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).

• L2L: a simple tool for discovering the hidden significance in microarray expression data.

  PMID 16168088 · PMC1242216 · Genome biology · 2005 · 8 claims · 4 setups

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  L2L systematically compares a user's differentially expressed gene list against a database of published differentially expressed gene lists to find statistically significant overlaps and generate hypotheses about shared mechanisms

  mammalian user-supplied diabetic uniprot compiled l2l re-analysis

• Gene- and evidence-based candidate gene selection for schizophrenia and gene feature analysis.

  PMID 19944577 · PMC2826526 · Artificial intelligence in medicine · 2010 · 8 claims · 5 setups

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  The SCOR method outperforms the CCOR method for prioritizing schizophrenia candidate genes

  schizophrenia genes ranked gene-based gene expression

• An integrated database of genes responsive to the Myc oncogenic transcription factor: identification of direct genomic targets.

  PMID 14519204 · PMC328458 · Genome biology · 2003 · 8 claims · 6 setups

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  The Myc Target Gene database integrates literature evidence to prioritize candidate Myc-responsive genes and cluster them into functional groups

  p493 rodent types quantitative chromatin northern

• Aberrant 5' splice sites in human disease genes: mutation pattern, nucleotide structure and comparison of computational tools that predict their utilization.

  PMID 17576681 · PMC1934990 · Nucleic acids research · 2007 · 8 claims · 4 setups

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  Cryptic 5'ss are best predicted by computational algorithms that accommodate nucleotide dependencies (e.g., Markov model, maximum entropy, maximum dependence decomposition) rather than by weight-matrix models

  disease mammalian compiled literature minigene computational

• iRefIndex: a consolidated protein interaction database with provenance.

  PMID 18823568 · PMC2573892 · BMC bioinformatics · 2008 · 6 claims · 3 setups

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  A reproducible key (ROG) for each protein interactor and a corresponding key (RIG) for each interaction record can be generated by anyone using only primary sequence, taxonomy identifier, and the SHA-1 algorithm (SEGUID).

  sequence nine interactor seguid parsing mapping

• Macrophages on the run: Exercise balances macrophage polarization for improved health.

  PMID 39476967 · PMC11585839 · Molecular metabolism · 2024 · 8 claims · 7 setups

  Has reproduction · 81

  Immediate/acute exercise triggers an M1 (pro-inflammatory) macrophage polarization surge.

  gene affymetrix pooled muscle meta-analysis stepminer gene

• Pathway-targeting gene matrix for Drosophila gene set enrichment analysis.

  PMID 34710184 · PMC8553153 · PloS one · 2021 · 8 claims · 4 setups

  Has reproduction · 95

  Gene matrix files for GSEA are largely unavailable for Drosophila, limiting pathway-level enrichment analysis in this model organism

  drosophila reactome kegg gene fluorescence manual

• Transcriptional regulation and chromatin architecture maintenance are decoupled functions at the Sox2 locus.

  PMID 35710138 · PMC9296009 · Genes & development · 2022 · 8 claims · 7 setups

  Has reproduction · 81

  Sox2 transcriptional activation is traced almost entirely to two key transcription factor-bound regions (SRR107 and SRR111) within the SCR

  escs esc sequence compiled allele-specific chip-seq motif

• A genome-wide survey of segmental duplications that mediate common human genetic variation of chromosomal architecture.

  PMID 15588494 · PMC3525102 · Human genomics · 2004 · 8 claims · 5 setups

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  PSD-mediated genomic architecture analogous to the 8p23/4p16 inversion regions is not unique to those loci but recurs genome-wide.

  genomic genome extracted pairwise online genome-wide

• 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