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).

• NETISCE: a network-based tool for cell fate reprogramming.

  PMID 35725577 · PMC9209484 · NPJ systems biology and applications · 2022 · 8 claims · 4 setups

  Has reproduction · 85

  NETISCE predicts cell fate reprogramming targets in static (GRN/signaling) networks without needing full kinetic parameterization of a dynamical model.

  ascidian pluripotent drosophila signal fvs-finding sfa

• Graph Random Forest: A Graph Embedded Algorithm for Identifying Highly Connected Important Features.

  PMID 37509188 · PMC10377046 · Biomolecules · 2023 · 8 claims · 3 setups

  Has reproduction · 89

  Graph Random Forest (GRF) embeds graph/network information directly into the decision-tree building process by splitting on features in the k-hop neighborhood of a data-driven head-splitting node.

  scale-free non-small embryonic simulation rna-seq

• The stem cell population of the human colon crypt: analysis via methylation patterns.

  PMID 17335343 · PMC1808490 · PLoS computational biology · 2007 · 8 claims · 3 setups

  Full-text index only

  A coalescent-based, full probabilistic model with MCMC Bayesian inference provides a more powerful alternative to prior forward-simulation approaches for analyzing methylation pattern data from crypts.

  colon computational simulated bisulfite coalescent posterior

• Massively parallel genomic perturbations with multi-target CRISPR interrogates Cas9 activity and DNA repair at endogenous sites.

  PMID 36064968 · PMC9481459 · Nature cell biology · 2022 · 8 claims · 6 setups

  Has reproduction · 98

  Multi-target gRNAs (mgRNAs) can direct Cas9 to over a hundred well-mapped endogenous genomic sites simultaneously, enabling massively parallel, high-throughput interrogation of Cas9 activity via short-read sequencing

  hg38 hela hek293t induced genome-wide high-throughput chip-seq

• Sequence polymorphisms cause many false cis eQTLs.

  PMID 17637838 · PMC1906859 · PloS one · 2007 · 8 claims · 7 setups

  Full-text index only

  Many reported local/cis eQTLs are false positives caused by probe-region sequence polymorphisms affecting hybridization rather than true cis-regulatory expression differences.

  lymphoblastoid hematopoietic caenorhabditis genome anova-based sanger eqtl

• Patrocles: a database of polymorphic miRNA-mediated gene regulation in vertebrates.

  PMID 19906729 · PMC2808989 · Nucleic acids research · 2010 · 8 claims · 6 setups

  Full-text index only

  Patrocles is a database compiling DSPs predicted to perturb miRNA-mediated gene regulation across seven vertebrate species, covering targets, miRNA precursors and silencing machinery.

  3'-utr mirbase hapmap comparative snp mirna

• An intergenic non-coding rRNA correlated with expression of the rRNA and frequency of an rRNA single nucleotide polymorphism in lung cancer cells.

  PMID 19838300 · PMC2759515 · PloS one · 2009 · 8 claims · 7 setups

  Full-text index only

  An nc-rRNA is transcribed from the intergenic spacer upstream of the rRNA transcription start site in human lung epithelial and lung cancer cells, spanning roughly -1000 to at least +203/+300.

  lung hpl1d rrna external pcr rt-pcr quantitative