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).

• Convergence of mutation and epigenetic alterations identifies common genes in cancer that predict for poor prognosis.

  PMID 18507500 · PMC2429944 · PLoS medicine · 2008 · 7 claims · 7 setups

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  At least 36 of the 189 newly mutated CAN genes are targets of promoter CpG island hypermethylation, often in both colon and breast cancer cell lines

  breast same selected hct116 expression methylation-specific rt-pcr

• Proteomic analysis of differential proteins in pancreatic carcinomas: Effects of MBD1 knock-down by stable RNA interference.

  PMID 18445260 · PMC2386481 · BMC cancer · 2008 · 8 claims · 5 setups

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  Stable RNAi-mediated MBD1 knock-down was successfully established in the BxPC-3 pancreatic cancer cell line using a recombinant siRNA plasmid

  bxpc-3 2-d maldi-tof-ms western

• A target enrichment method for gathering phylogenetic information from hundreds of loci: An example from the Compositae.

  PMID 25202605 · PMC4103609 · Applications in plant sciences · 2014 · 8 claims · 8 setups

  Has reproduction · 87

  A custom sequence capture probe set (9678 baits targeting 1061 orthologous genes) was designed to enrich COS loci across the Compositae.

  compositae same species helianthus targeted genome genomic

• Investigation of the human tear film proteome using multiple proteomic approaches.

  PMID 18334958 · PMC2268847 · Molecular vision · 2008 · 8 claims · 6 setups

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  Tear collection method (capillary vs. Schirmer strip) significantly impacts which proteins are detected in the tear film proteome.

  tear spectra 1d-sds-page 2d-sds-page mudpit

• A non-parametric meta-analysis approach for combining independent microarray datasets: application using two microarray datasets pertaining to chronic allograft nephropathy.

  PMID 18302764 · PMC2276496 · BMC genomics · 2008 · 8 claims · 6 setups

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  A novel non-parametric meta-analysis approach for combining independent microarray datasets is presented, requiring no distributional assumptions and being logically intuitive.

  kidney same identified additional microarray significance fisher's

• Commonality of functional annotation: a method for prioritization of candidate genes from genome-wide linkage studies.

  PMID 18263617 · PMC2275105 · Nucleic acids research · 2008 · 8 claims · 7 setups

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  Genes correlated with a common complex trait are more likely to share GO functional annotations than genes not correlated with that trait

  genes candidate simulated alzheimer's genome-wide term null-hypothesis

• Proteomic analysis of human aqueous humor using multidimensional protein identification technology.

  PMID 20019884 · PMC2793904 · Molecular vision · 2009 · 8 claims · 4 setups

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  Albumin/IgG depletion combined with MudPIT (2D-LC-MS/MS) enables high-confidence, extensive characterization of the human AH proteome

  pooled albumin-bound analysis mudpit immunoaffinity bca

• Network properties of complex human disease genes identified through genome-wide association studies.

  PMID 19956617 · PMC2779513 · PloS one · 2009 · 7 claims · 6 setups

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  Complex disease genes are significantly less central (lower degree/closeness, higher eccentricity) in the human interactome than essential and monogenic disease genes, occupying an intermediate niche between monogenic disease genes and non-disease genes

  complex interactome gene disease-sharing gene protein-protein

• In vivo pharmaco-proteomic analysis of hydroxyurea induced changes in the sickle red blood cell membrane proteome.

  PMID 19914412 · PMC2818491 · Journal of proteomics · 2010 · 8 claims · 4 setups

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  2D-DIGE combined with tandem mass spectrometry identified 32 distinct sickle RBC membrane proteins that significantly changed in abundance after in vivo HU therapy

  sickle excised patients 2d-dige tandem immunoblot

• MALDI profiling of human lung cancer subtypes.

  PMID 19890392 · PMC2767501 · PloS one · 2009 · 8 claims · 8 setups

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  PIMAC/MALDI-TOF peptide profiles combined with classification models can distinguish normal lung from tumor and differentiate NSCLC histological subtypes

  lung tryptic peak ffpe maldi-tof parallel stepwise

• Steps toward broad-spectrum therapeutics: discovering virulence-associated genes present in diverse human pathogens.

  PMID 19874620 · PMC2774872 · BMC genomics · 2009 · 8 claims · 8 setups

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  Phylogenetic profiling of protein clusters across pathogen and non-pathogen genomes can identify candidate generic virulence factors

  proteins cdc candidate yersinia all-against-all computational cross-species

• Candidate vaccine sequences to represent intra- and inter-clade HIV-1 variation.

  PMID 19812689 · PMC2753653 · PloS one · 2009 · 7 claims · 5 setups

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  Natural CTL immunodominance toward variable proteome regions increases epitope mismatch with challenge strains and recapitulates the escape-driven CTL failure seen in natural infection, contributing to HIV vaccine failure

  hiv-1 polyclonally shannon cross-clade ctl

• Effect of read-mapping biases on detecting allele-specific expression from RNA-sequencing data.

  PMID 19808877 · PMC2788925 · Bioinformatics (Oxford, England) · 2009 · 8 claims · 6 setups

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  Reads mapped to the reference genome show a significant bias toward the reference allele at heterozygous SNPs

  lymphoblastoid simulated hapmap genes rna-seq read-mapping eqtl

• Proteomic analysis of serum in lung cancer induced by 3-methylcholanthrene.

  PMID 19794824 · PMC2753780 · Journal of biomedicine & biotechnology · 2009 · 7 claims · 4 setups

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  141 protein spots are differentially expressed between normal rat sera and MCA-induced lung cancer rat sera (82 overexpressed, 59 underexpressed)

  serum lung excised two-dimensional maldi-tof-ms histopathology

• Haplotype frequencies at the DRD2 locus in populations of the East European Plain.

  PMID 19793394 · PMC2765450 · BMC genetics · 2009 · 8 claims · 4 setups

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  The three-locus TaqI B-TaqI D-TaqI A haplotype at DRD2 constitutes a powerful genetic marker reflecting the most ancient dispersal of anatomically modern humans

  genomic genotype rflp haplotype pcr-rflp hardy-weinberg pairwise

• Systems integration of biodefense omics data for analysis of pathogen-host interactions and identification of potential targets.

  PMID 19779614 · PMC2745575 · PloS one · 2009 · 8 claims · 8 setups

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  A protein-centric data integration approach (Master Protein Directory) enables integration and mining of heterogeneous pathogen-host omics data across multiple research centers

  macrophage hela vaccinia bacillus gene protein-protein comparative

• One-pot shotgun quantitative mass spectrometry characterization of histones.

  PMID 19764812 · PMC2798817 · Journal of proteome research · 2009 · 8 claims · 8 setups

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  One-pot propionylation and trypsin digestion of unfractionated bulk histones enables quantitative Bottom Up MS characterization of histone PTMs without prior off-line HPLC or SDS-PAGE purification

  hela wild-type set2δ yeast bottom rp-hplc one-pot

• Application of proteomics methods for pathogen discovery.

  PMID 19751767 · PMC7119679 · Journal of virological methods · 2010 · 8 claims · 6 setups

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  Proteomic techniques can detect and characterize unknown infectious agents in cell culture without prior knowledge of the pathogen

  hlf sequences synthetic conventional 2d-dige gelc-ms

• Human genomic diversity, viral genomics and proteomics, as exemplified by human papillomaviruses and H5N1 influenza viruses.

  PMID 19706363 · PMC3525194 · Human genomics · 2009 · 8 claims · 6 setups

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  A novel HPV type (HPV-85) was identified and phylogenetically characterized, showing closest relatedness to HPV-70/39/18/45/59 within the A7 genital HPV group

  novel hpv gene h5n1 whole-genome intrinsic statistical

• Endogenous retroviruses mediate transcriptional rewiring in response to oncogenic signaling in colorectal cancer.

  PMID 39018396 · PMC466953 · Science advances · 2024 · 8 claims · 8 setups

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  Primate-specific ERVs are a rich source of enhancers displaying cancer-specific activity across multiple tumor types

  cancer hct116 tcga colorectal atac-seq chip-seq bulk