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).

• Continued colonization of the human genome by mitochondrial DNA.

  PMID 15361937 · PMC515365 · PLoS biology · 2004 · 7 claims · 6 setups

  Full-text index only

  NUMT insertion into nuclear chromosomes is an ongoing process shaped by double-strand-break repair (as shown in yeast) and continuing in humans.

  homo genomic chimpanzee genome genome-wide pcr sanger

• Satellog: a database for the identification and prioritization of satellite repeats in disease association studies.

  PMID 15949044 · PMC1181805 · BMC bioinformatics · 2005 · 7 claims · 6 setups

  Full-text index only

  Satellog is a database cataloging all pure 1-16 unit satellite repeats in the human genome with supplementary polymorphism, gene-location, and expression data for prioritizing repeats in disease-association studies.

  reference unigene ensembl normal tandem polymorphism gene

• In silico meets in vivo.

  PMID 18304380 · PMC2374716 · Genome biology · 2008 · 8 claims · 8 setups

  Full-text index only

  About 10% of positions in multiple sequence alignments of the human genome with other vertebrate genomes are likely incorrect.

  genome lines prokaryotic genomes genome genome-wide gene

• miRGator: an integrated system for functional annotation of microRNAs.

  PMID 17942429 · PMC2238850 · Nucleic acids research · 2008 · 8 claims · 8 setups

  Full-text index only

  miRGator integrates target prediction, functional enrichment analysis (GO/pathway/disease), and expression data (miRNA/mRNA/protein) into one system for functional annotation of miRNAs

  genome predicted tissues organs computational functional mirna

• The many uses of a genome sequence.

  PMID 11423005 · PMC138940 · Genome biology · 2001 · 8 claims · 8 setups

  Full-text index only

  Solved protein structures from structural genomics efforts can be used to model many other proteins by homology, aiding function prediction

  recombinant mammalian chromosome chimpanzee x-ray quantitative tiling

• The 21st century hepatologist and a systems biology based approach to liver diseases.

  PMID 19026013 · PMC2712824 · Hepatology (Baltimore, Md.) · 2008 · 7 claims · 3 setups

  Full-text index only

  Network models covering the majority of an organism's genes can accurately predict phenotypic effects of gene perturbations in multicellular organisms

  caenorhabditis cohorts computational genome-wide whole-genome

• Proceedings of the First International Conference on Phylogenomics. March 15-19, 2006. Quebec, Canada.

  PMID 17288567 · PMC1796603 · BMC evolutionary biology · 2007 · 8 claims · 8 setups

  Full-text index only

  Gene tree parsimony applied to EST data with widespread gene duplication can infer an organismal phylogeny in excellent agreement with the expected angiosperm phylogeny.

  angiosperms animal oryza proteobacteria gene site-heterogeneous codon

• A genome-wide association analysis identifies 16 novel susceptibility loci for carpal tunnel syndrome.

  PMID 30833571 · PMC6399342 · Nature communications · 2019 · 6 claims · 8 setups

  Has reproduction · 90

  A GWAS of 12,312 CTS cases and 389,344 controls in UK Biobank identifies 16 novel genome-wide significant susceptibility loci for CTS

  biobank surgically gwas transformed genome-wide sequencing gene-based

• Identification of new ETV6 modulators through a high-throughput functional screening.

  PMID 35198911 · PMC8851229 · iScience · 2022 · 7 claims · 8 setups

  Has reproduction · 68

  A genome-wide shRNA screen in an engineered ETV6-dependent Blasticidin-sensitive pre-B ALL cell line can identify modulators of ETV6 repressive transcriptional activity

  reh genome-wide qrt-pcr chip-seq

• A genome-wide survey of segmental duplications that mediate common human genetic variation of chromosomal architecture.

  PMID 15588494 · PMC3525102 · Human genomics · 2004 · 8 claims · 5 setups

  Full-text index only

  PSD-mediated genomic architecture analogous to the 8p23/4p16 inversion regions is not unique to those loci but recurs genome-wide.

  genomic genome extracted pairwise online genome-wide

• A genome-wide approach to identify genetic loci with a signature of natural selection in the Irish population.

  PMID 16904005 · PMC1779589 · Genome biology · 2006 · 8 claims · 7 setups

  Full-text index only

  Eight SNPs with extreme European-branch locus-specific branch length (LSBL) were selected from a genome-wide FST dataset as candidates for selection in Europe.

  snp irish french fst-based microsatellite genome-wide

• Copy number variants and common disorders: filling the gaps and exploring complexity in genome-wide association studies.

  PMID 17953491 · PMC2039766 · PLoS genetics · 2007 · 8 claims · 5 setups

  Full-text index only

  CNVs are not easily tagged by SNPs and often fall in genomic regions poorly covered by whole-genome SNP arrays or not genotyped by HapMap, so current GWASs have largely missed their contribution to complex disorders.

  genome-wide genome cohorts array-based snp bac

• Genome-wide siRNA-based functional genomics of pigmentation identifies novel genes and pathways that impact melanogenesis in human cells.

  PMID 19057677 · PMC2585813 · PLoS genetics · 2008 · 7 claims · 8 setups

  Full-text index only

  Genome-wide siRNA screening identified 92 novel genes that support melanin production in human melanocytes with a low false discovery rate.

  mnt-1 melanocyte melanocytes genome-wide secondary quantitative

• Proteomic view of mitochondrial function.

  PMID 18331620 · PMC2374722 · Genome biology · 2008 · 8 claims · 8 setups

  Full-text index only

  Most modulators of basal mitochondrial function identified in the Drosophila RNAi screen are located outside the mitochondrion, since only 17 of 152 hits had a clear mitochondrial function.

  drosophila saccharomyces caenorhabditis yeast genome-wide phenotypic morphology

• A genome-wide deletion mutant screen identifies pathways affected by nickel sulfate in Saccharomyces cerevisiae.

  PMID 19917080 · PMC2784802 · BMC genomics · 2009 · 8 claims · 4 setups

  Full-text index only

  Genome-wide deletion screening identified 149 genes whose deletion causes NiSO4 sensitivity and 119 genes whose deletion confers NiSO4 resistance.

  cerevisiae lists yeast genome-wide functional protein-protein

• A simple and efficient algorithm for genome-wide homozygosity analysis in disease.

  PMID 19756043 · PMC2758715 · Molecular systems biology · 2009 · 8 claims · 4 setups

  Full-text index only

  A genome-wide AH analysis (GAHA) algorithm can identify disease-associated loci by comparing frequencies of homozygous segments between cases and controls using a z-statistic proportion test

  unrelated simulated selected genes genome-wide statistical logistic

• A genome-wide siRNA screen reveals diverse cellular processes and pathways that mediate genome stability.

  PMID 19647519 · PMC2772893 · Molecular cell · 2009 · 8 claims · 6 setups

  Full-text index only

  A genome-wide siRNA screen in HeLa cells using γH2AX as a readout identifies genes whose knockdown elevates DNA damage/genome instability

  hela candidate screen genome-wide propidium sirna

• QuadBase: genome-wide database of G4 DNA--occurrence and conservation in human, chimpanzee, mouse and rat promoters and 146 microbes.

  PMID 17962308 · PMC2238983 · Nucleic acids research · 2008 · 8 claims · 3 setups

  Full-text index only

  QuadBase is a compendium of G4 DNA (quadruplex) motifs focused on their occurrence and conservation in promoters, composed of EuQuad and ProQuad

  chimpanzee prokaryotic promoters genome-wide cross-species

• Phenotypic variation meets systems biology.

  PMID 19664197 · PMC2745761 · Genome biology · 2009 · 8 claims · 8 setups

  Full-text index only

  Cellular differentiation states are constrained by complex networks with substantial positive and negative regulation, challenging the concept of single 'master regulators'

  thp-1 arabidopsis unspecified mammalian deepcage protein-protein sequencing

• Data-driven projections of candidate enhancer-activating SNPs in immune regulation.

  PMID 40011812 · PMC11863423 · BMC genomics · 2025 · 7 claims · 7 setups

  Has reproduction · 57

  A data-driven computational protocol combining motif scanning, open-chromatin filtering, gene proximity, dbSNP validation, spacing, and cross-species conservation can prioritize SNPs likely to create functional GAS motifs.

  genome pbmc lung il4-stimulated motif chip-seq bulk