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).

• Gene duplication: the genomic trade in spare parts.

  PMID 15252449 · PMC449868 · PLoS biology · 2004 · 8 claims · 7 setups

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  Gene duplication relaxes selective constraint on one copy, allowing exploration of evolutionary space that is otherwise forbidden in single-copy genes, making duplication the major opportunity for new gene function evolution.

  great genome recently yeast genome-wide molecular comparative

• The sequence and de novo assembly of the giant panda genome.

  PMID 20010809 · PMC3951497 · Nature · 2010 · 8 claims · 8 setups

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  A draft giant panda genome was successfully generated and assembled de novo using only Illumina Genome Analyser short-read sequencing

  giant panda whole-genome novo read

• miRNAMap: genomic maps of microRNA genes and their target genes in mammalian genomes.

  PMID 16381831 · PMC1347497 · Nucleic acids research · 2006 · 6 claims · 6 setups

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  miRNAMap integrates known miRNA genes from miRBase, literature-curated validated targets, and computationally predicted miRNA genes and targets for human, mouse, rat and dog.

  conserved putative mirna-target normal comparative machine mirna

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

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

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  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

• 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

• The excess of 5' introns in eukaryotic genomes.

  PMID 16314314 · PMC1292992 · Nucleic acids research · 2005 · 7 claims · 4 setups

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  All 21 eukaryotic genomes studied show a statistically significant 5′-biased distribution of introns in protein-coding genes

  eukaryotic same housekeeping comparative chi-square bidirectional

• Comparative genomics of emerging human ehrlichiosis agents.

  PMID 16482227 · PMC1366493 · PLoS genetics · 2006 · 8 claims · 5 setups

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  Ehrlichia spp. and Anaplasma spp. display a unique large expansion of immunodominant outer membrane proteins (OMP-1/P44/Msp2 family) facilitating antigenic variation

  phagocytophilum representative concatenated rickettsiales whole-genome comparative phylogenetic

• GPCR genes are preferentially retained after whole genome duplication.

  PMID 18382678 · PMC2270905 · PloS one · 2008 · 8 claims · 6 setups

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  WGD-derived nGPCR duplicates in Tetraodon nigroviridis are retained at a significantly higher rate (23.5%) than the genome-wide average (15%)

  vertebrate ngpcr nigroviridis syntenic phylogenetic chromosomal

• Comparing whole genomes using DNA microarrays.

  PMID 18347592 · PMC7097741 · Nature reviews. Genetics · 2008 · 8 claims · 6 setups

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  DNA microarrays offer a relatively inexpensive and efficient alternative to genome sequencing for comparing all known classes of genomic diversity between closely related genomes.

  genome saccharomyces mitochondrial sars array comparative resequencing

• Identification of multiple independent horizontal gene transfers into poxviruses using a comparative genomics approach.

  PMID 18304319 · PMC2268676 · BMC evolutionary biology · 2008 · 8 claims · 4 setups

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  Comparative synteny conservation around a horizontally transferred gene (HTgene) can distinguish single versus multiple independent HGT events even without a robust phylogenetic tree.

  poxvirus core psi-blast comparative molecular

• A parsimony approach to biological pathway reconstruction/inference for genomes and metagenomes.

  PMID 19680427 · PMC2714467 · PLoS computational biology · 2009 · 8 claims · 6 setups

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  The naïve mapping approach (present if ≥1 associated function is found) leads to an inflated estimate of biological pathways and overestimates functional diversity of a sample.

  complete genome escherichia environmental comparative pathway local

• Genomic capacities for Reactive Oxygen Species metabolism across marine phytoplankton.

  PMID 37098087 · PMC10128935 · PloS one · 2023 · 8 claims · 3 setups

  Has reproduction · 38

  Genes encoding superoxide (O2•−) scavenging are ubiquitous across phytoplankton, but their fractional gene allocation decreases with increasing cell radius, consistent with a nearly fixed core gene set.

  diverse annotated same comparative enzyme trait

• 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

• Evolutionary Genomics of Sex-Related Chromosomes at the Base of the Green Lineage.

  PMID 34599324 · PMC8557840 · Genome biology and evolution · 2021 · 8 claims · 6 setups

  Has reproduction · 84

  The divergence of the MT+ and MT- alleles predates speciation events within the Ostreococcus genus

  mamiellales ostreococcus tauri shared comparative orthology synteny

• Comparative genomics of dairy-associated Staphylococcus aureus from selected sub-Saharan African regions reveals milk as reservoir for human-and animal-derived strains and identifies a putative animal-related clade with presumptive novel siderophore.

  PMID 36046020 · PMC9421002 · Frontiers in microbiology · 2022 · 7 claims · 8 setups

  Has reproduction · 89

  Milk serves as a reservoir for both human- and animal-derived S. aureus strains in sub-Saharan Africa

  aureus reduced genome cgmlst comparative

• 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

• 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

• 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

• The post-genomic era for a select few.

  PMID 14759254 · PMC395745 · Genome biology · 2004 · 8 claims · 8 setups

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  The Exofish comparative-genomics tool identifies protein-coding DNA segments by comparing two genome sequences and was used to compare pufferfish (Takifugu, Tetraodon) genomes with mammalian genomes, improving annotation of the human and mouse genomes.

  takifugu physcomitrella coli vibrio comparative genetic dna-microarray

• Large-scale trends in the evolution of gene structures within 11 animal genomes.

  PMID 16518452 · PMC1386723 · PLoS computational biology · 2006 · 8 claims · 5 setups

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  Change in intron–exon gene structure is gradual, clock-like, and largely independent of coding-sequence (protein) evolution

  annotated animal unannotated comparative all-against-all neighbor-joining