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).

• Investigating hookworm genomes by comparative analysis of two Ancylostoma species.

  PMID 15854223 · PMC1112591 · BMC genomics · 2005 · 8 claims · 8 setups

  Full-text index only

  Nearly 20,000 ESTs from 7 cDNA libraries define nearly 7,000 hookworm genes across A. caninum and A. ceylanicum

  caninum ceylanicum est bioinformatic functional

• Versatile online-offline engine for automated acquisition of high-resolution tandem mass spectra.

  PMID 18841935 · PMC2716176 · Analytical chemistry · 2008 · 7 claims · 6 setups

  Full-text index only

  An integrated hardware/software online-offline platform (TriVersa NanoMate + 12T LTQ FT Ultra + AUTOMATION WAREHOUSE) automates collection of high-resolution MS/MS data for polypeptides >3 kDa that cannot be acquired online on a chromatographic timescale

  acid-extracted hela online offline

• Extensive chromatin fragmentation improves enrichment of protein binding sites in chromatin immunoprecipitation experiments.

  PMID 18765474 · PMC2577354 · Nucleic acids research · 2008 · 6 claims · 6 setups

  Full-text index only

  Extensive sonication reduces crosslinked chromatin to an average fragment size of ~200 bp (range 75–300 bp) and fragmentation is largely random with respect to genomic region and nucleosome position.

  cerevisiae hela chip-qpcr nucleosome gel

• transXpress: a Snakemake pipeline for streamlined de novo transcriptome assembly and annotation.

  PMID 37016291 · PMC10074830 · BMC bioinformatics · 2023 · 6 claims · 7 setups

  Has reproduction · 95

  transXpress is a Snakemake pipeline that streamlines de novo transcriptome assembly, quantification, and annotation for non-model organisms

  piper assembled longum predicted rna-seq novo transcriptome

• 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

• Increased DNA microarray hybridization specificity using sscDNA targets.

  PMID 15847692 · PMC1090574 · BMC genomics · 2005 · 7 claims · 5 setups

  Full-text index only

  A single round of ribo-SPIA amplification produces sufficient sscDNA for microarray hybridization from as little as 5 ng of starting total RNA

  cuhr k562 input sscdna microarray quantitative capillary

• Protein isoaspartate methyltransferase prevents apoptosis induced by oxidative stress in endothelial cells: role of Bcl-Xl deamidation and methylation.

  PMID 18806875 · PMC2532751 · PloS one · 2008 · 8 claims · 8 setups

  Full-text index only

  PCMT overexpression protects porcine aortic endothelial cells (PAEC) from H2O2-induced apoptosis, raising the threshold H2O2 concentration required to trigger cell death.

  porcine paec umbilical huvec methyltransferase sds-page fragmentation

• Global mapping of the topography and magnitude of proteolytic events in apoptosis.

  PMID 18724940 · PMC2597167 · Cell · 2008 · 7 claims · 6 setups

  Full-text index only

  PROTOMAP, a method combining 1D SDS-PAGE fractionation with LC-MS/MS-derived sequence coverage and spectral counting visualized as 'peptographs', enables global mapping of proteolytic topography and magnitude

  jurkat sds-page fragmentation caspase-3

• Targeted KRAS mutation assessment on patient tumor histologic material in real time diagnostics.

  PMID 19888477 · PMC2768905 · PloS one · 2009 · 8 claims · 5 setups

  Full-text index only

  Q-PCR methods yield informative KRAS mutation results even on very fragmented FFPE-DNA where dideoxy-sequencing fails (p<0.0001)

  ffpe dideoxy-sequencing taqman-mgb dxs-kras

• Shotgun proteomics and biomarker discovery.

  PMID 12364816 · PMC3851423 · Disease markers · 2002 · 8 claims · 7 setups

  Full-text index only

  Shotgun (LC/LC-MS/MS, e.g. MudPIT) proteomic approaches show advantages over gel-based techniques in speed, sensitivity, scope of analysis, and dynamic range.

  urine yeast cysteine-containing hemoglobin 2d-ge lc-ms imac

• Evolution of variants of yeast site-specific recombinase Flp that utilize native genomic sequences as recombination target sites.

  PMID 17003057 · PMC1635253 · Nucleic acids research · 2006 · 8 claims · 8 setups

  Full-text index only

  Stepwise directed evolution using chimeric FLRT (FRT/genomic hybrid) intermediate sites can generate Flp variants capable of recombining native genomic FRT-like sequences from the human IL10 gene (FL-IL10A, FL-IL10B).

  coli flp il10 flp-holliday recombination site-specific computational