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).

• Target SNP selection in complex disease association studies.

  PMID 15248903 · PMC487897 · BMC bioinformatics · 2004 · 7 claims · 3 setups

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  A computational pipeline can retrieve gene sequence, collect SNP variation data, and annotate SNPs falling in functional motifs (promoter, exon-intron structure, AU-rich elements, TF binding sites, splice sites) with expression in target tissue

  genes pooled primer computational maldi-tof blast

• RetroSnake: A modular pipeline to detect human endogenous retroviruses in genome sequencing data.

  PMID 36339261 · PMC9626663 · iScience · 2022 · 8 claims · 4 setups

  Has reproduction · 79

  RetroSnake is an end-to-end, modular, computationally efficient Snakemake pipeline for detecting HERV-K insertions in short-read NGS data, from raw alignment files to an annotated interactive HTML report

  wgs single whole-genome nested capillary

• Virus variant quantification with Orthanq.

  PMID 41639627 · PMC12930645 · BMC bioinformatics · 2026 · 8 claims · 6 setups

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  Orthanq performs identification and uncertainty-aware quantification of known virus variants of any virus species, including in samples with mixed infections

  simulated real mixture sequencing sequencing-based pangenome variant

• MobiCT: a UMI-based circulating tumor DNA analysis pipeline.

  PMID 41503160 · PMC12770973 · NAR genomics and bioinformatics · 2026 · 7 claims · 7 setups

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  MobiCT is a Nextflow/nf-core UMI-based ctDNA pipeline (deduplication, alignment, variant calling with VarDict, annotation with VEP) achieving sensitivity, precision, and F1-score around 90% after comprehensive filtering.

  cfdna same tumor horizon targeted droplet ngs

• BLIT: an R package for seamless integration of command-line bioinformatics tool universe.

  PMID 42164079 · PMC13183670 · Bioinformatics advances · 2026 · 8 claims · 5 setups

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  BLIT provides a unified R6-based framework for seamless integration of command-line bioinformatics tools within R, replacing fragile string-based system() calls.

  core circrna clinical europe unit pipeline production

• 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

• Variation resources at UC Santa Cruz.

  PMID 17151077 · PMC1781230 · Nucleic acids research · 2007 · 8 claims · 8 setups

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  The UCSC Genome Browser variation resources integrate polymorphism data from public collections (dbSNP, HapMap, Affymetrix, Perlegen, SeattleSNPs) into a common format with additional annotations and genomic context.

  chimpanzee affymetrix hapmap perlegen snp fixed linkage

• Species-Wide Phylogenomics of the Staphylococcus aureus Agr Operon Revealed Convergent Evolution of Frameshift Mutations.

  PMID 35044202 · PMC8768832 · Microbiology spectrum · 2022 · 8 claims · 7 setups

  Has reproduction · 79

  AgrVATE, a novel kmer-based BLASTn and in silico PCR/Snippy pipeline, enables fast, standardized agr group typing and frameshift/null mutation detection from genome assemblies

  aureus complete extracted agr kmer-based sheep mash

• Patterns of evolutionary constraints on genes in humans.

  PMID 18840274 · PMC2587479 · BMC evolutionary biology · 2008 · 7 claims · 6 setups

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  BaseDiver, a novel framework integrating GERP score and derived allele frequency (DAF) at nonsynonymous coding SNPs, can classify GO functional categories by patterns of evolutionary constraint

  mammalian hapmap panther significant comparative population chi-square

• Metapipeline-DNA: A comprehensive germline and somatic genomics Nextflow pipeline.

  PMID 41850291 · PMC13030954 · Cell reports methods · 2026 · 8 claims · 7 setups

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  Metapipeline-DNA automates germline and somatic DNA sequencing analysis end-to-end, from raw reads through preprocessing, feature detection, QC, and visualization.

  pcawg giab pcawg-5 tumor-normal whole-genome germline somatic

• MetaPepticon: automated prediction of anticancer peptides from microbial genomes and metagenomes.

  PMID 41918857 · PMC13034871 · PeerJ · 2026 · 7 claims · 6 setups

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  MetaPepticon is a modular, end-to-end Snakemake pipeline that predicts ACP candidates directly from raw genomic, metagenomic, transcriptomic, metatranscriptomic reads, assembled contigs, or peptide sequences.

  validated gut representative predicted acp shotgun genome

• Assessing Bos taurus introgression in the UOA Bos indicus assembly.

  PMID 34922445 · PMC8684283 · Genetics, selection, evolution : GSE · 2021 · 7 claims · 6 setups

  Has reproduction · 86

  Aligning B. taurus samples to UOA_Brahman_1 detects up to 5 million more SNVs than aligning to ARS_UCD1.2, and aligning B. indicus samples to ARS_UCD1.2 detects 1.5 million more SNVs than aligning to UOA_Brahman_1, demonstrating reference-genome bias.

  cattle same per-breed merged whole-genome snv principal

• A comprehensive resequence analysis of the KLK15-KLK3-KLK2 locus on chromosome 19q13.33.

  PMID 19823874 · PMC2793378 · Human genetics · 2010 · 7 claims · 7 setups

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  Deep resequencing of a 56 kb region on chr19q13.33 identified 555 polymorphic loci, including 116 novel SNPs and 182 novel indels.

  individuals sequence resequencing snps targeted sequence genotype

• The genome sequence of the flat clown beetle, Hololepta plana (Sulzer, 1776) (Coleoptera: Histeridae).

  PMID 42255359 · PMC13237540 · Wellcome open research · 2026 · 8 claims · 8 setups

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  A chromosome-level genome assembly was produced for Hololepta plana (icHolPlan1) using the Darwin Tree of Life pipeline

  hololepta head abdomen hifi barcoding pacbio hi-c

• A comparison of random sequence reads versus 16S rDNA sequences for estimating the biodiversity of a metagenomic library.

  PMID 18682527 · PMC2532719 · Nucleic acids research · 2008 · 8 claims · 7 setups

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  Biodiversity observed by RSR analysis is consistent with that obtained by 16S rDNA analysis

  faecal rsr 16s sargasso shotgun blastn-based 16s

• The genome sequence of the Osiris Blue, Cupido osiris (Meigen, 1830) (Lepidoptera: Lycaenidae).

  PMID 41798706 · PMC12963831 · Wellcome open research · 2026 · 8 claims · 8 setups

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  A chromosome-level genome assembly was produced for Cupido osiris (Osiris Blue butterfly)

  cupido pacbio hi-c k-mer

• The genome sequence of the Mediterranean Skipper, Gegenes nostrodamus (Fabricius, 1793) (Lepidoptera: Hesperiidae).

  PMID 41908929 · PMC13019046 · Wellcome open research · 2026 · 6 claims · 7 setups

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  A chromosome-level genome assembly was generated for Gegenes nostrodamus (Mediterranean Skipper) as part of Project Psyche.

  gegenes pacbio hi-c k-mer

• 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

• Variation analysis and gene annotation of eight MHC haplotypes: the MHC Haplotype Project.

  PMID 18193213 · PMC2206249 · Immunogenetics · 2008 · 8 claims · 6 setups

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  Comparison of eight HLA-homozygous MHC haplotype sequences identified >44,000 variations (substitutions and indels), submitted to dbSNP

  hla-homozygous same mhc indel clone-by-clone gene hla

• The genome sequence of the Chalk Yellow-face Bee, Hylaeus dilatatus (Kirby, 1802) (Hymenoptera: Colletidae).

  PMID 41657665 · PMC12881847 · Wellcome open research · 2026 · 8 claims · 8 setups

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  A two-haplotype genome assembly of Hylaeus dilatatus was produced, with total lengths of 307.38 Mb (haplotype 1) and 314.32 Mb (haplotype 2)

  hylaeus pacbio assembled barcoding pacbio hi-c