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).

• Revealing an unexpectedly low electron injection threshold via reinforced shock acceleration.

  PMID 39805850 · PMC11730962 · Nature communications · 2025 · 8 claims · 4 setups

  Has reproduction · 68

  A reinforced shock acceleration model combining foreshock transients, wave-particle interactions, and variable stellar wind conditions operating across multiple scales enables electrons to consistently reach relativistic energies

  mms artemis foreshock six situ wave multi-event

• Direct observations of cross-scale wave-particle energy transfer in space plasmas.

  PMID 39919183 · PMC11804927 · Science advances · 2025 · 7 claims · 8 setups

  Has reproduction · 94

  Fluid-scale ULF waves resonate with reflected ions, modifying their velocity distributions and driving growth of ion-scale magnetosonic-whistler waves

  terrestrial mms observed simulated magnetic electric ion

• Parsimonious Gene Correlation Network Analysis (PGCNA): a tool to define modular gene co-expression for refined molecular stratification in cancer.

  PMID 30993001 · PMC6459838 · NPJ systems biology and applications · 2019 · 8 claims · 7 setups

  Has reproduction · 71

  Retaining only the top ~3 most correlated edges per gene (EPG3) combined with FastUnfold clustering (termed PGCNA) produces gene co-expression modules with significantly better separation and enrichment of known biology than using all edges or other clustering methods.

  breast colorectal brca representative gene comparative multi-omic

• Phenotypic characteristics of colo-rectal cancer in I1307K APC germline mutation carriers compared with sporadic cases.

  PMID 11720476 · PMC2375261 · British journal of cancer · 2001 · 8 claims · 5 setups

  Full-text index only

  I1307K APC germline mutation carriers were identified in 28 of 307 (9.1%) unselected Israeli CRC patients

  genomic pcr unselected i1307k mutation sequencing clinical

• The androgen receptor CAG repeat polymorphism and modification of breast cancer risk in BRCA1 and BRCA2 mutation carriers.

  PMID 15743497 · PMC1064126 · Breast cancer research : BCR · 2005 · 7 claims · 5 setups

  Full-text index only

  The AR CAG repeat polymorphism does not modify breast cancer risk in BRCA1 mutation carriers

  peripheral brca1 same simulated fluorescent cox weighted

• A homozygous R262Q mutation in the gonadotropin-releasing hormone receptor presenting as constitutional delay of growth and puberty with subsequent borderline oligospermia.

  PMID 16968799 · PMC1865483 · The Journal of clinical endocrinology and metabolism · 2006 · 7 claims · 8 setups

  Full-text index only

  A homozygous R262Q GNRHR mutation was identified in two brothers from an Asian Indian family, one of 11 families studied with delayed puberty or discordant IHH/delayed puberty siblings.

  blood serum younger brothers mutational hormone 24-hour

• Fast-evolving noncoding sequences in the human genome.

  PMID 17578567 · PMC2394770 · Genome biology · 2007 · 8 claims · 6 setups

  Full-text index only

  1,356 conserved noncoding sequences show human-specific accelerated substitution rates (ANC sequences) relative to chimpanzee

  chimpanzee genome hapmap comparative genomic segmental

• Identification of genomic regions contributing to etoposide-induced cytotoxicity.

  PMID 19089452 · PMC2714550 · Human genetics · 2009 · 7 claims · 6 setups

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  Etoposide-induced cytotoxicity in CEPH lymphoblastoid cell lines is heritable, with genetics explaining 17-25% of variation

  ceph subset hapmap simulated growth heritability non-parametric

• Association between the catechol-O-methyltransferase Val158Met polymorphism and cocaine dependence.

  PMID 18704099 · PMC2583214 · Neuropsychopharmacology : official publication of the American College of Neuropsychopharmacology · 2008 · 8 claims · 4 setups

  Full-text index only

  The COMT Val158Met polymorphism is significantly associated with cocaine dependence in individuals of African descent.

  cocaine-dependent duplicate genotype study snp genotype haplotype

• Bayesian survival analysis in genetic association studies.

  PMID 18617538 · PMC2530885 · Bioinformatics (Oxford, England) · 2008 · 7 claims · 5 setups

  Full-text index only

  A novel Bayesian method (BETA-Surv) extends prior case-control haplotype-clustering work to censored survival outcomes by clustering haplotypes via gene tree/perfect phylogeny topology and relative mutation age.

  simulated same sanad bayesian univariate partial

• Association testing of novel type 2 diabetes risk alleles in the JAZF1, CDC123/CAMK1D, TSPAN8, THADA, ADAMTS9, and NOTCH2 loci with insulin release, insulin sensitivity, and obesity in a population-based sample of 4,516 glucose-tolerant middle-aged Danes.

  PMID 18567820 · PMC2518507 · Diabetes · 2008 · 8 claims · 5 setups

  Full-text index only

  CDC123/CAMK1D rs12779790 risk allele (homozygous) is associated with decreased insulinogenic index, corrected insulin response (CIR), and AUC-insulin/AUC-glucose ratio, indicating impaired insulin release

  inter99 same taqman oral general

• Commonality of functional annotation: a method for prioritization of candidate genes from genome-wide linkage studies.

  PMID 18263617 · PMC2275105 · Nucleic acids research · 2008 · 8 claims · 7 setups

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  Genes correlated with a common complex trait are more likely to share GO functional annotations than genes not correlated with that trait

  genes candidate simulated alzheimer's genome-wide term null-hypothesis

• bakR: uncovering differential RNA synthesis and degradation kinetics transcriptome-wide with Bayesian hierarchical modeling.

  PMID 37028916 · PMC10275263 · RNA (New York, N.Y.) · 2023 · 8 claims · 4 setups

  Full-text index only

  bakR uses Bayesian hierarchical modeling to share information (specifically a replicate variability vs. read count trend) across transcripts, increasing statistical power for differential kinetic analysis

  simulated existing simulated nucleotide

• Warming Causes a Decline in Baltic Sea Coastal Sediment Microbial Abundance.

  PMID 41712959 · PMC12920023 · Environmental microbiology · 2026 · 6 claims · 5 setups

  Full-text index only

  Contrary to the expected increase in productivity, long-term warming decreased sediment microbial (bacterial and archaeal) cell abundance in the heated bay compared to the control bay

  baltic sediment 16s qpcr propidium 16s

• MIMIC: a flexible pipeline to register and summarize IMC-MSI experiments.

  PMID 41917425 · PMC13201759 · Communications biology · 2026 · 7 claims · 6 setups

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  MIMIC is a reproducible, semi-automated workflow that co-registers and jointly analyzes MALDI-MSI and IMC data using a chain of before/after microscopy images.

  liver regions artificial maldi-msi imaging multi-step

• Testing whether genetic variation explains correlation of quantitative measures of gene expression, and application to genetic network analysis.

  PMID 18444230 · PMC2729096 · Statistics in medicine · 2008 · 8 claims · 3 setups

  Full-text index only

  A statistical test (delta method and Steiger-Browne optimal linear composites) is developed to test equality of the marginal correlation and the partial correlation of two gene expression traits conditional on a set of covariates.

  simulated real analytical simulation application

• Gbdmr: identifying differentially methylated CpG regions in the human genome via generalized beta regressions.

  PMID 38443825 · PMC10916021 · BMC bioinformatics · 2024 · 8 claims · 4 setups

  Has reproduction · 62

  gbdmr models DNA methylation levels of CpG sites using a generalized beta distribution instead of assuming normality as in linear-regression-based methods

  simulated birth gene simulation methylation

• PHScaffolding: a hypergraph clustering and dual-weight integration strategy for scaffolding with Pore-C reads.

  PMID 41569288 · PMC12825295 · Briefings in bioinformatics · 2026 · 7 claims · 6 setups

  Full-text index only

  PHScaffolding builds a weighted hypergraph from Pore-C read-to-contig alignments, with hyperedges representing multi-way contig interactions and weighted by the geometric mean of per-contig alignment lengths

  hg002 gm12878 arabidopsis contig pore-c genome hypergraph

• Testing groups of genomic locations for enrichment in disease loci using linkage scan data: a method for hypothesis testing.

  PMID 16848972 · PMC3525155 · Human genomics · 2006 · 8 claims · 2 setups

  Full-text index only

  A method testing enrichment of a group of genomic locations for disease loci by comparing the average NPL score of the group to a null distribution from randomly drawn groups of equal size

  simulated pedigrees simulated real

• Integrated omics in Drosophila uncover a circadian kinome.

  PMID 32483184 · PMC7264355 · Nature communications · 2020 · 8 claims · 6 setups

  Has reproduction · 98

  iCMod, a computational pipeline integrating transcriptomic, proteomic, and phosphoproteomic circadian data, was developed to accurately identify normalized circadian p-sites (NCPs)

  drosophila analysis tmt-based sequencing western