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).

• Evaluating genome sequencing strategies: trio, singleton, and standard testing in rare disease diagnosis.

  PMID 40963120 · PMC12445032 · Genome medicine · 2025 · 7 claims · 4 setups

  Has reproduction · 88

  Trio genome sequencing (tGS) achieves higher prospective diagnostic yield than standard-of-care (SoC) and singleton genome sequencing (sGS) even when performed by a newly trained team.

  individuals index blood short-read exome array

• BFAST: an alignment tool for large scale genome resequencing.

  PMID 19907642 · PMC2770639 · PloS one · 2009 · 7 claims · 4 setups

  Full-text index only

  BFAST is a new algorithm and freely available software tool for aligning large-scale short-read sequencing data to large reference genomes with user-customizable speed and accuracy

  reference genome simulated real-world k-mer

• An improved assembly of the pearl millet reference genome using Oxford Nanopore long reads and optical mapping.

  PMID 36891809 · PMC10151396 · G3 (Bethesda, Md.) · 2023 · 8 claims · 8 setups

  Has reproduction · 90

  Combining ONT long reads with Bionano optical maps produced a substantially more complete and contiguous pearl millet Tift 23D2B1-P1-P5 assembly than the prior short-read assembly.

  pearl old oxford bionano illumina

• Deep transcriptomics reveals cell-specific isoforms of pan-neuronal genes.

  PMID 40379625 · PMC12084633 · Nature communications · 2025 · 8 claims · 5 setups

  Has reproduction · 84

  Pan-neuronal genes (expressed in many/all neurons) harbor highly cell-specific splice variants/isoforms restricted to single or few neuron types.

  elegans short-read whole-animal rt-pcr

• Hobbes: optimized gram-based methods for efficient read alignment.

  PMID 22199254 · PMC3315303 · Nucleic acids research · 2012 · 8 claims · 4 setups

  Has reproduction · 83

  Hobbes, a gram-based short-read mapper supporting Hamming and edit distance, is faster than all other read-mapping programs tested while maintaining high mapping quality.

  genome hg18 example reference read-mapping character-substitution algorithmic

• Inferring a spatial code of cell-cell interactions across a whole animal body.

  PMID 36395331 · PMC9714814 · PLoS computational biology · 2022 · 8 claims · 6 setups

  Has reproduction · 90

  cell2cell computes cell-cell interaction (CCI) potential using a novel modified Bray-Curtis score based on complementary coexpression of ligand-receptor pairs between cells

  elegans computational single-cell random genetic

• Environmental selection overturns the decay relationship of soil prokaryotic community over geographic distance across grassland biotas.

  PMID 35073255 · PMC8828049 · eLife · 2022 · 8 claims · 7 setups

  Has reproduction · 57

  Prokaryotic community similarity follows a significant U-shape relationship over geographic distance up to 4000 km, decreasing within biotas but increasing across biotas after a tipping point of 1760-1920 km

  soil grassland 16s plant soil

• A chromosome-level genome assembly of Plantago ovata.

  PMID 36707685 · PMC9883528 · Scientific reports · 2023 · 8 claims · 8 setups

  Has reproduction · 99

  A chromosome-level reference genome assembly of P. ovata was constructed using PacBio long reads and Hi-C scaffolding.

  plantago ovata pacbio hi-c k-mer

• Evaluation of core genome and whole genome multilocus sequence typing schemes for Campylobacter jejuni and Campylobacter coli outbreak detection in the USA.

  PMID 37133905 · PMC10272873 · Microbial genomics · 2023 · 8 claims · 8 setups

  Has reproduction · 92

  cgMLST, wgMLST and hqSNP WGS-based analysis methods clustered C. jejuni and C. coli isolates in concordance with epidemiological data.

  jejuni same subset isolate cgmlst hqsnp genome