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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Full-text index only
Using several pair-wise informant sequences for de novo prediction of alternatively spliced transcripts.
PMID 16925842 · PMC1810557 · Genome biology · 2006 · 8 claims · 4 setups
MARS, an extension of the Twinscan algorithm, uses multiple pairwise informant genomes to predict human alternatively spliced transcripts de novo without expressed sequence information.
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Has reproduction · 81
Whole-Genome Sequence of Cervid atadenovirus A from the Initial Cases of an Adenovirus Hemorrhagic Disease Epizootic of Black-Tailed Deer in Canada.
PMID 36129291 · PMC9584332 · Microbiology resource announcements · 2022 · 7 claims · 4 setups
A complete 30,616-nucleotide genome of Cervid atadenovirus A was determined from lung tissue of black-tailed deer that died of AHD in British Columbia in 2020
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Full-text index only
Visualization of shared genomic regions and meiotic recombination in high-density SNP data.
PMID 19696932 · PMC2725774 · PloS one · 2009 · 8 claims · 7 setups
SNPduo is a command-line (SNPduo++) and web-accessible tool that analyzes and visualizes relatedness between two individuals using identity by state (IBS) from SNP genotypes.
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Has reproduction · 75
The formation of avian montane diversity across barriers and along elevational gradients.
PMID 35022441 · PMC8755808 · Nature communications · 2022 · 8 claims · 8 setups
Genetic differentiation is generally greater across the oceanic barrier separating Buru and Seram than across the lowland barrier separating New Guinea mountain ranges.
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Has reproduction · 79
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
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
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Has reproduction · 69
Discovery and characterization of Alu repeat sequences via precise local read assembly.
PMID 26503250 · PMC4666360 · Nucleic acids research · 2015 · 7 claims · 8 setups
Combining Alu-supporting read detection (RetroSeq) with local de novo assembly (CAP3) reconstructs the full sequence of non-reference Alu insertions from Illumina paired-end WGS reads
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Has reproduction · 91
Genomic Description of 'Candidatus Abyssubacteria,' a Novel Subsurface Lineage Within the Candidate Phylum Hydrogenedentes.
PMID 30210471 · PMC6121073 · Frontiers in microbiology · 2018 · 8 claims · 7 setups
SURF_5 and SURF_17 are the first full genomes of a novel bacterial lineage, 'Candidatus Abyssubacteria,' within the candidate phylum Hydrogenedentes
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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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Has reproduction · 87
Insights into the Evolution of the New World Diploid Cottons (Gossypium, Subgenus Houzingenia) Based on Genome Sequencing.
PMID 30476109 · PMC6320677 · Genome biology and evolution · 2019 · 8 claims · 8 setups
Subgenus Houzingenia likely originated via transoceanic dispersal from Africa about 6.6 Ma
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Has reproduction · 83
Accurate prediction of metagenome-assembled genome completeness by MAGISTA, a random forest model built on alignment-free intra-bin statistics.
PMID 35248155 · PMC8898458 · Environmental microbiome · 2022 · 7 claims · 7 setups
MAGISTA, a random forest model built on alignment-free intra-bin distance-distribution statistics, can estimate MAG completeness and purity without relying on reference marker genes.
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Has reproduction · 100
Analysis of the Taxonomy, Synteny, and Virulence Factors for Soft Rot Pathogen Pectobacterium aroidearum in Amorphophallus konjac Using Comparative Genomics.
PMID 35910650 · PMC9326479 · Frontiers in microbiology · 2022 · 8 claims · 8 setups
The causal agent of konjac soft rot in China is Pectobacterium aroidearum, confirmed via in vitro/in vivo pathogenicity tests, ANI, dDDH, and phylogenomic analysis.
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Has reproduction · 92
Evaluation of core genome and whole genome multilocus sequence typing schemes for Campylobacter jejuni and Campylobacter coli outbreak detection in the USA.
PMID 37133905 · PMC10272873 · Microbial genomics · 2023 · 8 claims · 8 setups
cgMLST, wgMLST and hqSNP WGS-based analysis methods clustered C. jejuni and C. coli isolates in concordance with epidemiological data.
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Has reproduction · 82
Whole-genome analysis of a multidrug-resistant Klebsiella michiganensis environmental isolate from an orthopedic ward in Mwanza, Tanzania reveals IncF-family plasmid replicon signatures associated with resistance determinants.
PMID 41957580 · PMC13173886 · BMC genomics · 2026 · 6 claims · 8 setups
Genome-based taxonomy (GTDB-Tk and ANI) reclassified the isolate A55848, phenotypically identified as K. oxytoca, as Klebsiella michiganensis