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).

• Expanding the clinical spectrum of COL2A1 related disorders by a mass like phenotype.

  PMID 35296718 · PMC8927422 · Scientific reports · 2022 · 8 claims · 8 setups

  Has reproduction · 84

  Four FBN1-negative patients from three families with a MASS-like phenotype carry likely pathogenic or uncertain-significance missense variants in the propeptide-coding regions of COL2A1

  blood-derived four patients col2a1 targeted clinical transthoracic

• Comparative genomics of cyclin-dependent kinases suggest co-evolution of the RNAP II C-terminal domain and CTD-directed CDKs.

  PMID 15380029 · PMC521075 · BMC genomics · 2004 · 8 claims · 6 setups

  Full-text index only

  Cell-cycle related CDKs (orthologs of CDK1-6) are present in all sampled eukaryotic organisms, including the most ancestral protists.

  animals cdk encephalitozoon pfmrk comparative bayesian distance

• Zinc finger nucleases: custom-designed molecular scissors for genome engineering of plant and mammalian cells.

  PMID 16251401 · PMC1270952 · Nucleic acids research · 2005 · 8 claims · 8 setups

  Full-text index only

  ZFNs combining the FokI nuclease domain with custom zinc finger proteins can deliver site-specific double-strand breaks to plant and mammalian genomes.

  foki zif268-derived coli zfns limited foot-printing x-ray

• A new mutation in BFSP2 (G1091A) causes autosomal dominant congenital lamellar cataracts.

  PMID 18958306 · PMC2573734 · Molecular vision · 2008 · 8 claims · 7 setups

  Full-text index only

  The disease locus maps to chromosome 3q21-25, linked to markers D3S2322 and D3S1541

  four-generation bfsp2 wild-type microsatellite direct denaturing

• Mutation G61C in the CRYGD gene causing autosomal dominant congenital coralliform cataracts.

  PMID 18334953 · PMC2268897 · Molecular vision · 2008 · 8 claims · 6 setups

  Full-text index only

  A G61C (P.G61C) missense mutation in CRYGD causes autosomal dominant congenital coralliform cataracts in this family

  four-generation genomic crygd wild-type genotyping direct denaturing

• A novel DSPP mutation is associated with type II dentinogenesis imperfecta in a Chinese family.

  PMID 17686168 · PMC1995191 · BMC medical genetics · 2007 · 7 claims · 5 setups

  Full-text index only

  A novel mutation c.49C>T (p.Pro17Ser) in exon 1 of DSPP causes type II DGI in this Chinese family.

  family genomic affected linkage direct pcr

• Long-range regulation is a major driving force in maintaining genome integrity.

  PMID 19682388 · PMC2741452 · BMC evolutionary biology · 2009 · 7 claims · 5 setups

  Full-text index only

  Long-range transcriptional regulation is a major driving force in maintaining genome integrity by constraining where chromosomal breakpoints can become fixed.

  opossum genome comparative identification statistical

• ConNIS and labeling instability: New statistical methods for improving the detection of essential genes in TraDIS libraries.

  PMID 41790830 · PMC12991369 · PLoS computational biology · 2026 · 8 claims · 3 setups

  Has reproduction · 83

  ConNIS provides an analytic solution for the probability of observing the longest insertion-free sequence within a gene given its length and number of insertion sites under non-essentiality.

  simulated four real simulation semi-synthetic real-world

• A Reference DNA Barcode Library for UK Fungi associated with Bark and Ambrosia Beetles.

  PMID 41022899 · PMC12480477 · Scientific data · 2025 · 6 claims · 6 setups

  Has reproduction · 44

  A reference DNA barcode library of fungi associated with over 1000 UK bark and ambrosia beetles (25 native Scolytinae species) was generated, yielding 5274 identified fungal OTUs.

  bark sites sequencing fungal its2 passive sequence

• To Explore the Key Subgroup and Their Immune Microenvironment During the Formation of Coronary Plaque With scRNA-seq.

  PMID 40454289 · PMC12126265 · Cardiology research and practice · 2025 · 6 claims · 8 setups

  Has reproduction · 33

  C1 RACK1+ NK cells are a crucial subgroup for understanding coronary plaque formation, exhibiting the highest cell stemness/differentiation potential and positioned at the start of the pseudotime trajectory

  coronary scrna-seq five type single-cell doublet copy

• 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

• An extensive evaluation of read trimming effects on Illumina NGS data analysis.

  PMID 24376861 · PMC3871669 · PloS one · 2013 · 8 claims · 8 setups

  Has reproduction · 85

  Read trimming increases the quality and reliability of downstream NGS analyses (RNA-Seq mapping, SNP identification, genome assembly) while reducing execution time and computational resources.

  homo arabidopsis prunus saccharomyces rna-seq snp novo

• Genome informatics: taming the avalanche of genomic data.

  PMID 15642109 · PMC549058 · Genome biology · 2005 · 8 claims · 7 setups

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  Ultraconserved regions (>100 bp, 100% conserved among mammals) exist in the genome and their function remains unknown

  genes arabidopsis genome vertebrate comparative conservation whole-genome

• SNPdetector: a software tool for sensitive and accurate SNP detection.

  PMID 16261194 · PMC1274293 · PLoS computational biology · 2005 · 7 claims · 7 setups

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  SNPdetector, which models human visual inspection of sequencing traces, achieves low false positive and false negative rates in automated SNP and mutation detection

  inbred unrelated zebra same pcr manual comparative

• Mutations in UPF3B, a member of the nonsense-mediated mRNA decay complex, cause syndromic and nonsyndromic mental retardation.

  PMID 17704778 · PMC2872770 · Nature genetics · 2007 · 8 claims · 6 setups

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  Mutations in UPF3B cause syndromic (Lujan-Fryns syndrome, FG syndrome) and nonsyndromic X-linked mental retardation

  probands lymphoblastoid lcls tissues gene quantitative cycloheximide

• Of mice and men: comparative proteomics of bronchoalveolar fluid.

  PMID 20032019 · PMC3049194 · The European respiratory journal · 2010 · 8 claims · 8 setups

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  Comparative shotgun proteomics of human and mouse BALF identifies conserved pathways (immunity, defence response, protease activity) alongside species-specific divergent pathways.

  pooled oxidative unpooled balf shotgun functional protein-protein

• Comparative Genomics Provides Insight into the Function of Broad-Host Range Sponge Symbionts.

  PMID 34519538 · PMC8546597 · mBio · 2021 · 8 claims · 8 setups

  Has reproduction · 90

  Eleven new genomes were added to the Tethybacterales order and a novel family (Polydorabacteraceae) was identified

  tsitsikamma tethybacterales putative bin genome 16s multi-locus

• ChIP-seq guidelines and practices of the ENCODE and modENCODE consortia.

  PMID 22955991 · PMC3431496 · Genome research · 2012 · 8 claims · 8 setups

  Has reproduction · 74

  ENCODE/modENCODE define a set of working standards and guidelines for ChIP-seq covering antibody validation, experimental replication, sequencing depth, data/metadata reporting, and data quality assessment.

  small-genome nuclear whole-cell encode chip-seq chip-chip immunoblot

• Metabolic syndrome: from epidemiology to systems biology.

  PMID 18852695 · PMC2829312 · Nature reviews. Genetics · 2008 · 8 claims · 8 setups

  Full-text index only

  MetSyn component traits (obesity, insulin resistance, dyslipidaemia, hypertension) exhibit causal interactions and common etiologies rather than being independent conditions

  populations rats adipose four genome-wide linkage gene

• Comparative analysis of plant genomes allows the definition of the "Phytolongins": a novel non-SNARE longin domain protein family.

  PMID 19889231 · PMC2779197 · BMC genomics · 2009 · 8 claims · 6 setups

  Full-text index only

  A novel, plant-specific family of longin-related proteins, the 'Phytolongins', was identified in land plant genomes.

  genomes longin plant phytolongin iterative phylogenetic genomic