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).

• Mutations in pericentrin cause Seckel syndrome with defective ATR-dependent DNA damage signaling.

  PMID 18157127 · PMC2397541 · Nature genetics · 2008 · 8 claims · 8 setups

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  Homozygous truncating mutations in PCNT cause Seckel syndrome

  consanguineous genomic lymphoblastoid lcls snp-microarray sanger immunofluorescence

• Relative impact of nucleotide and copy number variation on gene expression phenotypes.

  PMID 17289997 · PMC2665772 · Science (New York, N.Y.) · 2007 · 8 claims · 5 setups

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  SNPs and CNVs capture largely non-overlapping signals of genetic variation affecting gene expression

  lymphoblastoid same computational subset gene snp array

• Population genomics: diversity and virulence in the Neisseria.

  PMID 18822386 · PMC2612085 · Current opinion in microbiology · 2008 · 8 claims · 8 setups

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  Horizontal genetic exchange (recombination) plays a central role in shaping bacterial speciation and population structure in Neisseria

  neisseria meningitidis meningococcal multi-locus microarray genome

• Key regulatory molecules of cartilage destruction in rheumatoid arthritis: an in vitro study.

  PMID 18205922 · PMC2374452 · Arthritis research & therapy · 2008 · 7 claims · 4 setups

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  A standardized 3D in vitro alginate bead model of chondrocytes stimulated with synovial fibroblast supernatants can be used to profile RA-related cartilage destruction genes

  sv40 articular differentially antibody-based oligonucleotide real-time

• The genetics of regulatory variation in the human genome.

  PMID 16004727 · PMC3525257 · Human genomics · 2005 · 8 claims · 7 setups

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  Naturally-occurring gene expression variation among individuals is common across species (yeast, Drosophila, mouse, fish, maize, primates, humans) and has a significant genetic component.

  ceph immortalised lymphoblastoid individuals reporter allelic microarray

• Identification of a PRDM1-regulated T cell network to regulate atherosclerotic plaque inflammation.

  PMID 41039608 · PMC12490039 · Genome medicine · 2025 · 6 claims · 7 setups

  Has reproduction · 100

  A distinct gene co-expression module with a prominent T cell signature is enriched in unstable plaques and distinguishes high-risk from low-risk lesions.

  carotid calcified atherosclerotic cell-specific microarray single-cell loss-of-function

• Vector algebra in the analysis of genome-wide expression data.

  PMID 11897023 · PMC88809 · Genome biology · 2002 · 8 claims · 6 setups

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  The angle θ between expression (experiment) vectors is the geometric counterpart of the Pearson correlation coefficient r, providing a rigorous measure of similarity between profiles.

  saccharomyces microarray

• Functional genomics of early cortex patterning.

  PMID 16515721 · PMC1431711 · Genome biology · 2006 · 7 claims · 6 setups

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  The neocortical protomap is established as continuous rostro-caudal gradients of gene expression in progenitor cells, not discrete compartments

  neocortex embryonic fgfr1-mutant cortex oligonucleotide situ microarray

• Variations in the transcriptome of Alzheimer's disease reveal molecular networks involved in cardiovascular diseases.

  PMID 18842138 · PMC2760875 · Genome biology · 2008 · 8 claims · 6 setups

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  AD-related genes (APOE, A2M, PON2, MAP4) and CVD-associated genes (COMT, CBS, WNK1) congregate in a single co-expression module, linking AD and CVD at the transcriptional level

  entorhinal subjects expression differentially microarray significance principal

• Whither genomics?

  PMID 11104516 · PMC138820 · Genome biology · 2000 · 8 claims · 8 setups

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  Genomics is both a science (understanding genome structure/evolution) and a tool (learning gene function) that collects comprehensive data on all genes, in contrast to genetics which studies a few genes controlling a phenotype

  mammalian budding yeast general expression genome-wide synthetic

• Newborn sex-specific transcriptome signatures and gestational exposure to fine particles: findings from the ENVIRONAGE birth cohort.

  PMID 28583124 · PMC5458481 · Environmental health : a global access science source · 2017 · 7 claims · 6 setups

  Has reproduction · 71

  Gestational PM2.5 exposure is associated with sex-specific gene expression changes in newborn cord blood, with major differences between boys and girls.

  cord maternal genes significant genome pm2.5 isolation

• Application of functional genomics to primate endometrium: insights into biological processes.

  PMID 17118168 · PMC1775064 · Reproductive biology and endocrinology : RB&E · 2006 · 8 claims · 7 setups

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  Gene expression profiles differ distinctly across proliferative, early-, mid-, and late-secretory phases of the human menstrual cycle, reflecting sequential estradiol and progesterone action.

  endometrial uterus whole-genome cdna oligonucleotide

• Genome-wide microRNA profiling in human fetal nervous tissues by oligonucleotide microarray.

  PMID 16983573 · PMC1705512 · Child's nervous system : ChNS : official journal of the International Society for Pediatric Neurosurgery · 2006 · 8 claims · 5 setups

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  72-83% of assayed miRNAs are expressed across human fetal organs, with G24w cerebrum showing the most miRNAs expressed

  fetal same microarray oligonucleotide northern microarray

• Effects of DNA-targeted ionizing radiation produced by 5-[125I]iodo-2'-deoxyuridine on global gene expression in primary human cells.

  PMID 17594496 · PMC1934370 · BMC genomics · 2007 · 8 claims · 7 setups

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  125I-IUdR-induced DNA damage alters expression of only a limited subset of genes in primary human cells

  ag09319 gm05388 nhfk whole-genome quantitative dna-associated

• Neonatal salivary analysis reveals global developmental gene expression changes in the premature infant.

  PMID 19959617 · PMC2853178 · Clinical chemistry · 2010 · 7 claims · 6 setups

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  Salivary genomic microarray analysis reveals global developmental gene expression changes in premature infants over postnatal age

  saliva amplified extracted differentially genome quality extraction

• Genomic transcriptional profiling identifies a candidate blood biomarker signature for the diagnosis of septicemic melioidosis.

  PMID 19903332 · PMC3091321 · Genome biology · 2009 · 6 claims · 5 setups

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  A candidate 37-transcript diagnostic signature distinguishes septicemic melioidosis from sepsis caused by other organisms with 100% accuracy in the training set and 78%/80% accuracy in two independent validation sets

  blood whole-genome unsupervised class

• Methods for genome-wide analysis of DNA methylation in intestinal tumors.

  PMID 19854208 · PMC2891386 · Mutation research · 2010 · 8 claims · 8 setups

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  Aberrant DNA methylation, including CpG island hypermethylation of tumor suppressors and genome-wide hypomethylation, is strongly linked to the origin and progression of colorectal cancer.

  cd19+ lung gpx1 tumor mira medip goldengate

• Have microarrays failed to deliver for developmental biology?

  PMID 12225576 · PMC139405 · Genome biology · 2002 · 8 claims · 8 setups

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  Despite predictions that microarrays would transform biology, very few published developmental biology microarray studies have generated novel insights.

  drosophila caenorhabditis developing xenopus cdna genome-wide microarray

• Similarities and differences in genome-wide expression data of six organisms.

  PMID 14737187 · PMC300882 · PLoS biology · 2004 · 8 claims · 8 setups

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  Coexpression of functionally related genes is frequently conserved across evolutionarily distant organisms

  saccharomyces caenorhabditis escherichia arabidopsis genome-wide large-scale developmental

• Systems biology approach for mapping the response of human urothelial cells to infection by Enterococcus faecalis.

  PMID 18047719 · PMC2099488 · BMC bioinformatics · 2007 · 8 claims · 5 setups

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  Deconvoluting gene expression variance into technical (Gaussian, ~6.5% relative SD) and biological components identifies hypervariable (HV) genes that reflect true biological response to infection without requiring replicates

  urothelial clustered genome-wide confocal k-means