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).

• Transcriptomic Data Meta-Analysis Sheds Light on High Light Response in Arabidopsis thaliana L.

  PMID 35457273 · PMC9026532 · International journal of molecular sciences · 2022 · 7 claims · 6 setups

  Has reproduction · 88

  Meta-analysis of five transcriptomic experiments identified 1151 differentially expressed genes that compose a coordinated gene network responding to high light stress

  arabidopsis deg promoter selected meta-analysis transcription hexamer

• Systematic analysis of CNGCs in cotton and the positive role of GhCNGC32 and GhCNGC35 in salt tolerance.

  PMID 35931984 · PMC9356423 · BMC genomics · 2022 · 8 claims · 8 setups

  Has reproduction

  114 CNGC genes were identified across the genomes of four cotton species (G. arboreum, G. raimondii, G. barbadense, G. hirsutum)

  arboreum cotton hirsutum ghcngc genome-wide phylogenetic gene

• Chromosome-level genome of the long-tailed marine-living ornate spiny lobster, Panulirus ornatus.

  PMID 38909031 · PMC11193758 · Scientific data · 2024 · 7 claims · 8 setups

  Has reproduction · 80

  A chromosome-level genome of P. ornatus was assembled spanning 2.65 Gb with contig N50 of 51.05 Mb, with 99.11% of sequence anchored to 73 chromosomes

  muscle eight genomic genome wgs hi-c rna-seq

• Identification of the Wheat (Triticum aestivum) IQD Gene Family and an Expression Analysis of Candidate Genes Associated with Seed Dormancy and Germination.

  PMID 35456910 · PMC9025732 · International journal of molecular sciences · 2022 · 8 claims · 8 setups

  Has reproduction · 78

  73 IQD gene family members were identified in the wheat genome and classified into six phylogenetic groups

  triticum taiqd wheat rice genome-wide phylogenetic gene

• 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

• Genome-wide identification and characterization of germin-like protein family in Brassica juncea reveals their role against biotic stress.

  PMID 41327045 · PMC12763953 · BMC plant biology · 2025 · 8 claims · 7 setups

  Has reproduction · 58

  Genome-wide identification revealed 102 GLPs in B. juncea, 51 in B. nigra, and 48 in B. rapa

  juncea promoter duplicated super genome-wide phylogenetic synteny

• 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

• 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 worldwide map of swine short tandem repeats and their associations with evolutionary and environmental adaptations.

  PMID 33892623 · PMC8063339 · Genetics, selection, evolution : GSE · 2021 · 8 claims · 8 setups

  Has reproduction · 63

  Identified 878,967 polymorphic STRs (pSTRs) from 394 deep-sequenced pig/Suidae genomes, the largest pSTR repository in pigs to date

  pigs sscrofa11.1 pig domestic whole-genome tandem repeat

• Phylogenetic variation and polymorphism at the toll-like receptor 4 locus (TLR4).

  PMID 11104518 · PMC31919 · Genome biology · 2000 · 7 claims · 7 setups

  Full-text index only

  The Tlr4 extracellular domain is far more variable than the cytoplasmic domain, both among mouse strains and among species

  tlr4 mus chimpanzee baboon genomic coding sequence

• Genome-wide analysis of the human Alu Yb-lineage.

  PMID 15588477 · PMC3525081 · Human genomics · 2004 · 8 claims · 6 setups

  Full-text index only

  1,733 Alu Yb-lineage elements are present on human autosomal chromosomes

  genome genomic non-human yb7 computational pcr-based pcr

• Classification of real and pseudo microRNA precursors using local structure-sequence features and support vector machine.

  PMID 16381612 · PMC1360673 · BMC bioinformatics · 2005 · 7 claims · 7 setups

  Full-text index only

  A 32-dimensional triplet structure-sequence feature vector combined with SVM (triplet-SVM) can distinguish real human pre-miRNAs from pseudo pre-miRNA hairpins with ~90% accuracy.

  pre-mirnas test conserved-hairpin cross-species secondary svm cross-species

• Pigs in sequence space: a 0.66X coverage pig genome survey based on shotgun sequencing.

  PMID 15885146 · PMC1142312 · BMC genomics · 2005 · 8 claims · 7 setups

  Full-text index only

  Pig sequence is closer to human than mouse is, across exons, UTRs, introns, intergenic regions, ultra-conserved elements, and miRNAs

  sus pig concatenated three-species whole-genome repeat comparative

• Retropseudogenes derived from the human Ro/SS-A autoantigen-associated hY RNAs.

  PMID 15817567 · PMC1074747 · Nucleic acids research · 2005 · 8 claims · 8 setups

  Full-text index only

  966 pseudogenes derived from the four human Y (hY) RNAs were characterized in the human genome

  genome chimpanzee pseudogenes genomic megablast blat sequence

• The MAPPER database: a multi-genome catalog of putative transcription factor binding sites.

  PMID 15608292 · PMC540057 · Nucleic acids research · 2005 · 8 claims · 6 setups

  Full-text index only

  Built a library of 1134 HMM models (359 matrix-derived, 718 factor-derived, 57 JASPAR-derived), corresponding to 863 distinct TF names, from TRANSFAC and JASPAR binding site data

  genome drosophila transfac b99 profile sequence case-study

• GeneTide--Terra Incognita Discovery Endeavor: a new transcriptome focused member of the GeneCards/GeneNote suite of databases.

  PMID 15608261 · PMC540076 · Nucleic acids research · 2005 · 8 claims · 7 setups

  Full-text index only

  GeneTide integrates UniGene, DoTS, AceView, BLAT/GeneLoc genomic alignment, and GeneAnnot probe-set data into a unified Consensus/Uniqueness/Score scheme to associate ESTs with GeneCards genes

  transcriptome genome spliced transcripts est genomic splice-orientation

• Genome-wide analyses of retrogenes derived from the human box H/ACA snoRNAs.

  PMID 17175533 · PMC1802619 · Nucleic acids research · 2007 · 8 claims · 6 setups

  Full-text index only

  202 novel box H/ACA RNA-related sequences were identified in the human genome

  genome chimpanzee aca flanking megablast comparative sequence

• Molecular phylogeny of the antiangiogenic and neurotrophic serpin, pigment epithelium derived factor in vertebrates.

  PMID 17020603 · PMC1609119 · BMC genomics · 2006 · 8 claims · 8 setups

  Full-text index only

  A single PEDF gene is present in all examined vertebrate species but is absent from invertebrates (D. melanogaster, C. elegans, C. intestinalis)

  vertebrate cdna pedf complete genomic rt-pcr phylogenetic

• Large-scale identification and characterization of alternative splicing variants of human gene transcripts using 56,419 completely sequenced and manually annotated full-length cDNAs.

  PMID 16914452 · PMC1557807 · Nucleic acids research · 2006 · 8 claims · 8 setups

  Full-text index only

  Analysis of 56,419 full-length cDNAs identified 6877 alternative splicing genes encoding 18,297 alternative splicing variants made of 37,670 exons.

  full-length deduced alternative panel cdna-to-genome manual motif

• Intronic alternative splicing regulators identified by comparative genomics in nematodes.

  PMID 16839192 · PMC1500816 · PLoS computational biology · 2006 · 8 claims · 6 setups

  Full-text index only

  Conserved intronic elements flanking alternative exons occur more often than expected from total intron sequence, consistent with selective pressure for splicing regulation

  elegans database transgenic comparative est cross-species