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).

• Improved epigenetic age prediction models by combining sex chromosome and autosomal markers.

  PMID 40665390 · PMC12261677 · Epigenetics & chromatin · 2025 · 7 claims · 5 setups

  Has reproduction · 48

  Combining sex chromosomal DNAm markers with autosomal age-informative markers can produce a high-accuracy age prediction model competitive with autosomal-only models

  blood buffy methylation random spearman

• A mechanistic model captures the emergence and implications of non-genetic heterogeneity and reversible drug resistance in ER+ breast cancer cells.

  PMID 34316714 · PMC8271219 · NAR cancer · 2021 · 7 claims · 8 setups

  Has reproduction · 85

  EMT and tamoxifen-resistance (TamR) regulatory axes can drive one another, enabling non-genetic heterogeneity via six co-existing phenotypes (ES, ER, HS, HR, MS, MR)

  gene same randomized publicly racipe stochastic randomized

• Predicting the pathogenicity of missense variants using features derived from AlphaFold2.

  PMID 37084271 · PMC10203375 · Bioinformatics (Oxford, England) · 2023 · 6 claims · 8 setups

  Has reproduction · 85

  AlphaFold2-derived structural features (solvent accessibility, amino acid network features, physicochemical environment, pLDDT) can be used to train a random forest classifier (AlphScore) that distinguishes proxy-benign from proxy-pathogenic missense variants.

  gnomad alphafold2-predicted alphscore proteins machine secondary physicochemical

• Gene Set Enrichment Analysis Reveals Individual Variability in Host Responses in Tuberculosis Patients.

  PMID 34421903 · PMC8375662 · Frontiers in immunology · 2021 · 8 claims · 8 setups

  Has reproduction · 71

  TB patients show substantial individual variability in the intensity of hallmark IFN responses, as well as in complement system, metabolic, and other pathway responses.

  blood cynomolgus external gene differential principal

• A temporal classifier predicts histopathology state and parses acute-chronic phasing in inflammatory bowel disease patients.

  PMID 36694043 · PMC9873918 · Communications biology · 2023 · 8 claims · 7 setups

  Has reproduction · 83

  The DSS phenotype-by-time interaction defines parsimonious temporal (dynamic) expression and splicing signatures of acute and chronic colitis distinct from time-specific differential expression.

  intestine colon dss distal bulk phenotypic h&e

• Optimal scaling of digital transcriptomes.

  PMID 24223126 · PMC3819321 · PloS one · 2013 · 8 claims · 8 setups

  Has reproduction · 67

  Fifteen existing and novel transcript-count normalization algorithms can be compared with two novel, mutually independent metrics: the number of "uniform" genes (sufficiently low coefficient of variation after normalization) and low average Spearman correlation between normalized expression profiles of gene pairs.

  tissues bodymap mapped 16-sample bulk read transcript

• Minimal metabolic pathway structure is consistent with associated biomolecular interactions.

  PMID 24987116 · PMC4299494 · Molecular systems biology · 2014 · 8 claims · 8 setups

  Has reproduction · 30

  MinSpan, a mixed-integer linear optimization algorithm, computes the shortest, linearly independent pathways (sparsest basis of the null space of the stoichiometric matrix S) for genome-scale metabolic networks, which convex approaches (extreme pathways, elementary flux modes) cannot do at genome scale.

  simplified genome-scale cerevisiae coli minspan spearman comparative

• A global view of protein expression in human cells, tissues, and organs.

  PMID 20029370 · PMC2824494 · Molecular systems biology · 2009 · 7 claims · 6 setups

  Full-text index only

  A high fraction (>65%) of proteins is expressed in most human cells and tissues, while very few proteins (<2%) are detected in any single cell type.

  normal computational hepatocytes same immunohistochemistry immunofluorescence unsupervised

• Extraction of human kinase mutations from literature, databases and genotyping studies.

  PMID 19758464 · PMC2745582 · BMC bioinformatics · 2009 · 7 claims · 6 setups

  Full-text index only

  A literature mining pipeline combining MutationFinder, false-positive filtering, and SVM-based classification can extract and disambiguate single-point mutation mentions from abstracts and full text

  pubmed large labeled swissprot literature supervised comparative

• Emergent dynamics of underlying regulatory network links EMT and androgen receptor-dependent resistance in prostate cancer.

  PMID 36851919 · PMC9957767 · Computational and structural biotechnology journal · 2023 · 8 claims · 7 setups

  Has reproduction · 78

  Simulations of the EMT-AR crosstalk network reveal four possible phenotypes: epithelial-sensitive (ES), epithelial-resistant (ER), mesenchymal-resistant (MR), and mesenchymal-sensitive (MS), with MS occurring rarely

  gene racipe clinical tcga racipe influence principal

• 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

• Genome-wide analysis of human disease alleles reveals that their locations are correlated in paralogous proteins.

  PMID 18989397 · PMC2565504 · PLoS computational biology · 2008 · 7 claims · 5 setups

  Full-text index only

  The locations of sequence variants are correlated between paralogous human proteins more than expected by chance.

  dbsnp best-hit omicia hgmd genome-wide correlation disease