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).

• Evaluation of the bacterial diversity among and within individual venous leg ulcers using bacterial tag-encoded FLX and titanium amplicon pyrosequencing and metagenomic approaches.

  PMID 19860898 · PMC2773781 · BMC microbiology · 2009 · 7 claims · 5 setups

  Full-text index only

  VLU infections are polymicrobial with no single bacterium colonizing the wounds

  individual pooled second btefap quantitative bulk

• Mapping protein abundance patterns in the brain using voxelation combined with liquid chromatography and mass spectrometry.

  PMID 19654045 · PMC2818068 · Methods (San Diego, Calif.) · 2010 · 8 claims · 5 setups

  Full-text index only

  Voxelation combined with LC-MS enables high-throughput spatial mapping of protein abundance across mouse brain voxels

  brain digested voxel amt-tag lc-ms bca

• Compressing DNA sequence databases with coil.

  PMID 18489794 · PMC2426707 · BMC bioinformatics · 2008 · 8 claims · 1 setups

  Full-text index only

  coil achieves higher compression ratio than state-of-the-art general-purpose compression tools on a large GenBank EST database file

  large sequence

• The Drosophila estrogen-related receptor promotes triglyceride storage within the larval fat body.

  PMID 40288680 · PMC12155637 · Journal of lipid research · 2025 · 8 claims · 8 setups

  Has reproduction · 88

  dERR autonomously promotes TAG accumulation within larval fat body cells

  mid-l2 larval dissected tag immunofluorescence nile

• A rational approach for discovering and validating cancer markers in very small samples using mass spectrometry and ELISA microarrays.

  PMID 15502246 · PMC3839270 · Disease markers · 2004 · 8 claims · 4 setups

  Full-text index only

  A two-stage strategy combining MS proteomics for discovery and ELISA microarrays for validation can identify and characterize cancer markers in very small samples

  complex naf minute clc-fticr tandem elisa

• Construction and analysis of tag single nucleotide polymorphism maps for six human-mouse orthologous candidate genes in type 1 diabetes.

  PMID 15720714 · PMC551616 · BMC genetics · 2005 · 7 claims · 5 setups

  Full-text index only

  None of the six candidate gene regions showed evidence of association with type 1 diabetes (all multi-locus/single-locus test P values > 0.2)

  genomic case-control nramp1 type sanger snp microsatellite

• NEIBank: genomics and bioinformatics resources for vision research.

  PMID 18648525 · PMC2480482 · Molecular vision · 2008 · 8 claims · 7 setups

  Full-text index only

  NEIBank is an integrated genomics and bioinformatics resource for vision research, combining EST/cDNA clone data, SAGE expression data, and eye disease gene databases.

  dissected eye retina cdna est serial sequence

• Power analysis for genome-wide association studies.

  PMID 17725844 · PMC2042984 · BMC genetics · 2007 · 8 claims · 6 setups

  Full-text index only

  Developed a method to compute genome-wide association study power using tag SNPs and representative population genotype data (HapMap), equivalent to the cumulative r2-adjusted power of Jorgenson and Witte.

  hapmap power pairwise tag

• Comparing cellular proteomes by mass spectrometry.

  PMID 19886975 · PMC2784314 · Genome biology · 2009 · 8 claims · 6 setups

  Full-text index only

  MS-based proteomics combined with cryo-electron tomography (CET) enables determination of absolute and relative protein abundances and localization

  leptospira saccharomyces specified shotgun selected cryo-electron

• Up regulation in gene expression of chromatin remodelling factors in cervical intraepithelial neoplasia.

  PMID 18248679 · PMC2277413 · BMC genomics · 2008 · 8 claims · 4 setups

  Full-text index only

  Chromatin remodelling-associated genes SMARCC1, NCOR1, MRFAP1 and MORF4L2 are upregulated during progression of cervical intraepithelial neoplasia

  cervical independent computational long real-time gene

• Integration of cytogenetic landmarks into the draft sequence of the human genome.

  PMID 11237021 · PMC7845515 · Nature · 2001 · 8 claims · 6 setups

  Full-text index only

  7,600 cytogenetically defined landmarks (from a set of 8,877 clones) were placed on the draft sequence of the human genome as a public resource

  large-insert bac ml-2 dgap012 fluorescence sts array

• Annotation and analysis of 10,000 expressed sequence tags from developing mouse eye and adult retina.

  PMID 14519200 · PMC328454 · Genome biology · 2003 · 8 claims · 5 setups

  Full-text index only

  Annotation of 8,633 high-quality non-mitochondrial/non-ribosomal ESTs shows 57% represent known genes and 43% are unknown or novel, with M15E having the highest proportion of novel ESTs

  embryonic high-quality unique m15e est sequence comparative

• Comparing protein abundance and mRNA expression levels on a genomic scale.

  PMID 12952525 · PMC193646 · Genome biology · 2003 · 8 claims · 8 setups

  Full-text index only

  Correlations between mRNA expression and protein abundance are generally poor or limited across most studies reviewed, including in yeast and human cancers

  yeast laser-dissected serum myeloid two-dimensional seldi-tof isotope-coded

• Post-translational generation of constitutively active cores from larger phosphatases in the malaria parasite, Plasmodium falciparum: implications for proteomics.

  PMID 15230980 · PMC459218 · BMC molecular biology · 2004 · 8 claims · 8 setups

  Full-text index only

  P. falciparum produces full-length PfCnA/PfCnB (calcineurin) and PP7 as well as proteolytically processed catalytic cores in vivo, likely as intermediates of a degradation pathway

  falciparum coli native falciparum-infected rt-pcr recombinant peptide

• A new family of giardial cysteine-rich non-VSP protein genes and a novel cyst protein.

  PMID 17183673 · PMC1762436 · PloS one · 2006 · 8 claims · 7 setups

  Full-text index only

  HCNCp is a novel invariant (non-variant) cyst protein belonging to a new family of high-cysteine membrane proteins (HCMp) abundant in the Giardia genome

  giardia serial northern western

• Association of autism with polymorphisms in the paired-like homeodomain transcription factor 1 (PITX1) on chromosome 5q31: a candidate gene analysis.

  PMID 18053270 · PMC2222245 · BMC medical genetics · 2007 · 8 claims · 6 setups

  Full-text index only

  PITX1 polymorphisms and haplotypes are significantly associated with autism

  agre pitx1 parental family-based extended haplotype

• Genome-wide identification of in vivo protein-DNA binding sites from ChIP-Seq data.

  PMID 18684996 · PMC2532738 · Nucleic acids research · 2008 · 8 claims · 7 setups

  Full-text index only

  SISSRs identifies binding sites from ChIP-Seq short reads with much higher resolution than the standard region-clustering approach

  cd4+ jurkat hela computational chip-seq novo motif

• Point mutations in GLI3 lead to misregulation of its subcellular localization.

  PMID 19829694 · PMC2758996 · PloS one · 2009 · 6 claims · 8 setups

  Full-text index only

  The MID1-α4-PP2A complex regulates the subcellular localization and transcriptional activity of GLI3.

  hela immunofluorescence real-time luciferase

• Nucleosome deposition and DNA methylation at coding region boundaries.

  PMID 19723310 · PMC2768978 · Genome biology · 2009 · 8 claims · 8 setups

  Full-text index only

  Nucleosomes and DNA methylation form distinct peaks just downstream of the start codon and just upstream of the stop codon, marking both ends of protein coding units genome-wide.

  yeast drosophila resting naive nucleosome methylation pol

• A well-conserved Plasmodium falciparum var gene shows an unusual stage-specific transcript pattern.

  PMID 12787360 · PMC2869446 · Molecular microbiology · 2003 · 8 claims · 8 setups

  Full-text index only

  Full-length var transcripts (detected by the complex var exon 2 probe) are present only in ring stages, not in pigmented trophozoites, across multiple parasite lines

  falciparum red northern static rt-pcr