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).

• 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

• Genome-wide scans for loci under selection in humans.

  PMID 16004726 · PMC3525256 · Human genomics · 2005 · 8 claims · 4 setups

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  Natural selection and population demographic history both distort patterns of genetic variation relative to the standard neutral model, so single-locus tests cannot unambiguously distinguish selection from demography.

  african-american european-american populations simulated tajima's fst coalescent

• Introduction: the challenge of incidental findings.

  PMID 18547190 · PMC2587006 · The Journal of law, medicine & ethics : a journal of the American Society of Law, Medicine & Ethics · 2008 · 8 claims · 5 setups

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  No consensus exists on how to handle incidental findings in human subjects research

  publicly healthy asymptomatic families empirical functional colonography

• A note on generalized Genome Scan Meta-Analysis statistics.

  PMID 15717930 · PMC551600 · BMC bioinformatics · 2005 · 7 claims · 3 setups

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  An Edgeworth series approximation to the null distribution of the weighted GSMA statistic provides a more accurate representation than the normal approximation, especially in the tails

  simulated schizophrenia monte genome numerical

• 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

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  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

• Population history and natural selection shape patterns of genetic variation in 132 genes.

  PMID 15361935 · PMC515367 · PLoS biology · 2004 · 7 claims · 5 setups

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  Developed a rigorous computational approach that corrects for multiple hypothesis testing and models population demographic history to test for natural selection

  genomic empirical snps chromosome comprehensive coalescent fst

• PRESTO: rapid calculation of order statistic distributions and multiple-testing adjusted P-values via permutation for one and two-stage genetic association studies.

  PMID 18620604 · PMC2483288 · BMC bioinformatics · 2008 · 8 claims · 4 setups

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  PRESTO is an order of magnitude faster than other existing permutation testing software for genetic association studies.

  case-control same wtccc genome-wide benchmark stratified

• PDA: Pooled DNA analyzer.

  PMID 16643673 · PMC1539032 · BMC bioinformatics · 2006 · 8 claims · 4 setups

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  No software existed prior to PDA for complete pooled-DNA analysis including data standardization, allele frequency estimation, and single/multipoint association tests

  heterozygous pools ordered peak pooled single-point

• PedGenie: an analysis approach for genetic association testing in extended pedigrees and genealogies of arbitrary size.

  PMID 16620382 · PMC1459209 · BMC bioinformatics · 2006 · 7 claims · 3 setups

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  PedGenie is a valid, flexible statistical tool for genetic association analysis in pedigrees of arbitrary size and structure using Monte Carlo significance testing

  simulated gaw12 breast monte pedigree-based genetic

• Size matters: just how big is BIG?: Quantifying realistic sample size requirements for human genome epidemiology.

  PMID 18676414 · PMC2639365 · International journal of epidemiology · 2009 · 7 claims · 2 setups

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  Conventional power calculations for case-control studies disregard analytic complexity (e.g. clinical assessment errors, unmeasured aetiological determinants) and can seriously underestimate true sample size requirements

  simulated simulation-based simulated

• The biological function of some human transcription factor binding motifs varies with position relative to the transcription start site.

  PMID 18367472 · PMC2377430 · Nucleic acids research · 2008 · 8 claims · 5 setups

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  1226 eight-letter DNA words show statistically significant positional preferences relative to the TSS across 7914 human promoter regions

  putative nonredundant homo genes computational pssm semantic

• 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

• 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

• AuPairWise: A Method to Estimate RNA-Seq Replicability through Co-expression.

  PMID 27082953 · PMC4833304 · PLoS computational biology · 2016 · 7 claims · 6 setups

  Has reproduction · 88

  Sample-sample correlation of transcript abundances is a misleading measure of replicability for assessing differential expression, because it is dominated by gene-specific dynamic ranges rather than condition-dependent variation.

  liver encode publicly co-expressed rna-seq meta-analysis computational

• Colorectal Cancer Prediction Based on Weighted Gene Co-Expression Network Analysis and Variational Auto-Encoder.

  PMID 32825264 · PMC7563725 · Biomolecules · 2020 · 6 claims · 7 setups

  Has reproduction · 80

  Combining WGCNA-derived hub genes with a VAE-derived 10-dimensional representation as features for an SVM classifier achieves high accuracy (0.9692) and AUC (0.9981) for colorectal cancer prediction.

  colorectal combined differentially crc microarray differential weighted

• SNP@Evolution: a hierarchical database of positive selection on the human genome.

  PMID 19732458 · PMC2755008 · BMC evolutionary biology · 2009 · 7 claims · 6 setups

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  SNP@Evolution is a hierarchical database integrating HET, FST, and iHS from HapMap Phase II and III to identify genome-wide positive selection signals

  hapmap autosomes simulated sliding snp sliding haplotype-based

• Genetical genomic determinants of alcohol consumption in rats and humans.

  PMID 19874574 · PMC2777866 · BMC biology · 2009 · 8 claims · 6 setups

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  A genetical genomics approach combining brain gene expression, bQTL, and eQTL analysis in HXB/BXH RI rats identifies candidate genes for alcohol consumption

  hxb naive caucasian two-bottle behavioral brain

• The origins of lactase persistence in Europe.

  PMID 19714206 · PMC2722739 · PLoS computational biology · 2009 · 8 claims · 5 setups

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  The −13,910*T allele first underwent selection among dairying farmers around 7,500 years ago in a region between the central Balkans and central Europe, possibly linked to the Linearbandkeramik culture.

  simulated simulation 910*t farming demic approximate comparison

• Using random walks to identify cancer-associated modules in expression data.

  PMID 24128261 · PMC4015830 · BioData mining · 2013 · 8 claims · 8 setups

  Has reproduction

  Walktrap-GM, a random-walk community detection algorithm adapted with stopping criteria (maximum modularity, maximum size, maximum module score), identifies modules significantly enriched with cancer genes in expression-weighted interaction networks.

  hepatocellular breast sporadic geo gene differential interaction

• Transcriptome analysis reveals differential splicing events in IPF lung tissue.

  PMID 24647608 · PMC3960165 · PloS one · 2014 · 8 claims · 6 setups

  Has reproduction · 81

  873 genes are differentially expressed in IPF lung tissue versus healthy controls at FDR<5%, with more up-regulated than down-regulated genes.

  lung discovery gene gse24206 sequencing rna-seq real-time