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 25

System / cell line: homology ✕ Assay: genome-wide ✕ Clear

Identification, characterization and comparative genomics of chimpanzee endogenous retroviruses.

PMID 16805923 · PMC1779541 · Genome biology · 2006 · 8 claims · 6 setups

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The chimpanzee genome contains at least 42 separate families of endogenous retroviruses, 9 newly identified

chimpanzee domains genomic hg16 genome-wide sequence ltr-ltr
Continued colonization of the human genome by mitochondrial DNA.

PMID 15361937 · PMC515365 · PLoS biology · 2004 · 7 claims · 6 setups

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NUMT insertion into nuclear chromosomes is an ongoing process shaped by double-strand-break repair (as shown in yeast) and continuing in humans.

homo genomic chimpanzee genome genome-wide pcr sanger
Systematic analysis of human kinase genes: a large number of genes and alternative splicing events result in functional and structural diversity.

PMID 16351747 · PMC1866387 · BMC bioinformatics · 2005 · 8 claims · 7 setups

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Systematic in silico search identified 5 novel human kinase genes (on chromosomes 1, 11, 13, 15, 16) and 1 pseudogene (chromosome X) absent from KinBase

genome genomic kinase psi-blast comparative genscan
DupyliCate: mining, classifying, and characterizing gene duplications.

PMID 42209743 · PMC13219399 · Scientific reports · 2026 · 8 claims · 8 setups

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DupyliCate is a Python tool for identifying and classifying gene duplication arrays, using BUSCO-based species-specific thresholds and offering integrated expression divergence and Ka/Ks analysis.

arabidopsis thaliana brassicales phytozome sequence duplication runtime
Similarities and differences in genome-wide expression data of six organisms.

PMID 14737187 · PMC300882 · PLoS biology · 2004 · 8 claims · 8 setups

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Coexpression of functionally related genes is frequently conserved across evolutionarily distant organisms

saccharomyces caenorhabditis escherichia arabidopsis genome-wide large-scale developmental
Mutations in dnaA and a cryptic interaction site increase drug resistance in Mycobacterium tuberculosis.

PMID 33253310 · PMC7738170 · PLoS pathogens · 2020 · 7 claims · 8 setups

Has reproduction · 98

Non-synonymous mutations in dnaA are statistically associated with drug resistance (INH, RIF, SM) in clinical M. tuberculosis strains across two independent GWAS cohorts (China and Vietnam)

clinical dnaa isogenic h37rv genome-wide structural deep-sequencing
Protein kinases of the human malaria parasite Plasmodium falciparum: the kinome of a divergent eukaryote.

PMID 15479470 · PMC526369 · BMC genomics · 2004 · 8 claims · 4 setups

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65 ePK sequences were identified in the P. falciparum genome and classified via phylogenetic analysis relative to the seven established ePK groups

falciparum individual recombinant cmgc-group genome-wide blastp kinase
The Proteomic Code: a molecular recognition code for proteins.

PMID 17999762 · PMC2206014 · Theoretical biology & medical modelling · 2007 · 8 claims · 8 setups

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The Proteomic Code is a set of rules by which genetic information is transferred into the physico-chemical properties of amino acids, determining protein-protein interactions and folding; it is part of the redundant Genetic Code.

anti-peptide sequence exon smooth radioimmunoassay pairwise genome-wide
Patterns of evolutionary constraints on genes in humans.

PMID 18840274 · PMC2587479 · BMC evolutionary biology · 2008 · 7 claims · 6 setups

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BaseDiver, a novel framework integrating GERP score and derived allele frequency (DAF) at nonsynonymous coding SNPs, can classify GO functional categories by patterns of evolutionary constraint

mammalian hapmap panther significant comparative population chi-square
The many uses of a genome sequence.

PMID 11423005 · PMC138940 · Genome biology · 2001 · 8 claims · 8 setups

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Solved protein structures from structural genomics efforts can be used to model many other proteins by homology, aiding function prediction

recombinant mammalian chromosome chimpanzee x-ray quantitative tiling
Discovery and hypothesis generation through bioinformatics.

PMID 16522224 · PMC1431734 · Genome biology · 2006 · 8 claims · 8 setups

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Bioinformatics should be used as a tool for discovery and hypothesis generation, not merely to manage biological data

genome chemokine gene-expression proteins genome-wide phylogenetic microarray
Symbiosis genes show a unique pattern of introgression and selection within a Rhizobium leguminosarum species complex.

PMID 32176601 · PMC7276703 · Microbial genomics · 2020 · 8 claims · 8 setups

Has reproduction · 79

196 R. leguminosarum sv. trifolii strains form a five-species complex (gsA-gsE) with generally little recent between-species gene transfer, aside from a few highly mobile genetic regions

rhizobium strains genotype genome whole-genome orthologous snp
Cryptic loxP sites in mammalian genomes: genome-wide distribution and relevance for the efficiency of BAC/PAC recombineering techniques.

PMID 17284462 · PMC1865043 · Nucleic acids research · 2007 · 6 claims · 6 setups

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Cryptic lox P sites occur frequently and are homogeneously distributed across the mouse genome (1.2 primary sites per megabase).

genome bac coli el350 genome-wide sequence bacterial
Identification of mitochondrial disease genes through integrative analysis of multiple datasets.

PMID 18930150 · PMC2774125 · Methods (San Diego, Calif.) · 2008 · 8 claims · 8 setups

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Data integration of multiple functional genomics datasets effectively predicts mitochondrial gene function and prioritizes candidate mitochondrial disease genes.

saccharomyces higher yeast mitochondria genome-wide rnai gene
Genome-wide linkage analysis of an autosomal recessive hypotrichosis identifies a novel P2RY5 mutation.

PMID 18692127 · PMC3341170 · Genomics · 2008 · 8 claims · 7 setups

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Autozygosity mapping identified a highly significant homozygous region on chromosome 13q14.11-q14.3 (Z/LOD=10.41)

family p2ry5 affected snp microsatellite sanger
Kinetoplastid genomics: the thin end of the wedge.

PMID 18675383 · PMC2676795 · Infection, genetics and evolution : journal of molecular epidemiology and evolutionary genetics in infectious diseases · 2008 · 8 claims · 8 setups

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Completion of the T. brucei, T. cruzi, and L. major genome sequencing projects enabled numerous studies that would otherwise have been difficult or impossible.

brucei major cruzi kinetoplastid whole-genome gene shotgun
EPGD: a comprehensive web resource for integrating and displaying eukaryotic paralog/paralogon information.

PMID 17984073 · PMC2238967 · Nucleic acids research · 2008 · 8 claims · 8 setups

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EPGD is a gene-centered, internet-accessible database integrating paralog family and paralogon information for 26 eukaryotic genomes.

sequences homologous proteins coding pairwise single sequence
Mutations in the formin gene INF2 cause focal segmental glomerulosclerosis.

PMID 20023659 · PMC2980844 · Nature genetics · 2010 · 8 claims · 8 setups

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Mutations in INF2, a formin family actin-regulating protein, cause autosomal dominant focal segmental glomerulosclerosis (FSGS)

families genes individuals kidney genome-wide sanger resequencing
A comprehensive resource of genomic, epigenomic and transcriptomic sequencing data for the black truffle Tuber melanosporum.

PMID 25392735 · PMC4228822 · GigaScience · 2014 · 8 claims · 8 setups

Has reproduction · 61

T. melanosporum shows a high rate of cytosine methylation (>44%) that selectively targets transposable elements rather than genes, with a strong preference for CpG sites.

tuber ectomycorrhizal melanosporum rna-seq whole-genome sequencing guided
Polymorphic segmental duplications at 8p23.1 challenge the determination of individual defensin gene repertoires and the assembly of a contiguous human reference sequence.

PMID 15588320 · PMC544879 · BMC genomics · 2004 · 8 claims · 8 setups

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The hg16 automatic assembly of the 8p23.1 DEF locus contains misassemblies caused by segmental duplications and interindividual/intraindividual genetic variation

bac genome metaphase overlapping manual repeat fluorescence

Experiments

Identification, characterization and comparative genomics of chimpanzee endogenous retroviruses.

Continued colonization of the human genome by mitochondrial DNA.

Systematic analysis of human kinase genes: a large number of genes and alternative splicing events result in functional and structural diversity.

DupyliCate: mining, classifying, and characterizing gene duplications.

Similarities and differences in genome-wide expression data of six organisms.

Mutations in dnaA and a cryptic interaction site increase drug resistance in Mycobacterium tuberculosis.

Protein kinases of the human malaria parasite Plasmodium falciparum: the kinome of a divergent eukaryote.

The Proteomic Code: a molecular recognition code for proteins.

Patterns of evolutionary constraints on genes in humans.

The many uses of a genome sequence.

Discovery and hypothesis generation through bioinformatics.

Symbiosis genes show a unique pattern of introgression and selection within a Rhizobium leguminosarum species complex.

Cryptic loxP sites in mammalian genomes: genome-wide distribution and relevance for the efficiency of BAC/PAC recombineering techniques.

Identification of mitochondrial disease genes through integrative analysis of multiple datasets.

Genome-wide linkage analysis of an autosomal recessive hypotrichosis identifies a novel P2RY5 mutation.

Kinetoplastid genomics: the thin end of the wedge.

EPGD: a comprehensive web resource for integrating and displaying eukaryotic paralog/paralogon information.

Mutations in the formin gene INF2 cause focal segmental glomerulosclerosis.

A comprehensive resource of genomic, epigenomic and transcriptomic sequencing data for the black truffle Tuber melanosporum.

Polymorphic segmental duplications at 8p23.1 challenge the determination of individual defensin gene repertoires and the assembly of a contiguous human reference sequence.