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

• Revealing the critical state and identifying individualized dynamic network biomarker for type 2 diabetes through advanced analysis methods on individual basis.

  PMID 39890881 · PMC11785715 · Scientific reports · 2025 · 8 claims · 5 setups

  Has reproduction · 75

  sJSD, NIG, and TNFE methods can detect critical states/tipping points before disease deterioration using only a single sample

  simulated adipose gastrocnemius dnb numerical microarray protein-protein

• A simple and efficient algorithm for genome-wide homozygosity analysis in disease.

  PMID 19756043 · PMC2758715 · Molecular systems biology · 2009 · 8 claims · 4 setups

  Full-text index only

  A genome-wide AH analysis (GAHA) algorithm can identify disease-associated loci by comparing frequencies of homozygous segments between cases and controls using a z-statistic proportion test

  unrelated simulated selected genes genome-wide statistical logistic

• nf-core/mag: a best-practice pipeline for metagenome hybrid assembly and binning.

  PMID 35118380 · PMC8808542 · NAR genomics and bioinformatics · 2022 · 8 claims · 7 setups

  Has reproduction · 100

  nf-core/mag is a Nextflow/nf-core pipeline for hybrid metagenome assembly, binning and taxonomic classification of MAGs.

  simulated assembled mags raw metagenomic novo genome

• A non-parametric meta-analysis approach for combining independent microarray datasets: application using two microarray datasets pertaining to chronic allograft nephropathy.

  PMID 18302764 · PMC2276496 · BMC genomics · 2008 · 8 claims · 6 setups

  Full-text index only

  A novel non-parametric meta-analysis approach for combining independent microarray datasets is presented, requiring no distributional assumptions and being logically intuitive.

  kidney same identified additional microarray significance fisher's

• Quantitative serum proteomics using dual stable isotope coding and nano LC-MS/MSMS.

  PMID 19817497 · PMC4684172 · Journal of proteome research · 2009 · 7 claims · 6 setups

  Full-text index only

  DSIC labeling achieves high efficiency: 100% for Cysteine (acrylamide) and 98% for Lysine (succinic anhydride)

  standard dsic-labeled immunodepleted serum labeling quantitative in-solution

• The fragile breakage versus random breakage models of chromosome evolution.

  PMID 16501665 · PMC1378107 · PLoS computational biology · 2006 · 8 claims · 6 setups

  Full-text index only

  Sankoff and Trinh's synteny block identification algorithm (ST-Synteny) is flawed, producing erroneous block identifications even in small toy examples.

  small synthetic synteny random whole-genome

• Glucokinase gene mutations: structural and genotype-phenotype analyses in MODY children from South Italy.

  PMID 18382660 · PMC2270336 · PloS one · 2008 · 8 claims · 6 setups

  Full-text index only

  16 of 30 patients with suspected MODY (53%) carry GCK mutations, confirming GCK MODY diagnosis

  genomic gck fasting pediatric direct molecular biochemical

• Speeding disease gene discovery by sequence based candidate prioritization.

  PMID 15766383 · PMC1274252 · BMC bioinformatics · 2005 · 7 claims · 8 setups

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  Disease genes (OMIM) differ significantly from non-disease genes in sequence-based features including gene/cDNA/protein size, exon number, homolog conservation, secretion signal, 3' UTR length, CpG islands, and distance to nearest gene.

  ensembl training same hgmd comparative machine tenfold