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).

Publications 1.3k Datasets 392.5k Experiments 4

System / cell line: brain ✕ Assay: common ✕ Clear

Phylogenetic reconstruction of ancestral character states for gene expression and mRNA splicing data.

PMID 15921519 · PMC1166541 · BMC bioinformatics · 2005 · 6 claims · 4 setups

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A minimum evolution algorithm (implemented in software 'phyrex') can reconstruct ancestral states of continuous characters like gene expression or splicing levels along a phylogeny

gene upstream chimpanzee reconstructed minimum sequence ancestral
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
Distinct senotypes in p16- and p21-positive cells across human and mouse aging tissues.

PMID 41162753 · PMC12669595 · The EMBO journal · 2025 · 8 claims · 8 setups

Has reproduction · 50

p16+ and p21+ senescent cells are largely distinct, non-overlapping populations across murine and human aging tissues, with only rare double-positive cells

young spleen brain single-cell mass velocity
Bioinformatics and system biology approaches to identify pathophysiological impact of COVID-19 to the progression and severity of neurological diseases.

PMID 34601390 · PMC8483812 · Computers in biology and medicine · 2021 · 8 claims · 8 setups

Has reproduction · 69

COVID-19 and neurological diseases (NDs) share pathophysiological connections that influence disease progression and severity

peripheral hippocampal spinal peritumoral microarray protein-protein

Experiments

Phylogenetic reconstruction of ancestral character states for gene expression and mRNA splicing data.

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

Distinct senotypes in p16- and p21-positive cells across human and mouse aging tissues.

Bioinformatics and system biology approaches to identify pathophysiological impact of COVID-19 to the progression and severity of neurological diseases.