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).

• 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

  Has reproduction · 87

  Subgenus Houzingenia likely originated via transoceanic dispersal from Africa about 6.6 Ma

  leaf trimmed species concatenated genome novo reference-assisted

• Genomic Correlates of Virulence Attenuation in the Deadly Amphibian Chytrid Fungus, Batrachochytrium dendrobatidis.

  PMID 26333840 · PMC4632049 · G3 (Bethesda, Md.) · 2015 · 8 claims · 8 setups

  Has reproduction · 58

  Virulence attenuation in the longer-passaged Bd isolate (JEL427-P39) is associated with loss of chromosome copy number relative to the shorter-passaged, more virulent isolate (JEL427-P9)

  strain jel427-p9 genes whole-genome snp indel

• Analysis of whole-genome re-sequencing data of ducks reveals a diverse demographic history and extensive gene flow between Southeast/South Asian and Chinese populations.

  PMID 33849442 · PMC8042899 · Genetics, selection, evolution : GSE · 2021 · 8 claims · 8 setups

  Has reproduction · 23

  Whole-genome resequencing reveals three geographically distinct genetic groups: local Chinese, wild, and local Southeast/South Asian duck populations

  newly duck southeast chinese whole-genome phylogenetic population

• Rise of the machines.

  PMID 18670625 · PMC2467494 · PLoS genetics · 2008 · 8 claims · 4 setups

  Full-text index only

  New short-read sequencing platforms (Illumina Genome Analyzer, 454 FLX, ABI SOLiD) enable rapid, scalable whole-genome resequencing that was previously restricted to dedicated sequencing centers using Sanger methods.

  bacillus independent subtilis whole-genome read

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

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

  Full-text index only

  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

• Insights into the differentiation and adaptation within Circaeasteraceae from Circaeaster agrestis genome sequencing and resequencing.

  PMID 36895650 · PMC9988679 · iScience · 2023 · 8 claims · 8 setups

  Has reproduction · 49

  C. agrestis and K. uniflora are sister species with contrasting reproductive modes, providing a natural system to test effects of sexual vs asexual reproduction on genome evolution

  circaeaster agrestis genome gene kmer-based

• A near complete genome for goat genetic and genomic research.

  PMID 34507524 · PMC8434745 · Genetics, selection, evolution : GSE · 2021 · 8 claims · 8 setups

  Has reproduction · 89

  Saanen_v1 is a near-complete de novo goat genome assembly generated from 117x PacBio and 118x Hi-C data, including the first goat Y chromosome scaffold

  saanen goat testicular nine pacbio illumina hi-c

• Searching for SNPs with cloud computing.

  PMID 19930550 · PMC3091327 · Genome biology · 2009 · 8 claims · 4 setups

  Full-text index only

  Crossbow combines the Bowtie short-read aligner and SOAPsnp SNP caller into a seamless, automatic Hadoop/MapReduce pipeline for whole-genome resequencing analysis

  han local short simulated whole-genome cloud

• Chromosome-scale Elaeis guineensis and E. oleifera assemblies: comparative genomics of oil palm and other Arecaceae.

  PMID 38918881 · PMC11373658 · G3 (Bethesda, Md.) · 2024 · 8 claims · 8 setups

  Has reproduction · 81

  Improved E. guineensis genome assembly achieved with substantially increased continuity and completeness compared to prior assemblies

  guineensis oleifera root pacbio proximity optical