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).

• AuPairWise: A Method to Estimate RNA-Seq Replicability through Co-expression.

  PMID 27082953 · PMC4833304 · PLoS computational biology · 2016 · 7 claims · 4 setups

  Has reproduction · 88

  Sample-sample correlation of transcript abundances is trivially high regardless of condition and gives misleading estimates of the replicability of conditional (differential) variation in expression.

  encode liver bulk rna-seq meta-analysis

• maxATAC: Genome-scale transcription-factor binding prediction from ATAC-seq with deep neural networks.

  PMID 36719906 · PMC9917285 · PLoS computational biology · 2023 · 8 claims · 6 setups

  Has reproduction · 98

  maxATAC is a suite of deep neural network models enabling state-of-the-art, genome-scale TFBS prediction from ATAC-seq, with models for 127 human transcription factors

  lines hepg2 types single chip-seq omni-atac-seq atac-seq

• CONTRAST: a discriminative, phylogeny-free approach to multiple informant de novo gene prediction.

  PMID 18096039 · PMC2246271 · Genome biology · 2007 · 8 claims · 5 setups

  Full-text index only

  CONTRAST predicts exact coding region structures for 65% more human genes than the previous state-of-the-art de novo predictor (N-SCAN)

  genome sequence drosophila novo gene coding

• 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

• Strong signature of natural selection within an FHIT intron implicated in prostate cancer risk.

  PMID 18953408 · PMC2568805 · PloS one · 2008 · 8 claims · 8 setups

  Full-text index only

  Re-sequencing and genotyping across a 28.5 kb region delineates the prostate cancer risk association within FHIT intron 5 to a 15 kb LD block in European-Americans.

  european-american yoruban japanese case sanger snp linkage