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).

• Genomic and bioinformatics analysis of human adenovirus type 37: new insights into corneal tropism.

  PMID 18471294 · PMC2397415 · BMC genomics · 2008 · 7 claims · 7 setups

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  The complete genome of HAdV-37 was sequenced and annotated (35,213 bp, 56.6% GC content, 35 predicted coding sequences plus 8 hypothetical ORFs)

  hadv-37 predicted select genome cpg global

• 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

• Narcisse: a mirror view of conserved syntenies.

  PMID 17981845 · PMC2238891 · Nucleic acids research · 2008 · 8 claims · 4 setups

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  Narcisse is a database/web tool providing an integrated, multi-level comparative analysis of sequence similarities and conserved chromosomal segments (syntenies) across animal, plant, fungal and bacterial completely sequenced genomes.

  annotated genome pairwise pairs sequence nucleic-level conserved

• Uprobe 2008: an online resource for universal overgo hybridization-based probe retrieval and design.

  PMID 18515352 · PMC2447791 · Nucleic acids research · 2008 · 7 claims · 7 setups

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  Uprobe provides new predesigned whole-genome universal overgo probe sets for screening marsupial, rodent, and carnivore BAC libraries.

  wallaby squirrel deer clouded overgo bac comparative

• 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

• Low conservation and species-specific evolution of alternative splicing in humans and mice: comparative genomics analysis using well-annotated full-length cDNAs.

  PMID 18838389 · PMC2582632 · Nucleic acids research · 2008 · 7 claims · 8 setups

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  Although 86% of individual human exons are conserved in the mouse genome, only a small fraction (431/20392, ~2%) of human AS variants are perfectly conserved AS variants in mice.

  genome full-length ~3x10^7 isoform whole-genome full-length polysome

• 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

• Viruses take center stage in cellular evolution.

  PMID 16787527 · PMC1779534 · Genome biology · 2006 · 8 claims · 6 setups

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  A large poxvirus-like dsDNA virus may have become the eukaryotic nucleus after being taken in by an ancestral cell (viral eukaryogenesis)

  acanthamoeba coccolithovirus nucleocytoplasmic dsdna whole-genome phylogenetic comparative

• Multiple whole genome alignments and novel biomedical applications at the VISTA portal.

  PMID 17488840 · PMC1933192 · Nucleic acids research · 2007 · 8 claims · 4 setups

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  A novel multiple whole-genome alignment algorithm treats all genomes symmetrically, avoiding dependence on a single base/reference genome

  genome vertebrate multi-species whole-genome conservation non-synonymous

• 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

• Insights into vertebrate evolution from the chicken genome sequence.

  PMID 15693954 · PMC551526 · Genome biology · 2005 · 8 claims · 6 setups

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  Chicken has expanded gene families involved in egg production (e.g., avidin) and feather/scale/claw formation (avian-specific keratins) not present or lost in mammals

  red chicken whole-genome comparative synteny

• Molecular correlates of host specialization in Staphylococcus aureus.

  PMID 17971880 · PMC2040198 · PloS one · 2007 · 8 claims · 6 setups

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  Genome sequencing of ET3-1 revealed genomic elements not previously identified in S. aureus, including homologs of virulence factors from other Gram-positive pathogens

  aureus sequenced et3-1 bovine whole-genome comparative substitution

• Comparative genomics of the neglected human malaria parasite Plasmodium vivax.

  PMID 18843361 · PMC2651158 · Nature · 2008 · 8 claims · 8 setups

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  P. vivax resembles other sequenced malaria parasites (P. falciparum, P. knowlesi, P. yoelii) in gene content and metabolic potential

  vivax genome comparative microsatellite

• More biology from the sequence.

  PMID 11532209 · PMC138951 · Genome biology · 2001 · 8 claims · 8 setups

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  The Schizosaccharomyces pombe genome has been sequenced to completion with no gaps, telomere to telomere.

  schizosaccharomyces chromosome genome cervical whole-genome sequence genome

• Of rats and men.

  PMID 15003114 · PMC395761 · Genome biology · 2004 · 8 claims · 10 setups

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  The rat genome has been sequenced to draft level, with over 90% of the genome sampled using more than 36 million sequence reads (assembly version 3.1)

  rattus cftr fugu transgenic whole-genome comparative genome

• The genome of the ant Tetramorium bicarinatum reveals a tandem organization of venom peptides genes allowing the prediction of their regulatory and evolutionary profiles.

  PMID 38245722 · PMC10800049 · BMC genomics · 2024 · 8 claims · 8 setups

  Has reproduction · 100

  44 venom peptide genes were identified, distributed across four of the eleven chromosomes and organized in tandem repeat clusters.

  tetramorium bicarinatum vpg venom whole-genome blast gene

• Genetic analysis of pathways regulated by the von Hippel-Lindau tumor suppressor in Caenorhabditis elegans.

  PMID 15361934 · PMC515368 · PLoS biology · 2004 · 7 claims · 8 setups

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  The HIF-1/VHL-1/EGL-9 hydroxylase pathway is tightly conserved in C. elegans

  elegans whole-genome rnase pharmacological

• The UCSC Genome Browser Database: update 2006.

  PMID 16381938 · PMC1347506 · Nucleic acids research · 2006 · 8 claims · 8 setups

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  The UCSC Genome Browser Database (GBD) provides integrated sequence and annotation data, with web tools (Genome Browser, Table Browser, Proteome Browser, Gene Sorter, BLAT, In Silico PCR) for visualizing and querying genomes of about a dozen vertebrate species and several model organisms.

  dog vertebrate encode genome comparative automated cross-species

• Identification of the REST regulon reveals extensive transposable element-mediated binding site duplication.

  PMID 16899447 · PMC1557810 · Nucleic acids research · 2006 · 8 claims · 8 setups

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  The RE1 PSSM identifies functional RE1 binding sites with greater sensitivity and selectivity than the previously used RE1 consensus sequence

  fibroblast hela hek293 set genome-wide electrophoretic rt-pcr

• The other side of comparative genomics: genes with no orthologs between the cow and other mammalian species.

  PMID 20003425 · PMC2808326 · BMC genomics · 2009 · 7 claims · 4 setups

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  3,801 bovine genes have no orthologs in human, mouse and dog, and 1,010 human genes have no orthologs in cow despite having orthologs in mouse and dog

  bovine cow coding blast-based ensembl gene