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).

• Macrophages on the run: Exercise balances macrophage polarization for improved health.

  PMID 39476967 · PMC11585839 · Molecular metabolism · 2024 · 8 claims · 7 setups

  Has reproduction · 81

  Immediate/acute exercise triggers an M1 (pro-inflammatory) macrophage polarization surge.

  gene affymetrix pooled muscle meta-analysis stepminer gene

• A genome annotation-driven approach to cloning the human ORFeome.

  PMID 15461802 · PMC545604 · Genome biology · 2004 · 8 claims · 8 setups

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  Existing human cDNA clone collections together provide only 60% coverage of full-length chromosome 22 ORFs, with the best single collection (MGC) providing 48%

  chromosome pooled t-tailed naga comparative rt-pcr sanger

• Systematic identification of ACE2 expression modulators reveals cardiomyopathy as a risk factor for mortality in COVID-19 patients.

  PMID 35012625 · PMC8743438 · Genome biology · 2022 · 7 claims · 8 setups

  Has reproduction · 68

  GENEVA is a semi-automated, study-design-agnostic framework that mines large-scale public RNA-seq data to identify conditions modulating a gene of interest's expression

  gtex lncap heart breast bulk rna-seq meta-analysis

• Improvements to cardiovascular gene ontology.

  PMID 19046747 · PMC2706316 · Atherosclerosis · 2009 · 8 claims · 8 setups

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  Gene Ontology (GO) provides a controlled vocabulary that links current functional knowledge of genes to high-throughput genomic and proteomic datasets, aiding data interpretation.

  coronary phospholamban mammalian lines gene expression large-scale

• Systems genetics of alcoholism.

  PMID 23584748 · PMC3860445 · Alcohol research & health : the journal of the National Institute on Alcohol Abuse and Alcoholism · 2008 · 8 claims · 8 setups

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  Alcoholism is a multifactorial disease driven by interacting genetic, social, and environmental factors, with genetics accounting for 50-60% of risk.

  families drosophila mice han linkage metabolic gene

• SNP-RFLPing: restriction enzyme mining for SNPs in genomes.

  PMID 16503968 · PMC1386656 · BMC genomics · 2006 · 8 claims · 2 setups

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  SNP-RFLPing accepts three flexible input types (dbSNP rs#/ss# IDs, HUGO gene name/Entrez gene ID, or free-form SNP-in-sequence including IUPAC or [dNTP1/dNTP2] formats) for human, rat, and mouse genomes

  software existing string-matching feature

• Generic injuries are sufficient to induce ectopic Wnt organizers in Hydra.

  PMID 33779545 · PMC8049744 · eLife · 2021 · 8 claims · 6 setups

  Has reproduction · 100

  The initial transcriptional and chromatin response to mid-gastric bisection is identical at oral and aboral wounds at 3 hpa and only diverges by 8 hpa.

  hydra rna-seq atac-seq transcription

• An accurate method for identifying recent recombinants from unaligned sequences.

  PMID 35025988 · PMC8963311 · Bioinformatics (Oxford, England) · 2022 · 8 claims · 4 setups

  Has reproduction · 84

  A novel algorithm combining the JHMM (Zilversmit et al. 2013) mosaic representation with a distance-based triple comparison can identify recombinant sequences and their parents from unaligned, gene-length sequences without a reference panel.

  simulated dblα coalescent comparative recombinant

• Serum protein profile in systemic-onset juvenile idiopathic arthritis differentiates response versus nonresponse to therapy.

  PMID 15987476 · PMC1175022 · Arthritis research & therapy · 2005 · 8 claims · 8 setups

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  SELDI-TOF MS can differentiate serum protein profiles of active versus well-controlled SJIA

  serum clustered pooled trypsin-digested seldi-tof cart immunoprecipitation

• High-precision mapping of protein protein interfaces: an integrated genetic strategy combining en masse mutagenesis and DNA-level parallel analysis on a yeast two-hybrid platform.

  PMID 17702760 · PMC2018616 · Nucleic acids research · 2007 · 7 claims · 4 setups

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  An integrated strategy combining en masse pentapeptide insertion mutagenesis, yeast two-hybrid screening, and parallel genetic footprinting can map protein-protein interfaces at amino acid precision and is generally applicable to any interacting protein pair.

  saccharomyces plasmid pooled individual yeast pcr-based restriction

• The functional importance of disease-associated mutation.

  PMID 12220483 · PMC128831 · BMC bioinformatics · 2002 · 6 claims · 1 setups

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  Disease-associated mutations occur in conserved regions of genes and can be used to identify likely disease-causing mutations

  disease-associated sequence

• High performance imputation of structural and single nucleotide variants using low-coverage whole genome sequencing.

  PMID 40155798 · PMC11951665 · Genetics, selection, evolution : GSE · 2025 · 7 claims · 6 setups

  Has reproduction · 85

  SNVs are imputed with high accuracy and recall across all tested WGS depths (1-4x), including in samples external to the reference panel.

  atlantic low-coverage genotyping genome

• Molecular cloning, genomic characterization and over-expression of a novel gene, XRRA1, identified from human colorectal cancer cell HCT116Clone2_XRR and macaque testis.

  PMID 12908878 · PMC194569 · BMC genomics · 2003 · 8 claims · 7 setups

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  XRRA1 is a novel gene down-regulated ~2-fold in XR-resistant HCT116 Clone2_XRR relative to HCT116 Clone10, identified via cDNA microarray

  hct116 macaque cos-7 genomic cdna est molecular

• Biomarkers that discriminate multiple myeloma patients with or without skeletal involvement detected using SELDI-TOF mass spectrometry and statistical and machine learning tools.

  PMID 17124346 · PMC3862287 · Disease markers · 2006 · 8 claims · 5 setups

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  SELDI-TOF MS serum profiling can discriminate MM patients with vs without skeletal (bone lesion) involvement using peak biomarkers

  serum seldi seldi-tof serum univariate

• Large-scale mutagenesis in p19(ARF)- and p53-deficient mice identifies cancer genes and their collaborative networks.

  PMID 18485879 · PMC2405818 · Cell · 2008 · 8 claims · 8 setups

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  A large-scale retroviral insertional mutagenesis screen identified 10,806 insertion sites implicating over 300 loci in tumorigenesis

  p53 tumor tumors computational retroviral linker-mediated flow

• Automated recognition of retroviral sequences in genomic data--RetroTector.

  PMID 17636050 · PMC1976444 · Nucleic acids research · 2007 · 8 claims · 8 setups

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  RetroTector uses 'fragment threading' (detection of chains of conserved retroviral motifs satisfying distance constraints) combined with LTR detection and protein reconstruction to identify ERVs in genomic sequences

  reference genome chimpanzee red motif whole-genome simulated

• What makes species unique? The contribution of proteins with obscure features.

  PMID 16859532 · PMC1779552 · Genome biology · 2006 · 7 claims · 8 setups

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  POFs constitute 18-38% (average 26%) of a typical eukaryotic proteome

  eukaryotic animal cerevisiae homo hmmpfam blast tblastn

• Utilization of genomic signatures to identify phenotype-specific drugs.

  PMID 19714244 · PMC2729377 · PloS one · 2009 · 8 claims · 8 setups

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  A RAS pathway gene expression signature applied to NCI-60 cells identifies compounds selectively active against RAS-activated cells, including the MEK inhibitor Hypothemycin

  nci-60 breast mda-mb-231 signature-drug gene signature