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).

• A comprehensive literature review of haplotyping software and methods for use with unrelated individuals.

  PMID 15814067 · PMC3525117 · Human genomics · 2005 · 7 claims · 2 setups

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  Forty-six haplotyping programs were identified and reviewed, split into 43 designed for individual genotype data and three designed for pooled DNA samples.

  pubmed identified literature software

• MasterOfPores: A Workflow for the Analysis of Oxford Nanopore Direct RNA Sequencing Datasets.

  PMID 32256520 · PMC7089958 · Frontiers in genetics · 2020 · 8 claims · 5 setups

  Has reproduction · 50

  MasterOfPores is a scalable, parallelizable, containerized (Docker/Singularity) NextFlow workflow for analyzing Oxford Nanopore direct RNA sequencing datasets

  cerevisiae barcoded direct polya modification

• QuasiFlow: a Nextflow pipeline for analysis of NGS-based HIV-1 drug resistance data.

  PMID 36699347 · PMC9722223 · Bioinformatics advances · 2022 · 6 claims · 8 setups

  Has reproduction · 78

  QuasiFlow is a Nextflow pipeline that runs entirely locally via command-line tools and a local HIVdb database copy to analyze NGS-based HIV-1 drug resistance testing data.

  hiv-1 same paired-end reads ngs-based concordance read

• Tracing human genetic histories and natural selection with precise local ancestry inference.

  PMID 40379651 · PMC12084304 · Nature communications · 2025 · 7 claims · 7 setups

  Has reproduction · 76

  Orchestra, a two-stage LAI method combining a recombination-distance base layer with a deep learning (convolutional + attention) smoothing module, outperforms RFmix, FLARE and Gnomix in precision and recall across simulated admixture generations.

  1kgp-16pops independent simulated 1kgp simulated population-level local

• 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

• Discovery of protein-protein interactions using a combination of linguistic, statistical and graphical information.

  PMID 15941473 · PMC1164402 · BMC bioinformatics · 2005 · 8 claims · 5 setups

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  A combined linguistic+statistical+rule-based method achieves precision 0.61 and recall 0.97 (f=0.74) detecting yeast protein-protein interactions across 12,300 Medline abstracts.

  yeast yeast-related interaction random dictionary-based manual graph

• ADaCGH: A parallelized web-based application and R package for the analysis of aCGH data.

  PMID 17710137 · PMC1940324 · PloS one · 2007 · 8 claims · 4 setups

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  ADaCGH implements eight CNA detection methods, including the best-performing ones from recent reviews (CBS, GLAD, CGHseg, HMM)

  30-node web-based cluster simulated computational web comparison

• The specificity and polymorphism of the MHC class I prevents the global adaptation of HIV-1 to the monomorphic proteasome and TAP.

  PMID 18949050 · PMC2569417 · PloS one · 2008 · 6 claims · 5 setups

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  Within individual hosts, proteasome and TAP escape mutations in HIV-1 occur frequently

  hiv-1 hla-genotyped predicted bioinformatic longitudinal ancestral

• Manual validation finds ultra-long-read sequencing best enables faithful, population-level structural variant calling in Drosophila melanogaster euchromatin with nanopore.

  PMID 41806374 · PMC13148403 · G3 (Bethesda, Md.) · 2026 · 8 claims · 5 setups

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  Only ultra-long long-reads (N50 > 50 kb) are capable of accurately calling structural variants of any size in D. melanogaster euchromatin

  inbred downsampled aligned putative ont illumina novo

• Identification of Radiation-Induced Injury Pathways and Hub Genes from RNA-Seq Data Based on Integrative Bioinformatics Approach.

  PMID 42074497 · PMC13116960 · Genes · 2026 · 8 claims · 6 setups

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  Ionizing radiation induces extensive transcriptome reprogramming in mouse bone marrow HSCs 3 days after whole-body irradiation.

  bone deg transcriptome deg-encoded rna-seq gene kegg

• scATD: a high-throughput and interpretable framework for single-cell cancer drug resistance prediction and biomarker identification.

  PMID 40501071 · PMC12159290 · Briefings in bioinformatics · 2025 · 8 claims · 6 setups

  Has reproduction · 62

  scATD enables high-throughput single-cell drug sensitivity prediction for new patients without model parameter retraining via bidirectional Bi-AdaIN style transfer

  panglaodb cancer geo gse137829 single-cell bulk

• singIST: An integrative method for comparative single-cell transcriptomics between disease models and humans.

  PMID 41838773 · PMC13008255 · PLoS computational biology · 2026 · 8 claims · 7 setups

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  singIST provides explainable quantitative measures of disease model similarity to a human reference at the pathway, cell type, and gene levels

  skin ear simulated scrna-seq simulation