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).

• EGASP: Introduction.

  PMID 16925831 · PMC1810546 · Genome biology · 2006 · 8 claims · 5 setups

  Full-text index only

  Computational gene finding methods, when compared to the GENCODE golden standard annotation, show that the human genome annotation is nearly complete in terms of novel protein-coding loci.

  genome computational manual rt-pcr

• GenomeTrafac: a whole genome resource for the detection of transcription factor binding site clusters associated with conventional and microRNA encoding genes conserved between mouse and human gene orthologs.

  PMID 17178752 · PMC1781107 · Nucleic acids research · 2007 · 8 claims · 5 setups

  Full-text index only

  GenomeTrafac is a web-accessible database enabling genome-wide detection of conserved cis-element clusters in human-mouse gene orthologs, covering both conventional and microRNA genes

  human-mouse genome blastz-aligned itgb1bp2 comparative transcription sequence

• Smart spatial omics (S2-omics) optimizes region of interest selection to capture molecular heterogeneity in diverse tissues.

  PMID 41298871 · PMC12662399 · Nature cell biology · 2025 · 7 claims · 6 setups

  Has reproduction · 100

  S2-omics is an end-to-end workflow that automatically selects ROIs from H&E histology images to maximize molecular information content for spatial omics profiling.

  gastric colorectal additional breast xenium visium histology

• Mutations in the UBIAD1 gene, encoding a potential prenyltransferase, are causal for Schnyder crystalline corneal dystrophy.

  PMID 17668063 · PMC1925147 · PloS one · 2007 · 8 claims · 7 setups

  Full-text index only

  Mutations in UBIAD1 are causal for Schnyder crystalline corneal dystrophy

  pedigrees pedigree genomic ubiad1 microsatellite fine direct

• Identification of STRA6 and SKI sequence variants in patients with anophthalmia/microphthalmia.

  PMID 19112531 · PMC2610290 · Molecular vision · 2008 · 8 claims · 4 setups

  Full-text index only

  A novel STRA6 missense variant (p.G217E, exon 8) and a novel STRA6 nonsense variant (p.Q592X, exon 18) were identified in one A/M subject and absent from 89 controls, implicating STRA6 in this subject's A/M phenotype.

  genomic stra6 direct variant

• Exome sequencing in 38 patients with intracranial aneurysms and subarachnoid hemorrhage.

  PMID 32367296 · PMC7419486 · Journal of neurology · 2020 · 8 claims · 6 setups

  Has reproduction · 78

  Sequence variants in PCNT, RNF213 and THSD1 support a role as susceptibility factors for cerebrovascular disease (UIA/aSAH)

  unrelated affected additional 75-patient exome sanger gene

• High-throughput discovery of rare human nucleotide polymorphisms by Ecotilling.

  PMID 16893952 · PMC1540726 · Nucleic acids research · 2006 · 7 claims · 6 setups

  Full-text index only

  Ecotilling can be adapted to accurately discover and genotype human SNPs, with error rates low relative to resequencing

  genomic ecotilling non-synonymous ecotilling sanger universal-primer

• A novel de novo PAX6 mutation in an Ashkenazi-Jewish family with aniridia.

  PMID 18334930 · PMC2255027 · Molecular vision · 2008 · 7 claims · 5 setups

  Full-text index only

  A novel heterozygous de novo PAX6 frameshift mutation (c.577_578insG, insG@Gly72) in exon 6 causes autosomal dominant aniridia with congenital cataract, nystagmus, and glaucoma in this family.

  genomic pax6 direct microsatellite blast

• A non-parametric meta-analysis approach for combining independent microarray datasets: application using two microarray datasets pertaining to chronic allograft nephropathy.

  PMID 18302764 · PMC2276496 · BMC genomics · 2008 · 8 claims · 6 setups

  Full-text index only

  A novel non-parametric meta-analysis approach for combining independent microarray datasets is presented, requiring no distributional assumptions and being logically intuitive.

  kidney same identified additional microarray significance fisher's

• A2TEA: Identifying trait-specific evolutionary adaptations.

  PMID 37224329 · PMC10186066 · F1000Research · 2022 · 8 claims · 7 setups

  Has reproduction · 90

  A2TEA integrates gene family expansion analysis with differential expression data across species to identify genes that were targets of evolutionary adaptation to a given stress/treatment

  user-provided multi-species genes sequences rna-seq orthologous phylogenetic

• Improved precision of epigenetic clock estimates across tissues and its implication for biological ageing.

  PMID 31443728 · PMC6708158 · Genome medicine · 2019 · 8 claims · 6 setups

  Has reproduction · 68

  The proportion of variance in chronological age explained by all DNA methylation probes is close to 1, so a near-perfect age predictor is in principle achievable with sufficient training data.

  blood unrelated training lbc1921 methylation reml age

• Medical sequencing of candidate genes for nonsyndromic cleft lip and palate.

  PMID 16327884 · PMC1298935 · PLoS genetics · 2005 · 8 claims · 8 setups

  Full-text index only

  Point mutations in FOXE1, GLI2, JAG2, LHX8, MSX1, MSX2, SATB2, SKI, SPRY2, and TBX10 may be rare causes of isolated CL/P

  family additional unrelated mutant direct linkage targeted

• DG-CST (Disease Gene Conserved Sequence Tags), a database of human-mouse conserved elements associated to disease genes.

  PMID 15608249 · PMC539965 · Nucleic acids research · 2005 · 5 claims · 8 setups

  Full-text index only

  Comparative human-mouse genome analysis identifies conserved sequence tags (CSTs, >=70% identity over >=100bp) that frequently correspond to non-coding elements with putative regulatory or structural roles

  identified cst csts comparative coding exon

• ATM variants and cancer risk in breast cancer patients from Southern Finland.

  PMID 16914028 · PMC1592307 · BMC cancer · 2006 · 8 claims · 6 setups

  Full-text index only

  Neither 5557G>A nor ivs38-8T>C, nor any haplotype containing them, was significantly associated with breast cancer risk in any patient group

  familial brca1 same genotype genotyping denaturing direct

• Backseat drivers take the wheel.

  PMID 18068625 · PMC2705833 · Cancer cell · 2007 · 8 claims · 8 setups

  Full-text index only

  Systematic resequencing combined with functional validation can distinguish rare driver FLT3 mutations from passenger mutations in AML patients negative for known activating mutations

  pretreatment baf3 additional normal targeted baf3 immunoprecipitation

• An integrated genomic analysis of human glioblastoma multiforme.

  PMID 18772396 · PMC2820389 · Science (New York, N.Y.) · 2008 · 8 claims · 7 setups

  Full-text index only

  IDH1 is recurrently mutated at its active site (R132) in 12% of GBM patients, a previously unrecognized alteration in GBM.

  gbm additional missense exome targeted snp

• Comparative analysis reveals signatures of differentiation amid genomic polymorphism in Lake Malawi cichlids.

  PMID 18616806 · PMC2530870 · Genome biology · 2008 · 8 claims · 8 setups

  Full-text index only

  Lake Malawi cichlids are phenotypically and behaviorally diverse but appear genetically like a single subdivided population rather than distinct species

  five cichlid pairwise lake low-coverage blastx multi-species

• Exome sequencing identifies the cause of a mendelian disorder.

  PMID 19915526 · PMC2847889 · Nature genetics · 2010 · 8 claims · 7 setups

  Full-text index only

  Exome sequencing of a small number of unrelated affected individuals, combined with filtering against public SNP databases and HapMap exomes, is sufficient to identify the causal gene for a monogenic disorder of unknown etiology.

  patients chromosomes dhodh utero exome directed sanger

• Inventory and analysis of the protein subunits of the ribonucleases P and MRP provides further evidence of homology between the yeast and human enzymes.

  PMID 16998185 · PMC1636426 · Nucleic acids research · 2006 · 8 claims · 6 setups

  Full-text index only

  Fungal Pop8 is evolutionarily related to the Rpp14/Pop5 protein family, suggesting Pop8 is the fungal orthologue of Rpp14

  sequences sequence eukaryotic mrp psi-blast phylogenetic hmm

• Pairagon+N-SCAN_EST: a model-based gene annotation pipeline.

  PMID 16925839 · PMC1810554 · Genome biology · 2006 · 7 claims · 5 setups

  Full-text index only

  Pairagon+N-SCAN_EST, using only native alignments, was as accurate as ENSEMBL and ExoGean in the EGASP mRNA/EST evidence assessment

  encode genome cdna-to-genome novo comparative