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).

• Accelerated Evolution of Tissue-Specific Genes Mediates Divergence Amidst Gene Flow in European Green Lizards.

  PMID 33988711 · PMC8382678 · Genome biology and evolution · 2021 · 8 claims · 8 setups

  Has reproduction · 23

  The Adriatic lineage is a sister taxon to L. bilineata based on mitogenome and autosomal phylogenies

  adriatic mitochondrial autosomal brain whole-genome phylogenetic d-statistics

• Pooled DNA genotyping on Affymetrix SNP genotyping arrays.

  PMID 16480507 · PMC1382214 · BMC genomics · 2006 · 7 claims · 4 setups

  Full-text index only

  Pooled genotyping on Affymetrix 10K arrays estimates allele frequency differences between pools with accuracy comparable to lower-throughput pooling platforms.

  pools individual same parental pooled individual test-retest

• Previously described sequence variant in CDK5RAP2 gene in a Pakistani family with autosomal recessive primary microcephaly.

  PMID 17764569 · PMC2072945 · BMC medical genetics · 2007 · 7 claims · 4 setups

  Full-text index only

  A nonsense mutation in CDK5RAP2 exon 4, correctly designated 246T>A (Y82X), was identified in all four affected individuals of a Pakistani family linked to MCPH3

  pakistani affected unrelated one microsatellite sanger mutation

• VarDetect: a nucleotide sequence variation exploratory tool.

  PMID 19091032 · PMC2638149 · BMC bioinformatics · 2008 · 8 claims · 2 setups

  Full-text index only

  VarDetect is a stand-alone software tool that automatically detects nucleotide variation (SNPs) from fluorescence-based chromatogram traces using pre-calculated peak content ratios and artifact-handling rules.

  genomic vardetect automatic software

• Detecting tipping points of complex diseases by network information entropy.

  PMID 38960408 · PMC11221888 · Briefings in bioinformatics · 2024 · 8 claims · 4 setups

  Has reproduction · 78

  NIEE can detect critical states or tipping points in diverse data types, including bulk and single-sample expression data

  real stringdb individual genes network background sample-specific

• Gene Set Enrichment Analysis Reveals Individual Variability in Host Responses in Tuberculosis Patients.

  PMID 34421903 · PMC8375662 · Frontiers in immunology · 2021 · 8 claims · 8 setups

  Has reproduction · 71

  TB patients show substantial individual variability in the intensity of hallmark IFN responses, as well as in complement system, metabolic, and other pathway responses.

  blood cynomolgus external gene differential principal

• A procedure for the detection of linkage with high density SNP arrays in a large pedigree with colorectal cancer.

  PMID 17222328 · PMC1784097 · BMC cancer · 2007 · 7 claims · 8 setups

  Full-text index only

  A workflow combining Alohomora, Mega2, MENDEL, SNPLINK and SimWalk2 enables linkage analysis with high-density SNP arrays in large pedigrees (>35-40 bits) that exceed the capacity of single existing programs

  peripheral pedigree nuclear family snp two-point multipoint

• Exhaustive prediction of disease susceptibility to coding base changes in the human genome.

  PMID 18793467 · PMC2537574 · BMC bioinformatics · 2008 · 8 claims · 7 setups

  Full-text index only

  Inter-species conservation is the strongest single predictor of disease-associated coding mutations among the factors tested.

  hgmd refseq aligned svm svm reciprocal inter-species

• TPRpred: a tool for prediction of TPR-, PPR- and SEL1-like repeats from protein sequences.

  PMID 17199898 · PMC1774580 · BMC bioinformatics · 2007 · 7 claims · 8 setups

  Full-text index only

  TPRpred detects divergent/remote-homolog TPR repeat units that existing resources (Pfam, SMART, REP) fail to detect

  scop-derived malt nr-70 scop profile-based dali remote

• Mutation survey of known LCA genes and loci in the Saudi Arabian population.

  PMID 18936139 · PMC2695987 · Investigative ophthalmology & visual science · 2009 · 7 claims · 4 setups

  Full-text index only

  Mutations in the 13 known LCA genes were identified in only 24% (9/37) of Saudi Arabian LCA families, far lower than the ~65% mutation detection rate reported in European populations

  leukocyte affected kkesh-060 direct str homozygosity

• SNiPer: improved SNP genotype calling for Affymetrix 10K GeneChip microarray data.

  PMID 16262895 · PMC1280925 · BMC genomics · 2005 · 8 claims · 5 setups

  Full-text index only

  Poorly performing SNPs (NoCall rate ≥25%) fail primarily due to inadequate training/localization of the MPAM statistical model call zone, not detection filter failure

  genomic genotype genotyped chromosomal snp clustering mendelian

• A genome-wide association study of social and non-social autistic-like traits in the general population using pooled DNA, 500 K SNP microarrays and both community and diagnosed autism replication samples.

  PMID 20012890 · PMC2797846 · Behavior genetics · 2010 · 6 claims · 4 setups

  Full-text index only

  SNP Microarrays and Pooling (SNP-MaP) is a valid economical method for genome-wide screening of quantitative trait extremes using pooled DNA on microarrays

  teds diagnosed ceph snp individual transmission

• Intratumoral heterogeneity in microsatellite instability status at single-cell resolution.

  PMID 41767255 · PMC12936829 · iScience · 2026 · 8 claims · 7 setups

  Has reproduction · 100

  A novel computational (Snakemake) pipeline quantifies intratumoral heterogeneity in MSI status at single-cell resolution

  colorectal cancer aggregated msisensor-rna single-cell cnv-based

• siRNA screen of the human signaling proteome identifies the PtdIns(3,4,5)P3-mTOR signaling pathway as a primary regulator of transferrin uptake.

  PMID 17640392 · PMC2323231 · Genome biology · 2007 · 8 claims · 8 setups

  Full-text index only

  The PtdIns(3,4,5)P3-mTOR signaling pathway is a primary positive regulator of transferrin uptake.

  hela sirna secondary synthetic

• Enhanced Generalizability of RNA Secondary Structure Prediction via Convolutional Block Attention Network and Ensemble Learning.

  PMID 40871599 · PMC12388828 · Molecules (Basel, Switzerland) · 2025 · 8 claims · 8 setups

  Has reproduction · 87

  TrioFold integrates base-pairing clues from thermodynamic- and DL-based methods via ensemble learning and a convolutional block attention mechanism to enhance RSS prediction generalizability.

  testseta bprna-new ts-inter individual jaccard pca ensemble

• SNPAnalyzer: a web-based integrated workbench for single-nucleotide polymorphism analysis.

  PMID 15980517 · PMC1160189 · Nucleic acids research · 2005 · 8 claims · 4 setups

  Full-text index only

  SNPAnalyzer is an integrated web-based workbench that performs four statistical SNP analyses (Hardy-Weinberg equilibrium, haplotype estimation, linkage disequilibrium, and QTL analysis) in one common computational environment.

  african simulated hardy-weinberg haplotype linkage

• Proteomic identification of nitrated brain proteins in amnestic mild cognitive impairment: a regional study.

  PMID 17760844 · PMC3823261 · Journal of cellular and molecular medicine · 2007 · 8 claims · 5 setups

  Full-text index only

  Total protein nitration (3-NT immunoreactivity) is significantly increased in MCI hippocampus and IPL compared to age-matched control brain

  postmortem excised mci 2d-page sypro in-gel

• Rapid detection of SMARCB1 sequence variation using high resolution melting.

  PMID 20003390 · PMC2801682 · BMC cancer · 2009 · 8 claims · 6 setups

  Full-text index only

  HRM screening of SMARCB1 amplicons has a zero false negative rate compared to direct sequencing

  genomic same tumor rhabdoid high direct hrm

• Proteomic analysis of Alzheimer's disease cerebrospinal fluid from neuropathologically diagnosed subjects.

  PMID 19689240 · PMC2832860 · Current Alzheimer research · 2009 · 8 claims · 6 setups

  Full-text index only

  2D DIGE analysis of postmortem V-CSF pools identified 21-22 protein spots that significantly differ among neuropathologically-diagnosed AD, non-demented controls (NDC), and non-AD dementia (non-ADD) groups

  postmortem trypsin-digested individual subjects difference mass micro

• Exploring Gene Expression Patterns in Alzheimer's Disease Using a Human Microarray Data Meta-Analysis.

  PMID 41744654 · PMC12938635 · Biology · 2026 · 7 claims · 7 setups

  Has reproduction · 100

  A meta-analysis of eight microarray studies (10 sub-studies) produced a combined list of 4218 statistically significant DEGs between AD and healthy brain at an adjP cut-off of 0.001

  post-mortem combined sub-studies down-regulated microarray differential statistical