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).

• p16INK4 gene mutations are relatively frequent in ampullary carcinomas.

  PMID 9414654 · PMC5921281 · Japanese journal of cancer research : Gann · 1997 · 8 claims · 2 setups

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  P16INK4 gene mutations are relatively frequent in sporadic ampullary carcinomas

  sporadic loss mutational

• Most microsatellite unstable sporadic colorectal carcinomas carry MBD4 mutations.

  PMID 11104560 · PMC2363466 · British journal of cancer · 2000 · 8 claims · 2 setups

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  MBD4 mutations occur in 89% (17/19) of RER+ sporadic colorectal carcinomas when microdissected tumor sites are analyzed

  microdissected frozen pcr comparison

• A common founder for the V126D CDKN2A mutation in seven North American melanoma-prone families.

  PMID 11506491 · PMC2364106 · British journal of cancer · 2001 · 8 claims · 2 setups

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  All seven North American melanoma-prone families carrying V126D share a haplotype consistent with a single common founder/ancestor for the mutation

  melanoma-prone haplotype microsatellite maximum

• VISTA Enhancer Browser--a database of tissue-specific human enhancers.

  PMID 17130149 · PMC1716724 · Nucleic acids research · 2007 · 8 claims · 2 setups

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  Comparative genome analysis can identify candidate human enhancer elements whose tissue-specific in vivo activity can then be experimentally validated in transgenic mice.

  genomic genome transgenic comparative

• GenePING: secure, scalable management of personal genomic data.

  PMID 16638151 · PMC1524750 · BMC genomics · 2006 · 8 claims · 2 setups

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  GenePING extends the PING personal health record system to securely store and efficiently share large genome-sized datasets

  geneping threat computational

• Overview of microarray analysis of gene expression and its applications to cervical cancer investigation.

  PMID 18182341 · PMC7129792 · Taiwanese journal of obstetrics & gynecology · 2007 · 6 claims · 5 setups

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  Oligonucleotide microarray and cDNA microarray are the two main microarray platforms used to study gene expression genome-wide.

  cervical cdna microarray combinatorial

• Serum proteomic analysis focused on fibrosis in patients with hepatitis C virus infection.

  PMID 17625010 · PMC1971245 · Journal of translational medicine · 2007 · 8 claims · 2 setups

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  Seven serum protein spots show significantly altered expression between mild (F0-F1) and advanced (F3-F4) fibrosis in chronic hepatitis C patients

  serum digitized polyacrylamide image

• AutoCSA, an algorithm for high throughput DNA sequence variant detection in cancer genomes.

  PMID 17485433 · PMC5947781 · Bioinformatics (Oxford, England) · 2007 · 7 claims · 2 setups

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  AutoCSA is an automated algorithm, extended from the CSA protocol, that detects DNA sequence variants in cancer genomes with minimal manual intervention

  training kinase capillary targeted

• Negotiating the boundary between medicine and consumer culture: online marketing of nutrigenetic tests.

  PMID 20022680 · PMC2824846 · Social science & medicine (1982) · 2010 · 8 claims · 3 setups

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  Nutrigenetic testing companies create a new social/marketing space for their products positioned between medicine and consumer culture, rather than being simply delegitimized by boundary work.

  webpages same fda qualitative framing document

• Detecting tipping points of complex diseases by network information entropy.

  PMID 38960408 · PMC11221888 · Briefings in bioinformatics · 2024 · 8 claims · 4 setups

  Has reproduction · 78

  NIEE can detect critical states or tipping points in diverse data types, including bulk and single-sample expression data

  real stringdb individual genes network background sample-specific

• Gene Expression Analysis Platform (GEAP): A highly customizable, fast, versatile and ready-to-use microarray analysis platform.

  PMID 34927664 · PMC8754388 · Genetics and molecular biology · 2021 · 8 claims · 2 setups

  Has reproduction · 83

  GEAP is a GUI-based microarray analysis platform combining a C# front-end with an R (RTerm) back-end via the rgeap package, enabling analysis independent of manufacturer/platform.

  sqlite microarray software microarray

• Vibrio cholerae pathogenic clones.

  PMID 16318732 · PMC3367346 · Emerging infectious diseases · 2005 · 8 claims · 1 setups

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  The US Gulf clone, the Australian clone, and 3 prepandemic El Tor strains are related to the seventh pandemic clone.

  vibrio multilocus

• Getting knit-PI3Ky: PIK3CA mutation status to direct multimodality therapy?

  PMID 19903790 · PMC3400141 · Clinical cancer research : an official journal of the American Association for Cancer Research · 2009 · 8 claims · 1 setups

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  PIK3CA mutations are associated with local disease recurrence in rectal cancer patients

  tumor retrospective

• Having a BLAST with bioinformatics (and avoiding BLASTphemy).

  PMID 11597340 · PMC138974 · Genome biology · 2001 · 8 claims · 4 setups

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  BLAST is the most widely used tool for searching biological sequences for regions of local similarity

  superfamilies blocks query pairwise phylogenetic sequence heuristic

• Mice and more.

  PMID 14519193 · PMC328447 · Genome biology · 2003 · 8 claims · 7 setups

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  A multispecies weighted conservation score, which accounts for each species' divergence rate, can identify conserved non-coding sequences (multispecies conserved sequences, MCSs) likely to be biologically significant

  cftr ciona embryonic chromosome comparative genome bac-based

• Highlights of international conference of immunogenomics and immunomics, October 8-12, 2006 Budapest, Hungary.

  PMID 17470366 · PMC7130317 · Cellular immunology · 2006 · 8 claims · 8 setups

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  An 'immunological constant of rejection' involving interferon-stimulated genes (ISGs) and innate immune effector functions (IEF) underlies diverse immune-mediated tissue destruction processes (allograft rejection, cancer rejection, autoimmunity, infection)

  hla-b44 plasma macrophages complement proteomics shotgun cap

• The ASAP II database: analysis and comparative genomics of alternative splicing in 15 animal species.

  PMID 17108355 · PMC1669709 · Nucleic acids research · 2007 · 8 claims · 4 setups

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  ASAP II expands human alternative splicing data ~3-fold over the previous ASAP database, to ~89,078 distinct alternative splicing relationships in 11,717 genes

  genome animal aligned est genome-wide comparative est

• The future is genome-wide.

  PMID 16934105 · PMC1779592 · Genome biology · 2006 · 8 claims · 8 setups

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  Noncoding SNPs near NRG1 associated with schizophrenia likely act by influencing NRG1 expression level

  schizophrenia myocardial individuals infectious genetic candidate gene

• Splicing bioinformatics to biology.

  PMID 16732900 · PMC1779529 · Genome biology · 2006 · 8 claims · 8 setups

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  Mutually exclusive selection of Dscam exon 6 variants is governed by base pairing between a conserved intronic docking site and selector sequences adjacent to each alternative exon.

  dscam alternative heterologous expressing comparative dicodon reporter

• Rats go genomic.

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

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  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