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).

• Exonic remnants of whole-genome duplication reveal cis-regulatory function of coding exons.

  PMID 19969543 · PMC2831330 · Nucleic acids research · 2010 · 8 claims · 8 setups

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  38 candidate cis-regulatory coding exons (RCEs) with predicted target genes were identified genome-wide

  hg18 zebrafish bystander human-mouse comparative synteny orthologous

• From microarrays to genome duplications.

  PMID 12914655 · PMC193639 · Genome biology · 2003 · 8 claims · 8 setups

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  Gene3D shows that most genes across sequenced genomes can be assigned to known structural domain families, many of which are shared across kingdoms of life

  tumor cancer plated saccharomyces comparative nonsense-mediated cell-based

• Comparative genomics comes of age.

  PMID 12186641 · PMC139393 · Genome biology · 2002 · 8 claims · 8 setups

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  Only about 50% of conserved sequence elements (exons+introns) in orthologous human-mouse genes correspond to exons, implying substantial non-exonic conservation

  orthologous chromosome chimpanzee somatic-cell comparative targeted tiled

• SVC: structured visualization of evolutionary sequence conservation.

  PMID 15991338 · PMC1160265 · Nucleic acids research · 2005 · 7 claims · 5 setups

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  SVC aligns protein-coding sequences of orthologous gene pairs and maps them back onto their encoding exons/introns to generate a scaffold of conserved gene structure.

  orthologous exonic tblastx blastn sliding-window

• Differences in the evolutionary history of disease genes affected by dominant or recessive mutations.

  PMID 16817963 · PMC1534034 · BMC genomics · 2006 · 8 claims · 8 setups

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  Dominant disease genes are more conserved at the protein level (mouse orthologues) than recessive disease genes.

  disease human-chimpanzee human-mouse-dog elegans sequence paralogue coding

• Exhaustive prediction of disease susceptibility to coding base changes in the human genome.

  PMID 18793467 · PMC2537574 · BMC bioinformatics · 2008 · 8 claims · 7 setups

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  Inter-species conservation is the strongest single predictor of disease-associated coding mutations among the factors tested.

  hgmd refseq aligned svm svm reciprocal inter-species

• 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

• Benchmarking ortholog identification methods using functional genomics data.

  PMID 16613613 · PMC1557999 · Genome biology · 2006 · 8 claims · 7 setups

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  InParanoid is the best overall ortholog identification method for identifying functionally equivalent proteins when sensitivity and selectivity are combined into an overall score.

  known human-mouse expression interpro co-expression

• Correlation of microsynteny conservation and disease gene distribution in mammalian genomes.

  PMID 19909546 · PMC2779822 · BMC genomics · 2009 · 7 claims · 8 setups

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  Density of mouse orthologs of human disease genes correlates with regions of conserved microsynteny in the mouse genome

  genes autosomes dog genome comparative blat sliding-window

• Comparative genomic analysis reveals a novel mitochondrial isoform of human rTS protein and unusual phylogenetic distribution of the rTS gene.

  PMID 16162288 · PMC1261261 · BMC genomics · 2005 · 8 claims · 5 setups

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  A novel rTS protein isoform, rTSγ, exists with a 27-residue longer N-terminus generated from an alternative upstream start codon relative to rTSβ.

  rts rtsβ ccrf-cem comparative mitochondrial subcellular

• 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

• Catalogues of mammalian long noncoding RNAs: modest conservation and incompleteness.

  PMID 19895688 · PMC3091318 · Genome biology · 2009 · 8 claims · 6 setups

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  MacroRNA and lincRNA exons are subject to the same relatively low degree of sequence constraint, contrary to prior reports that lincRNAs are far more conserved

  macrorna sequence comparative mouse-human population

• lncEvo: automated identification and conservation study of long noncoding RNAs.

  PMID 33563213 · PMC7871587 · BMC bioinformatics · 2021 · 8 claims · 5 setups

  Has reproduction · 61

  lncEvo is an integrated Nextflow/Docker pipeline combining transcriptome assembly, lncRNA identification, and cross-species conservation analysis into a single workflow.

  chimp assembled pairwise raw bulk lncrna comparative

• Organismal complexity, cell differentiation and gene expression: human over mouse.

  PMID 17881362 · PMC2095826 · Nucleic acids research · 2007 · 8 claims · 7 setups

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  Human shows a greater fraction of tissue-specific genes and a greater ratio of total expression of tissue-specific to housekeeping genes than mouse across 32 homologous tissues

  human-mouse oligonucleotide exon comparative

• Prioritization of candidate cancer genes--an aid to oncogenomic studies.

  PMID 18710882 · PMC2566894 · Nucleic acids research · 2008 · 8 claims · 8 setups

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  Computational classifiers using combinations of protein conservation, gene structure, protein domains, protein interactions, and regulatory data can distinguish known cancer genes (CD/CR) from unlabelled human genes

  genes cancer interpro interactome averaged cross-validation domain

• QuadBase: genome-wide database of G4 DNA--occurrence and conservation in human, chimpanzee, mouse and rat promoters and 146 microbes.

  PMID 17962308 · PMC2238983 · Nucleic acids research · 2008 · 8 claims · 3 setups

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  QuadBase is a compendium of G4 DNA (quadruplex) motifs focused on their occurrence and conservation in promoters, composed of EuQuad and ProQuad

  chimpanzee prokaryotic promoters genome-wide cross-species

• Heterotachy in mammalian promoter evolution.

  PMID 16683025 · PMC1449885 · PLoS genetics · 2006 · 8 claims · 5 setups

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  The rate of promoter evolution relative to control sequences is not consistent between or within mammalian lineages over time (heterotachy)

  promoter ancient chimpanzee comparative ancient micro-indel

• 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

• A clustering property of highly-degenerate transcription factor binding sites in the mammalian genome.

  PMID 16670430 · PMC1456330 · Nucleic acids research · 2006 · 8 claims · 7 setups

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  Highly-degenerate RE1 sites are significantly enriched in promoters of validated and putative REST target genes compared to control promoters

  orthologous randomized high-score promoters pssm-based comparative motif

• A global definition of expression context is conserved between orthologs, but does not correlate with sequence conservation.

  PMID 16423292 · PMC1382217 · BMC genomics · 2006 · 7 claims · 6 setups

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  Expression context is largely conserved between orthologs across four eukaryote species.

  elegans pairwise orthologs cerevisiae microarray ortholog functional