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 65

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

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

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

Full-text index only

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
Towards the identification of essential genes using targeted genome sequencing and comparative analysis.

PMID 17052348 · PMC1624830 · BMC genomics · 2006 · 8 claims · 8 setups

Full-text index only

Phyletic retention (ortholog presence across organisms) is the single most predictive feature of gene essentiality in both E. coli and S. cerevisiae.

coli cerevisiae comparative machine single-gene
The Princeton Protein Orthology Database (P-POD): a comparative genomics analysis tool for biologists.

PMID 17712414 · PMC1942082 · PloS one · 2007 · 8 claims · 5 setups

Full-text index only

P-POD is the first comparative genomics database to combine results from multiple computational ortholog/homolog prediction methods with manually curated literature-derived experimental evidence of functional conservation.

sequences orthomcl yeast orthomcl jaccard phylogenetic
Comparative genomics of emerging human ehrlichiosis agents.

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

Full-text index only

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
The dystrobrevin-binding protein 1 gene: features and networks.

PMID 18663367 · PMC2859304 · Molecular psychiatry · 2009 · 8 claims · 6 setups

Full-text index only

DTNBP1 gene structure, protein-coding sequence, and dysbindin domain are conserved across 13 vertebrate species, while noncoding sequence is diverse.

vertebrate dtnbp1 comparative cross-species molecular
A Meta-Analysis of Wolbachia Transcriptomics Reveals a Stage-Specific Wolbachia Transcriptional Response Shared Across Different Hosts.

PMID 32718933 · PMC7467002 · G3 (Bethesda, Md.) · 2020 · 7 claims · 8 setups

Has reproduction · 89

Across datasets re-analyzed with a unified workflow, there is a general lack of global Wolbachia gene regulation.

wolbachia wbm differentially rna-seq comparative co-expression
Computational verification of protein-protein interactions by orthologous co-expression.

PMID 15740634 · PMC555590 · BMC bioinformatics · 2005 · 7 claims · 8 setups

Full-text index only

Co-expression of orthologous protein pairs across multiple species can verify/predict S. cerevisiae PPIs with better performance than S. cerevisiae co-expression alone.

cerevisiae orthologs cdc28 yeast co-expression ortholog orthologous
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

Full-text index only

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
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

Full-text index only

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

yeast familial human-mouse comparative gene mutation
Correlation of microsynteny conservation and disease gene distribution in mammalian genomes.

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

Full-text index only

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
Emerging genomic and proteomic evidence on relationships among the animal, plant and fungal kingdoms.

PMID 15629046 · PMC5172449 · Genomics, proteomics & bioinformatics · 2004 · 8 claims · 7 setups

Full-text index only

Sequence-based molecular phylogenies widely support a sister relationship between animals and fungi, grouped as the Opisthokonta

nine animals completed fungal combined sequence biochemical
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

Full-text index only

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

genome genomic chromosome randomization
Investigating hookworm genomes by comparative analysis of two Ancylostoma species.

PMID 15854223 · PMC1112591 · BMC genomics · 2005 · 8 claims · 8 setups

Full-text index only

Nearly 20,000 ESTs from 7 cDNA libraries define nearly 7,000 hookworm genes across A. caninum and A. ceylanicum

caninum ceylanicum est bioinformatic functional
Comparative genomic analysis of three Leishmania species that cause diverse human disease.

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

Full-text index only

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
Reconstruction of human protein interolog network using evolutionary conserved network.

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

Full-text index only

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
Comparative analysis reveals signatures of differentiation amid genomic polymorphism in Lake Malawi cichlids.

PMID 18616806 · PMC2530870 · Genome biology · 2008 · 8 claims · 8 setups

Full-text index only

Lake Malawi cichlids are phenotypically and behaviorally diverse but appear genetically like a single subdivided population rather than distinct species

five cichlid pairwise lake low-coverage blastx multi-species
A map of human protein interactions derived from co-expression of human mRNAs and their orthologs.

PMID 18414481 · PMC2387231 · Molecular systems biology · 2008 · 8 claims · 6 setups

Full-text index only

Comparing human mRNA co-expression with co-expression of orthologous gene pairs in five other organisms identifies proteins that physically associate

genes hela proteins worm co-expression quantitative functional
Rapid bursts of androgen-binding protein (Abp) gene duplication occurred independently in diverse mammals.

PMID 18269759 · PMC2291036 · BMC evolutionary biology · 2008 · 8 claims · 5 setups

Full-text index only

The mouse Abp gene repertoire is twice as large as previously reported, comprising 30 Abpa and 34 Abpbg genes/pseudogenes

c57bl mus rodent genomic comparative pcr phylogenetic
Divergence of exonic splicing elements after gene duplication and the impact on gene structures.

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

Full-text index only

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

paralogous human-mouse duplicated comparative ortholog binomial
A new procedure for determining the genetic basis of a physiological process in a non-model species, illustrated by cold induced angiogenesis in the carp.

PMID 19852815 · PMC2771047 · BMC genomics · 2009 · 8 claims · 5 setups

Full-text index only

The Conditional Stepped Reciprocal Best Hit (CSRBH) approach, combining direct RBH and zebrafish-stepped RBH (SRBH), outperformed other ortholog assignment methods and attained 8,726 carp-human functional homolog relationships for 16,650 carp contigs

carp randomly zebrafish reciprocal sequence microarray

Experiments

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

Towards the identification of essential genes using targeted genome sequencing and comparative analysis.

The Princeton Protein Orthology Database (P-POD): a comparative genomics analysis tool for biologists.

Comparative genomics of emerging human ehrlichiosis agents.

The dystrobrevin-binding protein 1 gene: features and networks.

A Meta-Analysis of Wolbachia Transcriptomics Reveals a Stage-Specific Wolbachia Transcriptional Response Shared Across Different Hosts.

Computational verification of protein-protein interactions by orthologous co-expression.

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

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.

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

Emerging genomic and proteomic evidence on relationships among the animal, plant and fungal kingdoms.

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

Investigating hookworm genomes by comparative analysis of two Ancylostoma species.

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

Reconstruction of human protein interolog network using evolutionary conserved network.

Comparative analysis reveals signatures of differentiation amid genomic polymorphism in Lake Malawi cichlids.

A map of human protein interactions derived from co-expression of human mRNAs and their orthologs.

Rapid bursts of androgen-binding protein (Abp) gene duplication occurred independently in diverse mammals.

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

A new procedure for determining the genetic basis of a physiological process in a non-model species, illustrated by cold induced angiogenesis in the carp.