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).

• Inconsistencies in Neanderthal genomic DNA sequences.

  PMID 17937503 · PMC2014787 · PLoS genetics · 2007 · 8 claims · 6 setups

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  The Noonan et al. and Green et al. Neanderthal nuclear DNA datasets yield mutually inconsistent estimates of population split time and Neanderthal admixture proportion when analyzed with the same method

  neanderthal green neanderthal-specific population-genetic fragment-length-stratified hapmap

• Sequence diversity within the HA-1 gene as detected by melting temperature assay without oligonucleotide probes.

  PMID 16202172 · PMC1260020 · BMC medical genetics · 2005 · 8 claims · 3 setups

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  HA-1 allele and genotype frequencies were determined in 131 unrelated Italian subjects (HA-1H=0.43, HA-1R=0.57), consistent with Hardy-Weinberg equilibrium and prior North American Caucasian data.

  genomic sequence-specific direct melting

• Emerging genomic and proteomic evidence on relationships among the animal, plant and fungal kingdoms.

  PMID 15629046 · PMC5172449 · Genomics, proteomics & bioinformatics · 2004 · 8 claims · 7 setups

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  Sequence-based molecular phylogenies widely support a sister relationship between animals and fungi, grouped as the Opisthokonta

  nine animals completed fungal combined sequence biochemical

• Endonuclease-independent insertion provides an alternative pathway for L1 retrotransposition in the human genome.

  PMID 17517773 · PMC1920257 · Nucleic acids research · 2007 · 8 claims · 5 setups

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  An endonuclease-independent pathway (NCLI) for L1 insertion has been active in recent human genome evolution

  genome chimpanzee genomic pcr computational triple pcr

• Germline mutations of the INK4a-ARF gene in patients with suspected genetic predisposition to melanoma.

  PMID 14735200 · PMC2409576 · British journal of cancer · 2004 · 8 claims · 2 setups

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  Seven germline INK4a-ARF changes (five novel) were found in 7 of 89 patients (8%) suspected of genetic predisposition to melanoma.

  genomic pcr real-time

• Genome-wide analysis of the human Alu Yb-lineage.

  PMID 15588477 · PMC3525081 · Human genomics · 2004 · 8 claims · 6 setups

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  1,733 Alu Yb-lineage elements are present on human autosomal chromosomes

  genome genomic non-human yb7 computational pcr-based pcr

• Evolutionary comparison provides evidence for pathogenicity of RMRP mutations.

  PMID 16244706 · PMC1262189 · PLoS genetics · 2005 · 7 claims · 5 setups

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  Putative pathogenic RMRP mutations are located in highly conserved nucleotides across mammals, whereas polymorphisms are located in non-conserved positions.

  genomic rmrp family non-finnish sequencing comparative microsatellite

• Mitochondrial localization and function of a subset of 22q11 deletion syndrome candidate genes.

  PMID 18775783 · PMC2729512 · Molecular and cellular neurosciences · 2008 · 8 claims · 8 setups

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  Six 22q11 genes (Mrpl40, Prodh, Slc25a1, Txnrd2, T10, Zdhhc8) encode proteins that localize to mitochondria, including neuronal/synaptic mitochondria.

  orthologues nih-3t3 3t3 mefs bioinformatic egfp co-transfection

• Conservation and losses of non-coding RNAs in avian genomes.

  PMID 25822729 · PMC4378963 · PloS one · 2015 · 8 claims · 6 setups

  Has reproduction · 100

  34 lncRNA-associated loci are conserved between birds and mammals, and 12 of these were validated in chicken by RNA-seq.

  avian bird chicken covariance-model trna mirna

• Accelerated evolution of the ASPM gene controlling brain size begins prior to human brain expansion.

  PMID 15045028 · PMC374243 · PLoS biology · 2004 · 8 claims · 6 setups

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  The ASPM gene shows accelerated (positively selected) evolution in the African hominoid clade, and this acceleration precedes hominid brain expansion by several million years.

  chimpanzee retrofitted primate aspm tar restriction genomic

• Double-strand breaks in the myotonic dystrophy type 1 and the fragile X syndrome triplet repeat sequences induce different types of mutations in DNA flanking sequences in Escherichia coli.

  PMID 17012280 · PMC1636463 · Nucleic acids research · 2006 · 7 claims · 5 setups

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  DSBs induced at the TRS/vector junction (EcoRV site) generate numerous mutagenic events in flanking sequences, whereas DSBs within the repeat tract (EcoRI site) produce no such mutants

  coli plasmids plasmid white plasmid sequencing non-b

• The genome of the simian and human malaria parasite Plasmodium knowlesi.

  PMID 18843368 · PMC2656934 · Nature · 2008 · 8 claims · 7 setups

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  The P. knowlesi (H strain) nuclear genome was sequenced and assembled: 23.5 Mb across 14 chromosomes with 5,188 predicted protein-encoding genes.

  knowlesi predicted type whole-genome comparative pfam

• Severe insulin resistance and intrauterine growth deficiency associated with haploinsufficiency for INSR and CHN2: new insights into synergistic pathways involved in growth and metabolism.

  PMID 19720790 · PMC2780873 · Diabetes · 2009 · 7 claims · 8 setups

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  INSR is disrupted by the chromosome 19 breakpoint, causing INSR haploinsufficiency (monoallelic expression) that explains the insulin resistance/dysglycemia phenotype

  metaphase genomic ebv-transformed serum fluorescence multiplex sanger

• PA-GOSUB: a searchable database of model organism protein sequences with their predicted Gene Ontology molecular function and subcellular localization.

  PMID 15608166 · PMC540074 · Nucleic acids research · 2005 · 7 claims · 4 setups

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  PA-GOSUB significantly extends the coverage of GO molecular function and subcellular localization annotations for 10 model organism proteomes compared with existing databases (GOA, Swiss-Prot).

  sequences query swiss-prot naive-bayes blast feature

• Mucospheres produced by a mixotrophic protist impact ocean carbon cycling.

  PMID 35288549 · PMC8921327 · Nature communications · 2022 · 8 claims · 8 setups

  Has reproduction · 58

  P. cf. balticum constructs carbon-rich mucospheres that attract, capture and immobilise microbial prey to facilitate phago-heterotrophic consumption

  tara four xenic balticum 18s its toxin

• 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

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  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

• High-resolution metagenomic reconstruction of the freshwater spring bloom.

  PMID 36698172 · PMC9878933 · Microbiome · 2023 · 8 claims · 8 setups

  Has reproduction · 69

  High-frequency metagenomic sampling (57 samples, 3 filter sizes, 2 depths, 37 days) recovers thousands of prokaryotic, eukaryotic, and viral genomes tracking spring bloom succession in fine detail

  freshwater phytoplankton heterotrophic reservoir 16s 18s shotgun

• TccP2-mediated subversion of actin dynamics by EPEC 2 - a distinct evolutionary lineage of enteropathogenic Escherichia coli.

  PMID 17526832 · PMC2884950 · Microbiology (Reading, England) · 2007 · 7 claims · 8 setups

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  tccP2 is present in 26 of 27 (96.2%) EPEC 2 lineage strains and absent from all 34 EPEC 1 strains tested

  clinical pcr-negative representative whole-cell conventional colony locus-specific