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).

• A macaque's-eye view of human insertions and deletions: differences in mechanisms.

  PMID 17941704 · PMC1976337 · PLoS computational biology · 2007 · 7 claims · 4 setups

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  Insertion and deletion rates are differentially associated with replication- versus recombination-related genomic features, indicating the two mutation types are driven in part by distinct mechanisms

  chimpanzee non-overlapping 1-mb 100-kb comparative regression kruskal-wallis

• Quadratic regression analysis for gene discovery and pattern recognition for non-cyclic short time-course microarray experiments.

  PMID 15850479 · PMC1127068 · BMC bioinformatics · 2005 · 8 claims · 8 setups

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  A step-down quadratic regression method (fitting quadratic, then linear, then null models per gene) identifies differentially expressed genes and classifies them into 9 temporal expression patterns using continuous time information.

  olfactory present same anova-significant microarray step-down peddada

• Long-term trends in evolution of indels in protein sequences.

  PMID 17298668 · PMC1805498 · BMC evolutionary biology · 2007 · 8 claims · 5 setups

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  More than one third of protein domains show a statistically significant tendency to increase or decrease in size over evolutionary distance.

  curated individual cdd linear pearson binomial

• Fractional ridge regression: a fast, interpretable reparameterization of ridge regression.

  PMID 33252656 · PMC7702219 · GigaScience · 2020 · 7 claims · 2 setups

  Has reproduction · 84

  Ridge regression can be reparameterized in terms of the fraction γ between the L2-norms of the regularized and unregularized coefficient solutions (fractional ridge regression, FRR).

  synthetic brain benchmarking general

• Projecting contact matrices in 177 geographical regions: An update and comparison with empirical data for the COVID-19 era.

  PMID 34310590 · PMC8354454 · PLoS computational biology · 2021 · 7 claims · 6 setups

  Has reproduction · 98

  Updated synthetic contact matrices were generated for 177 geographical locations covering 97.2% of the world's population (up from 152 locations/95.9% in 2017).

  polymod geographical dhs locations bayesian synthetic household

• Epistemic uncertainty challenges aging clock reliability in predicting rejuvenation effects.

  PMID 39072888 · PMC11561706 · Aging cell · 2024 · 8 claims · 8 setups

  Has reproduction · 93

  DNA methylation profiles observed across cellular reprogramming are poorly represented in the training data of existing aging clocks, introducing high out-of-distribution/epistemic uncertainty in their age estimates

  males skin liver linear dnam epigenetic

• Integrated drug resistance and leukemic stemness gene-expression scores predict outcomes in large cohort of over 3500 AML patients from 10 trials.

  PMID 39090192 · PMC11294346 · NPJ precision oncology · 2024 · 7 claims · 6 setups

  Has reproduction · 50

  A 5-gene ADE-Resistance Score (ADE-RS5), derived via LASSO regression from 67 pharmacologically relevant genes, predicts MRD positivity, EFS and OS in pediatric AML.

  pediatric combined lasso gene-expression-based integrated

• Computationally scalable regression modeling for ultrahigh-dimensional omics data with ParProx.

  PMID 34254998 · PMC8575036 · Briefings in bioinformatics · 2021 · 6 claims · 4 setups

  Has reproduction · 79

  ParProx implements overlapping and non-overlapping (latent) group lasso regression for time-to-event (Cox) and classification (logistic) analysis with variables grouped by biological priors.

  tcga breast liver synthetic somatic gene methylation-based

• Elucidating the Prognostic and Therapeutic Implications of Insulin Resistance Genes in Breast Cancer: A Machine Learning-Powered Analysis.

  PMID 40427728 · PMC12109394 · Biology · 2025 · 8 claims · 8 setups

  Has reproduction · 84

  A seven-gene IRG prognostic signature (LIFR, EZR, TBC1D4, NSF, RPL5, SAA1, PGK1) predicts overall survival in breast cancer across training and four validation cohorts

  tcga-brca triple-negative ffpe bulk univariate kaplan-meier

• A pharmacogene database enhanced by the 1000 Genomes Project.

  PMID 19745786 · PMC2935084 · Pharmacogenetics and genomics · 2009 · 7 claims · 4 setups

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  The database provides a convenient portal for immediate utilization of newly released 1000 Genomes Project (KGP) data in pharmacogenetic studies

  ceu hapmap lymphoblastoid genotype-phenotype whole-genome low-coverage

• Statistical analysis of real-time PCR data.

  PMID 16504059 · PMC1395339 · BMC bioinformatics · 2006 · 8 claims · 2 setups

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  Four statistical models (multiple regression, ANCOVA, t-test, Wilcoxon test) were developed to estimate ΔΔCt with associated significance/confidence intervals

  real-time linear

• Imputation-based analysis of association studies: candidate regions and quantitative traits.

  PMID 17676998 · PMC1934390 · PLoS genetics · 2007 · 8 claims · 2 setups

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  Imputation-based Bayesian regression increases power to detect association compared with standard single-SNP tests, even when the causal variant is directly typed

  study phenotyped genotype bayesian

• Asterias: integrated analysis of expression and aCGH data using an open-source, web-based, parallelized software suite.

  PMID 17488846 · PMC1933128 · Nucleic acids research · 2007 · 8 claims · 2 setups

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  Asterias is an integrated, open-source, web-based software suite for analysis of gene expression and aCGH data

  asterias pomelo functional cross-browser

• The indirect effect of mRNA-based COVID-19 vaccination on healthcare workers' unvaccinated household members.

  PMID 35246536 · PMC8897446 · Nature communications · 2022 · 5 claims · 4 setups

  Has reproduction

  mRNA-based COVID-19 vaccination of healthcare workers is associated with reduced SARS-CoV-2 infections among their unvaccinated adult household members (indirect effectiveness).

  vaccinated unvaccinated double observational

• Positive Relationships between Intraocular Pressure and Thyroid Function in Graves' Ophthalmopathy: A Three-Aspect Evidence Analysis.

  PMID 40992768 · PMC12479196 · Yonsei medical journal · 2025 · 6 claims · 4 setups

  Has reproduction · 68

  Increased thyroid function is a risk factor for elevated IOP in patients with Graves' ophthalmopathy.

  patients nhanes gtex geo retrospective cross-sectional summary-data-based

• Detecting imbalanced expression of SNP alleles by minisequencing on microarrays.

  PMID 15500681 · PMC529269 · BMC biotechnology · 2004 · 8 claims · 7 setups

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  Both microarray minisequencing formats accurately quantify SNP allele ratios, with R2 > 0.95 for the majority of regression lines

  genomic huvec microarray solid-phase real-time

• Promoting human promoters.

  PMID 16760901 · PMC1681504 · Molecular systems biology · 2006 · 8 claims · 5 setups

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  A computational protocol using MARS on known sequence motifs can quantify transcription factor effects on human gene expression despite noise and data size challenges

  gene liver cycle genes computational expression time-course

• A genomic pathway approach to a complex disease: axon guidance and Parkinson disease.

  PMID 17571925 · PMC1904362 · PLoS genetics · 2007 · 8 claims · 5 setups

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  A genomic pathway approach using axon-guidance pathway SNPs strongly predicts PD susceptibility, survival free of PD, and age at onset of PD

  cases patients postmortem whole-genome cox linear

• Merger of ayurveda and tissue culture-based functional genomics: inspirations from systems biology.

  PMID 18348714 · PMC2311278 · Journal of translational medicine · 2008 · 8 claims · 8 setups

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  Crude LASH extract and its purified components (withanone, withaferin A) act through distinct but partially overlapping molecular gene-regulatory networks

  tumor-derived tumor lash gene cytotoxicity sirna ribozyme

• Clear detection of ADIPOQ locus as the major gene for plasma adiponectin: results of genome-wide association analyses including 4659 European individuals.

  PMID 20018283 · PMC2845297 · Atherosclerosis · 2010 · 8 claims · 7 setups

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  The ADIPOQ locus is the only major gene locus for plasma adiponectin, reaching genome-wide significance in combined and sex-stratified analyses

  population-based cohorts gwa plasma genome-wide replication candidate