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).

• Mucospheres produced by a mixotrophic protist impact ocean carbon cycling.

  PMID 35288549 · PMC8921327 · Nature communications · 2022 · 8 claims · 8 setups

  Has reproduction · 58

  P. cf. balticum constructs carbon-rich mucospheres that attract, capture and immobilise microbial prey to facilitate phago-heterotrophic consumption

  tara four xenic balticum 18s its toxin

• Genotyping of genetically monomorphic bacteria: DNA sequencing in Mycobacterium tuberculosis highlights the limitations of current methodologies.

  PMID 19915672 · PMC2772813 · PloS one · 2009 · 8 claims · 8 setups

  Full-text index only

  MLSA of 89 genes across 108 global MTBC strains yields a single, highly robust phylogeny with virtually no homoplasy, congruent across parsimony, NJ, ML, and Bayesian methods.

  global mtbc miru-vntr multilocus spoligotyping 15-loci-miru-vntr

• Having a BLAST with bioinformatics (and avoiding BLASTphemy).

  PMID 11597340 · PMC138974 · Genome biology · 2001 · 8 claims · 4 setups

  Full-text index only

  BLAST is the most widely used tool for searching biological sequences for regions of local similarity

  superfamilies blocks query pairwise phylogenetic sequence heuristic

• 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

  Has reproduction · 91

  SURF_5 and SURF_17 are the first full genomes of a novel bacterial lineage, 'Candidatus Abyssubacteria,' within the candidate phylum Hydrogenedentes

  deep co-assembled surf_17 surf_5 whole-genome novo 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

• A target enrichment method for gathering phylogenetic information from hundreds of loci: An example from the Compositae.

  PMID 25202605 · PMC4103609 · Applications in plant sciences · 2014 · 8 claims · 8 setups

  Has reproduction · 87

  A custom sequence capture probe set (9678 baits targeting 1061 orthologous genes) was designed to enrich COS loci across the Compositae.

  compositae same species helianthus targeted genome genomic

• Genomic and bioinformatics analysis of human adenovirus type 37: new insights into corneal tropism.

  PMID 18471294 · PMC2397415 · BMC genomics · 2008 · 7 claims · 7 setups

  Full-text index only

  The complete genome of HAdV-37 was sequenced and annotated (35,213 bp, 56.6% GC content, 35 predicted coding sequences plus 8 hypothetical ORFs)

  hadv-37 predicted select genome cpg global

• Characterization of the influenza A H5N1 viruses of the 2008-09 outbreaks in India reveals a third introduction and possible endemicity.

  PMID 19924254 · PMC2775943 · PloS one · 2009 · 7 claims · 5 setups

  Full-text index only

  All 2008-09 Indian H5N1 isolates belong to the EMA3 sublineage of clade 2.2

  h5n1 gene genome phylogenetic bayesian

• The role of genomics in tracking the evolution of influenza A virus.

  PMID 19855818 · PMC2739293 · PLoS pathogens · 2009 · 8 claims · 5 setups

  Full-text index only

  Antigenic drift, driven by selection for amino acid changes in exposed hemagglutinin epitope sites, is the main mechanism by which influenza A evades pre-existing immunity between pandemics.

  hemagglutinin influenza ferrets nonsynonymous antigenic whole-genome

• Assessing the genomic evidence for conserved transcribed pseudogenes under selection.

  PMID 19754956 · PMC2753554 · BMC genomics · 2009 · 8 claims · 8 setups

  Full-text index only

  1750 transcribed pseudogene annotations (TPAs) were identified in the human genome, ~11.5% of all human pseudogene annotations.

  genome rhesus vega-annotated tpas transcript-to-genome same synteny

• A Deluge of Complex Repeats: The Solanum Genome.

  PMID 26241045 · PMC4524691 · PloS one · 2015 · 8 claims · 7 setups

  Has reproduction · 94

  ~50–60% of the S. tuberosum and S. lycopersicum genomes are composed of repetitive elements

  tuberosum orthologous identified de-novo genome-wide transcriptional

• Eurasian and African mitochondrial DNA influences in the Saudi Arabian population.

  PMID 17331239 · PMC1810519 · BMC evolutionary biology · 2007 · 8 claims · 4 setups

  Full-text index only

  The majority (85%) of Saudi Arab mtDNA lineages have a western Asia (Eurasian) provenance

  saudi mtdna rflp complete

• The integrated world of functional genomics.

  PMID 12537543 · PMC151279 · Genome biology · 2003 · 8 claims · 8 setups

  Full-text index only

  Integrating chromatin immunoprecipitation (promoter-binding) data with expression data reveals the yeast cell-cycle transcriptional regulatory network, including network motifs such as autoregulation, multi-component loops, and feedforward loops.

  cerevisiae sequenced elegans drosophila chromatin integration comparative

• The Bifidobacterium dentium Bd1 genome sequence reflects its genetic adaptation to the human oral cavity.

  PMID 20041198 · PMC2788695 · PLoS genetics · 2009 · 8 claims · 8 setups

  Full-text index only

  The B. dentium Bd1 genome was sequenced to completion, revealing a single circular 2,636,368 bp chromosome with 2,143 predicted ORFs

  dentium core whole-genome 3d-structure comparative