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).

• G-quadruplexes: the beginning and end of UTRs.

  PMID 18832370 · PMC2577360 · Nucleic acids research · 2008 · 8 claims · 5 setups

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  UTRs show significant strand asymmetry with C-PQS more common than G-PQS, consistent with general depletion of G-quadruplex-forming RNA

  genome 5'-utr simulated protein-coding computational high-resolution utr

• Chimp genome: branching out.

  PMID 16136102 · PMC7420934 · Nature · 2005 · 8 claims · 8 setups

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  The Chimpanzee Sequencing and Analysis Consortium published the initial draft chimpanzee genome sequence and compared it to the human genome.

  chimpanzee primate rhesus fossil whole-genome phylogenetic genome

• Widespread ectopic expression of olfactory receptor genes.

  PMID 16716209 · PMC1508154 · BMC genomics · 2006 · 8 claims · 6 setups

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  OR genes show widespread, locus-dependent, heterogeneous ectopic expression across dozens of non-olfactory human and mouse tissues

  tissues olfactory intact probesets microarray est custom

• Understanding incidental findings in the context of genetics and genomics.

  PMID 18547195 · PMC2581745 · The Journal of law, medicine & ethics : a journal of the American Society of Law, Medicine & Ethics · 2008 · 8 claims · 3 setups

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  No consensus exists on researchers' responsibilities to disclose individual genetic/genomic research results to participants.

  individual population whole-genome genome-wide

• Whole genome and transcriptome maps of the entirely black native Korean chicken breed Yeonsan Ogye.

  PMID 30010758 · PMC6065499 · GigaScience · 2018 · 8 claims · 6 setups

  Has reproduction · 91

  A draft genome (Ogye_1.1) was assembled using a hybrid de novo method combining high-depth Illumina short reads (376.6X) and low-depth PacBio long reads (9.7X)

  yeonsan ogye_1.1 locus tissues whole-genome genome structural

• Genome of the endangered Guatemalan Beaded Lizard, Heloderma charlesbogerti, reveals evolutionary relationships of squamates and declines in effective population sizes.

  PMID 36226801 · PMC9713440 · G3 (Bethesda, Md.) · 2022 · 8 claims · 7 setups

  Has reproduction · 84

  The assembled draft genome of H. charlesbogerti totals 2.31 Gb, similar in size to related species

  blood charlesbogerti reptile annotated whole-genome novo repeat

• Kinetoplastid genomics: the thin end of the wedge.

  PMID 18675383 · PMC2676795 · Infection, genetics and evolution : journal of molecular epidemiology and evolutionary genetics in infectious diseases · 2008 · 8 claims · 8 setups

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  Completion of the T. brucei, T. cruzi, and L. major genome sequencing projects enabled numerous studies that would otherwise have been difficult or impossible.

  brucei major cruzi kinetoplastid whole-genome gene shotgun

• Cis-regulatory evolution reveals sensory trade-offs as a genetic basis for temporal niche evolution in tapirs.

  PMID 41779860 · PMC12959415 · Science advances · 2026 · 8 claims · 8 setups

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  Tapirs reverted from a cathemeral ancestor to a nocturnal/crepuscular niche, accompanied by coordinated sensory reallocation: regressive vision (corneal opacity, reduced acuity) with enhanced auditory and chemosensory systems.

  terrestris single-copy mammalian tapir whole-genome comparative ancestral

• Comparative genomics and understanding of microbial biology.

  PMID 10998382 · PMC2627966 · Emerging infectious diseases · 2000 · 8 claims · 7 setups

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  GC content varies widely among prokaryotic genomes (29% in B. burgdorferi to 68% in M. tuberculosis) and shapes codon usage and amino acid composition.

  completed same sequenced mycobacterium whole-genome comparative phylogenomic

• The genome and development-dependent transcriptomes of Pyronema confluens: a window into fungal evolution.

  PMID 24068976 · PMC3778014 · PLoS genetics · 2013 · 8 claims · 8 setups

  Has reproduction · 76

  The 50 Mb P. confluens genome with 13,369 predicted protein-coding genes is more characteristic of higher filamentous ascomycetes than of the large, repeat-rich Tuber melanosporum genome, showing that the truffle's expanded genome is not typical of the Pezizales.

  pyronema confluens fungal whole-genome k-mer rna-seq

• Functional genomics in zebrafish permits rapid characterization of novel platelet membrane proteins.

  PMID 19109564 · PMC2680375 · Blood · 2009 · 8 claims · 6 setups

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  Zebrafish morpholino knockdown combined with a laser-induced arterial thrombosis assay is a fast, powerful method for initial functional screening of novel platelet genes.

  blood platelets platelet-rich platelet whole-genome quantitative flow

• The Bifidobacterium dentium Bd1 genome sequence reflects its genetic adaptation to the human oral cavity.

  PMID 20041198 · PMC2788695 · PLoS genetics · 2009 · 8 claims · 8 setups

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  The B. dentium Bd1 genome was sequenced to completion, revealing a single circular 2,636,368 bp chromosome with 2,143 predicted ORFs

  dentium core whole-genome 3d-structure comparative

• The promise and reality of personal genomics.

  PMID 19723346 · PMC2768970 · Genome biology · 2009 · 7 claims · 6 setups

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  Despite being the most complete and accurate individually sequenced human genome to date, AK1 sequencing still misses a substantial fraction of variants, showing sequencing technology remains far from complete/reliable.

  ak1 six whole-genome copy-number genotyping-based

• GenBank.

  PMID 16381837 · PMC1347519 · Nucleic acids research · 2006 · 8 claims · 8 setups

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  GenBank is a comprehensive public database of nucleotide sequences with supporting bibliographic and biological annotation, built and distributed by NCBI.

  sapiens organisms genbank large-scale genome expressed blast

• Multi-organ expression profiling uncovers a gene module in coronary artery disease involving transendothelial migration of leukocytes and LIM domain binding 2: the Stockholm Atherosclerosis Gene Expression (STAGE) study.

  PMID 19997623 · PMC2780352 · PLoS genetics · 2009 · 8 claims · 6 setups

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  Functionally associated gene modules, not individual genes, underlie CAD development and can be identified via multi-organ expression clustering

  liver atherosclerotic 128-gene independent two-way gene bioinformatic

• Ecotype diversity and conversion in Photobacterium profundum strains.

  PMID 24824441 · PMC4019646 · PloS one · 2014 · 8 claims · 8 setups

  Has reproduction · 77

  No single gene restricts the environmental niche of each bathytype; instead a set of strain-specific genetic features confers depth-specific stress tolerance (temperature, pressure, nutrients).

  photobacterium profundum predicted orthologous whole-genome pulsed-field comparative

• Effects of DNA mass on multiple displacement whole genome amplification and genotyping performance.

  PMID 16168060 · PMC1249558 · BMC biotechnology · 2005 · 8 claims · 6 setups

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  Increased gDNA input into the MDA WGA reaction increases the proportion of double-stranded and human-specific PCR-amplifiable wgaDNA and improves genotyping performance.

  lymphoblastoid gdna ntc wgadna quantification displacement str

• Critical care: applying genomics to inflammation outcomes.

  PMID 16330338 · PMC1314943 · Environmental health perspectives · 2005 · 8 claims · 6 setups

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  Genetic factors drive key aspects of an individual's inflammatory outcome after trauma, burns, or sepsis

  leukocytes whole-blood healthy peripheral genomewide whole-genome microarray

• The past and future of tuberculosis research.

  PMID 19855821 · PMC2745564 · PLoS pathogens · 2009 · 8 claims · 6 setups

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  Integrating systems biology with epidemiology ('systems epidemiology') will be required to better predict TB's trajectory and eliminate the disease

  clinical mycobacterium mtbc patients fingerprinting whole-genome microarray

• Metabolic resistance of the tiger mosquito to pyrethroid insecticides in La Réunion Island likely results from local adaptation.

  PMID 41718473 · PMC12963046 · Genome biology and evolution · 2026 · 8 claims · 5 setups

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  Deltamethrin resistance in La Réunion Ae. albopictus is not associated with known target-site (Kdr) mutations in the VGSC gene

  aedes who genome rna-seq