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 410

System / cell line: phylogenetic ✕ Clear

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
Comparative analysis of plant genomes allows the definition of the "Phytolongins": a novel non-SNARE longin domain protein family.

PMID 19889231 · PMC2779197 · BMC genomics · 2009 · 8 claims · 6 setups

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A novel, plant-specific family of longin-related proteins, the 'Phytolongins', was identified in land plant genomes.

genomes longin plant phytolongin iterative phylogenetic genomic
Searching for new clues about the molecular cause of endomyocardial fibrosis by way of in silico proteomics and analytical chemistry.

PMID 19823676 · PMC2757908 · PloS one · 2009 · 8 claims · 4 setups

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Cross-reactivity of antibodies against C-terminal sequences of ribosomal P proteins from several animals, plants and protozoa with heart tissue may mediate EMF similarly to how T. cruzi C-termini mediate Chaga's disease

tcp0 tcp2β blast-p phylogenetic structure
Addressing pandemic-wide systematic errors in the SARS-CoV-2 phylogeny.

PMID 41663577 · PMC12982125 · Nature methods · 2026 · 6 claims · 3 setups

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Most SARS-CoV-2 genomes were sequenced using tiled amplicon methods, which introduce systematic errors unless assembly software is aware of the amplicon scheme and the error modes of amplicon sequencing

sars-cov-2 amplicon-aware simulation global
Identification of the Wheat (Triticum aestivum) IQD Gene Family and an Expression Analysis of Candidate Genes Associated with Seed Dormancy and Germination.

PMID 35456910 · PMC9025732 · International journal of molecular sciences · 2022 · 8 claims · 8 setups

Has reproduction · 78

73 IQD gene family members were identified in the wheat genome and classified into six phylogenetic groups

triticum taiqd wheat rice genome-wide phylogenetic gene
Genome-wide identification and characterization of germin-like protein family in Brassica juncea reveals their role against biotic stress.

PMID 41327045 · PMC12763953 · BMC plant biology · 2025 · 8 claims · 7 setups

Has reproduction · 58

Genome-wide identification revealed 102 GLPs in B. juncea, 51 in B. nigra, and 48 in B. rapa

juncea promoter duplicated super genome-wide phylogenetic synteny
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
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
The cohesin complex: sequence homologies, interaction networks and shared motifs.

PMID 11276426 · PMC30708 · Genome biology · 2001 · 8 claims · 8 setups

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Mouse Mmip1 and Smc3 (SMCD) share 99% sequence identity and are products of the same gene

smc1 smc3 mmip1 smc psi-blast phylogenetic sequence
Genotyping, Orientalis-like Yersinia pestis, and plague pandemics.

PMID 15498160 · PMC3320270 · Emerging infectious diseases · 2004 · 6 claims · 6 setups

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Multiple spacer typing (MST), based on intergenic spacer sequencing, differentiates the three Y. pestis biovars

pestis combined dental contemporary spacer phylogenetic pcr
Comparative genomics of cyclin-dependent kinases suggest co-evolution of the RNAP II C-terminal domain and CTD-directed CDKs.

PMID 15380029 · PMC521075 · BMC genomics · 2004 · 8 claims · 6 setups

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Cell-cycle related CDKs (orthologs of CDK1-6) are present in all sampled eukaryotic organisms, including the most ancestral protists.

animals cdk encephalitozoon pfmrk comparative bayesian distance
Ancient adaptive evolution of the primate antiviral DNA-editing enzyme APOBEC3G.

PMID 15269786 · PMC479043 · PLoS biology · 2004 · 7 claims · 6 setups

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APOBEC3G has been under strong, recurrent positive selection throughout primate evolution (~33 million years)

apobec3g pairwise human-chimpanzee apobec1 pcr phylogenetic sliding
Accelerated evolution of the ASPM gene controlling brain size begins prior to human brain expansion.

PMID 15045028 · PMC374243 · PLoS biology · 2004 · 8 claims · 6 setups

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The ASPM gene shows accelerated (positively selected) evolution in the African hominoid clade, and this acceleration precedes hominid brain expansion by several million years.

chimpanzee retrofitted primate aspm tar restriction genomic
GeneSeer: a sage for gene names and genomic resources.

PMID 16176584 · PMC1266031 · BMC genomics · 2005 · 7 claims · 4 setups

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GeneSeer aggregates gene name synonyms from GenBank, FlyBase, ExPASy, HUGO, ENSEMBL, UCSC and Gene Ontology into a name-translation database that maps any familiar name to a reference (SOFAR) identifier.

sofar clusters rnai gene blast sequence shrna
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
Chimp genome: branching out.

PMID 16136102 · PMC7420934 · Nature · 2005 · 8 claims · 8 setups

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The Chimpanzee Sequencing and Analysis Consortium published the initial draft chimpanzee genome sequence and compared it to the human genome.

chimpanzee primate rhesus fossil whole-genome phylogenetic genome
Molecular evolution and multilocus sequence typing of 145 strains of SARS-CoV.

PMID 16112670 · PMC7118731 · FEBS letters · 2005 · 8 claims · 7 setups

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145 SARS-CoV genomes can be divided into three groups: animal-origin viruses, first-epidemic clinical viruses, and GD03T0013

complete mutation sars-cov spike sequence phylogenetic selection
Genomic sequence and analysis of a vaccinia virus isolate from a patient with a smallpox vaccine-related complication.

PMID 17062162 · PMC1635044 · Virology journal · 2006 · 8 claims · 6 setups

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VACV-DUKE is most similar to VACV-ACAM2000 and VACV-CLONE3, confirming it as a Dryvax-derived isolate

vacv-duke whole-genome phylogenetic comparative
Heterogeneous genomic molecular clocks in primates.

PMID 17029560 · PMC1592237 · PLoS genetics · 2006 · 7 claims · 7 setups

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Non-CpG site substitutions show clear generation-time dependency, consistent with a replication-error origin

baboon chimpanzee same human-chimpanzee relative phylogenetic four-species
Inventory and analysis of the protein subunits of the ribonucleases P and MRP provides further evidence of homology between the yeast and human enzymes.

PMID 16998185 · PMC1636426 · Nucleic acids research · 2006 · 8 claims · 6 setups

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Fungal Pop8 is evolutionarily related to the Rpp14/Pop5 protein family, suggesting Pop8 is the fungal orthologue of Rpp14

sequences sequence eukaryotic mrp psi-blast phylogenetic hmm

Experiments

GPCR genes are preferentially retained after whole genome duplication.

Comparative analysis of plant genomes allows the definition of the "Phytolongins": a novel non-SNARE longin domain protein family.

Searching for new clues about the molecular cause of endomyocardial fibrosis by way of in silico proteomics and analytical chemistry.

Addressing pandemic-wide systematic errors in the SARS-CoV-2 phylogeny.

Identification of the Wheat (Triticum aestivum) IQD Gene Family and an Expression Analysis of Candidate Genes Associated with Seed Dormancy and Germination.

Genome-wide identification and characterization of germin-like protein family in Brassica juncea reveals their role against biotic stress.

Comparative Genomics Provides Insight into the Function of Broad-Host Range Sponge Symbionts.

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.

The cohesin complex: sequence homologies, interaction networks and shared motifs.

Genotyping, Orientalis-like Yersinia pestis, and plague pandemics.

Comparative genomics of cyclin-dependent kinases suggest co-evolution of the RNAP II C-terminal domain and CTD-directed CDKs.

Ancient adaptive evolution of the primate antiviral DNA-editing enzyme APOBEC3G.

Accelerated evolution of the ASPM gene controlling brain size begins prior to human brain expansion.

GeneSeer: a sage for gene names and genomic resources.

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

Chimp genome: branching out.

Molecular evolution and multilocus sequence typing of 145 strains of SARS-CoV.

Genomic sequence and analysis of a vaccinia virus isolate from a patient with a smallpox vaccine-related complication.

Heterogeneous genomic molecular clocks in primates.

Inventory and analysis of the protein subunits of the ribonucleases P and MRP provides further evidence of homology between the yeast and human enzymes.