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).

• Identification and Characterization of Small Noncoding RNAs in Genome Sequences of the Edible Fungus Pleurotus ostreatus.

  PMID 27703969 · PMC5040776 · BioMed research international · 2016 · 7 claims · 8 setups

  Has reproduction · 95

  Genome-scale identification detected 254 small noncoding RNAs (snRNAs, snoRNAs, tRNAs, miRNAs, and other Rfam-classified sncRNAs) in the P. ostreatus CCEF00389 genome assembly

  pleurotus ostreatus ccef00389 sncrnas whole-genome rna-seq rfam

• The formation of avian montane diversity across barriers and along elevational gradients.

  PMID 35022441 · PMC8755808 · Nature communications · 2022 · 8 claims · 8 setups

  Has reproduction · 75

  Genetic differentiation is generally greater across the oceanic barrier separating Buru and Seram than across the lowland barrier separating New Guinea mountain ranges.

  forest population individuals single whole-genome f_st principal

• 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

• Utility of Triti-Map for bulk-segregated mapping of causal genes and regulatory elements in Triticeae.

  PMID 35605195 · PMC9284283 · Plant communications · 2022 · 8 claims · 4 setups

  Has reproduction · 95

  Triti-Map is a computational package suite plus web interface specifically optimized for bulk-segregated gene mapping in Triticeae, accepting DNA-seq, RNA-seq/ChIP-seq, and traditional QTL data as input

  wheat hordeum bulk-segregated interval novo

• Using several pair-wise informant sequences for de novo prediction of alternatively spliced transcripts.

  PMID 16925842 · PMC1810557 · Genome biology · 2006 · 8 claims · 4 setups

  Full-text index only

  MARS, an extension of the Twinscan algorithm, uses multiple pairwise informant genomes to predict human alternatively spliced transcripts de novo without expressed sequence information.

  genome tissues novo pairwise rt-pcr

• CONTRAST: a discriminative, phylogeny-free approach to multiple informant de novo gene prediction.

  PMID 18096039 · PMC2246271 · Genome biology · 2007 · 8 claims · 5 setups

  Full-text index only

  CONTRAST predicts exact coding region structures for 65% more human genes than the previous state-of-the-art de novo predictor (N-SCAN)

  genome sequence drosophila novo gene coding

• 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

• HGA: de novo genome assembly method for bacterial genomes using high coverage short sequencing reads.

  PMID 26945881 · PMC4779561 · BMC genomics · 2016 · 8 claims · 7 setups

  Has reproduction · 58

  HGA leads to significant improvement in assembly quality (N50 and corrected N50) for all 7 evaluated GAGE-B bacterial datasets using most of the 8 evaluated assemblers

  bacillus mycobacterium rhodobacter vibrio novo contigs-combining re-assembly

• rMAP: the Rapid Microbial Analysis Pipeline for ESKAPE bacterial group whole-genome sequence data.

  PMID 34110280 · PMC8461470 · Microbial genomics · 2021 · 8 claims · 8 setups

  Has reproduction · 50

  rMAP is a pipeline capable of profiling the resistomes of ESKAPE pathogens using Illumina WGS data

  eskape same novo snp phylogenetic

• Inference of transcriptional regulation using gene expression data from the bovine and human genomes.

  PMID 17683551 · PMC1978505 · BMC genomics · 2007 · 7 claims · 8 setups

  Full-text index only

  Using human reference promoter sequences is a useful approach for studying gene expression regulation in species with limited or non-existing genomic sequence, such as cattle.

  muscle-specific bovine refseq cardiac novo est blastn

• Optimizing open data to support one health: best practices to ensure interoperability of genomic data from bacterial pathogens.

  PMID 33103064 · PMC7568946 · One health outlook · 2020 · 8 claims · 3 setups

  Has reproduction · 85

  An open-access pathogen surveillance database (NCBI Pathogen Detection) plus contributor Best Practices enables FAIR, interoperable genomic data across human, animal, food, and environmental sources for One Health surveillance.

  salmonella ncbi-pd illumina empirical coverage

• A Deluge of Complex Repeats: The Solanum Genome.

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

  Has reproduction · 94

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

  tuberosum orthologous novo synteny orthologous

• geneshot: gene-level metagenomics identifies genome islands associated with immunotherapy response.

  PMID 33952321 · PMC8097837 · Genome biology · 2021 · 8 claims · 6 setups

  Has reproduction · 75

  geneshot identifies microbial genomic islands consistently associated with ICI response across independent cohorts

  stool deduplicated cag reference gene-level novo co-abundance

• A whole genome duplication drives the genome evolution of Phytophthora betacei, a closely related species to Phytophthora infestans.

  PMID 34740326 · PMC8571832 · BMC genomics · 2021 · 8 claims · 7 setups

  Has reproduction · 95

  P. betacei P8084 has the largest sequenced genome in the Phytophthora genus (270 Mb)

  betacei predicted genome k-mer busco

• 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

  Has reproduction · 55

  Generated the first draft genome assembly of A. coronaria by Illumina sequencing a haploid androgenetic plant

  haploid mistral assembled masked whole-genome k-mer genome-wide

• Telomere-to-telomere reference genome for Panax ginseng highlights the evolution of saponin biosynthesis.

  PMID 38883331 · PMC11179851 · Horticulture research · 2024 · 8 claims · 8 setups

  Has reproduction · 92

  A telomere-to-telomere reference genome of P. ginseng was assembled (3.45 Gb, 24 chromosomes, 77266 protein-coding genes)

  panax ginseng whole-genome genome rna-seq

• The sequence and de novo assembly of the giant panda genome.

  PMID 20010809 · PMC3951497 · Nature · 2010 · 8 claims · 8 setups

  Full-text index only

  A draft giant panda genome was successfully generated and assembled de novo using only Illumina Genome Analyser short-read sequencing

  giant panda whole-genome novo read

• Whole genome amplification and de novo assembly of single bacterial cells.

  PMID 19724646 · PMC2731171 · PloS one · 2009 · 8 claims · 6 setups

  Full-text index only

  FACS-based single-cell isolation combined with strict handling procedures virtually eliminates contaminating DNA from single-cell MDA reactions

  prochlorococcus single-cell seven sag genome spike-in amplification

• Whole genome and transcriptome maps of the entirely black native Korean chicken breed Yeonsan Ogye.

  PMID 30010758 · PMC6065499 · GigaScience · 2018 · 8 claims · 6 setups

  Has reproduction · 91

  A draft genome (Ogye_1.1) was assembled using a hybrid de novo method combining high-depth Illumina short reads (376.6X) and low-depth PacBio long reads (9.7X)

  yeonsan ogye_1.1 locus tissues whole-genome genome structural

• 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

  Has reproduction · 79

  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

  rhizobium strains genotype genome whole-genome orthologous snp