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).

• A chromosome-level genome assembly of Plantago ovata.

  PMID 36707685 · PMC9883528 · Scientific reports · 2023 · 8 claims · 8 setups

  Has reproduction · 99

  A chromosome-level reference genome assembly of P. ovata was constructed using PacBio long reads and Hi-C scaffolding.

  plantago ovata pacbio hi-c k-mer

• 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

• Spontaneous mutations in hlyD and tuf genes result in resistance of Dickeya solani IPO 2222 to phage ϕD5 but cause decreased bacterial fitness and virulence in planta.

  PMID 37160956 · PMC10169776 · Scientific reports · 2023 · 7 claims · 8 setups

  Full-text index only

  Spontaneous ΦD5-resistant D. solani mutants DsR34 and DsR207 show significantly reduced virulence and colonization ability in planta compared to wild-type

  potato solani planta maceration genome

• Genome-wide identification of conserved and novel microRNAs in one bud and two tender leaves of tea plant (Camellia sinensis) by small RNA sequencing, microarray-based hybridization and genome survey scaffold sequences.

  PMID 29157210 · PMC5697157 · BMC plant biology · 2017 · 8 claims · 8 setups

  Has reproduction · 91

  175 conserved miRNAs (39 families) and 83 novel miRNAs were identified in C. sinensis one bud and two tender leaves using small RNA sequencing combined with genome survey scaffold data

  one sinensis small-molecular-weight leaves small genome mirna

• 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

• 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

• Multiple whole genome alignments and novel biomedical applications at the VISTA portal.

  PMID 17488840 · PMC1933192 · Nucleic acids research · 2007 · 8 claims · 4 setups

  Full-text index only

  A novel multiple whole-genome alignment algorithm treats all genomes symmetrically, avoiding dependence on a single base/reference genome

  genome vertebrate multi-species whole-genome conservation non-synonymous

• HTSQualC is a flexible and one-step quality control software for high-throughput sequencing data analysis.

  PMID 34548573 · PMC8455540 · Scientific reports · 2021 · 8 claims · 5 setups

  Has reproduction · 89

  HTSQualC is a standalone, one-step QC software that performs filtering and trimming of raw HTS data in a single run

  cotton sugarcane tomato illumina single-end paired-end runtime

• Discovery of a novel filamentous prophage in the genome of the Mimosa pudica microsymbiont Cupriavidus taiwanensis STM 6018.

  PMID 36925474 · PMC10011098 · Frontiers in microbiology · 2023 · 8 claims · 8 setups

  Has reproduction · 74

  The STM 6018 genome contains two prophages: a complete Mu-like capsular phage and a filamentous phage that integrates into a putative dif site.

  cupriavidus stm taiwanensis genome 16s average

• Narcisse: a mirror view of conserved syntenies.

  PMID 17981845 · PMC2238891 · Nucleic acids research · 2008 · 8 claims · 4 setups

  Full-text index only

  Narcisse is a database/web tool providing an integrated, multi-level comparative analysis of sequence similarities and conserved chromosomal segments (syntenies) across animal, plant, fungal and bacterial completely sequenced genomes.

  annotated genome pairwise pairs sequence nucleic-level conserved

• Comparative Genome Analysis of 16SrXII-A 'Candidatus Phytoplasma solani' POT Transmitted by Hyalesthes obsoletus.

  PMID 41597744 · PMC12843639 · Microorganisms · 2026 · 8 claims · 8 setups

  Has reproduction · 95

  The complete 832,614 bp circular genome of H. obsoletus-transmitted 'Ca. P. solani' 16SrXII-A strain POT was assembled and annotated

  hyalesthes pot long insect genome taxonomic

• Human Retrotransposons and Effective Computational Detection Methods for Next-Generation Sequencing Data.

  PMID 36295018 · PMC9605557 · Life (Basel, Switzerland) · 2022 · 8 claims · 7 setups

  Has reproduction

  Retrotransposons mobilize via a copy-and-paste mechanism involving transcription of an RNA intermediate and reinsertion as a cDNA copy, unlike DNA transposons which cut-and-paste.

  drosophila normal genomic genome synthetic whole-genome computational

• Oxidative stress protection and growth promotion activity of Pseudomonas mercuritolerans sp. nov., in forage plants under mercury abiotic stress conditions.

  PMID 36560952 · PMC9763275 · Frontiers in microbiology · 2022 · 8 claims · 8 setups

  Has reproduction · 54

  Inoculation with SAICEUPSM^T significantly reduces the oxidative stress enzymatic response (CAT, APX, SOD, GR) in Lupinus albus grown under mercury stress

  lupinus saiceupsm^t greenhouse enzymatic mercury

• The fungal pathogen Rhizoctonia solani AG-8 has 2 nuclear haplotypes that differ in abundance.

  PMID 41124349 · PMC12774589 · G3 (Bethesda, Md.) · 2026 · 8 claims · 8 setups

  Full-text index only

  R. solani isolates AG8-1 and AG8-3 each possess 2 distinct nuclear haplotypes, each ~50 Mbp assembled into 16 chromosomes

  solani ag8-1 rhizoctonia annotated pacbio hi-c stranded

• The genome sequence of the Roundleaf geranium, Geranium rotundifolium L. (Geraniales: Geraniaceae).

  PMID 42021764 · PMC13096780 · Wellcome open research · 2026 · 8 claims · 8 setups

  Full-text index only

  The genome assembly of Geranium rotundifolium has a total length of 497.00 megabases, with 97.57% scaffolded into 13 chromosomal pseudomolecules.

  leaf silica-dried pacbio alternate flow barcoding pacbio