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).

• Exploration of the omics evidence landscape: adding qualitative labels to predicted protein-protein interactions.

  PMID 17880677 · PMC2375035 · Genome biology · 2007 · 7 claims · 8 setups

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  Combining pairs of omics evidence types into two-dimensional 'evidence landscapes' allows regions to be identified that specifically and purely predict either physical or metabolic protein interactions

  saccharomyces correlated chip-chip gene

• More breast cancer genes?

  PMID 11305950 · PMC138680 · Breast cancer research : BCR · 2001 · 8 claims · 7 setups

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  A new high-risk breast cancer gene termed BRCAX may exist on chromosome 13q, identified via CGH and linkage analysis in Nordic families

  tumours five independent ataxia-telangiectasia comparative haplotype linkage

• A comparative study on recombination activity in cattle.

  PMID 41942849 · PMC13067647 · Genetics, selection, evolution : GSE · 2026 · 8 claims · 8 setups

  Has reproduction · 93

  Genotype data with high systematic missingness across breeds and arrays can be streamlined and analysed with three complementary recombination-estimation approaches (HMM-based LINKPHASE3, deterministic hsphase, likelihood-based hsrecombi)

  six paternal alphasimr-simulated brown snp recombination simulation

• Emerging genomic and proteomic evidence on relationships among the animal, plant and fungal kingdoms.

  PMID 15629046 · PMC5172449 · Genomics, proteomics & bioinformatics · 2004 · 8 claims · 7 setups

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  Sequence-based molecular phylogenies widely support a sister relationship between animals and fungi, grouped as the Opisthokonta

  nine animals completed fungal combined sequence biochemical

• Environmental Drivers of Genetic Divergence in Two Corals From the Florida Keys.

  PMID 40589611 · PMC12206660 · Evolutionary applications · 2025 · 8 claims · 8 setups

  Has reproduction · 64

  Temperature was not the most important driver of coral genetic divergence in the Florida Keys; depth and water chemistry were more important

  agaricia agaricites coral sites 2brad population hierarchical

• Phenotypic features and genetic characterization of male breast cancer families: identification of two recurrent BRCA2 mutations in north-east of Italy.

  PMID 16764716 · PMC1586026 · BMC cancer · 2006 · 8 claims · 6 setups

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  The 9106C>T (Q2960X) and IVS16-2A>G BRCA2 mutations are recurrent in MBC families from North-East Italy and may reflect a founder effect.

  blood germline tumor family mutation mlpa microsatellite

• The post-genomic era for a select few.

  PMID 14759254 · PMC395745 · Genome biology · 2004 · 8 claims · 8 setups

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  The Exofish comparative-genomics tool identifies protein-coding DNA segments by comparing two genome sequences and was used to compare pufferfish (Takifugu, Tetraodon) genomes with mammalian genomes, improving annotation of the human and mouse genomes.

  takifugu physcomitrella coli vibrio comparative genetic dna-microarray

• Comparative genome and phenotypic analysis of Clostridium difficile 027 strains provides insight into the evolution of a hypervirulent bacterium.

  PMID 19781061 · PMC2768977 · Genome biology · 2009 · 8 claims · 7 setups

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  The 027 genomes (CD196 and R20291) contain 234 additional genes compared to strain 630, spread across at least 50 regions of genetic difference, including a phage island, transposon genes, two-component response regulators, drug resistance genes and transporters

  difficile toxin whole-genome toxin paloc

• Population Genomic Analyses Suggest a Hybrid Origin, Cryptic Sexuality, and Decay of Genes Regulating Seed Development for the Putatively Strictly Asexual Kingdonia uniflora (Circaeasteraceae, Ranunculales).

  PMID 36674965 · PMC9866071 · International journal of molecular sciences · 2023 · 8 claims · 8 setups

  Has reproduction · 51

  K. uniflora shows high allelic heterozygosity (negative F_IS) consistent with theoretical expectations under asexual evolution

  uniflora whole-genome phylogenomic population

• Toxicogenomics research consortium sails into uncharted waters.

  PMID 12460811 · PMC1241122 · Environmental health perspectives · 2002 · 8 claims · 8 setups

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  The NIEHS-funded $37 million Toxicogenomics Research Consortium (TRC) combines the NIEHS Microarray Center with five academic institutions (UNC, Duke, Fred Hutchinson/UW, MIT, OHSU) to define genetic variability, set gene expression standards, and study environmental stress responses.

  strains nervous mice liver microarray gene toxicogenomic

• Identification of potential therapeutic targets for nonischemic cardiomyopathy in European ancestry: an integrated multiomics analysis.

  PMID 39267096 · PMC11396958 · Cardiovascular diabetology · 2024 · 8 claims · 7 setups

  Has reproduction · 89

  Two-sample MR analysis identified 255 circulating plasma proteins associated with NISCM

  european cis-pqtl myocardial geo mendelian bayesian differential

• Human disease classification in the postgenomic era: a complex systems approach to human pathobiology.

  PMID 17625512 · PMC1948102 · Molecular systems biology · 2007 · 8 claims · 5 setups

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  Current syndromic disease classification lacks specificity despite historically serving clinicians well

  prostate neurodegenerative experimental genetic reverse-engineered protein-protein gene

• GABRG1 and GABRA2 as independent predictors for alcoholism in two populations.

  PMID 18818659 · PMC2656604 · Neuropsychopharmacology : official publication of the American College of Neuropsychopharmacology · 2009 · 8 claims · 8 setups

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  GABRG1 SNPs and haplotypes are significantly associated with alcohol use disorder (AUD) in both Finnish Caucasians and Plains American Indians

  finnish plains population hapmap snp haplotype ancestry

• The estrogen hypothesis of schizophrenia implicates glucose metabolism: association study in three independent samples.

  PMID 18460190 · PMC2391158 · BMC medical genetics · 2008 · 8 claims · 4 setups

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  A novel candidate-gene selection strategy combining unbiased schizophrenia expression/linkage data with the estrogen hypothesis as a biological filter identifies glycolysis as a candidate pathway network for schizophrenia

  case-control same compilation snp haplotype pairwise

• Genomic insight into the influence of selection, crossbreeding, and geography on population structure in poultry.

  PMID 36670351 · PMC9854048 · Genetics, selection, evolution : GSE · 2023 · 6 claims · 8 setups

  Has reproduction · 100

  Dutch traditional chicken breeds display a complex, admixed, subdivided population structure that broadly matches historical management-based clustering (past-productive, ornamental, country fowl, Lakenvelder).

  individuals dutch phased drenthe whole-genome principal phylogenetic

• The integrated world of functional genomics.

  PMID 12537543 · PMC151279 · Genome biology · 2003 · 8 claims · 8 setups

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  Integrating chromatin immunoprecipitation (promoter-binding) data with expression data reveals the yeast cell-cycle transcriptional regulatory network, including network motifs such as autoregulation, multi-component loops, and feedforward loops.

  cerevisiae sequenced elegans drosophila chromatin integration comparative

• Insights into the differentiation and adaptation within Circaeasteraceae from Circaeaster agrestis genome sequencing and resequencing.

  PMID 36895650 · PMC9988679 · iScience · 2023 · 8 claims · 8 setups

  Has reproduction · 49

  C. agrestis and K. uniflora are sister species with contrasting reproductive modes, providing a natural system to test effects of sexual vs asexual reproduction on genome evolution

  circaeaster agrestis genome gene kmer-based