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 244

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

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
Comparative genomics comes of age.

PMID 12186641 · PMC139393 · Genome biology · 2002 · 8 claims · 8 setups

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Only about 50% of conserved sequence elements (exons+introns) in orthologous human-mouse genes correspond to exons, implying substantial non-exonic conservation

orthologous chromosome chimpanzee somatic-cell comparative targeted tiled
The post-genomic era for a select few.

PMID 14759254 · PMC395745 · Genome biology · 2004 · 8 claims · 8 setups

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The Exofish comparative-genomics tool identifies protein-coding DNA segments by comparing two genome sequences and was used to compare pufferfish (Takifugu, Tetraodon) genomes with mammalian genomes, improving annotation of the human and mouse genomes.

takifugu physcomitrella coli vibrio comparative genetic dna-microarray
Identification of polymorphisms and balancing selection in the male infertility candidate gene, ornithine decarboxylase antizyme 3.

PMID 16542438 · PMC1526716 · BMC medical genetics · 2006 · 8 claims · 6 setups

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Mutations in the OAZ3 gene are not a common cause of male infertility

genomic coding inferred oaz3 direct sscp haplotype
Comparative analysis of cancer genes in the human and chimpanzee genomes.

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

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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
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
Physiology engages with functional genomics - at last.

PMID 16086845 · PMC1273626 · Genome biology · 2005 · 8 claims · 8 setups

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Large-scale QTL phenotyping in rat strains reveals that most hypertension-related traits are sexually dimorphic

wild-type caenorhabditis kidney pcr qtl enu copas
Better smelling through genetics: mammalian odor perception.

PMID 18938244 · PMC2590501 · Current opinion in neurobiology · 2008 · 8 claims · 8 setups

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Odorant receptor (OR) gene repertoire size and pseudogene fraction vary dramatically across mammalian species

mammals subjects v1r trpc2 comparative genetic targeted
Complete genome sequence of Treponema pallidum ssp. pallidum strain SS14 determined with oligonucleotide arrays.

PMID 18482458 · PMC2408589 · BMC microbiology · 2008 · 8 claims · 6 setups

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CGS combined with targeted DDT sequencing and whole genome fingerprinting (WGF) can accurately determine a treponemal genome sequence using only three arrays, at accuracy comparable to or better than finished DDT sequencing

treponema pcr-amplified ss14 pcr comparative dideoxy-terminator genome
Biodefense versus bioterrorism.

PMID 18771576 · PMC2575524 · Genome biology · 2008 · 5 claims · 4 setups

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Whole-genome sequencing and comparative genomics of the attack strain were used to trace the anthrax letters to a specific laboratory flask

bacillus ancestral cultures anthrax whole-genome comparative colony
A genomics-based approach to biodefence preparedness.

PMID 14708013 · PMC7097618 · Nature reviews. Genetics · 2004 · 7 claims · 8 setups

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Genome sequence data are now available for essentially all 25-30 principal human bacterial pathogens, including most CDC category A-C bioterror agents

bacillus brucella neisseria gastric comparative transcriptome two-dimensional
Genomic diversity and evolution of Mycobacterium ulcerans revealed by next-generation sequencing.

PMID 19806175 · PMC2736377 · PLoS pathogens · 2009 · 8 claims · 6 setups

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Genome sequencing of three M. ulcerans strains (NM20/02, NM31/04, Jp8756) identified thousands of SNPs relative to reference strain Agy99

ulcerans collection snp whole-genome comparative read
Getting positive about selection.

PMID 12914654 · PMC193638 · Genome biology · 2003 · 8 claims · 4 setups

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Purifying selection is the predominant form of molecular evolution, preserving fitness by eliminating deleterious mutations, while positive selection is rare but critical for adaptation.

genome chimpanzee human-chimpanzee humans whole-genome ratio maximum-likelihood
Microbial metagenomics.

PMID 16207365 · PMC1257460 · Genome biology · 2005 · 8 claims · 8 setups

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Metagenomic sequencing of the human GI tract reveals microbial community composition (e.g., Actinobacteria and Archaea prominence) differing from prior culture-based estimates dominated by Firmicutes and Bacteroides

gastrointestinal acid ocean group metagenomic shotgun comparative
Characterizing natural variation using next-generation sequencing technologies.

PMID 19801172 · PMC3994700 · Trends in genetics : TIG · 2009 · 8 claims · 8 setups

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Next-generation sequencing enables complete, genome-wide surveys of genetic variation at unprecedented resolution, overcoming limitations of genotyping panels and microarrays.

pichia individuals saccharomyces individual whole-genome partial comparative
The vertebrate genome annotation (Vega) database.

PMID 18003653 · PMC2238886 · Nucleic acids research · 2008 · 8 claims · 8 setups

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Vega is a database for viewing manual genome annotation of human, mouse and zebrafish genomic sequences produced at the Wellcome Trust Sanger Institute.

genome zebrafish pig nod manual comparative transcript
The key role of genomics in modern vaccine and drug design for emerging infectious diseases.

PMID 19855822 · PMC2752168 · PLoS genetics · 2009 · 8 claims · 8 setups

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Reverse vaccinology (in silico genome screening for surface/secreted proteins) can identify vaccine candidates far faster than conventional approaches, as demonstrated by the MenB project.

neisseria streptococcus coli vibrio reverse pan-genomic comparative
Investigating hookworm genomes by comparative analysis of two Ancylostoma species.

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

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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 Metagenomic Analysis of Biosynthetic Diversity across Sponge Microbiomes Highlights Metabolic Novelty, Conservation, and Diversification.

PMID 35862823 · PMC9426513 · mSystems · 2022 · 8 claims · 5 setups

Has reproduction · 56

The vast majority of recovered gene cluster families (GCFs) in sponge microbiomes show no similarity to any characterized BGC, revealing extreme biosynthetic novelty

microbiomes sponge shotgun nonpareil 16s
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

Chimp genome: branching out.

Comparative genomics comes of age.

The post-genomic era for a select few.

Identification of polymorphisms and balancing selection in the male infertility candidate gene, ornithine decarboxylase antizyme 3.

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

The many uses of a genome sequence.

Physiology engages with functional genomics - at last.

Better smelling through genetics: mammalian odor perception.

Complete genome sequence of Treponema pallidum ssp. pallidum strain SS14 determined with oligonucleotide arrays.

Biodefense versus bioterrorism.

A genomics-based approach to biodefence preparedness.

Genomic diversity and evolution of Mycobacterium ulcerans revealed by next-generation sequencing.

Getting positive about selection.

Microbial metagenomics.

Characterizing natural variation using next-generation sequencing technologies.

The vertebrate genome annotation (Vega) database.

The key role of genomics in modern vaccine and drug design for emerging infectious diseases.

Investigating hookworm genomes by comparative analysis of two Ancylostoma species.

Comparative Metagenomic Analysis of Biosynthetic Diversity across Sponge Microbiomes Highlights Metabolic Novelty, Conservation, and Diversification.

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.