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 of TYR, TYRP1, DCT and LARP7 as related biomarkers and immune infiltration characteristics of vitiligo via comprehensive strategies.

  PMID 34107850 · PMC8806433 · Bioengineered · 2021 · 7 claims · 8 setups

  Has reproduction · 55

  131 robust DEGs (89 upregulated, 42 downregulated) were identified by RRA integration of three vitiligo datasets and are closely associated with melanogenesis and vitiligo development

  lesional merged robust verification gene robust weighted

• Natural clines and human management impact the genetic structure of Algerian honey bee populations.

  PMID 38114899 · PMC10729559 · Genetics, selection, evolution : GSE · 2023 · 7 claims · 8 setups

  Has reproduction · 55

  Algerian honey bees show no significant admixture from European reference honey bee populations

  haploid combined ld-pruned algerian whole-genome variant principal

• SGCP: a spectral self-learning method for clustering genes in co-expression networks.

  PMID 38956463 · PMC11221046 · BMC bioinformatics · 2024 · 7 claims · 4 setups

  Has reproduction · 51

  SGCP, a spectral self-learning method, yields gene co-expression modules with higher GO enrichment than WGCNA, CoExpNets, and CEMiTool across 12 real gene expression datasets.

  real microarray rna-seq same gene dna-microarray rna-sequencing

• The mouse gastric surface epithelial cell and its response to early Helicobacter pylori infection.

  PMID 41824631 · PMC13020875 · Virulence · 2026 · 8 claims · 6 setups

  Has reproduction · 100

  SMCs show high gene expression for mucus-secreted proteins (Tff1, Gkn1, Gkn2, Psca, Muc5ac), mitoribosome RNA, and cytoskeleton proteins

  laser-microdissected gastric ffpe oct-embedded sequencing glycomics immunofluorescence

• Identification of Novel Therapeutic Candidates Against SARS-CoV-2 Infections: An Application of RNA Sequencing Toward mRNA Based Nanotherapeutics.

  PMID 35983322 · PMC9378778 · Frontiers in microbiology · 2022 · 6 claims · 7 setups

  Has reproduction · 75

  RPL29 (60S ribosomal protein L29) is highly/consistently expressed across all COVID-19 infected groups regardless of severity, suggesting it as a novel host therapeutic target for mRNA-based nanomedicines.

  pbmcs pbmc aligned bulk read transcript

• Functional differentiation determines the molecular basis of the symbiotic lifestyle of Ca. Nanohaloarchaeota.

  PMID 36242054 · PMC9563170 · Microbiome · 2022 · 8 claims · 8 setups

  Has reproduction · 99

  Three MAGs from a stratified salt crust represent a novel order, Nucleotidisoterales, within Ca. Nanohaloarchaeota

  stratified salt nanohaloarchaeota reconstructed 16s metagenomic phylogenomic

• What the Phage: a scalable workflow for the identification and analysis of phage sequences.

  PMID 36399058 · PMC9673492 · GigaScience · 2022 · 8 claims · 7 setups

  Has reproduction · 76

  WtP combines 11 tools (14 approaches) for phage prediction in a parallel, containerized Nextflow workflow

  assembled illumina phage-predicted predicted multitool metagenome gene

• QuasiFlow: a Nextflow pipeline for analysis of NGS-based HIV-1 drug resistance data.

  PMID 36699347 · PMC9722223 · Bioinformatics advances · 2022 · 6 claims · 8 setups

  Has reproduction · 78

  QuasiFlow is a Nextflow pipeline that runs entirely locally via command-line tools and a local HIVdb database copy to analyze NGS-based HIV-1 drug resistance testing data.

  hiv-1 same paired-end reads ngs-based concordance read

• Gap-free telomere-to-telomere haplotype assembly of the tomato hind (Cephalopholis sonnerati).

  PMID 39578472 · PMC11584678 · Scientific data · 2024 · 8 claims · 8 setups

  Has reproduction · 90

  Two T2T gap-free haplotype assemblies of C. sonnerati (YSFRI_Csonn_HA_1.0 and YSFRI_Csonn_HB_1.0) were successfully generated, each spanning 24 chromosomes with no gaps.

  cephalopholis analysis next-generation pacbio ont

• Environmental Drivers of Genetic Divergence in Two Corals From the Florida Keys.

  PMID 40589611 · PMC12206660 · Evolutionary applications · 2025 · 8 claims · 8 setups

  Has reproduction · 64

  Temperature was not the most important driver of coral genetic divergence in the Florida Keys; depth and water chemistry were more important

  agaricia agaricites coral sites 2brad population hierarchical

• Vector algebra in the analysis of genome-wide expression data.

  PMID 11897023 · PMC88809 · Genome biology · 2002 · 8 claims · 6 setups

  Full-text index only

  The angle θ between expression (experiment) vectors is the geometric counterpart of the Pearson correlation coefficient r, providing a rigorous measure of similarity between profiles.

  saccharomyces microarray

• p53 as a potential predictive factor of response to chemotherapy: feasibility of p53 assessment using a functional test in yeast from trucut biopsies in breast cancer patients.

  PMID 11875738 · PMC2375302 · British journal of cancer · 2002 · 8 claims · 6 setups

  Full-text index only

  p53 status can be reliably determined by yeast functional assay from single frozen sections of trucut biopsies

  frozen plasmids single extracted p53 sanger laser

• HLA-A gene polymorphism defined by high-resolution sequence-based typing in 161 Northern Chinese Han people.

  PMID 15629059 · PMC5172246 · Genomics, proteomics & bioinformatics · 2003 · 7 claims · 5 setups

  Full-text index only

  HLA-A gene shows high polymorphism in the Northern Chinese Han population, with 74 gene types and 36 alleles detected in 161 individuals

  genomic ihwg peripheral allele sequence-based pcr sbt

• DiagHunter and GenoPix2D: programs for genomic comparisons, large-scale homology discovery and visualization.

  PMID 14519203 · PMC328457 · Genome biology · 2003 · 7 claims · 5 setups

  Full-text index only

  DiagHunter identifies large-scale synteny blocks within or between genomes efficiently despite background noise and genomic discontinuities, without performing sequence alignment

  arabidopsis synthetic blastp-based blastn-based simulation

• Recent segmental and gene duplications in the mouse genome.

  PMID 12914656 · PMC193640 · Genome biology · 2003 · 8 claims · 8 setups

  Full-text index only

  33.6 Mb (1.2%) of the February 2003 mouse genome assembly (2,695 Mb) is involved in recent segmental duplications

  genome gene ensembl-annotated chromosome pairwise gene blat

• RNAseq analysis of the parasitic nematode Strongyloides stercoralis reveals divergent regulation of canonical dauer pathways.

  PMID 23145190 · PMC3493385 · PLoS neglected tropical diseases · 2012 · 8 claims · 8 setups

  Has reproduction · 66

  S. stercoralis possesses homologs of nearly all C. elegans dauer genes, but with significant differences in protein structure, developmental regulation, and gene family expansion.

  strongyloides stercoralis mongolian adapter-ligated polyadenylated novo comparative

• Spotted-fever group Rickettsia in Dermacentor variabilis, Maryland.

  PMID 15496254 · PMC3320417 · Emerging infectious diseases · 2004 · 8 claims · 6 setups

  Full-text index only

  SFG Rickettsia infection prevalence in Maryland D. variabilis was 3.8% (15/392)

  dermacentor tick-derived glta field pcr single sequencing

• Structural genomics of membrane proteins.

  PMID 15059248 · PMC395774 · Genome biology · 2004 · 9 claims · 8 setups

  Full-text index only

  Membrane proteins comprise less than 1 in 100 of structures deposited in the Protein Data Bank despite being a large fraction of the proteome.

  membrane detergent-solubilized lysate-based x-ray solution solid-state

• RNA-Seq transcriptome profiling of upland cotton (Gossypium hirsutum L.) root tissue under water-deficit stress.

  PMID 24324815 · PMC3855774 · PloS one · 2013 · 8 claims · 8 setups

  Has reproduction · 38

  A total of 1,530 transcripts were differentially expressed between well-watered and water-deficit stressed field-grown upland cotton root tissues (913 up-regulated, 617 down-regulated).

  gossypium uppermost root reads bulk leaf rt-qpcr

• Hyb: a bioinformatics pipeline for the analysis of CLASH (crosslinking, ligation and sequencing of hybrids) data.

  PMID 24211736 · PMC3969109 · Methods (San Diego, Calif.) · 2014 · 8 claims · 6 setups

  Has reproduction · 71

  The 'hyb' pipeline detects, calls, folds and annotates chimeric reads from CLASH high-throughput sequencing data.

  ago1 test clash multiplexed clash benchmarking demultiplexing