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).

• Assessing Bos taurus introgression in the UOA Bos indicus assembly.

  PMID 34922445 · PMC8684283 · Genetics, selection, evolution : GSE · 2021 · 7 claims · 6 setups

  Has reproduction · 86

  Aligning divergent (cross-subspecies) sequence data detects substantially more SNVs than aligning to a same-subspecies reference, indicating reference/assembly bias in variant calling.

  cattle breed-pooled indian merged whole-genome snv template

• Repression of Divergent Noncoding Transcription by a Sequence-Specific Transcription Factor.

  PMID 30576656 · PMC6310685 · Molecular cell · 2018 · 8 claims · 8 setups

  Has reproduction

  Depletion of Rap1 induces divergent noncoding transcription at a large fraction of Rap1-regulated gene promoters

  cerevisiae rap1-aid northern western poly

• Evidence for a minimal eukaryotic phosphoproteome?

  PMID 17712425 · PMC1945084 · PloS one · 2007 · 8 claims · 3 setups

  Full-text index only

  Divergence in eukaryotic kinases at the primary sequence level is not reflected at the level of substrate phosphorylation.

  lysates lysate pepchip peptide labelling statistical

• Metagenomic analysis of human diarrhea: viral detection and discovery.

  PMID 18398449 · PMC2290972 · PLoS pathogens · 2008 · 8 claims · 7 setups

  Full-text index only

  Micro-mass sequencing (minimal stool input, minimal purification, ~384 reads/sample) can detect known enteric viruses in diarrhea specimens

  stool divergent extract preparations sequence-independent maximum enzyme

• Comparative analysis of circular RNAs between soybean cytoplasmic male-sterile line NJCMS1A and its maintainer NJCMS1B by high-throughput sequencing.

  PMID 30208848 · PMC6134632 · BMC genomics · 2018 · 8 claims · 7 setups

  Has reproduction · 50

  2867 circRNAs were identified in soybean flower buds via high-throughput sequencing with RNase R enrichment, of which 1009 were differentially expressed between NJCMS1A and NJCMS1B

  flower roots analysis parental high-throughput quantitative pcr

• Expression and Secretion of Circular RNAs in the Parasitic Nematode, Ascaris suum.

  PMID 35711944 · PMC9194832 · Frontiers in genetics · 2022 · 8 claims · 7 setups

  Has reproduction · 20

  A. suum expresses 1,997 distinct circRNAs identified via next-generation sequencing in adult female body wall and ovary-enriched tissue

  suum circrna qrt-pcr drug

• Microarray analysis: genome-scale hypothesis scanning.

  PMID 14551912 · PMC212694 · PLoS biology · 2003 · 8 claims · 5 setups

  Full-text index only

  Microarrays can be used to both test and generate hypotheses, not merely to fish for candidate genes.

  drosophila yeast diffuse breast microarray integrated gene

• 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

  Has reproduction · 84

  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.

  ophiodon single lingcod subset radseq genome bayesian

• A genetic variation map for chicken with 2.8 million single-nucleotide polymorphisms.

  PMID 15592405 · PMC2263125 · Nature · 2004 · 8 claims · 8 setups

  Full-text index only

  A genetic variation map of 2.8 million SNPs was constructed for chicken by comparing 3 domestic breeds to Red Jungle Fowl

  domestic red same white partial comparative pcr

• Genome-wide signatures of convergent evolution in echolocating mammals.

  PMID 24005325 · PMC3836225 · Nature · 2013 · 8 claims · 8 setups

  Has reproduction

  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.

  four raw orthologous mammalian whole-genome novo homology-based

• Phenotypic screening, transcriptional profiling, and comparative genomic analysis of an invasive and non-invasive strain of Candida albicans.

  PMID 18950481 · PMC2579918 · BMC microbiology · 2008 · 8 claims · 8 setups

  Full-text index only

  Strain SC5314 is invasive and virulent whereas strain ATCC10231 is non-invasive and strongly attenuated in virulence

  albicans hep-2 rhe blood phenotypic growth adhesion

• Analysis of chimpanzee history based on genome sequence alignments.

  PMID 18421364 · PMC2278377 · PLoS genetics · 2008 · 8 claims · 6 setups

  Full-text index only

  Bonobos and common chimpanzees separated approximately 1.29 million years ago

  bonobo bonobos chimpanzee simulated shotgun sequenom principal

• 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

• Genetic polymorphisms of Echinococcus tapeworms in China as determined by mitochondrial and nuclear DNA sequences.

  PMID 19800346 · PMC2823955 · International journal for parasitology · 2010 · 8 claims · 7 setups

  Full-text index only

  Species identification by mitochondrial (cox1) and nuclear (ef1a) markers was identical across isolates, indicating introgressive hybridization among sympatric Echinococcus species is infrequent.

  granulosus multilocularis shiquicus echinococcus mitochondrial nuclear statistical

• Application of genomics to toxicology research.

  PMID 12634120 · PMC1241273 · Environmental health perspectives · 2002 · 8 claims · 3 setups

  Full-text index only

  Toxic chemical exposures alter gene expression, producing a diagnostic transcriptional 'fingerprint' that can be matched against known toxicants to classify untested chemicals' toxic potential.

  yeast rodents rodent microarray proposed cross-species

• With the finished human genome in hand, what next?

  PMID 12844356 · PMC193627 · Genome biology · 2003 · 8 claims · 8 setups

  Full-text index only

  Gene Ontology (GO) provides a syntax/query framework for functional classification of genes, expanding beyond E. coli origins into anatomy, pathology, and phenotype data.

  domestic saccharomyces systemic schistosoma comparative functional genetic

• 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