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).

• Integrative functional genomics.

  PMID 15239826 · PMC463286 · Genome biology · 2004 · 8 claims · 8 setups

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  Ultra-conserved noncoding elements exist across human, mouse and rat genomes at very high sequence identity, often far from genes

  yeast tissue-cultured mammalian genomic comparative targeted chip-chip

• Enhancing cell subpopulation discovery in cancer by integrating single-cell transcriptome and expressed variants.

  PMID 41647537 · PMC12869734 · Fundamental research · 2026 · 6 claims · 3 setups

  Has reproduction · 68

  scCluster, an end-to-end deep clustering model integrating gene expression and expressed variant (eSNP) features, stratifies cell subpopulations in cancer scRNA-seq data.

  raw real-world expressed gene deep

• BRCA1 and BRCA2 missense variants of high and low clinical significance influence lymphoblastoid cell line post-irradiation gene expression.

  PMID 18497862 · PMC2375115 · PLoS genetics · 2008 · 8 claims · 6 setups

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  BRCA1 and BRCA2 pathogenic mutation carriers have similar post-irradiation LCL gene expression profiles to each other, more so than to BRCAX samples without an LCS variant

  lymphoblastoid lcl gene microarray unsupervised t-test

• Similarities and Differences in Gene Expression Networks Between the Breast Cancer Cell Line Michigan Cancer Foundation-7 and Invasive Human Breast Cancer Tissues.

  PMID 34056582 · PMC8155268 · Frontiers in artificial intelligence · 2021 · 8 claims · 8 setups

  Has reproduction · 92

  MCF-7 cell lines and human breast cancer tissues share only minimal similarity in biological processes, though fundamental functions such as cell cycle are conserved

  mcf-7 breast wgcna top bulk microarray weighted

• Trans-ethnic association study of blood pressure determinants in over 750,000 individuals.

  PMID 30578418 · PMC6365102 · Nature genetics · 2019 · 8 claims · 8 setups

  Has reproduction

  Discovery and replication GWAS of SBP, DBP and pulse pressure in up to 776,078 individuals identified 208 novel common blood pressure SNPs and 53 rare variants.

  mvp tissues kidney gwas genome-wide transcriptome-wide

• Population genomics of human gene expression.

  PMID 17873874 · PMC2683249 · Nature genetics · 2007 · 8 claims · 8 setups

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  Gene expression levels in lymphoblastoid cell lines are a heritable trait

  ebv-transformed ceu lymphoblastoid unrelated genome-wide custom cis-eqtl

• Aryl hydrocarbon receptor nuclear translocator (ARNT) gene as a positional and functional candidate for type 2 diabetes and prediabetic intermediate traits: Mutation detection, case-control studies, and gene expression analysis.

  PMID 18366646 · PMC2323364 · BMC medical genetics · 2008 · 7 claims · 8 setups

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  Common ARNT variants are not associated with type 2 diabetes in European American or African American case-control cohorts

  european african individuals nondiabetic snp variant direct

• Integrative analyses reveal signaling pathways underlying familial breast cancer susceptibility.

  PMID 26969729 · PMC4812528 · Molecular systems biology · 2016 · 7 claims · 6 setups

  Has reproduction · 67

  Cell adhesion (cell-cell and cell-ECM) pathways are significantly and consistently dysregulated in women who develop familial breast cancer across multiple omic data types and tissues.

  peripheral pbmcs normal snap-frozen gene exome western

• High resolution analysis of the human transcriptome: detection of extensive alternative splicing independent of transcriptional activity.

  PMID 19804644 · PMC2768739 · BMC genetics · 2009 · 8 claims · 6 setups

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  The human GWSA uses exon body and exon-exon junction probes to directly measure over 280,000 known and predicted splicing events genome-wide.

  universal same lim erythrocyte genome-wide cross-platform rt-pcr

• The UCSC Genome Browser database: update 2010.

  PMID 19906737 · PMC2808870 · Nucleic acids research · 2010 · 8 claims · 5 setups

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  The UCSC Genome Browser provides a large database of publicly available sequence and annotation data with an integrated tool set for examining, comparing, aligning, and displaying genomes

  genome vertebrate individuals personal snp sequence genome-wide

• Accelerating rare disease diagnostics by linking DNA and RNA through an explainable and interactive RNA-guided workflow.

  PMID 41685349 · PMC12891912 · NAR genomics and bioinformatics · 2026 · 7 claims · 7 setups

  Has reproduction

  An integrated RNA-guided variant interpretation workflow combining OUTRIDER, FRASER, MOLGENIS VIP, and Borzoi enhances clinical variant interpretation and reclassification of VUS in rare disease cases.

  udn blood skin snvs whole-genome bulk splice-altering

• Expanding the vision of environmental health at UNC-CH.

  PMID 15248304 · PMC1247395 · Environmental health perspectives · 2004 · 8 claims · 8 setups

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  Human breast tumors arise from at least two distinct cell types, basal and luminal epithelial, with different clinical behavior

  breast chinese carolina rodent microarray functional genetic

• Cell type-specific eQTL analysis of COVID-19 based on single-cell transcriptomic data.

  PMID 41064594 · PMC12501775 · NAR genomics and bioinformatics · 2025 · 8 claims · 8 setups

  Has reproduction · 51

  Single-cell eQTL analysis across eight immune cell types identified 2593 genes whose expression is significantly associated with common genetic polymorphisms, with most genes showing cell type-specific effects

  pbmcs eight pbmc monocytes scrna-seq genetic cis-eqtl

• Toxicogenomics research consortium sails into uncharted waters.

  PMID 12460811 · PMC1241122 · Environmental health perspectives · 2002 · 8 claims · 8 setups

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  The NIEHS-funded $37 million Toxicogenomics Research Consortium (TRC) combines the NIEHS Microarray Center with five academic institutions (UNC, Duke, Fred Hutchinson/UW, MIT, OHSU) to define genetic variability, set gene expression standards, and study environmental stress responses.

  strains nervous mice liver microarray gene toxicogenomic

• Variants in the estrogen receptor alpha gene and its mRNA contribute to risk for schizophrenia.

  PMID 18424448 · PMC2465798 · Human molecular genetics · 2008 · 8 claims · 8 setups

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  Genotype CC (rs2234693/PvuII) and C-allele-containing haplotypes in ESR1 intron 1 are more frequent in African American schizophrenics than controls

  genomic postmortem nimhgi esr1 targeted case-control family-based

• Patrocles: a database of polymorphic miRNA-mediated gene regulation in vertebrates.

  PMID 19906729 · PMC2808989 · Nucleic acids research · 2010 · 8 claims · 6 setups

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  Patrocles is a database compiling DSPs predicted to perturb miRNA-mediated gene regulation across seven vertebrate species, covering targets, miRNA precursors and silencing machinery.

  3'-utr mirbase hapmap comparative snp mirna

• Proteogenomic analysis prioritises functional single nucleotide variants in cancer samples.

  PMID 29221171 · PMC5707065 · Oncotarget · 2017 · 8 claims · 6 setups

  Has reproduction · 73

  A customised SAAV peptide database built from RNA-seq/WGS variant calls can be used to search proteomics data and detect single amino acid variant (SAAV)-containing peptides at the protein level

  jurkat rna-seq genome proteomics

• Ancient variation of the AvrPm17 gene in powdery mildew limits the effectiveness of the introgressed rye Pm17 resistance gene in wheat.

  PMID 35857869 · PMC9335242 · Proceedings of the National Academy of Sciences of the United States of America · 2022 · 6 claims · 8 setups

  Has reproduction · 80

  AvrPm17 is encoded by a paralogous, tandemly duplicated effector gene pair located in a pericentromeric, mildew sublineage-specific effector cluster (family E003) showing signs of recurring gene conversion.

  b.g parental nicotiana benthamiana qtl comparative rna-sequencing

• More breast cancer genes?

  PMID 11305950 · PMC138680 · Breast cancer research : BCR · 2001 · 8 claims · 7 setups

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  A new high-risk breast cancer gene termed BRCAX may exist on chromosome 13q, identified via CGH and linkage analysis in Nordic families

  tumours five independent ataxia-telangiectasia comparative haplotype linkage

• ECgene: genome annotation for alternative splicing.

  PMID 15608289 · PMC540072 · Nucleic acids research · 2005 · 8 claims · 5 setups

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  ECgene combines genome-based EST clustering with a graph-theoretic transcript assembly procedure to predict gene models including alternative splicing events.

  brca2 rgs17 organs cdna genomic genome transcript