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).

• Associations between polycyclic aromatic hydrocarbon-related exposures and p53 mutations in breast tumors.

  PMID 20064791 · PMC2854728 · Environmental health perspectives · 2010 · 8 claims · 5 setups

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  PAH-related exposures are associated with breast cancer differently according to tumor p53 mutation status, type, effect, and number

  archived breast peripheral study surveyor immunohistochemistry competitive

• MILANO--custom annotation of microarray results using automatic literature searches.

  PMID 15661078 · PMC547913 · BMC bioinformatics · 2005 · 7 claims · 4 setups

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  MILANO annotates microarray gene lists by counting literature co-occurrences of each gene with user-defined secondary terms

  well-known list over-producing known medline generif microarray

• 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

• Sex differences in cancer risk among germline p53 mutation carriers.

  PMID 15280910 · PMC2409855 · British journal of cancer · 2004 · 6 claims · 3 setups

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  Cancer risk in germline p53 mutation carriers differs by sex, with females at higher risk than males in adulthood, was first reported by Chompret et al 2000, three years before a confirmatory study by Hwang et al 2003 claimed similar findings without citing the earlier work.

  children first-degree p53 germline family-based

• Characterization of mutations and loss of heterozygosity of p53 and K-ras2 in pancreatic cancer cell lines by immobilized polymerase chain reaction.

  PMID 12877750 · PMC183853 · BMC biotechnology · 2003 · 6 claims · 5 setups

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  Polony technology can detect intragenic mutations in well-defined hotspots of p53 (codons 175, 245, 248, 249, 273, 282) and K-ras2 (codons 12, 13, 61)

  panc-1 aspc-1 capan-1 immobilized polony-based

• An oncogenomics-based in vivo RNAi screen identifies tumor suppressors in liver cancer.

  PMID 19012953 · PMC2990916 · Cell · 2008 · 7 claims · 8 setups

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  shRNA pools targeting genes recurrently deleted in human HCC accelerate hepatocarcinogenesis in vivo, whereas randomly selected shRNA pools do not.

  hepatocellular p53 genomic hepatoma array-based pooled shrna

• Investigations on a clinically and functionally unusual and novel germline p53 mutation.

  PMID 12085209 · PMC2746598 · British journal of cancer · 2002 · 8 claims · 7 setups

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  A novel germline 7 base pair insertion in exon 5 of p53 (causing frameshift from codon 161 with a stop at codon 182) was identified in a patient with osteosarcoma at age 22 and choroid plexus papilloma at age 29.

  peripheral yeast saos-2 genomic fasay apoptotic

• Genome amplification of single sperm using multiple displacement amplification.

  PMID 15942023 · PMC1143700 · Nucleic acids research · 2005 · 8 claims · 7 setups

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  MDA was applied for the first time to whole-genome amplification of single sperm cell DNA

  single sperm pcr sanger real-time

• GeneSeer: a sage for gene names and genomic resources.

  PMID 16176584 · PMC1266031 · BMC genomics · 2005 · 7 claims · 4 setups

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  GeneSeer aggregates gene name synonyms from GenBank, FlyBase, ExPASy, HUGO, ENSEMBL, UCSC and Gene Ontology into a name-translation database that maps any familiar name to a reference (SOFAR) identifier.

  sofar clusters rnai gene blast sequence shrna

• High-resolution aCGH and expression profiling identifies a novel genomic subtype of ER negative breast cancer.

  PMID 17925008 · PMC2246289 · Genome biology · 2007 · 7 claims · 8 setups

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  A novel subtype of high-grade ER-negative breast cancer exists, characterized by a low genomic instability index (GII)

  breast computational array-cgh gene bac

• Cyclic olefin homopolymer-based microfluidics for protein crystallization and in situ X-ray diffraction.

  PMID 19690369 · PMC2733880 · Acta crystallographica. Section D, Biological crystallography · 2009 · 8 claims · 7 setups

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  A COP-based microfluidics system (SpinX cards, 500 chambers of 320 nl each) was established for protein crystallization and in situ X-ray diffraction.

  chicken bovine p53 arabidopsis microbatch situ vapour-diffusion

• Genomic and mutational profiling to assess clonal relationships between multiple non-small cell lung cancers.

  PMID 19671847 · PMC2892178 · Clinical cancer research : an official journal of the American Association for Cancer Research · 2009 · 8 claims · 5 setups

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  Genomic profiling by aCGH can distinguish clonal tumors from independent primaries with high confidence by identifying matching versus non-matching regions of allelic gain/loss.

  fresh-frozen same banked resected array mutational pcr

• PIK3CA alterations in Middle Eastern ovarian cancers.

  PMID 19638206 · PMC2724395 · Molecular cancer · 2009 · 8 claims · 7 setups

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  PIK3CA gene amplification is frequent in Middle Eastern EOC, found in 54/152 (35.5%) cases

  eoc fluorescence pcr step-down

• Somatic mutations in mitochondria: the chicken or the egg?

  PMID 16207343 · PMC1257449 · Arthritis research & therapy · 2005 · 6 claims · 6 setups

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  Patients with RA have a higher incidence of somatic mtDNA mutations (in MT-ND1 transcripts) in synoviocytes and synovial tissue compared with OA patients

  mutated synovial sequencing mhc expression

• A scalable, open-source implementation of a large-scale mechanistic model for single cell proliferation and death signaling.

  PMID 35729113 · PMC9213456 · Nature communications · 2022 · 7 claims · 5 setups

  Has reproduction · 84

  Developed a python-based, scalable model creation and simulation pipeline that converts structured text files into an SBML-standard model and is high-performance/cloud-computing ready.

  sparced mcf10a deterministic hybrid comparison

• Complex genetic diseases: controversy over the Croesus code.

  PMID 11532206 · PMC138948 · Genome biology · 2001 · 8 claims · 3 setups

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  The common disease/common variant hypothesis is predicted by population genetic theory (founder population dynamics, mutation-drift-selection balance) and supported by empirical examples such as APOE*E4.

  chromosome northern disease large-scale genome-wide database