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).

• ORFer--retrieval of protein sequences and open reading frames from GenBank and storage into relational databases or text files.

  PMID 12493080 · PMC139979 · BMC bioinformatics · 2002 · 6 claims · 6 setups

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  ORFer retrieves protein and nucleic acid sequences and annotations from NCBI GenBank using the XML sequence format

  sequences parsed bacillus anopheles large-scale sequence orf

• Digital evolution.

  PMID 14551915 · PMC212697 · PLoS biology · 2003 · 7 claims · 5 setups

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  Digital organisms (Avidians) evolved from simple self-replicators, through an unexpected transitional form, to complex performers of many logic functions, with the full genealogy traceable and no missing links.

  digital bacteria long-term digital test gene-expression

• PRESTO: rapid calculation of order statistic distributions and multiple-testing adjusted P-values via permutation for one and two-stage genetic association studies.

  PMID 18620604 · PMC2483288 · BMC bioinformatics · 2008 · 8 claims · 4 setups

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  PRESTO is an order of magnitude faster than other existing permutation testing software for genetic association studies.

  case-control same wtccc genome-wide benchmark stratified

• Integrating herbarium specimen observations into global phenology data systems.

  PMID 30937223 · PMC6426164 · Applications in plant sciences · 2019 · 7 claims · 5 setups

  Has reproduction · 60

  A new PPO release adds terms and properties to relate observations of parts of plants to whole plants, enabling integration of herbarium phenology data with field observation data.

  plant prunus serotina ontology phenological integration

• Shiny-Calorie: a context-aware application for indirect calorimetry data analysis and visualization using R.

  PMID 41640623 · PMC12867577 · Bioinformatics advances · 2026 · 8 claims · 8 setups

  Has reproduction · 100

  Shiny-Calorie is an open-source interactive application for transparent data and metadata integration, statistical analysis, and visualization of indirect calorimetry datasets.

  datasets clinical calr imported indirect import physical

• Serum diagnosis of diffuse large B-cell lymphomas and further identification of response to therapy using SELDI-TOF-MS and tree analysis patterning.

  PMID 18163913 · PMC2242801 · BMC cancer · 2007 · 8 claims · 8 setups

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  SELDI-TOF-MS serum proteomic patterns analyzed by decision tree classification (Biomarker Pattern Software) can discriminate DLBCL patients from healthy controls with high sensitivity and specificity.

  serum seldi dlbcl pooled seldi-tof-ms proteinchip decision

• Sustainable data analysis with Snakemake.

  PMID 34035898 · PMC8114187 · F1000Research · 2021 · 8 claims · 4 setups

  Has reproduction · 71

  Reproducibility alone is insufficient for sustainable data analysis; transparency and adaptability are equally important additional properties.

  snakemake example citation software readability

• GoMiner: a resource for biological interpretation of genomic and proteomic data.

  PMID 12702209 · PMC154579 · Genome biology · 2003 · 8 claims · 4 setups

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  GoMiner organizes 'interesting' gene lists (e.g., differentially expressed genes) into the Gene Ontology hierarchy for biological interpretation, displaying results as both a tree and a directed acyclic graph (DAG).

  du145 gene gominer cdna flow category

• Hyb: a bioinformatics pipeline for the analysis of CLASH (crosslinking, ligation and sequencing of hybrids) data.

  PMID 24211736 · PMC3969109 · Methods (San Diego, Calif.) · 2014 · 8 claims · 6 setups

  Has reproduction · 71

  The 'hyb' pipeline detects, calls, folds and annotates chimeric reads from CLASH high-throughput sequencing data.

  ago1 test clash multiplexed clash benchmarking demultiplexing

• Compression of structured high-throughput sequencing data.

  PMID 24260313 · PMC3832420 · PloS one · 2013 · 8 claims · 7 setups

  Has reproduction · 43

  Leveraging an explicit data schema (separate field encoding, field modeling, template compression, domain modeling) enables stronger compression of HTS alignment data than general-purpose compression of serialized bytes.

  benchmark ten rna-seq exome genome

• Genome-wide copy number profiling on high-density bacterial artificial chromosomes, single-nucleotide polymorphisms, and oligonucleotide microarrays: a platform comparison based on statistical power analysis.

  PMID 17363414 · PMC2779891 · DNA research : an international journal for rapid publication of reports on genes and genomes · 2007 · 8 claims · 6 setups

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  High-density oligonucleotide/SNP platforms are superior to the BAC platform for genome-wide detection of copy-number variations smaller than 1 Mb

  genomic normalized simulated tiling-resolution snp oligonucleotide

• A case study for large-scale human microbiome analysis using JCVI's metagenomics reports (METAREP).

  PMID 22719821 · PMC3374610 · PloS one · 2012 · 8 claims · 7 setups

  Has reproduction · 78

  METAREP version 1.3.1 is an open-source, scalable tool for querying, browsing and comparing extremely large volumes of metagenomic annotations, with an extended data model, dynamic weighting, distributed searches and advanced clustering.

  microbiome pooled hmp metarep genome assembly-based enzymatic

• Genomic variation in myeloma: design, content, and initial application of the Bank On A Cure SNP Panel to detect associations with progression-free survival.

  PMID 18778477 · PMC2553089 · BMC medicine · 2008 · 7 claims · 7 setups

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  A custom BOAC SNP panel of 3404 SNPs in 983 genes was developed using the Affymetrix GeneChip Targeted Genotyping Platform, focused on non-synonymous coding SNPs and regulatory-region SNPs in candidate genes.

  coriell myeloma duplicate snp targeted genotyping machine