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).
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Has reproduction · 74
Discovery of a novel filamentous prophage in the genome of the Mimosa pudica microsymbiont Cupriavidus taiwanensis STM 6018.
PMID 36925474 · PMC10011098 · Frontiers in microbiology · 2023 · 8 claims · 8 setups
The STM 6018 genome contains two prophages: a complete Mu-like capsular phage and a filamentous phage that integrates into a putative dif site.
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Insights into vertebrate evolution from the chicken genome sequence.
PMID 15693954 · PMC551526 · Genome biology · 2005 · 8 claims · 6 setups
Chicken has expanded gene families involved in egg production (e.g., avidin) and feather/scale/claw formation (avian-specific keratins) not present or lost in mammals
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Has reproduction · 55
Genome-Wide Survey and Development of the First Microsatellite Markers Database (AnCorDB) in Anemone coronaria L.
PMID 35328546 · PMC8949970 · International journal of molecular sciences · 2022 · 8 claims · 8 setups
Generated the first draft genome assembly of A. coronaria by Illumina sequencing a haploid androgenetic plant
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Genome sequence, comparative analysis, and population genetics of the domestic horse.
PMID 19892987 · PMC3785132 · Science (New York, N.Y.) · 2009 · 8 claims · 7 setups
Produced a high-quality draft genome assembly of the domestic horse (EquCab2.0)
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Assessing the gene space in draft genomes.
PMID 19042974 · PMC2615622 · Nucleic acids research · 2009 · 6 claims · 7 setups
The proportion of mapped CEGs in a draft genome assembly is a useful metric for describing gene space completeness, complementing N50 and x-fold coverage.
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Has reproduction · 92
Genome Sequencing of Methicillin-Resistant and Methicillin-Susceptible Mammaliicoccus sciuri from Diseased Animals.
PMID 36125295 · PMC9583799 · Microbiology resource announcements · 2022 · 7 claims · 7 setups
Draft genomes of a methicillin-resistant Mammaliicoccus sciuri strain (2254A, from an armadillo) and a methicillin-susceptible strain (6942A, from a cow) are reported.
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Has reproduction · 84
Strong population differentiation in lingcod (Ophiodon elongatus) is driven by a small portion of the genome.
PMID 33294007 · PMC7691466 · Evolutionary applications · 2020 · 7 claims · 8 setups
Lingcod comprise two distinct genetic clusters separated latitudinally at a break near Point Reyes off Northern California, with a high frequency of admixed individuals near the break.
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Helminth genomics: The implications for human health.
PMID 19855829 · PMC2757907 · PLoS neglected tropical diseases · 2009 · 8 claims · 7 setups
More than two billion people (one-third of humanity) are infected with helminth parasites, causing major morbidity, mortality, and poverty maintenance
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Has reproduction · 84
Genomic profiling of Streptococcus agalactiae (Group B Streptococcus) isolates from pregnant women in northeastern Mexico: clonal complexes, virulence factors, and antibiotic resistance.
PMID 40416609 · PMC12103846 · PeerJ · 2025 · 8 claims · 6 setups
GBS colonization was detected in 51 of 1,924 (2.7%) pregnant women screened
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Has reproduction · 98
Large-scale quality assessment of prokaryotic genomes with metashot/prok-quality.
PMID 35136576 · PMC8804904 · F1000Research · 2021 · 8 claims · 6 setups
metashot/prok-quality is a container-enabled Nextflow pipeline for quality assessment and dereplication of draft prokaryotic genomes
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Has reproduction · 84
Genome of the endangered Guatemalan Beaded Lizard, Heloderma charlesbogerti, reveals evolutionary relationships of squamates and declines in effective population sizes.
PMID 36226801 · PMC9713440 · G3 (Bethesda, Md.) · 2022 · 8 claims · 7 setups
The assembled draft genome of H. charlesbogerti totals 2.31 Gb, similar in size to related species
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Of rats and men.
PMID 15003114 · PMC395761 · Genome biology · 2004 · 8 claims · 10 setups
The rat genome has been sequenced to draft level, with over 90% of the genome sampled using more than 36 million sequence reads (assembly version 3.1)
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Has reproduction · 92
Draft Genome Sequences of Antimicrobial-Resistant Shigella Clinical Isolates from Pakistan.
PMID 31346012 · PMC6658682 · Microbiology resource announcements · 2019 · 6 claims · 6 setups
Draft genome sequences are reported for three multidrug-resistant Shigella clinical isolates from Pakistan (two S. flexneri and one S. sonnei).
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Has reproduction · 74
MicroPIPE: validating an end-to-end workflow for high-quality complete bacterial genome construction.
PMID 34172000 · PMC8235852 · BMC genomics · 2021 · 8 claims · 8 setups
MicroPIPE, an end-to-end Nextflow/Singularity-based pipeline built from systematically validated tool choices, produces high-quality complete bacterial genome assemblies without manual intervention.
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Has reproduction
Genome-wide signatures of convergent evolution in echolocating mammals.
PMID 24005325 · PMC3836225 · Nature · 2013 · 8 claims · 8 setups
Genome-wide convergent sequence evolution between echolocating lineages is not rare but widespread and continuously distributed, with signatures consistent with convergence in nearly 200 loci out of 2,326 examined.
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The TIGR Gene Indices: clustering and assembling EST and known genes and integration with eukaryotic genomes.
PMID 15608288 · PMC540018 · Nucleic acids research · 2005 · 8 claims · 8 setups
The TIGR Gene Indices (TGI) are a collection of 77 species-specific databases that cluster and assemble EST and known gene sequences into tentative consensus (TC) sequences to identify and characterize expressed transcripts.
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Has reproduction · 89
DFAST and DAGA: web-based integrated genome annotation tools and resources.
PMID 27867804 · PMC5107635 · Bioscience of microbiota, food and health · 2016 · 8 claims · 7 setups
DFAST is a web-based bacterial genome annotation and DDBJ submission pipeline with integrated CheckM quality assessment and ANI taxonomic assessment.
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Organization and evolution of the Cyp2 gene cluster on mouse chromosome 7, and comparison with the syntenic human cluster.
PMID 14630516 · PMC1241748 · Environmental health perspectives · 2003 · 8 claims · 6 setups
The mouse Cyp2a-t cluster on chromosome 7 contains 22 loci from the same six CYP2 subfamilies (Cyp2a, Cyp2b, Cyp2f, Cyp2g, Cyp2s, Cyp2t) found in the human cluster
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Has reproduction · 66
RNAseq analysis of the parasitic nematode Strongyloides stercoralis reveals divergent regulation of canonical dauer pathways.
PMID 23145190 · PMC3493385 · PLoS neglected tropical diseases · 2012 · 8 claims · 8 setups
S. stercoralis possesses homologs of nearly all C. elegans dauer genes, but with significant differences in protein structure, developmental regulation, and gene family expansion.
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Has reproduction · 73
Genomics of Environmental Salmonella: Engaging Students in the Microbiology and Bioinformatics of Foodborne Pathogens.
PMID 33967968 · PMC8100199 · Frontiers in microbiology · 2021 · 8 claims · 8 setups
An undergraduate CURE combining field sampling, wet-lab microbiology, and genomic bioinformatics can be used to isolate and characterize environmental S. enterica strains.