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).

Publications 1.3k Datasets 392.5k Experiments 21

System / cell line: test ✕ Assay: ortholog ✕ Clear

Evola: Ortholog database of all human genes in H-InvDB with manual curation of phylogenetic trees.

PMID 17982176 · PMC2238928 · Nucleic acids research · 2008 · 6 claims · 7 setups

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Evola combines genome synteny-based computational ortholog detection with manual curation of phylogenetic trees by experts to yield more reliable orthologs than automated pairwise methods

genome h-invdb gene sets genome transcript-to-genome coding
Mining expressed sequence tags identifies cancer markers of clinical interest.

PMID 17078886 · PMC1635568 · BMC bioinformatics · 2006 · 8 claims · 6 setups

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An EST-mining approach (Fisher Exact Test on tumor vs. non-tumor library hit counts) identifies differentially expressed transcripts with an estimated false discovery rate below 22% when human and mouse screens are combined.

dbest cancer gene est human-mouse leave-one-out
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
Reconstruction of human protein interolog network using evolutionary conserved network.

PMID 17493278 · PMC1885812 · BMC bioinformatics · 2007 · 8 claims · 7 setups

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A relative conservation score derived from maximal quasi-cliques in protein interaction networks, combined with other interaction features, can score and rank predicted human interologs for confidence.

ppi sequences interaction predicted interolog orthology quasi-clique
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
BLASTO: a tool for searching orthologous groups.

PMID 17483516 · PMC1933156 · Nucleic acids research · 2007 · 7 claims · 2 setups

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BLASTO treats each orthologous group as a unit and outputs a ranked list of orthologous groups instead of single sequences

randomly sequences blast blasto
Human synthetic lethal inference as potential anti-cancer target gene detection.

PMID 20015360 · PMC2804737 · BMC systems biology · 2009 · 7 claims · 8 setups

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Targeting the synthetic lethal partner of a gene mutated in cancer selectively damages tumor cells while sparing healthy cells, offering a rationale for anti-cancer drug design

saccharomyces sapiens ihsln genes database phylogenetic gene
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
Unusual linkage patterns of ligands and their cognate receptors indicate a novel reason for non-random gene order in the human genome.

PMID 16277660 · PMC1309615 · BMC evolutionary biology · 2005 · 8 claims · 5 setups

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Ligands are not more closely linked (shorter physical distance) to their cognate receptors than expected by chance

genome genomic chromosome randomization
Empirical codon substitution matrix.

PMID 15927081 · PMC1173088 · BMC bioinformatics · 2005 · 8 claims · 5 setups

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The authors present the first empirical codon substitution matrix built entirely from alignments of vertebrate coding DNA sequences.

orthologous million codon same pairwise empirical comparative
Predictive screening for regulators of conserved functional gene modules (gene batteries) in mammals.

PMID 15882449 · PMC1134656 · BMC genomics · 2005 · 8 claims · 4 setups

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A predictive computational screen covering ~40% of annotated protein-coding genes identified 21 co-expressed gene clusters with statistically supported sharing of cis-regulatory motifs.

upstream co-expression pre-b microarray-based motif gene
Gene losses during human origins.

PMID 16464126 · PMC1361800 · PLoS biology · 2006 · 7 claims · 7 setups

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A comparative genomic screen identified 67 new human-specific nonprocessed pseudogenes, bringing the total (with 13 from prior literature) to 80 human-specific pseudogenes.

pseudogene chimpanzee human-specific population comparative phylogenetic fisher's
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
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
Chemical genomics informs antibiotic and essential gene function in Acinetobacter baumannii.

PMID 40153700 · PMC11975115 · PLoS genetics · 2025 · 8 claims · 6 setups

Has reproduction · 71

The vast majority of A. baumannii essential genes show significant chemical-gene interactions upon knockdown

baumannii ranked lpta representative pooled string mic
Evolution and codon usage bias of mitochondrial and nuclear genomes in Aspergillus section Flavi.

PMID 36305682 · PMC9836360 · G3 (Bethesda, Md.) · 2023 · 8 claims · 8 setups

Has reproduction · 85

18 new mitochondrial genomes were assembled for Aspergillus section Flavi species, complementing 3 existing reference mitogenomes, for a total of 20 species analyzed.

aspergillus circularized core orthologous mitogenome read organellar
Design factors that influence PCR amplification success of cross-species primers among 1147 mammalian primer pairs.

PMID 17029642 · PMC1635982 · BMC genomics · 2006 · 8 claims · 7 setups

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The number of index-species (IS) mismatches in a primer pair significantly reduces amplification success, with an estimated 6-8% decrease in success rate per additional mismatch.

dog hamster pcr primer pcr blast sequence
Protein function assignment through mining cross-species protein-protein interactions.

PMID 18253506 · PMC2216687 · PloS one · 2008 · 8 claims · 6 setups

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CSIDOP predicts protein molecular function with 95.42% accuracy using 2,972 GO functional categories in H. sapiens

sapiens cross-species majority simple
Genome of the endangered Guatemalan Beaded Lizard, Heloderma charlesbogerti, reveals evolutionary relationships of squamates and declines in effective population sizes.

PMID 36226801 · PMC9713440 · G3 (Bethesda, Md.) · 2022 · 8 claims · 7 setups

Has reproduction · 84

The assembled draft genome of H. charlesbogerti totals 2.31 Gb, similar in size to related species

blood charlesbogerti reptile annotated whole-genome novo repeat
Ordinal-level phylogenomics of the arthropod class Diplopoda (millipedes) based on an analysis of 221 nuclear protein-coding loci generated using next-generation sequence analyses.

PMID 24236165 · PMC3827447 · PloS one · 2013 · 8 claims · 8 setups

Has reproduction · 82

An ordinal-level phylogeny of Diplopoda reconstructed from 221 nuclear protein-coding loci (61,641 aligned amino acid columns) differs from existing classifications in fundamental ways.

exemplar paired-end cleaned assembled transcriptome read novo

Experiments

Evola: Ortholog database of all human genes in H-InvDB with manual curation of phylogenetic trees.

Mining expressed sequence tags identifies cancer markers of clinical interest.

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

Reconstruction of human protein interolog network using evolutionary conserved network.

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

BLASTO: a tool for searching orthologous groups.

Human synthetic lethal inference as potential anti-cancer target gene detection.

The excess of 5' introns in eukaryotic genomes.

Unusual linkage patterns of ligands and their cognate receptors indicate a novel reason for non-random gene order in the human genome.

Empirical codon substitution matrix.

Predictive screening for regulators of conserved functional gene modules (gene batteries) in mammals.

Gene losses during human origins.

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

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

Chemical genomics informs antibiotic and essential gene function in Acinetobacter baumannii.

Evolution and codon usage bias of mitochondrial and nuclear genomes in Aspergillus section Flavi.

Design factors that influence PCR amplification success of cross-species primers among 1147 mammalian primer pairs.

Protein function assignment through mining cross-species protein-protein interactions.

Genome of the endangered Guatemalan Beaded Lizard, Heloderma charlesbogerti, reveals evolutionary relationships of squamates and declines in effective population sizes.

Ordinal-level phylogenomics of the arthropod class Diplopoda (millipedes) based on an analysis of 221 nuclear protein-coding loci generated using next-generation sequence analyses.