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 114

System / cell line: comparative ✕ Assay: phylogenetic ✕ Clear

Genetic parallels in biomineralization of the calcareous sponge Sycon ciliatum and stony corals.

PMID 40922549 · PMC12419799 · eLife · 2025 · 8 claims · 8 setups

Has reproduction · 50

829 genes are overexpressed in the oscular region of increased calcite spicule formation in S. ciliatum

sycon ciliatum sponges differential go-term genome
Identification of functional SNPs in the 5-prime flanking sequences of human genes.

PMID 15717931 · PMC550646 · BMC genomics · 2005 · 6 claims · 5 setups

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7 of 10 candidate SNPs tested by EMSA showed reproducible allele-specific differences in TF-DNA complex binding/stability

flanking synthetic genomic cloned comparative electrophoretic rflp
Distinctive pattern of sequence polymorphism in the NS3 protein of hepatitis C virus type 1b reflects conflicting evolutionary pressures.

PMID 18632963 · PMC2577380 · The Journal of general virology · 2008 · 7 claims · 6 setups

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NS3 shows less evidence of purifying selection acting on its CTL epitopes than the other 9 HCV proteins, while outside the CTL epitopes NS3 is more conserved than the other proteins.

complete hcv-1b sequence nonsynonymous comparative neighbor-joining maximum
Steps toward broad-spectrum therapeutics: discovering virulence-associated genes present in diverse human pathogens.

PMID 19874620 · PMC2774872 · BMC genomics · 2009 · 8 claims · 8 setups

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Phylogenetic profiling of protein clusters across pathogen and non-pathogen genomes can identify candidate generic virulence factors

proteins cdc candidate yersinia all-against-all computational cross-species
Protozoan genomics for drug discovery.

PMID 16151400 · PMC7096809 · Nature biotechnology · 2005 · 8 claims · 3 setups

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Complete genome sequences of five protozoan parasites (Theileria parva, T. annulata, Leishmania major, Trypanosoma brucei, T. cruzi) were reported, enabling comparative genomics.

theileria leishmania plasmodium whole-genome comparative
Genomic analysis of the TRIM family reveals two groups of genes with distinct evolutionary properties.

PMID 18673550 · PMC2533329 · BMC evolutionary biology · 2008 · 8 claims · 6 setups

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The human TRIM family is split into two groups (group 1 and group 2) that differ in domain structure, genomic organization, and evolutionary properties.

redundant mammalian genomic vertebrates blast pattern-hit tblastn
Identifying the important HIV-1 recombination breakpoints.

PMID 18787691 · PMC2522274 · PLoS computational biology · 2008 · 8 claims · 3 setups

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Local sequence identity between co-packaged parental RNAs strongly influences the probability of strand-transfer/breakpoint location, with fewer breakpoints occurring near mismatches

inter-subtype parental copy-choice probabilistic comparative
From single cells to whole organisms.

PMID 16420683 · PMC1414103 · Genome biology · 2005 · 8 claims · 8 setups

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The genetic-interaction map in S. cerevisiae is roughly four times as complex as the protein-protein interaction map, and genetic interactions do not overlap with physical interactions but instead predict functional neighborhoods

saccharomyces caenorhabditis mammalian cylindromatosis automated interference rnai
Molecular analysis of Plasmodium ovale variants.

PMID 15324543 · PMC3323326 · Emerging infectious diseases · 2004 · 8 claims · 5 setups

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P. ovale isolates separate into two genetically distinct types, classic (Nigerian I/CDC) and variant (LS), consistent across four independent gene loci.

ovale plasmodium pcr first comparative
Evolutionary modeling of rate shifts reveals specificity determinants in HIV-1 subtypes.

PMID 18989394 · PMC2566816 · PLoS computational biology · 2008 · 7 claims · 4 setups

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A novel Bayesian method, RASER, can detect site-specific evolutionary rate shifts and the lineages in which they occurred without pre-specifying candidate lineages.

hiv-1 simulated bayesian simulation structural
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
Sequence context affects the rate of short insertions and deletions in flies and primates.

PMID 18291026 · PMC2374710 · Genome biology · 2008 · 8 claims · 6 setups

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The rate of insertion or deletion of specific lengths can vary by more than 100-fold depending on the surrounding sequence context

chimpanzee simulans chimp primate comparative direct nucleotide
Integrative functional genomics.

PMID 15239826 · PMC463286 · Genome biology · 2004 · 8 claims · 8 setups

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Ultra-conserved noncoding elements exist across human, mouse and rat genomes at very high sequence identity, often far from genes

yeast tissue-cultured mammalian genomic comparative targeted chip-chip
CoMoDis: composite motif discovery in mammalian genomes.

PMID 17130158 · PMC1702496 · Nucleic acids research · 2007 · 7 claims · 4 setups

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CoMoDis is a new bioinformatics tool that streamlines computational identification of novel regulatory modules starting from a single seed motif

ncbi35 gata-1 gene imr90 computational microarray seed-motif-anchored
The first single-stranded DNA virus targeting Pectobacterium belongs to the family Microviridae and demonstrates a broad host range to Pectobacterium brasiliense soft rot pathogens.

PMID 41739249 · PMC12935840 · Archives of virology · 2026 · 7 claims · 7 setups

Has reproduction · 90

Phage Mimer is the first described single-stranded DNA phage targeting Pectobacterium and belongs to the family Microviridae, subfamily Bullavirinae.

pectobacterium phage cscl-purified pbr phage whole-genome genome
Comprehensive Genomic and Phenotypic Characterization of Escherichia coli O78:H9 Strain HPVN24 Isolated from Diarrheic Poultry in Vietnam.

PMID 41156725 · PMC12565876 · Microorganisms · 2025 · 7 claims · 8 setups

Has reproduction · 86

HPVN24 is an avian pathogenic E. coli serotype O78:H9, sequence type ST23, with a 5.05 Mb genome and 50.57% GC content.

coli hpvn24 strain hemolysis antibiotic
Human Lsg1 defines a family of essential GTPases that correlates with the evolution of compartmentalization.

PMID 16209721 · PMC1262696 · BMC biology · 2005 · 8 claims · 9 setups

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hLsg1 is the human orthologue of yeast Lsg1p and defines a family of circularly permuted GTPases named YRG (YlqF Related GTPases)

multi-species recombinant immunoprecipitated hela phylogenetic gtp gtpase
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
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

Experiments

Genetic parallels in biomineralization of the calcareous sponge Sycon ciliatum and stony corals.

Identification of functional SNPs in the 5-prime flanking sequences of human genes.

Distinctive pattern of sequence polymorphism in the NS3 protein of hepatitis C virus type 1b reflects conflicting evolutionary pressures.

Steps toward broad-spectrum therapeutics: discovering virulence-associated genes present in diverse human pathogens.

Protozoan genomics for drug discovery.

Genomic analysis of the TRIM family reveals two groups of genes with distinct evolutionary properties.

Identifying the important HIV-1 recombination breakpoints.

From single cells to whole organisms.

Molecular analysis of Plasmodium ovale variants.

Evolutionary modeling of rate shifts reveals specificity determinants in HIV-1 subtypes.

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.

Sequence context affects the rate of short insertions and deletions in flies and primates.

Integrative functional genomics.

CoMoDis: composite motif discovery in mammalian genomes.

The first single-stranded DNA virus targeting Pectobacterium belongs to the family Microviridae and demonstrates a broad host range to Pectobacterium brasiliense soft rot pathogens.

Comprehensive Genomic and Phenotypic Characterization of Escherichia coli O78:H9 Strain HPVN24 Isolated from Diarrheic Poultry in Vietnam.

Human Lsg1 defines a family of essential GTPases that correlates with the evolution of compartmentalization.

Gene losses during human origins.

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.