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).

• Duplication count distributions in DNA sequences.

  PMID 19256873 · PMC3121164 · Physical review. E, Statistical, nonlinear, and soft matter physics · 2008 · 8 claims · 8 setups

  Full-text index only

  Duplication count distributions N(c) for complex 40-mers show power-law-like decay for c roughly 3 to 50 (or higher) across human, C. elegans, A. thaliana, and D. melanogaster genomes.

  genome elegans thaliana melanogaster genome-wide transposable homogeneous

• Prediction of prognostic signatures in triple-negative breast cancer based on the differential expression analysis via NanoString nCounter immune panel.

  PMID 33138797 · PMC7607642 · BMC cancer · 2020 · 8 claims · 7 setups

  Has reproduction · 72

  edgeR identifies 9 DEGs associated with pCR and 13 DEGs associated with relapse from 579 immune genes in a small TNBC sample set (n=55)

  ffpe same nanostring training nanostring immunohistochemistry differential

• Boosting accuracy of automated classification of fluorescence microscope images for location proteomics.

  PMID 15207009 · PMC449699 · BMC bioinformatics · 2004 · 8 claims · 8 setups

  Full-text index only

  New classifiers (SVMs, ensembles) and new wavelet-derived (Gabor, Daubechies) features improve recognition of protein subcellular location patterns over the previous neural network approach

  hela automated stepwise training-set-size

• Speeding disease gene discovery by sequence based candidate prioritization.

  PMID 15766383 · PMC1274252 · BMC bioinformatics · 2005 · 7 claims · 8 setups

  Full-text index only

  Disease genes (OMIM) differ significantly from non-disease genes in sequence-based features including gene/cDNA/protein size, exon number, homolog conservation, secretion signal, 3' UTR length, CpG islands, and distance to nearest gene.

  ensembl training same hgmd comparative machine tenfold

• The impact of peptide abundance and dynamic range on stable-isotope-based quantitative proteomic analyses.

  PMID 18798661 · PMC2746028 · Journal of proteome research · 2008 · 8 claims · 7 setups

  Full-text index only

  Over half of confidently identified peptides in complex mixtures have S/N ratios below 10 on both FT-ICR and Orbitrap instruments

  jurkat silac-based sds-page database

• The biological function of some human transcription factor binding motifs varies with position relative to the transcription start site.

  PMID 18367472 · PMC2377430 · Nucleic acids research · 2008 · 8 claims · 5 setups

  Full-text index only

  1226 eight-letter DNA words show statistically significant positional preferences relative to the TSS across 7914 human promoter regions

  putative nonredundant homo genes computational pssm semantic

• Conserved elements with potential to form polymorphic G-quadruplex structures in the first intron of human genes.

  PMID 18187510 · PMC2275096 · Nucleic acids research · 2008 · 8 claims · 6 setups

  Full-text index only

  G-richness downstream of the TSS is strand-biased, concentrated on the nontemplate strand, with a peak at +200 to +300 bp

  refseq chicken random genome-wide quadparser regulatory

• Automatic discovery of 100-miRNA signature for cancer classification using ensemble feature selection.

  PMID 31533612 · PMC6751684 · BMC bioinformatics · 2019 · 7 claims · 8 setups

  Has reproduction · 69

  An ensemble feature selection method based on classifier consensus identifies a robust 100-miRNA signature from TCGA data.

  tcga geo 100-mirna mirna feature bibliographic

• Severe COVID-19 Shares a Common Neutrophil Activation Signature with Other Acute Inflammatory States.

  PMID 35269470 · PMC8909161 · Cells · 2022 · 7 claims · 7 setups

  Has reproduction · 88

  COVID-19 and HLH share immunological pathways, yielding 237 common up-regulated DEGs dominated by cytokine/chemokine signaling and neutrophil-mediated immune responses.

  peripheral leukocytes plasma degs bulk single-cell plasma

• Discovery of protein-protein interactions using a combination of linguistic, statistical and graphical information.

  PMID 15941473 · PMC1164402 · BMC bioinformatics · 2005 · 8 claims · 5 setups

  Full-text index only

  A combined linguistic+statistical+rule-based method achieves precision 0.61 and recall 0.97 (f=0.74) detecting yeast protein-protein interactions across 12,300 Medline abstracts.

  yeast yeast-related interaction random dictionary-based manual graph

• A comparative study of techniques for differential expression analysis on RNA-Seq data.

  PMID 25119138 · PMC4132098 · PloS one · 2014 · 8 claims · 8 setups

  Has reproduction · 58

  edgeR performs slightly better than DESeq and Cuffdiff2 in terms of the ability to uncover true positives.

  brain neurospheres lymphoblastoid simulation single-end paired-end rna-seq

• Assessing the genomic evidence for conserved transcribed pseudogenes under selection.

  PMID 19754956 · PMC2753554 · BMC genomics · 2009 · 8 claims · 8 setups

  Full-text index only

  1750 transcribed pseudogene annotations (TPAs) were identified in the human genome, ~11.5% of all human pseudogene annotations.

  genome rhesus vega-annotated tpas transcript-to-genome same synteny