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).

• FEDRANN: effective long-read overlap detection based on dimensionality reduction and approximate nearest neighbors.

  PMID 42102720 · PMC13201080 · GigaScience · 2026 · 8 claims · 6 setups

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  A pipeline combining IDF transformation, sparse random projection (SRP), and NNDescent (the FEDRANN strategy) enables accurate overlap detection across diverse long-read datasets

  real same chromosome genome overlap exact simulated

• Duplex-Indel: a Snakemake pipeline for somatic Indel calling in Tn5 transposase-based duplex sequencing data.

  PMID 42046229 · PMC13171174 · Bioinformatics (Oxford, England) · 2026 · 8 claims · 8 setups

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  Duplex-Indel is a Snakemake pipeline for somatic Indel calling from Tn5 transposase-based duplex sequencing data that requires consensus support from both DNA strands to minimize technical artifacts.

  colo829-t colo829-bl colo829-blt duplex tn5 bulk cosine

• Computational verification of protein-protein interactions by orthologous co-expression.

  PMID 15740634 · PMC555590 · BMC bioinformatics · 2005 · 7 claims · 8 setups

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  Co-expression of orthologous protein pairs across multiple species can verify/predict S. cerevisiae PPIs with better performance than S. cerevisiae co-expression alone.

  cerevisiae orthologs cdc28 yeast co-expression ortholog orthologous

• TransOrGAN: An Artificial Intelligence Mapping of Rat Transcriptomic Profiles between Organs, Ages, and Sexes.

  PMID 37200521 · PMC10433534 · Chemical research in toxicology · 2023 · 8 claims · 5 setups

  Has reproduction · 84

  TransOrGAN can infer transcriptomic profiles between any 2 of 9 rat organs with an average cosine similarity of 0.984 versus real profiles

  fischer computational transcriptomic same bulk gan-based autoencoder

• CellFishing.jl: an ultrafast and scalable cell search method for single-cell RNA sequencing.

  PMID 30744683 · PMC6371477 · Genome biology · 2019 · 8 claims · 5 setups

  Has reproduction · 97

  CellFishing.jl achieves accuracy comparable to state-of-the-art software (scmap-cell) but is markedly faster

  scrna-seq shekhar2016 svd lsh hamming

• A taxonomy of epithelial human cancer and their metastases.

  PMID 20017941 · PMC2806369 · BMC medical genomics · 2009 · 8 claims · 6 setups

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  Unsupervised hierarchical clustering of 1566 primary epithelial tumors yields large tissue-enriched clusters (breast, colon/GI, lung, ovary, kidney) plus smaller prostate, thyroid-kidney, and mixed clusters

  epithelial tumor metastatic breast microarray gene fisher

• Uncovering Cas9 PAM diversity through metagenomic mining and machine learning.

  PMID 41656299 · PMC12996302 · Nature communications · 2026 · 8 claims · 6 setups

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  CRISPR-PAMdb is a publicly accessible database compiling Cas9 protein sequences from 3.8 million bacterial/archaeal genomes and PAM profiles from 7.4 million phage/plasmid sequences

  bacterial phage cas9 experimentally hmm-based spacer-protospacer machine

• stDyer-image improves clustering analysis of spatially resolved transcriptomics and proteomics with morphological images.

  PMID 41692960 · PMC12960910 · Bioinformatics (Oxford, England) · 2026 · 8 claims · 5 setups

  Has reproduction · 75

  stDyer-image directly associates the image modality with predicted cluster labels rather than using images to enhance/impute gene expression data

  non-small morphology brain breast spatial image

• An informatics research platform to make public gene expression time-course datasets reusable for more scientific discoveries.

  PMID 33247935 · PMC7698665 · Database : the journal of biological databases and curation · 2020 · 8 claims · 6 setups

  Has reproduction · 75

  GETc enables discovery and visualization of time-course gene expression data and analytical results from GEO

  geo time-course researcher filtered regular metamap ode-based