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).

• CDKN2A and CDK4 mutation analysis in Italian melanoma-prone families: functional characterization of a novel CDKN2A germ line mutation.

  PMID 11556834 · PMC2375081 · British journal of cancer · 2001 · 7 claims · 6 setups

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  Germ line CDKN2A mutations were found in 5 of 15 (33.3%) Italian melanoma-prone families, including one novel mutation (P48T) and three known pathogenic mutations (R24P, G101W, N71S)

  genomic radiolabelled tig-er u2os sscp protein-protein retroviral

• Predicting preferential DNA vector insertion sites: implications for functional genomics and gene therapy.

  PMID 18047689 · PMC2106846 · Genome biology · 2007 · 8 claims · 6 setups

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  Vector insertion site preferences differ substantially between viral vectors and transposons, affecting both oncogenic risk in gene therapy and utility for functional genomics

  hela liver gene peripheral retroviral transposon hydrodynamic

• 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

• 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

• Genome-wide location analysis and expression studies reveal a role for p110 CUX1 in the activation of DNA replication genes.

  PMID 18003658 · PMC2248751 · Nucleic acids research · 2008 · 8 claims · 8 setups

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  p110 CUX1 is recruited to promoters of cell cycle-related target genes preferentially during S phase

  hela hs578t nih3t3 genomic chap-chip conventional scanning

• A distinct epigenetic signature at targets of a leukemia protein.

  PMID 17266773 · PMC1796549 · BMC genomics · 2007 · 7 claims · 7 setups

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  Combining gene expression microarray analysis with bioinformatic search for AML1-consensus sequences identifies direct AML1 targets that expression analysis alone cannot resolve

  32d sequence gene bioinformatic real-time

• Application of two machine learning algorithms to genetic association studies in the presence of covariates.

  PMID 19014573 · PMC2620353 · BMC genetics · 2008 · 8 claims · 3 setups

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  The relative performance of RF and MARS for detecting genotype-trait associations depends on both the strategy used to handle covariates and the true underlying model of association (e.g., confounding vs. mediation vs. interaction).

  simulated cohort simulation applied

• Novel point mutation in the extracellular domain of the granulocyte colony-stimulating factor (G-CSF) receptor in a case of severe congenital neutropenia hyporesponsive to G-CSF treatment.

  PMID 10449521 · PMC2195597 · The Journal of experimental medicine · 1999 · 7 claims · 8 setups

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  A novel C→A point mutation at nucleotide 850 of GCSFR cDNA causes a Pro→His substitution at position 206 (P206H) in the proline-rich hinge of the CRH domain of the G-CSF receptor extracellular domain in an SCN patient hyporesponsive to G-CSF.

  bone fibroblast 32d.cl8.6 32d rt-pcr genomic flow

• Inflammatory bowel disease and mutations affecting the interleukin-10 receptor.

  PMID 19890111 · PMC2787406 · The New England journal of medicine · 2009 · 8 claims · 8 setups

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  Homozygous loss-of-function mutations in IL10RA or IL10RB cause severe early-onset enterocolitis

  consanguineous patients ebv-transformed pbmcs genetic-linkage single-nucleotide-polymorphism candidate-gene

• A paradigm for virus-host coevolution: sequential counter-adaptations between endogenous and exogenous retroviruses.

  PMID 17997604 · PMC2065879 · PLoS pathogens · 2007 · 8 claims · 5 setups

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  Two enJSRV proviruses (enJS56A1 and enJSRV-20) independently acquired a defective, transdominant Gag (R21W substitution) that blocks late replication steps of exogenous JSRV/ENTV

  sheep nih3t3 domestic enjsrv bac retroviral locus-specific

• Dynamic Proteomics: a database for dynamics and localizations of endogenous fluorescently-tagged proteins in living human cells.

  PMID 19820112 · PMC2808965 · Nucleic acids research · 2010 · 8 claims · 6 setups

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  The Dynamic Proteomics database compiles fluorescence dynamics and localization data for endogenously YFP/Venus-tagged human proteins from the LARC library studied by Cohen et al.

  h1299 cdna user-submitted time-lapse cd-tagging race

• Identification, characterization and comparative genomics of chimpanzee endogenous retroviruses.

  PMID 16805923 · PMC1779541 · Genome biology · 2006 · 8 claims · 6 setups

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  The chimpanzee genome contains at least 42 separate families of endogenous retroviruses, 9 newly identified

  chimpanzee domains genomic hg16 genome-wide sequence ltr-ltr

• A homozygous CARD9 mutation in a family with susceptibility to fungal infections.

  PMID 19864672 · PMC2793117 · The New England journal of medicine · 2009 · 7 claims · 7 setups

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  A homozygous CARD9 point mutation (Q295X, premature termination codon) is associated with autosomal recessive susceptibility to chronic mucocutaneous candidiasis.

  family patients peripheral-blood peripheral snp microsatellite sanger

• DNA methylation of cancer genome.

  PMID 19960550 · PMC2940836 · Birth defects research. Part C, Embryo today : reviews · 2009 · 8 claims · 7 setups

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  Cancer epigenome alterations fall into two main categories: hypermethylation of tumor suppressor genes and hypomethylation of oncogenes or heterochromatin.

  embryonic germ heterozygous cancer gene hypomorphic methyltransferase

• 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