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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Phenotypic categorization of genetic skin diseases reveals new relations between phenotypes, genes and pathways.
PMID 19744994 · PMC2773259 · Bioinformatics (Oxford, England) · 2009 · 8 claims · 5 setups
560 genetic skin diseases can be decomposed into 71 elementary phenotypic features (42 dermatologic, 29 systemic) that combine to represent each disease as a point in a multidimensional phenotype space
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Human epigenome project--up and running.
PMID 14691553 · PMC300691 · PLoS biology · 2003 · 7 claims · 4 setups
Epigenetic modifications (e.g., DNA methylation) rather than DNA sequence differences explain phenotypic differences between genetically identical individuals, such as monozygotic twins or inbred mice.
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Phenotypic screening, transcriptional profiling, and comparative genomic analysis of an invasive and non-invasive strain of Candida albicans.
PMID 18950481 · PMC2579918 · BMC microbiology · 2008 · 8 claims · 8 setups
Strain SC5314 is invasive and virulent whereas strain ATCC10231 is non-invasive and strongly attenuated in virulence
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Information-based methods for predicting gene function from systematic gene knock-downs.
PMID 18959798 · PMC2596148 · BMC bioinformatics · 2008 · 8 claims · 4 setups
Information-based metrics, which incorporate a phenotype's genomic frequency, outperform non-information-based metrics for detecting gene-gene functional similarity from phenotypic knock-down profiles.
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Has reproduction · 78
GenTB: A user-friendly genome-based predictor for tuberculosis resistance powered by machine learning.
PMID 34461978 · PMC8407037 · Genome medicine · 2021 · 8 claims · 6 setups
GenTB is a free, open, web-based application offering two ML predictors (Random Forest and WDNN) that predict resistance to 13 and 10 anti-TB drugs, respectively.
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Physiology engages with functional genomics - at last.
PMID 16086845 · PMC1273626 · Genome biology · 2005 · 8 claims · 8 setups
Large-scale QTL phenotyping in rat strains reveals that most hypertension-related traits are sexually dimorphic
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Has reproduction · 100
Computational modeling demonstrates that glioblastoma cells can survive spatial environmental challenges through exploratory adaptation.
PMID 31836713 · PMC6911112 · Nature communications · 2019 · 8 claims · 6 setups
Stochastic exploration of the gene-regulatory network structure confers enhanced adaptive capacity, enabling GBM cells to converge to new target phenotypes in novel environments.
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Has reproduction · 83
A temporal classifier predicts histopathology state and parses acute-chronic phasing in inflammatory bowel disease patients.
PMID 36694043 · PMC9873918 · Communications biology · 2023 · 8 claims · 7 setups
The DSS phenotype-by-time interaction defines parsimonious temporal (dynamic) expression and splicing signatures of acute and chronic colitis distinct from time-specific differential expression.
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Has reproduction · 64
Genetic introgression from commercial European pigs to the indigenous Chinese Lijiang breed and associated changes in phenotypes.
PMID 38566006 · PMC10985947 · Genetics, selection, evolution : GSE · 2024 · 7 claims · 7 setups
Significant genetic introgression from commercial European pigs (EP) into the Lijiang pig (LJP) and other domestic Chinese pig breeds was detected.
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Has reproduction · 99
The systematic assessment of completeness of public metadata accompanying omics studies in the Gene Expression Omnibus data repository.
PMID 40926267 · PMC12421755 · Genome biology · 2025 · 8 claims · 3 setups
Over 25% of critical metadata are omitted, with only 74.8% of relevant phenotypes available in publications or public repositories.
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Has reproduction · 87
Next-generation phenotyping integrated in a national framework for patients with ultrarare disorders improves genetic diagnostics and yields new molecular findings.
PMID 39039281 · PMC11319204 · Nature genetics · 2024 · 6 claims · 5 setups
A structured multidisciplinary exome sequencing framework established molecular genetic diagnoses in 32% of patients with suspected ultrarare disorders, comprising 370 distinct molecular causes.
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Sequencing of 16S rRNA gene: a rapid tool for identification of Bacillus anthracis.
PMID 12396926 · PMC2730316 · Emerging infectious diseases · 2002 · 7 claims · 4 setups
All 86 B. anthracis isolates tested share an identical 16S rRNA gene sequence, designated 16S type 6
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Gene loss rate: a probabilistic measure for the conservation of eukaryotic genes.
PMID 17158152 · PMC1802574 · Nucleic acids research · 2007 · 8 claims · 8 setups
GLR is a novel maximum-likelihood measure of gene loss rate that probabilistically weighs all possible ancestral phyletic patterns rather than relying on a single parsimonious reconstruction.
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A well-conserved Plasmodium falciparum var gene shows an unusual stage-specific transcript pattern.
PMID 12787360 · PMC2869446 · Molecular microbiology · 2003 · 8 claims · 8 setups
Full-length var transcripts (detected by the complex var exon 2 probe) are present only in ring stages, not in pigmented trophozoites, across multiple parasite lines