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).

• 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

• Cancer genome standards for long-read sequencing using cancer cell line mixtures.

  PMID 41934171 · PMC13137868 · GigaScience · 2026 · 8 claims · 6 setups

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  Long-read variant calling tools achieve recall rates comparable to short-read gold standards

  colo829 same whole-genome short-read 5mc

• Nimbus: a design-driven analyses suite for amplicon-based NGS data.

  PMID 29538618 · PMC6084620 · Bioinformatics (Oxford, England) · 2018 · 7 claims · 5 setups

  Has reproduction · 64

  Nimbus tracks the source amplicon of reads throughout alignment and SNP/InDel calling

  blood na15510 twin haloplex haloplex spiked-in humanexome-12

• Identification and characterisation of the angiotensin converting enzyme-3 (ACE3) gene: a novel mammalian homologue of ACE.

  PMID 17597519 · PMC1925091 · BMC genomics · 2007 · 7 claims · 7 setups

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  A novel single-domain ACE-like gene, ACE3, exists in mouse, rat, cow, dog and human genomes, located on the same chromosome downstream of ACE.

  dog predicted ace3 panel blast sequence homology

• Genome wide identification of recessive cancer genes by combinatorial mutation analysis.

  PMID 18846217 · PMC2557123 · PloS one · 2008 · 7 claims · 4 setups

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  A combinatorial mutation analysis identified 154 candidate recessive cancer genes (pRecessiveCancer<1.5x10-7, FDR=0.39)

  refseq tp53 tumor 154-gene est paired array

• B lymphocytes of xeroderma pigmentosum or Cockayne syndrome patients with inherited defects in nucleotide excision repair are fully capable of somatic hypermutation of immunoglobulin genes.

  PMID 9236193 · PMC2198998 · The Journal of experimental medicine · 1997 · 6 claims · 3 setups

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  EBV-transformed B cells from NER-defective patients (XP-B, XP-D, XP-V, CS-A) show a high frequency of point mutations in Ig heavy and light chain V regions but not in C regions

  ebv-transformed cloned rt-pcr southern sequence

• Repurposing public sarcoma multi-omics for neoantigen discovery.

  PMID 42012689 · PMC13100081 · Cancer immunology, immunotherapy : CII · 2026 · 8 claims · 7 setups

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  Reanalysis of legacy CKS multi-omic data shows that standard genome-wide metrics frequently underestimate the true immunogenic potential of these tumors.

  paired cks peptides whole-exome rna-seq hla

• MODBASE, a database of annotated comparative protein structure models and associated resources.

  PMID 18948282 · PMC2686492 · Nucleic acids research · 2009 · 8 claims · 8 setups

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  MODBASE contains 5,152,695 reliable comparative protein structure models for 1,593,209 unique protein sequences.

  sequences chains template chain comparative pairwise ligand

• TrEMOLO: accurate transposable element allele frequency estimation using long-read sequencing data combining assembly and mapping-based approaches.

  PMID 37013657 · PMC10069131 · Genome biology · 2023 · 6 claims · 6 setups

  Has reproduction · 89

  TrEMOLO combines an assembly-based INSIDER module and a mapping-based OUTSIDER module to detect TE insertions/deletions from long-read sequencing data and estimate their allele frequency

  melanogaster simulated long-read whole-genome genome

• Ensembl 2013.

  PMID 23203987 · PMC3531136 · Nucleic acids research · 2013 · 8 claims · 8 setups

  Has reproduction · 85

  Ensembl (http://www.ensembl.org) provides genome information for sequenced chordate genomes, currently supporting 70 species with a focus on human, mouse, zebrafish and rat.

  genome species supported variants evidence-based rna-seq chip-seq

• Integrative transcriptome sequencing identifies trans-splicing events with important roles in human embryonic stem cell pluripotency.

  PMID 24131564 · PMC3875859 · Genome research · 2014 · 8 claims · 8 setups

  Has reproduction · 100

  TSscan, a computational pipeline integrating long- and short-read transcriptome sequencing from multiple hESC lines, can detect trans-splicing while minimizing false positives from experimental artifacts and genetic rearrangements.

  hesc hescs long-read short-read rt-pcr

• Microsatellite instability analysis in hereditary non-polyposis colon cancer using the Bethesda consensus panel of microsatellite markers in the absence of proband normal tissue.

  PMID 16426447 · PMC1373649 · BMC medical genetics · 2006 · 7 claims · 4 setups

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  MSI status can be determined in the absence of proband non-tumor tissue by comparing tumor alleles to alleles carried by the proband's progenitors

  proband's peripheral hmsh2 microsatellite direct targeted

• Mutation analysis in primary immunodeficiency diseases: case studies.

  PMID 19841577 · PMC2774237 · Current opinion in allergy and clinical immunology · 2009 · 8 claims · 8 setups

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  Genomic DNA Sanger sequencing is the standard first-line approach for identifying PIDD-causing mutations but has limitations that can yield false-negative or false-positive results

  mother parents ebv-transformed nemo genomic flow northern