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).

• MoDLE: high-performance stochastic modeling of DNA loop extrusion interactions.

  PMID 36451166 · PMC9710047 · Genome biology · 2022 · 8 claims · 6 setups

  Has reproduction · 50

  MoDLE is a high-performance stochastic model/software for simulating DNA-DNA contacts generated by loop extrusion genome-wide

  h1-hesc five synthetic chip-seq stochastic molecular

• A workflow reproducibility scale for automatic validation of biological interpretation results.

  PMID 37150537 · PMC10164546 · GigaScience · 2022 · 8 claims · 4 setups

  Has reproduction · 100

  Comparing output files by checksum alone is insufficient to verify reproducibility, since checksums can differ even when the underlying biological interpretation is unchanged

  nf-core sam vcf workflow checksum biological workflow

• StatsDB: platform-agnostic storage and understanding of next generation sequencing run metrics.

  PMID 24627795 · PMC3938176 · F1000Research · 2013 · 8 claims · 6 setups

  Has reproduction · 43

  StatsDB is an open-source software package for storage and analysis of next generation sequencing run metrics, backed by an SQL (MySQL) database with Perl and Java APIs.

  fastq mysql perl java fastqc relational programmatic

• Segzoo: a turnkey system that summarizes genome annotations.

  PMID 42087325 · PMC13189851 · Bioinformatics (Oxford, England) · 2026 · 7 claims · 4 setups

  Full-text index only

  Segzoo is a turnkey system that automates downloading of reference data and running of analyses to summarize SAGA genome annotations, requiring only a BED-format annotation file as input

  embryonic segway chip-seq segway segtools

• Alignoth: portable and interactive visualization of read alignments.

  PMID 41392197 · PMC12777968 · Bioinformatics (Oxford, England) · 2026 · 8 claims · 3 setups

  Full-text index only

  Alignoth is a command-line tool that generates self-contained, portable HTML reports of DNA sequencing read alignment pileups, with export to PNG, SVG, PDF, and JSON.

  synthetic test genomic report browser output

• HTSQualC is a flexible and one-step quality control software for high-throughput sequencing data analysis.

  PMID 34548573 · PMC8455540 · Scientific reports · 2021 · 8 claims · 5 setups

  Has reproduction · 89

  HTSQualC is a standalone, one-step QC software that performs filtering and trimming of raw HTS data in a single run

  cotton sugarcane tomato illumina single-end paired-end runtime

• Cyrface: An interface from Cytoscape to R that provides a user interface to R packages.

  PMID 24715956 · PMC3962008 · F1000Research · 2013 · 8 claims · 6 setups

  Has reproduction · 67

  Cyrface is a Cytoscape app/Java library providing a general interface from Cytoscape (Java) to any R function or package.

  cytoscape generated prior-knowledge iris software datarail logic

• Genetic requirement for pneumococcal ear infection.

  PMID 18670623 · PMC2593789 · PloS one · 2007 · 7 claims · 8 setups

  Full-text index only

  STM screening of 5,280 S. pneumoniae ST556 mutants in a chinchilla middle ear infection model identified 169 genes required for ear infection

  pneumoniae bioluminescent balb signature-tagged bioluminescent transmission

• Development of animal models to test the fundamental basis of gene-environment interactions.

  PMID 19037209 · PMC2703424 · Obesity (Silver Spring, Md.) · 2008 · 8 claims · 8 setups

  Full-text index only

  Selective breeding for low and high intrinsic aerobic treadmill running capacity produced divergent rat lines (LCR and HCR) that contrast in propensity for complex disease

  nih-derived lcr carotid treadmill body maximal

• Detecting purely epistatic multi-locus interactions by an omnibus permutation test on ensembles of two-locus analyses.

  PMID 19761607 · PMC2759961 · BMC bioinformatics · 2009 · 8 claims · 5 setups

  Full-text index only

  2LOmb performs an omnibus permutation test on ensembles of two-locus analyses via a four-step algorithm (two-locus analysis, permutation test, global p-value determination, progressive ensemble search)

  simulated same snp type two-locus 2lomb benchmark

• The origins of lactase persistence in Europe.

  PMID 19714206 · PMC2722739 · PLoS computational biology · 2009 · 8 claims · 5 setups

  Full-text index only

  The −13,910*T allele first underwent selection among dairying farmers around 7,500 years ago in a region between the central Balkans and central Europe, possibly linked to the Linearbandkeramik culture.

  simulated simulation 910*t farming demic approximate comparison

• Optimizing data-driven excellence: Canada's approach to using pathogen test datasets for quality control, pipeline development and training initiatives.

  PMID 41591806 · PMC12847982 · Microbial genomics · 2026 · 8 claims · 5 setups

  Full-text index only

  Standardized SARS-CoV-2 test datasets (Illumina and Nanopore) were developed as benchmarks for validating sequencing/bioinformatics pipelines across Canadian public health labs

  sars-cov-2 extracted nasopharyngeal bioinformatic whole-genome triplex extraction

• Defining the signature of deformable and infectious Plasmodium falciparum gametocytes.

  PMID 42064353 · PMC13126010 · Wellcome open research · 2026 · 7 claims · 7 setups

  Full-text index only

  Deformable gametocytes are immediately infectious upon release from the bone marrow into circulation.

  synchronized falciparum blood microsphere bulk exflagellation

• The evolutionary dynamics of a rapidly mutating virus within and between hosts: the case of hepatitis C virus.

  PMID 19911046 · PMC2768904 · PLoS computational biology · 2009 · 8 claims · 3 setups

  Full-text index only

  The replication rate of the strain that initiates an infection has a strong effect on the fitness of the infection at the between-host level, even though the virus evolves rapidly within the host.

  computational same simulation stochastic parameter-sweep multivariate

• Accurate prediction of metagenome-assembled genome completeness by MAGISTA, a random forest model built on alignment-free intra-bin statistics.

  PMID 35248155 · PMC8898458 · Environmental microbiome · 2022 · 7 claims · 7 setups

  Has reproduction · 83

  MAGISTA, a random forest model built on alignment-free intra-bin distance-distribution statistics, can estimate MAG completeness and purity without relying on reference marker genes.

  pooled hc227 contig sets shotgun novo alignment-free

• Asterias: integrated analysis of expression and aCGH data using an open-source, web-based, parallelized software suite.

  PMID 17488846 · PMC1933128 · Nucleic acids research · 2007 · 8 claims · 2 setups

  Full-text index only

  Asterias is an integrated, open-source, web-based software suite for analysis of gene expression and aCGH data

  asterias pomelo functional cross-browser

• Metavisitor, a Suite of Galaxy Tools for Simple and Rapid Detection and Discovery of Viruses in Deep Sequence Data.

  PMID 28045932 · PMC5207757 · PloS one · 2017 · 7 claims · 5 setups

  Has reproduction · 78

  Metavisitor is an open-source suite of modular Galaxy tools and preset workflows for detecting and assembling viral genomes from deep sequencing data.

  drosophila viral sequence use small novo read

• Insights into the Evolution of the New World Diploid Cottons (Gossypium, Subgenus Houzingenia) Based on Genome Sequencing.

  PMID 30476109 · PMC6320677 · Genome biology and evolution · 2019 · 8 claims · 8 setups

  Has reproduction · 87

  Subgenus Houzingenia likely originated via transoceanic dispersal from Africa about 6.6 Ma

  leaf trimmed species concatenated genome novo reference-assisted

• Gut-derived Lactobacillus from exceptional responders mitigates chemoradiotherapy-induced intestinal injury through methionine-driven epigenetic modulation.

  PMID 40469520 · PMC12130557 · iMeta · 2025 · 8 claims · 8 setups

  Has reproduction · 89

  High pretreatment abundance of Lactobacillus (and Bifidobacterium) in gut microbiota correlates with absence of ACRIII in rectal cancer patients

  fecal bacterial whole-abdomen cecal metagenomic random fecal

• Enhanced Generalizability of RNA Secondary Structure Prediction via Convolutional Block Attention Network and Ensemble Learning.

  PMID 40871599 · PMC12388828 · Molecules (Basel, Switzerland) · 2025 · 8 claims · 8 setups

  Has reproduction · 87

  TrioFold integrates base-pairing clues from thermodynamic- and DL-based methods via ensemble learning and a convolutional block attention mechanism to enhance RSS prediction generalizability.

  testseta bprna-new ts-inter individual jaccard pca ensemble