 5 setups
FeatureScan transforms nucleotide sequences into numerical signals of physico-chemical/conformational properties and compares them via a convolution/correlation (Fourier transform) method rather than comparing letters
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Comparative genomic study reveals a transition from TA richness in invertebrates to GC richness in vertebrates at CpG flanking sites: an indication for context-dependent mutagenicity of methylated CpG sites.
PMID 19329065 · PMC5054122 · Genomics, proteomics & bioinformatics · 2008 · 8 claims · 8 setups
Nucleotide preference at CpG flanking sites transitions from 5' T (invertebrates) to 5' A (vertebrates) at the invertebrate-vertebrate boundary
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Repeating patterns of mimicry.
PMID 17048984 · PMC1617347 · PLoS biology · 2006 · 7 claims · 4 setups
The Yb locus controls presence of a yellow wing band in H. melpomene
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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 · 23
Analysis of whole-genome re-sequencing data of ducks reveals a diverse demographic history and extensive gene flow between Southeast/South Asian and Chinese populations.
PMID 33849442 · PMC8042899 · Genetics, selection, evolution : GSE · 2021 · 8 claims · 8 setups
Whole-genome resequencing reveals three geographically distinct genetic groups: local Chinese, wild, and local Southeast/South Asian duck populations
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Speeding disease gene discovery by sequence based candidate prioritization.
PMID 15766383 · PMC1274252 · BMC bioinformatics · 2005 · 7 claims · 8 setups
Disease genes (OMIM) differ significantly from non-disease genes in sequence-based features including gene/cDNA/protein size, exon number, homolog conservation, secretion signal, 3' UTR length, CpG islands, and distance to nearest gene.
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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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Human blood plasma preparation for two-dimensional gel electrophoresis.
PMID 17174613 · PMC7105212 · Journal of chromatography. B, Analytical technologies in the biomedical and life sciences · 2007 · 8 claims · 6 setups
Plasma protein concentrations reflect the physiological/health state of an individual and can serve as disease biomarkers
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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 · 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 hierarchical and modular approach to the discovery of robust associations in genome-wide association studies from pooled DNA samples.
PMID 18194558 · PMC2248205 · BMC genetics · 2008 · 8 claims · 5 setups
A hierarchical/modular approach integrating quality control, LD, physical distance, and gene ontology identifies authentic associations among those found by statistical tests in pooled DNA GWAS
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Towards alignment independent quantitative assessment of homology detection.
PMID 17205117 · PMC1762415 · PloS one · 2006 · 8 claims · 6 setups
The Fhom Estimator uses the prevalence of a conserved protein feature (X) in two protein sets to estimate the fraction of true homologs among paired proteins, independent of alignment quality.