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).

• Connecting synthetic chemistry decisions to cell and genome biology using small-molecule phenotypic profiling.

  PMID 19825513 · PMC2787914 · Current opinion in chemical biology · 2009 · 8 claims · 8 setups

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  Multidimensional phenotypic profiling leverages information content from multiple parallel or multiplexed measurements of compound action on cells, unlike hierarchical screening which filters to few 'interesting' compounds.

  one nci60 cerevisiae cancer multidimensional cellular two-color

• GenTB: A user-friendly genome-based predictor for tuberculosis resistance powered by machine learning.

  PMID 34461978 · PMC8407037 · Genome medicine · 2021 · 8 claims · 6 setups

  Has reproduction · 78

  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.

  clinical tuberculosis registered whole-genome targeted retraining

• 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

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  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

  genodermatoses phenotype disease gene-phenotype manual correlation principal

• Information-based methods for predicting gene function from systematic gene knock-downs.

  PMID 18959798 · PMC2596148 · BMC bioinformatics · 2008 · 8 claims · 4 setups

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  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.

  caenorhabditis elegans saccharomyces interference computational genome-wide

• Environmental genomics: an opportunity for the NIEHS.

  PMID 16393638 · PMC1332673 · Environmental health perspectives · 2006 · 8 claims · 5 setups

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  Intrauterine exposure to endocrine-disrupting pesticides can produce transgenerational adverse effects on male fertility

  intrauterine offspring monozygotic specified phenotypic methylation receptor

• Human epigenome project--up and running.

  PMID 14691553 · PMC300691 · PLoS biology · 2003 · 7 claims · 4 setups

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  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.

  expressed bat8 genetically methylation genome-wide phenotypic

• A genome-wide deletion mutant screen identifies pathways affected by nickel sulfate in Saccharomyces cerevisiae.

  PMID 19917080 · PMC2784802 · BMC genomics · 2009 · 8 claims · 4 setups

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  Genome-wide deletion screening identified 149 genes whose deletion causes NiSO4 sensitivity and 119 genes whose deletion confers NiSO4 resistance.

  cerevisiae lists yeast genome-wide functional protein-protein

• Gene function in the mammalian genome, courtesy of the mouse.

  PMID 12537544 · PMC151280 · Genome biology · 2003 · 8 claims · 8 setups

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  Mosaicism of Mus musculus domesticus and Mus musculus musculus haplotypes exists across the inbred laboratory mouse genome, and genome-wide haplotype mapping can enhance positional cloning

  inbred genome mice model genome-wide large-scale phenotypic

• From microarrays to genome duplications.

  PMID 12914655 · PMC193639 · Genome biology · 2003 · 8 claims · 8 setups

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  Gene3D shows that most genes across sequenced genomes can be assigned to known structural domain families, many of which are shared across kingdoms of life

  tumor cancer plated saccharomyces comparative nonsense-mediated cell-based

• Prediction of Antimicrobial Resistance in Gram-Negative Bacteria From Whole-Genome Sequencing Data.

  PMID 32528441 · PMC7262952 · Frontiers in microbiology · 2020 · 8 claims · 5 setups

  Has reproduction · 100

  WGS-derived antibiotic resistance gene (ARG) coverage can be used to predict antimicrobial resistance in Gram-negative bacteria via machine learning

  gram-negative in-house args curated shotgun genome phenotypic

• Cost-effectively dissecting the genetic architecture of complex wool traits in rabbits by low-coverage sequencing.

  PMID 36401180 · PMC9673297 · Genetics, selection, evolution : GSE · 2022 · 8 claims · 8 setups

  Has reproduction · 50

  BaseVar + STITCH at 1.0X sequencing depth with a sample size >300 achieves the highest genotyping accuracy among tested imputation strategies (genotype concordance >98.8%, genotype accuracy >0.97).

  angora domesticated candidate low-coverage multivariate principal

• Estimation of genetic parameters and genome-wide association study for carcass traits in native chickens.

  PMID 40211845 · PMC12229932 · Animal bioscience · 2025 · 8 claims · 7 setups

  Has reproduction · 71

  Carcass traits (SW, EW, ThW, and their percentages except SP) show moderate to high heritability (0.20-0.50), while SP has low heritability (0.08)

  sanhuang breast whole-genome genome-wide heritability

• 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

  Has reproduction · 64

  Significant genetic introgression from commercial European pigs (EP) into the Lijiang pig (LJP) and other domestic Chinese pig breeds was detected.

  unrelated chinese ljp individuals whole-genome d-statistic local

• PD-1 and TIGIT coexpression identifies a circulating CD8 T cell subset predictive of response to anti-PD-1 therapy.

  PMID 33188038 · PMC7668369 · Journal for immunotherapy of cancer · 2020 · 7 claims · 6 setups

  Has reproduction · 75

  The frequency of circulating PD-1+TIGIT+ (DPOS) CD8+ T cells after 1 month of anti-PD-1 therapy is associated with clinical response and overall survival

  pbmcs sorted expanded cancer multiparameter receptor targeted

• Putting proteins in one place.

  PMID 12790144 · PMC1316915 · Environmental health perspectives · 2003 · 8 claims · 7 setups

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  Rapamycin inhibits TOR, causing the silencing protein Sir3 to detach from chromatin at stress-response genes, triggering a coordinated multigene stress response that halts cancer cell proliferation

  saccharomyces yeast vascular skin chemical chromatin microarray

• Common genomic features of Campylobacter jejuni subsp. doylei strains distinguish them from C. jejuni subsp. jejuni.

  PMID 17535437 · PMC1892558 · BMC microbiology · 2007 · 8 claims · 6 setups

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  Cjd strains are phylogenetically distinct from Cjj strains based on MLST and CGI analysis

  geographically cjd novel jejuni multilocus comparative phenotypic

• The UCSC Genome Browser Database: update 2009.

  PMID 18996895 · PMC2686463 · Nucleic acids research · 2009 · 8 claims · 6 setups

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  The UCSC Genome Browser Database (GBD) is a publicly available, integrated collection of genome assembly sequences and annotations across many organisms, including extensive comparative-genomic resources.

  chimp vertebrate mrnas genome genome-wide multiz blat

• MBGD update 2010: toward a comprehensive resource for exploring microbial genome diversity.

  PMID 19906735 · PMC2808943 · Nucleic acids research · 2010 · 8 claims · 6 setups

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  MBGD allows users to create ortholog groups using a specified subgroup of organisms, distinguishing it from other comparative genomics resources

  complete user-submitted ortholog mbgd hierarchical automated phylogenetic

• QTLs for heat-induced stomatal anatomy underpin gas exchange variation in field-grown wheat.

  PMID 42231893 · PMC13223016 · Frontiers in plant science · 2026 · 8 claims · 6 setups

  Has reproduction · 100

  Heat stress via delayed sowing reduces stomatal conductance (gs) and gas exchange efficiency (gse) despite unchanged theoretical maximum anatomical conductance (gsmax), revealing a decoupling of structural potential and physiological performance under stress.

  field-grown microscope wheat field stomatal in-field deep

• Genomic insights into the diversity, virulence, and antimicrobial resistance of group B Streptococcus clinical isolates from Saudi Arabia.

  PMID 38711928 · PMC11070470 · Frontiers in cellular and infection microbiology · 2024 · 8 claims · 8 setups

  Has reproduction · 69

  Sequenced GBS isolates from Saudi Arabia show high genetic diversity, with 28 sequence types and nine distinct serotypes including uncommon serotypes VII and VIII

  gbs whole-genome multilocus capsular