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).

• A novel splice-site mutation of TULP1 underlies severe early-onset retinitis pigmentosa in a consanguineous Israeli Muslim Arab family.

  PMID 18432314 · PMC2329669 · Molecular vision · 2008 · 6 claims · 5 setups

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  A novel homozygous splice-site mutation, c.1495+2_1495+3insT, in the donor splice-site of TULP1 intron 14 underlies autosomal recessive early-onset RP in family TB13.

  genomic tulp1 y79 haplotype direct mismatch-primer

• OptiType: precision HLA typing from next-generation sequencing data.

  PMID 25143287 · PMC4441069 · Bioinformatics (Oxford, England) · 2014 · 8 claims · 8 setups

  Has reproduction · 95

  OptiType, an ILP-based HLA genotyping algorithm, produces accurate four-digit HLA-I predictions from NGS data not enriched for the HLA cluster.

  colorectal lymphoblastic hapmap genomes rna-seq low-coverage exome

• Bladder tumour-derived somatic TSC1 missense mutations cause loss of function via distinct mechanisms.

  PMID 18397877 · PMC2427143 · Human molecular genetics · 2008 · 8 claims · 8 setups

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  All six somatic TSC1 missense mutations found in bladder tumours cause loss of TSC1 function, but via distinct molecular mechanisms.

  hcv29 lines tsc1 bladder immunoblotting real-time co-immunoprecipitation

• A novel recessive Nefl mutation causes a severe, early-onset axonal neuropathy.

  PMID 20039262 · PMC4439312 · Annals of neurology · 2009 · 8 claims · 8 setups

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  A homozygous NEFL nonsense mutation (E210X) causes a severe, early-onset recessive axonal neuropathy in four siblings of a consanguineous family

  family sural nefl-null sw-13 clinical genetic immunohistochemistry

• Mutations in the formin gene INF2 cause focal segmental glomerulosclerosis.

  PMID 20023659 · PMC2980844 · Nature genetics · 2010 · 8 claims · 8 setups

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  Mutations in INF2, a formin family actin-regulating protein, cause autosomal dominant focal segmental glomerulosclerosis (FSGS)

  families genes individuals kidney genome-wide sanger resequencing

• Angiotensin I-converting enzyme mutation (Trp1197Stop) causes a dramatic increase in blood ACE.

  PMID 20011602 · PMC2788243 · PloS one · 2009 · 8 claims · 8 setups

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  A novel heterozygous Trp1197Stop (W1197X) mutation in the ACE gene causes a 13-fold increase in blood ACE activity in an African-American family

  plasma genomic cho heparinized ace plate conformational

• Construction of a high-resolution genetic linkage map and comparative genome analysis for the reef-building coral Acropora millepora.

  PMID 19900279 · PMC3091320 · Genome biology · 2009 · 8 claims · 6 setups

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  This is the first genetic linkage map constructed for any coral species or any non-Bilaterian animal

  acropora millepora coral snp genetic segregation

• Assessing the genomic evidence for conserved transcribed pseudogenes under selection.

  PMID 19754956 · PMC2753554 · BMC genomics · 2009 · 8 claims · 8 setups

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  1750 transcribed pseudogene annotations (TPAs) were identified in the human genome, ~11.5% of all human pseudogene annotations.

  genome rhesus vega-annotated tpas transcript-to-genome same synteny

• Congenital bovine spinal dysmyelination is caused by a missense mutation in the SPAST gene.

  PMID 19714378 · PMC2854348 · Neurogenetics · 2010 · 8 claims · 5 setups

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  A missense mutation (R560Q) in the SPAST gene's ATPase domain causes bovine spinal dysmyelination

  cattle bovine coli affinity-purified snp reverse cdna

• Mutations at codons 178, 200-129, and 232 contributed to the inherited prion diseases in Korean patients.

  PMID 19698114 · PMC2749045 · BMC infectious diseases · 2009 · 8 claims · 7 setups

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  Three PRNP mutations—D178N, E200K, and M232R—were identified in heterozygosity in Korean probable CJD patients, marking their first report in this population.

  csf 293t genomic pcr western recombinant sequencing

• Fifty Generations of Amitosis: Tracing Asymmetric Allele Segregation in Polyploid Cells with Single-Cell DNA Sequencing.

  PMID 34576874 · PMC8467633 · Microorganisms · 2021 · 7 claims · 7 setups

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  Amitosis causes random assortment of somatic alleles (IESs) in the highly polyploid Paramecium macronucleus, which can be tracked without phenotypic markers using scDNA-seq.

  paramecium tetraurelia telomere-capped simulated single-cell bulk bias

• Pharmacogenomic screening identifies and repurposes leucovorin and dyclonine as pro-oligodendrogenic compounds in brain repair.

  PMID 39537633 · PMC11561360 · Nature communications · 2024 · 8 claims · 8 setups

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  A pharmacogenomic scoring strategy (OligoScore) combining transcriptomic signatures and curated oligodendrogenesis gene sets identifies compounds with pro-oligodendrogenic transcriptional activity

  brain neonatal gene cerebellar bulk transcriptomic pharmacogenomic

• Epimutations driven by RNAi or heterochromatin evoke transient antimicrobial drug resistance in pathogenic Mucor fungi.

  PMID 41628159 · PMC12863538 · PLoS biology · 2026 · 8 claims · 8 setups

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  In M. bainieri, most (90%) FK506-resistant isolates are unstable/transient and revert to drug sensitivity without any detectable DNA mutation

  mucor fk506-resistant bainieri drug sanger serial

• Genomic analysis of the Ixworth chicken: insights into a local dual-purpose breed.

  PMID 41814148 · PMC13064311 · BMC genomics · 2026 · 6 claims · 8 setups

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  The Ixworth chicken is genetically distinct from red junglefowl, commercial broilers, and commercial layers.

  ixworth six pairwise whole-genome variant principal

• Divergent clonal evolution and tumor microenvironment remodeling shape gastric cancer peritoneal metastasis.

  PMID 41882239 · PMC13181027 · Communications biology · 2026 · 8 claims · 7 setups

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  Substantial intra-patient heterogeneity exists between GCPM and primary tumors at both genetic and functional (transcriptomic) levels

  gastric wgs paired genes whole-genome whole-transcriptome mutational

• nf-core/viralmetagenome: A novel pipeline for untargeted viral genome reconstruction.

  PMID 42057295 · PMC13141149 · Bioinformatics (Oxford, England) · 2026 · 8 claims · 5 setups

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  nf-core/viralmetagenome is a Nextflow pipeline that automates untargeted reconstruction and variant analysis of eukaryotic DNA and RNA viruses from short-read metagenomic or hybridisation-capture data.

  real simulated seven pipeline metagenomic simulated clinical

• Accessing medically relevant complex regions with a pangenome graph of 20 near-complete Japanese haplotypes.

  PMID 42203797 · PMC13216315 · Nature communications · 2026 · 8 claims · 8 setups

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  Generated 20 near-complete haplotypes from 10 Japanese male individuals using PacBio HiFi, ONT ultra-long, and Omni-C reads, all with contig N50 exceeding 100 Mbp

  japanese pacbio oxford omni-c

• DupyliCate: mining, classifying, and characterizing gene duplications.

  PMID 42209743 · PMC13219399 · Scientific reports · 2026 · 8 claims · 8 setups

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  DupyliCate is a Python tool for identifying and classifying gene duplication arrays, using BUSCO-based species-specific thresholds and offering integrated expression divergence and Ka/Ks analysis.

  arabidopsis thaliana brassicales phytozome sequence duplication runtime

• A pan-cancer single cell landscape reveals heterogeneity and functional diversity of double-negative T cells.

  PMID 41484771 · PMC12882460 · Molecular cancer · 2026 · 7 claims · 5 setups

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  Integration of pan-cancer scRNA-seq data yields a comprehensive single-cell atlas of 157,025 high-quality DNT cells across 23 cancer types.

  tumor dnt ffpe mc38 scrna-seq tcr multiplex

• Effector gene silencing coordinated by histone methylation and small RNAs enhances host adaptation in a plant pathogen.

  PMID 41505097 · PMC12781887 · Nucleic acids research · 2026 · 8 claims · 8 setups

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  CRISPR/Cas9 editing of PsSu(z)12 abolishes H3K27me3 deposition at Avr1b and Avr3a, causing transcriptional reactivation and loss of avirulence

  sojae soybean crispr homology-directed virulence