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).

• Rats go genomic.

  PMID 16522223 · PMC1431730 · Genome biology · 2006 · 7 claims · 8 setups

  Full-text index only

  A systems biology approach combining genome-wide expression profiling with expression QTL (eQTL) mapping can identify candidate genes underlying complex-disease QTLs

  recombinant genes serotonin adenomatous genome-wide targeted knockout

• Population differentiation and epidemic tracking of Bursaphelenchus xylophilus in China based on chromosome-level assembly and whole-genome sequencing data.

  PMID 34839581 · PMC9300093 · Pest management science · 2022 · 6 claims · 8 setups

  Has reproduction · 44

  Generated the first chromosome-level genome assembly (AH1) of B. xylophilus using PacBio, Illumina, BioNano, and Hi-C data

  xylophilus snp smrt short-read bionano

• A golden age of brain exploration.

  PMID 15660159 · PMC544547 · PLoS biology · 2005 · 8 claims · 3 setups

  Full-text index only

  Over 99% of neuroscience literature focuses on only 1% of the ~15,000–16,000 genes expressed in the brain, leaving most brain-expressed genes uncharacterized.

  brain transgenic situ microarray bacterial

• Integrated genomic approaches implicate osteoglycin (Ogn) in the regulation of left ventricular mass.

  PMID 18443592 · PMC2742198 · Nature genetics · 2008 · 8 claims · 8 setups

  Full-text index only

  Osteoglycin (Ogn) is a major candidate regulator of rat LVM, with increased Ogn protein expression associated with elevated LVM

  heart ogn cos-1 neonatal eqtl quantitative genome-wide

• Animal models of gene-nutrient interactions.

  PMID 19037208 · PMC2703433 · Obesity (Silver Spring, Md.) · 2008 · 8 claims · 5 setups

  Full-text index only

  Mice and rats are well-suited models for human food selection because they share food preferences with humans and are supported by extensive genetic tools (sequenced genome, inbred strains, gene targeting, Cre-lox).

  interbred inbred pubmed genome qtl strain bibliometric

• Gene function in the mammalian genome, courtesy of the mouse.

  PMID 12537544 · PMC151280 · Genome biology · 2003 · 8 claims · 8 setups

  Full-text index only

  Mosaicism of Mus musculus domesticus and Mus musculus musculus haplotypes exists across the inbred laboratory mouse genome, and genome-wide haplotype mapping can enhance positional cloning

  inbred genome mice model genome-wide large-scale phenotypic

• Can we find the genes involved in complex traits?

  PMID 15461809 · PMC545590 · Genome biology · 2004 · 8 claims · 8 setups

  Full-text index only

  Large regions of the mouse genome exist in linkage disequilibrium (LD), including a 40 Mb region on the X chromosome, reflecting selection against recombination to preserve allelic combinations.

  inbred strains 000-strain recombinant snp expression eqtl

• 6th annual meeting of the Complex Trait Consortium.

  PMID 17906895 · PMC2042027 · Mammalian genome : official journal of the International Mammalian Genome Society · 2007 · 8 claims · 7 setups

  Full-text index only

  The NIEHS Perlegen/resequencing project has generated over 8.5 million SNPs from 15 inbred mouse strains but shows a high false-negative discovery rate, with an estimated 45 million SNPs actually present.

  inbred recombinant yeast gallstone genome affymetrix microarray

• Genetical genomics: spotlight on QTL hotspots.

  PMID 18949031 · PMC2563687 · PLoS genetics · 2008 · 8 claims · 4 setups

  Full-text index only

  Distant eQTL hotspots are rare and difficult to reliably verify across published genetical genomics studies

  adipose saccharomyces genome-wide permutation gene

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

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

  Full-text index only

  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

• Sequence polymorphisms cause many false cis eQTLs.

  PMID 17637838 · PMC1906859 · PloS one · 2007 · 8 claims · 7 setups

  Full-text index only

  Many reported local/cis eQTLs are false positives caused by probe-region sequence polymorphisms affecting hybridization rather than true cis-regulatory expression differences.

  lymphoblastoid hematopoietic caenorhabditis genome anova-based sanger eqtl

• Genomics: applications in mechanism elucidation.

  PMID 19166886 · PMC2698023 · Advanced drug delivery reviews · 2009 · 8 claims · 8 setups

  Full-text index only

  Genomic tools require no a priori knowledge of a compound's mode of action and can reveal biological pathways (metabolism, distribution, off-target effects) in addition to the precise mechanism of action.

  extract panel saccharomyces inbred affinity cytotoxicity genome-wide

• Phylogenetic variation and polymorphism at the toll-like receptor 4 locus (TLR4).

  PMID 11104518 · PMC31919 · Genome biology · 2000 · 7 claims · 7 setups

  Full-text index only

  The Tlr4 extracellular domain is far more variable than the cytoplasmic domain, both among mouse strains and among species

  tlr4 mus chimpanzee baboon genomic coding sequence

• Proteomic solutions for analytical challenges associated with alcohol research.

  PMID 23584870 · PMC3860482 · Alcohol research & health : the journal of the National Institute on Alcohol Abuse and Alcoholism · 2008 · 7 claims · 4 setups

  Full-text index only

  Protein-level meta-analyses analogous to the transcriptome meta-analysis by Mulligan et al. (2006) are not yet possible because proteins lack a uniform sample preparation/analysis method and span up to 8 orders of magnitude in abundance.

  general complex plasma selected shotgun label-free targeted

• The mammalian phenotype ontology: enabling robust annotation and comparative analysis.

  PMID 20052305 · PMC2801442 · Wiley interdisciplinary reviews. Systems biology and medicine · 2009 · 8 claims · 6 setups

  Full-text index only

  The Mammalian Phenotype (MP) Ontology enables classification and organization of phenotypic data for mouse and other mammalian species in a computationally useful, standardized manner.

  genotypes neural inbred viable phenotype phylogenetic comparative

• Asthma investigators begin to reap the fruits of genomics.

  PMID 14611649 · PMC329104 · Genome biology · 2003 · 7 claims · 8 setups

  Full-text index only

  Microarray profiling of animal models of allergic asthma can identify novel differentially expressed candidate genes involved in inflammation and airway remodeling.

  monkey models lung inbred cdna oligonucleotide northern

• TEMP: a computational method for analyzing transposable element polymorphism in populations.

  PMID 24753423 · PMC4066757 · Nucleic acids research · 2014 · 8 claims · 8 setups

  Has reproduction · 61

  TEMP combines pair-end (discordant) read and split (soft-clipped) read information to identify both presence and absence of TE insertions in genomic DNA from heterogeneous/pooled samples.

  drosophila five four melanogaster simulated comparative whole-genome

• Endotoxin-tolerant mice have mutations in Toll-like receptor 4 (Tlr4).

  PMID 9989976 · PMC2192941 · The Journal of experimental medicine · 1999 · 8 claims · 8 setups

  Full-text index only

  The Lps locus was fine-mapped to a 0.9-cM interval spanning a 1.7-Mb genomic contig on mouse chromosome 4.

  c3h genomic bac multiple-tissue genetic yac direct

• Bias of selection on human copy-number variants.

  PMID 16482228 · PMC1366494 · PLoS genetics · 2006 · 8 claims · 8 setups

  Full-text index only

  Human CNVs are significantly overrepresented near telomeres and centromeres and enriched in simple tandem repeats relative to the genome as a whole

  genome human-mouse cnv-encompassed inbred comparative randomization molecular

• Neuroscience in the era of functional genomics and systems biology.

  PMID 19829370 · PMC3645852 · Nature · 2009 · 8 claims · 7 setups

  Full-text index only

  Omics/discovery-based approaches do not eschew hypotheses but elevate hypothesis testing to high-throughput hypothesis generation and prioritization.

  developing hippocampus bac-transgenic fetal situ gene bac-transgenic