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).

• 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

• Programmed genetic instability: a tumor-permissive mechanism for maintaining the evolvability of higher species through methylation-dependent mutation of DNA repair genes in the male germ line.

  PMID 18535014 · PMC2464741 · Molecular biology and evolution · 2008 · 8 claims · 7 setups

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  Repair genes are numerically less common than apoptosis genes in the genomes of multicellular organisms

  yeast familial human-mouse comparative gene mutation

• GenomeTrafac: a whole genome resource for the detection of transcription factor binding site clusters associated with conventional and microRNA encoding genes conserved between mouse and human gene orthologs.

  PMID 17178752 · PMC1781107 · Nucleic acids research · 2007 · 8 claims · 5 setups

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  GenomeTrafac is a web-accessible database enabling genome-wide detection of conserved cis-element clusters in human-mouse gene orthologs, covering both conventional and microRNA genes

  human-mouse genome blastz-aligned itgb1bp2 comparative transcription sequence

• Evolution of insect proteomes: insights into synapse organization and synaptic vesicle life cycle.

  PMID 18257909 · PMC2374702 · Genome biology · 2008 · 8 claims · 3 setups

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  Compiled a list of 120 core presynaptic gene prototypes (PS120) and catalogued their conservation across insect proteomes.

  insect vamp2 ps120 comparative sequence protein-protein

• Comparative analysis of cancer genes in the human and chimpanzee genomes.

  PMID 16438707 · PMC1382208 · BMC genomics · 2006 · 7 claims · 6 setups

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  All 333 examined human cancer genes have intact, highly conserved orthologs in the chimpanzee genome (99.38% protein identity).

  chimpanzee non-human cancer comparative pcr targeted

• 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

• 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

• Genomic organization, annotation, and ligand-receptor inferences of chicken chemokines and chemokine receptor genes based on comparative genomics.

  PMID 15790398 · PMC1082905 · BMC genomics · 2005 · 8 claims · 6 setups

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  Twenty-three chemokine genes and 14 chemokine receptor genes were identified in the chicken genome, including 12 new chemokines and 7 new receptors beyond prior reports.

  chicken comparative amino phylogenetic

• Combining comparative genomics with de novo motif discovery to identify human transcription factor DNA-binding motifs.

  PMID 17217514 · PMC1780116 · BMC bioinformatics · 2006 · 6 claims · 4 setups

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  A novel method combining 8-species comparative genomics with de novo motif discovery identifies human TF DNA-binding motifs overrepresented and conserved in upstream regions of co-regulated genes

  muscle-specific novo comparative

• ARED Organism: expansion of ARED reveals AU-rich element cluster variations between human and mouse.

  PMID 17984078 · PMC2238997 · Nucleic acids research · 2008 · 6 claims · 4 setups

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  ARED Organism and ARED-Integrated are new/updated public databases cataloguing ARE-containing mRNAs/genes in human, mouse and rat

  6x6 ortholog 3'utr comparative chi-squared

• 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

• Divergence of exonic splicing elements after gene duplication and the impact on gene structures.

  PMID 19883501 · PMC3091315 · Genome biology · 2009 · 8 claims · 7 setups

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  ESEs and ESSs diverge especially fast shortly after gene duplication, correlating with time since duplication (Ks)

  paralogous human-mouse duplicated comparative ortholog binomial

• Comparative gene finding in chicken indicates that we are closing in on the set of multi-exonic widely expressed human genes.

  PMID 15809229 · PMC1074396 · Nucleic acids research · 2005 · 8 claims · 6 setups

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  Comparative gene finding (SGP2) between human and chicken, followed by RT-PCR verification, adds at most ~0.2% new genes to the multi-exonic human gene catalog

  chicken predicted human-chicken cdna comparative blastp pairwise

• Genomic view of the evolution of the complement system.

  PMID 16896831 · PMC2480602 · Immunogenetics · 2006 · 8 claims · 6 setups

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  Bony fish and higher vertebrates share practically the same set of complement genes, indicating most complement gene duplications occurred by the teleost/mammalian divergence (~500 MYA)

  chicken complement sponge shark comparative phylogenetic reverse

• Comparative genomic analysis of three Leishmania species that cause diverse human disease.

  PMID 17572675 · PMC2592530 · Nature genetics · 2007 · 8 claims · 6 setups

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  L. infantum and L. braziliensis genomes were sequenced and show marked conservation of synteny with L. major, with only ~200 genes differentially distributed among the three species

  infantum major braziliensis leishmania whole-genome comparative pcr

• Identification and characterization of insect-specific proteins by genome data analysis.

  PMID 17407609 · PMC1852559 · BMC genomics · 2007 · 8 claims · 7 setups

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  Comparative genome analysis across five holometabolous insects and three non-insect eukaryotes (opisthokonts) identifies 154 insect-specific orthologous groups (refined to 51 proteins) and 466 eukaryote/opisthokont-core orthologous groups

  drosophila insect-core locusta insect-specific comparative est functional

• 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

• Expansion of the human mitochondrial proteome by intra- and inter-compartmental protein duplication.

  PMID 19930686 · PMC3091328 · Genome biology · 2009 · 8 claims · 6 setups

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  The human mitochondrial proteome expanded via two prevailing gene duplication modes: intra-mitochondrial and inter-compartmental duplication

  cerevisiae mitocarta mitochondrial tissues comparative subcellular gene

• PReMod: a database of genome-wide mammalian cis-regulatory module predictions.

  PMID 17148480 · PMC1761432 · Nucleic acids research · 2007 · 8 claims · 3 setups

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  PReMod is a database of genome-wide predicted cis-regulatory modules (pCRMs) for the human and mouse genomes.

  genome chip-chip comparative

• Adaptive history of single copy genes highly expressed in the term human placenta.

  PMID 18848617 · PMC2759754 · Genomics · 2009 · 8 claims · 6 setups

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  222 single copy eutherian genes are highly expressed (>=3x median) in the term human placenta

  term single same lists microarray comparative site