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).

• The global landscape of sequence diversity.

  PMID 17996061 · PMC2258180 · Genome biology · 2007 · 7 claims · 5 setups

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  Eukaryotic sequence datasets show substantially greater genetic diversity (higher sequence/gene family discovery rates) than bacterial datasets, likely related to differences in modes of genetic inheritance.

  fully eukaryotic complete gene blast-based est gene

• From Pasteur to genomics: progress and challenges in infectious diseases.

  PMID 15516917 · PMC7096024 · Nature medicine · 2004 · 8 claims · 8 setups

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  Genomic sequencing has revealed the blueprint of most pathogens, enabling new diagnostics, therapeutics and vaccines including for previously uncultivable agents.

  bacterial neisseria sars hiv-infected whole-genome reverse nucleic

• Human chromosome 7: DNA sequence and biology.

  PMID 12690205 · PMC2882961 · Science (New York, N.Y.) · 2003 · 6 claims · 2 setups

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  Presents the DNA sequence and annotation of the entire human chromosome 7

  chromosome genomic comparative

• Exogean: a framework for annotating protein-coding genes in eukaryotic genomic DNA.

  PMID 16925841 · PMC1810556 · Genome biology · 2006 · 8 claims · 5 setups

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  Exogean is a framework using directed acyclic coloured multigraphs (DACMs) to represent biological objects (mRNA, ESTs, protein alignments, exons) and iteratively combine them into complex protein-coding transcript models.

  genome sequences automatic manual sequence

• Dark matter in a deep-sea vent and in human mouth.

  PMID 17803764 · PMC2040194 · Environmental microbiology · 2007 · 7 claims · 8 setups

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  The first genome sequence from the uncultured TM7 phylum was obtained by capturing and sequencing DNA from a single cell using a microfluidic device, yielding a 2.86 Mb assembly with 3245 predicted genes.

  uncultured mycoplasma cyanidioschyzon kineococcus single-cell genome whole-genome

• Visualizing the genome: techniques for presenting human genome data and annotations.

  PMID 12149135 · PMC119855 · BMC bioinformatics · 2002 · 8 claims · 4 setups

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  Web-based client-server genome browsers (e.g., LocusLink evidence viewer, UCSC genome browser) are limited by lack of true interactivity, requiring server round-trips for navigation

  flj22324 snurf arg1 plat cdna-to-genomic multi-track frame-of-translation

• Genome-wide survey for biologically functional pseudogenes.

  PMID 16680195 · PMC1456316 · PLoS computational biology · 2006 · 8 claims · 6 setups

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  A subset of ancient, cross-species-conserved pseudogenes (30 of 1,453 candidate quartets) show evidence consistent with retained biological function

  human-mouse chimpanzee cross-species maximum-likelihood synteny

• Accelerating rare disease diagnostics by linking DNA and RNA through an explainable and interactive RNA-guided workflow.

  PMID 41685349 · PMC12891912 · NAR genomics and bioinformatics · 2026 · 7 claims · 7 setups

  Has reproduction

  An integrated RNA-guided variant interpretation workflow combining OUTRIDER, FRASER, MOLGENIS VIP, and Borzoi enhances clinical variant interpretation and reclassification of VUS in rare disease cases.

  udn blood skin snvs whole-genome bulk splice-altering

• Genomics research and malaria control: great expectations.

  PMID 14624242 · PMC261879 · PLoS biology · 2003 · 8 claims · 8 setups

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  Genomics research on humans, P. falciparum, and An. gambiae holds great promise for developing new drugs, vaccines, diagnostics, and vector control tools for malaria.

  plasmodium anopheles malaria whole-genome computational microarray

• EpiToolKit--a web server for computational immunomics.

  PMID 18440979 · PMC2447732 · Nucleic acids research · 2008 · 7 claims · 3 setups

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  EpiToolKit is a web server integrating five MHC class I and two MHC class II epitope prediction methods in a unified, user-friendly interface.

  randomly novel minor mhc polymorphic

• The human L-threonine 3-dehydrogenase gene is an expressed pseudogene.

  PMID 12361482 · PMC131051 · BMC genetics · 2002 · 8 claims · 7 setups

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  The human TDH gene is located at chromosome 8p23-22, spans 10 kb, and has 8 exons that would be expected to encode a 369-residue ORF.

  genomic predicted cdna tissues genomic sequence pcr

• Cis sequence effects on gene expression.

  PMID 17727713 · PMC2077339 · BMC genomics · 2007 · 6 claims · 4 setups

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  Approximately one in four genes (8 of 30, 26.7%) exhibit statistically significant cis sequence effects on gene expression in this study, consistent with a literature-wide weighted average of 26.2%

  lymphoblastoid genomic oligonucleotide gene candidate snp

• Recent segmental and gene duplications in the mouse genome.

  PMID 12914656 · PMC193640 · Genome biology · 2003 · 8 claims · 8 setups

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  33.6 Mb (1.2%) of the February 2003 mouse genome assembly (2,695 Mb) is involved in recent segmental duplications

  genome gene ensembl-annotated chromosome pairwise gene blat

• Comparative genomics.

  PMID 14624258 · PMC261895 · PLoS biology · 2003 · 8 claims · 7 setups

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  Conserved DNA between species tends to encode shared functional features, while divergent DNA underlies species differences

  caenorhabditis yeast mammalian vertebrate whole-genome comparative interspecies-similarity-informed

• Application of genomics to toxicology research.

  PMID 12634120 · PMC1241273 · Environmental health perspectives · 2002 · 8 claims · 3 setups

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  Toxic chemical exposures alter gene expression, producing a diagnostic transcriptional 'fingerprint' that can be matched against known toxicants to classify untested chemicals' toxic potential.

  yeast rodents rodent microarray proposed cross-species

• Genomic approaches to the genetics of alcoholism.

  PMID 12875046 · PMC6683845 · Alcohol research & health : the journal of the National Institute on Alcohol Abuse and Alcoholism · 2002 · 8 claims · 4 setups

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  Alcoholism is a complex disease that develops from a combination of numerous genetic and environmental factors, unlike single-gene disorders such as cystic fibrosis or Huntington's disease.

  specified genomic gene genomic exon

• Evolutionary sequence analysis of complete eukaryote genomes.

  PMID 15762985 · PMC1274250 · BMC bioinformatics · 2005 · 8 claims · 6 setups

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  A conservative genome-comparison method (MIA) identifies panorthologs — strict single-copy 1:1 orthologs containing only species divergences, no paralogy — to minimize errors from gene duplication in evolutionary sequence analysis.

  complete panortholog concatenated individual reciprocal sequence neighbor-joining

• Computational disease gene identification: a concert of methods prioritizes type 2 diabetes and obesity candidate genes.

  PMID 16757574 · PMC1475747 · Nucleic acids research · 2006 · 6 claims · 8 setups

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  Applying seven independent computational disease-gene prioritization methods in concert to 9556 positional candidate genes identifies a prioritized set of likely T2D and obesity candidate genes

  pubmed genes same randomly geneseeker evoc disease

• Evolution of the NANOG pseudogene family in the human and chimpanzee genomes.

  PMID 16469101 · PMC1457002 · BMC evolutionary biology · 2006 · 7 claims · 5 setups

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  The NANOG gene and all pseudogenes except NANOGP8 occupy orthologous chromosomal positions in the chimpanzee genome, indicating they originated before the human-chimpanzee divergence.

  chimpanzee megablast pcr flanking-sequence

• 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