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).

• NGSTroubleFinder: a tool for detection and quantification of contamination and kinship across human NGS data.

  PMID 41608734 · PMC12838523 · NAR genomics and bioinformatics · 2026 · 8 claims · 8 setups

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  NGSTroubleFinder detects cross-sample contamination, sample swaps, kinship, and sex mismatches from BAM/CRAM files without requiring additional variant-calling steps

  genomes 1000gp internal whole-genome whole-transcriptome wgs

• AMR-GNN: a multi-representation graph neural network framework to enable genomic antimicrobial resistance prediction.

  PMID 41792137 · PMC13087051 · Nature communications · 2026 · 7 claims · 8 setups

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  AMR-GNN, a graph neural network integrating multiple genomic representations (unitigs, SNPs, FCGR) via low-rank multimodal fusion, improves AMR phenotype prediction in P. aeruginosa compared to single-representation baseline models.

  pseudomonas aeruginosa escherichia coli whole-genome elastic convolutional

• Finding signals that regulate alternative splicing in the post-genomic era.

  PMID 12429065 · PMC244920 · Genome biology · 2002 · 8 claims · 8 setups

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  Alternative splicing generates protein and regulatory diversity from a limited number of genes and modulates isoform levels in a cell-context-specific manner

  intron-containing genome brain-specific cell-free computational comparative selex

• SVNeoPP: A Workflow for Structural-Variant-Derived Neoantigen Prediction and Prioritization Using Multi-Omics Data.

  PMID 41892252 · PMC13024079 · Biology · 2026 · 8 claims · 7 setups

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  SVNeoPP is an end-to-end Snakemake workflow that takes WGS and RNA-seq as input to call/annotate SVs, reconstruct altered transcripts and coding sequences in an isoform-aware, traceable manner, and generate candidate peptides.

  tumor hcc sv-derived candidate whole-genome rna-seq peptide

• DMN-seq enriches DNA hypomethylated regions for biomarker discovery using 5-methylcytosine glycosylase.

  PMID 41673887 · PMC13097799 · Genome biology · 2026 · 8 claims · 9 setups

  Has reproduction · 80

  DMN-seq (DMN+) uses DME to nick DNA specifically at 5mC sites, enabling 5mC detection at single-base resolution via selective adaptor ligation

  synthetic partially embryonic mesc glycosylase dmn-seq ultrafast

• Genome-wide identification of Hfq-regulated small RNAs in the fire blight pathogen Erwinia amylovora discovered small RNAs with virulence regulatory function.

  PMID 24885615 · PMC4070566 · BMC genomics · 2014 · 8 claims · 8 setups

  Has reproduction · 50

  A total of 40 candidate Hfq-dependent sRNAs were identified genome-wide in E. amylovora by combining RNA-seq with a Rho-independent terminator search.

  erwinia intergenic candidate wounded small northern race

• A single-nucleotide enhancer mutation overrides chromosomal sex to drive XX male development.

  PMID 41957362 · PMC13066550 · Nature communications · 2026 · 8 claims · 7 setups

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  A 3 bp deletion or a 1 bp insertion in the Enh13 SOX9 binding site causes complete XX female-to-male sex reversal in adult homozygous mice

  c57bl6 6-week-old 6-week e12.5 crispr-cas9 gross immunostaining

• Computational comparison of two mouse draft genomes and the human golden path.

  PMID 12537546 · PMC151282 · Genome biology · 2003 · 8 claims · 7 setups

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  The Celera and public mouse genome assemblies differ in about 10% of the mouse genome, with complementary strengths (Celera higher base-pair accuracy and overall coverage; public assembly higher quality in some finished BAC regions and freely accessible)

  newly genome chromosome genomic blat blastn repeat

• Adjustment of genomic waves in signal intensities from whole-genome SNP genotyping platforms.

  PMID 18784189 · PMC2577347 · Nucleic acids research · 2008 · 8 claims · 6 setups

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  Genomic waves are present in both Illumina and Affymetrix SNP genotyping arrays, confirming they are not platform-specific

  representative illumina six snp serial concentration

• GeneMark: web software for gene finding in prokaryotes, eukaryotes and viruses.

  PMID 15980510 · PMC1160247 · Nucleic acids research · 2005 · 8 claims · 2 setups

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  The GeneMark website provides web interfaces to the GeneMark family of ab initio gene-finding programs for prokaryotic, eukaryotic and viral genomic sequences

  escherichia arabidopsis initio

• BIPASS: BioInformatics Pipeline Alternative Splicing Services.

  PMID 17584795 · PMC1933140 · Nucleic acids research · 2007 · 8 claims · 4 setups

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  BIPASS offers two complementary services for alternative splicing (AS) research: BIPAS-SpliceDB, a queryable pre-computed AS data warehouse, and BIPAS-Align&Splice, an online pipeline for user-submitted sequences.

  transcript aligned pre-computed user-submitted sequence alternative database

• The truth about mouse, human, worms and yeast.

  PMID 15601543 · PMC3525071 · Human genomics · 2004 · 8 claims · 8 setups

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  Comparing genomes in pairs or larger sets (mouse-human, C. elegans-C. briggsae, multiple Saccharomyces, human-pufferfish, etc.) reveals unsuspected genes and helps eliminate false-positive gene predictions

  mouse-human homo tetraodon region comparative est cross-species

• The evolution of human influenza A viruses from 1999 to 2006: a complete genome study.

  PMID 18325125 · PMC2311284 · Virology journal · 2008 · 8 claims · 6 setups

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  H3N2 was the prevalent influenza A strain in Denmark from 1999 to 2006, except the 2000–2001 season when H1N1 dominated

  danish representative h3n2 influenza phylogenetic complete haemagglutination

• A novel 154-bp deletion in the human mitochondrial DNA control region in healthy individuals.

  PMID 18629826 · PMC2697596 · Human mutation · 2008 · 8 claims · 5 setups

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  A novel 154-bp mtDNA control region deletion (m.16154_16307del154) was identified in a healthy family

  blood-derived mtdna pcr fragment mtdna

• Unleashing the potential of mRNA-seq to uncover the microbiome structure and their crosstalk with host cells: the vulvar ecosystem.

  PMID 42098796 · PMC13154700 · Microbiome · 2026 · 8 claims · 5 setups

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  Poly(A)-enriched mRNA-seq can reliably reconstruct microbiome composition, validated against a quantitative mock community standard and metagenomic analysis

  zymobiomics vls-vscc vulvar subset mrna-seq rna-seq poly

• Large-scale analysis of human alternative protein isoforms: pattern classification and correlation with subcellular localization signals.

  PMID 15860772 · PMC1087780 · Nucleic acids research · 2005 · 8 claims · 8 setups

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  Constructed a large-scale dataset of 6876 human alternative protein isoforms from 2624 genes by combining H-Invitational full-length cDNA data and SwissProt VARSPLIC entries

  full-length alternative refseq genome pairwise mitochondrial signal

• RNA-Seq transcriptome profiling of upland cotton (Gossypium hirsutum L.) root tissue under water-deficit stress.

  PMID 24324815 · PMC3855774 · PloS one · 2013 · 8 claims · 8 setups

  Has reproduction · 38

  A total of 1,530 transcripts were differentially expressed between well-watered and water-deficit stressed field-grown upland cotton root tissues (913 up-regulated, 617 down-regulated).

  gossypium uppermost root reads bulk leaf rt-qpcr

• RExPrimer: an integrated primer designing tool increases PCR effectiveness by avoiding 3' SNP-in-primer and mis-priming from structural variation.

  PMID 19958502 · PMC2788391 · BMC genomics · 2009 · 7 claims · 4 setups

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  RExPrimer integrates local SNP, indel, pseudogene, and CNV/structural variation databases with the Primer3 core algorithm to avoid mis-priming and SNP-in-Primer effects.

  genomic cyp2d6 genome pcr penta-plex sequence