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).

• Coverage and characteristics of the Affymetrix GeneChip Human Mapping 100K SNP set.

  PMID 16680197 · PMC1456318 · PLoS genetics · 2006 · 7 claims · 7 setups

  Full-text index only

  SNPs in the Affymetrix 100K set are undersampled from coding regions (both synonymous and nonsynonymous) and oversampled from regions outside genes, relative to HapMap SNPs

  genome autosomal hapmap chromosome snp chromosomal minor

• Discovery-based science education: functional genomic dissection in Drosophila by undergraduate researchers.

  PMID 15719063 · PMC548953 · PLoS biology · 2005 · 8 claims · 3 setups

  Full-text index only

  Discovery-based genomics research can be integrated into an undergraduate curriculum, engaging large numbers of students in professional-quality research without compromising didactic training

  drosophila genomic flp p-element molecular

• Functional nsSNPs from carcinogenesis-related genes expressed in breast tissue: potential breast cancer risk alleles and their distribution across human populations.

  PMID 16595073 · PMC3500178 · Human genomics · 2006 · 7 claims · 5 setups

  Full-text index only

  A bioinformatics strategy cross-referencing carcinogenesis-related gene lists with breast-tissue expression data can identify candidate breast cancer risk nsSNPs.

  breast carcinogenesis-related nssnp-containing african gene snp functional

• The Vertebrate Genome Annotation (Vega) database.

  PMID 15608237 · PMC540089 · Nucleic acids research · 2005 · 8 claims · 8 setups

  Full-text index only

  Vega is a community database for browsing manual annotation of finished vertebrate genome sequences, based on an extended Ensembl-style schema.

  chromosomes genomic manual sequence initio

• A novel and dual digestive symbiosis scales up the nutrition and immune system of the holobiont Rimicaris exoculata.

  PMID 36333777 · PMC9636832 · Microbiome · 2022 · 7 claims · 6 setups

  Has reproduction · 64

  Genome-resolved metagenomics of separated foregut and midgut reconstructed 20 MAGs including novel lineages of Hepatoplasmataceae (foregut) and Deferribacteres (midgut).

  rimicaris foregut deferribacteres shotgun fluorescence yoyo-1

• A cell biological perspective on genome research.

  PMID 8522596 · PMC2120688 · The Journal of cell biology · 1995 · 7 claims · 7 setups

  Full-text index only

  Genome sequencing represents a sixth stage in the historical progression of structural biology (comparative anatomy through crystallography), and will be similarly valuable once related to function.

  saccharomyces caenorhabditis selected fruit genomic saturation physical

• Genome-wide identification of human functional DNA using a neutral indel model.

  PMID 16410828 · PMC1326222 · PLoS computational biology · 2006 · 8 claims · 8 setups

  Full-text index only

  A neutral indel model predicting a geometric distribution of intergap segment (IGS) lengths fits human-mouse ancestral repeat (AR) alignment data excellently

  chromosome human-mouse genome individual whole-genome probabilistic comparative

• The genome of the ant Tetramorium bicarinatum reveals a tandem organization of venom peptides genes allowing the prediction of their regulatory and evolutionary profiles.

  PMID 38245722 · PMC10800049 · BMC genomics · 2024 · 8 claims · 8 setups

  Has reproduction · 100

  44 venom peptide genes were identified, distributed across four of the eleven chromosomes and organized in tandem repeat clusters.

  tetramorium bicarinatum vpg venom whole-genome blast gene

• The complete genome sequence of Vibrio cholerae: a tale of two chromosomes and of two lifestyles.

  PMID 11178241 · PMC138858 · Genome biology · 2000 · 8 claims · 4 setups

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  The V. cholerae O1 (El Tor) genome consists of two chromosomes with asymmetrically distributed gene functions

  vibrio whole-genome microarray expression

• The vertebrate genome annotation (Vega) database.

  PMID 18003653 · PMC2238886 · Nucleic acids research · 2008 · 8 claims · 8 setups

  Full-text index only

  Vega is a database for viewing manual genome annotation of human, mouse and zebrafish genomic sequences produced at the Wellcome Trust Sanger Institute.

  genome zebrafish pig nod manual comparative transcript

• Analysis of recent segmental duplications in the bovine genome.

  PMID 19951423 · PMC2796684 · BMC genomics · 2009 · 8 claims · 6 setups

  Full-text index only

  Recently duplicated sequence (≥1 kb, ≥90% identity) comprises 3.11% (94.4 Mb) of the bovine genome assembly (Btau_4.0)

  bos bovine genes cattle genome fluorescent repeat

• Genome-wide detection of segmental duplications and potential assembly errors in the human genome sequence.

  PMID 12702206 · PMC154576 · Genome biology · 2003 · 8 claims · 6 setups

  Full-text index only

  Segmental duplications comprise 3.53% (107.4/3,043.1 Mb) of the June 2002 human genome assembly

  genome refseq-annotated chromosome chromosome-wide e-pcr ambsnp

• The Li2 mutation results in reduced subgenome expression bias in elongating fibers of allotetraploid cotton (Gossypium hirsutum L.).

  PMID 24598808 · PMC3944810 · PloS one · 2014 · 8 claims · 7 setups

  Has reproduction · 58

  The Li2 mutation significantly reduces subgenome (homeolog) expression bias in the elongating fiber transcriptome.

  developing rna-seq expressed subgenome-biased paired-end rna-seq rt-qpcr

• Molecular characterization of retinitis pigmentosa in Saudi Arabia.

  PMID 19956407 · PMC2786884 · Molecular vision · 2009 · 8 claims · 7 setups

  Full-text index only

  The causative mutation was identified in 51 of 52 (94%/98%) Saudi RP patients, including seven novel mutations.

  blood-derived families pcr-amplified ethnically genome-wide linkage bidirectional

• An OMICs-based meta-analysis to support infection state stratification.

  PMID 33560295 · PMC8388022 · Bioinformatics (Oxford, England) · 2021 · 7 claims · 6 setups

  Has reproduction · 44

  Multi-class machine learning models built from cross-platform microarray meta-analysis can distinguish bacterial, viral and no-infection states with high accuracy (best model: 93% bacterial, 89% viral correct).

  blood merged affymetrix-optimized gene feature out-of-sample

• Insights into the evolution of cotton diploids and polyploids from whole-genome re-sequencing.

  PMID 23979935 · PMC3789805 · G3 (Bethesda, Md.) · 2013 · 8 claims · 8 setups

  Has reproduction · 91

  An index of 23,859,893 (~24 million) homoeo-SNPs distinguishing A-genome from D-genome cotton was constructed at a density of one SNP per 32.3 bases of the D5 reference.

  gossypium longicalyx nine diploids whole-genome wgs read