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).

• Genetic determinants of virulence in pathogenic lineage 2 West Nile virus strains.

  PMID 18258114 · PMC2600181 · Emerging infectious diseases · 2008 · 8 claims · 7 setups

  Full-text index only

  The nonstructural genes, especially NS5, are the most variable regions between highly and less neuroinvasive lineage 2 WNV strains

  lineage mice patients complete phylogenetic nucleotide

• A taxonomy of epithelial human cancer and their metastases.

  PMID 20017941 · PMC2806369 · BMC medical genomics · 2009 · 8 claims · 6 setups

  Full-text index only

  Unsupervised hierarchical clustering of 1566 primary epithelial tumors yields large tissue-enriched clusters (breast, colon/GI, lung, ovary, kidney) plus smaller prostate, thyroid-kidney, and mixed clusters

  epithelial tumor metastatic breast microarray gene fisher

• Exonic remnants of whole-genome duplication reveal cis-regulatory function of coding exons.

  PMID 19969543 · PMC2831330 · Nucleic acids research · 2010 · 8 claims · 8 setups

  Full-text index only

  38 candidate cis-regulatory coding exons (RCEs) with predicted target genes were identified genome-wide

  hg18 zebrafish bystander human-mouse comparative synteny orthologous

• The vaginal bacterial communities of Japanese women resemble those of women in other racial groups.

  PMID 19912342 · PMC2868947 · FEMS immunology and medical microbiology · 2010 · 7 claims · 5 setups

  Full-text index only

  The types of vaginal bacterial communities found in Japanese women closely resemble those previously found in White and Black North American women.

  vaginal japanese t-rflp clone cluster

• Inverse symmetry in complete genomes and whole-genome inverse duplication.

  PMID 19898631 · PMC2771390 · PloS one · 2009 · 8 claims · 5 setups

  Full-text index only

  Reverse and complement symmetries are essentially absent in genomic sequences at all scales.

  complete coli individual coding k-mer comparison segmental

• Genomic variability associated with the presence of occult hepatitis B virus in HIV co-infected individuals.

  PMID 19889143 · PMC3032083 · Journal of viral hepatitis · 2010 · 7 claims · 8 setups

  Full-text index only

  O-HBV-associated mutations in PreS/S/polymerase regions likely contribute to undetectable HBsAg by interfering with serologic detection, altering antigen secretion, and/or decreasing replicative fitness

  serum hbv full-length o-hbv nested phylogenetic quasispecies

• Saudi Arabian Y-Chromosome diversity and its relationship with nearby regions.

  PMID 19772609 · PMC2759955 · BMC genetics · 2009 · 8 claims · 5 setups

  Full-text index only

  Saudi Arabia differs from other Arabian Peninsula countries by a significantly higher presence of J2-M172 lineages.

  saudi same j1-m267 y-chromosome y-str amova

• Prodepth: predict residue depth by support vector regression approach from protein sequences only.

  PMID 19759917 · PMC2742725 · PloS one · 2009 · 8 claims · 8 setups

  Full-text index only

  Residue depth can be reliably predicted solely from protein primary sequence using support vector regression on sequence-derived features.

  structure sequences sequence residue dssp psi-blast

• Proteomic analysis of integrin-associated complexes identifies RCC2 as a dual regulator of Rac1 and Arf6.

  PMID 19738201 · PMC2857963 · Science signaling · 2009 · 8 claims · 8 setups

  Full-text index only

  A novel ligand-affinity/cross-linking proteomic methodology enables isolation of labile integrin-associated signaling complexes

  α5+ computational k562 embryonic ligand tandem hierarchical

• Teasing apart the joint effect of demography and natural selection in the birth of a contact zone.

  PMID 36093739 · PMC9828440 · The New phytologist · 2022 · 8 claims · 8 setups

  Full-text index only

  Natural selection contributed to the establishment and maintenance of the Scandinavian contact zone between the NFE and CSE genetic clusters.

  picea swedish subsets exome principal umap

• WEPP: Phylogenetic placement achieves near-haplotype resolution in wastewater-based epidemiology.

  PMID 41911220 · PMC13048486 · PLoS computational biology · 2026 · 8 claims · 5 setups

  Full-text index only

  WEPP is a pathogen-agnostic pipeline that uses phylogenetic placement of sequencing reads onto mutation-annotated trees (MATs) to identify candidate haplotypes and estimate their abundances

  sars-cov-2 mutation-annotated simulated synthetic real-world

• Loss of long-range co-expression is a common feature in cancer.

  PMID 41935098 · PMC13247121 · NPJ systems biology and applications · 2026 · 8 claims · 7 setups

  Full-text index only

  In cancer, the strongest co-expressed gene pairs (top MI values) are predominantly intra-chromosomal, unlike in normal tissue.

  tissues same bladder cancer bulk differential bootstrap

• Determining the quality and complexity of next-generation sequencing data without a reference genome.

  PMID 25514851 · PMC4298064 · Genome biology · 2014 · 8 claims · 8 setups

  Has reproduction · 78

  kPAL, an open-source alignment-free package, assesses sequencing data quality and complexity using k-mer frequency profiles and pairwise distances between them, without a reference sequence.

  rna-seq genome wgs exome k-mer rna-seq read

• Identification of novel DNA sequence motifs that modulate transcription in T cells.

  PMID 41514212 · PMC12879379 · BMC genomics · 2026 · 8 claims · 8 setups

  Full-text index only

  Identified 2,036 novel DNA motifs enriched in regulatory regions of T-cell-specific genes

  t-cell non-t-cell cd4+ sequences rna-seq dnase-seq h3k27ac

• Spatiotemporal dynamics of spermatogenesis: insights from high-resolution spatial transcriptomics and pseudotime trajectories in mouse testes.

  PMID 41602862 · PMC12832764 · Frontiers in reproductive health · 2025 · 8 claims · 7 setups

  Full-text index only

  Salus-STS (1 μm resolution) combined with the Salus Cellbins Algorithm enables accurate subcellular segmentation of individual testicular cells in dense tissue

  testicular testis seminiferous top high-resolution integration pseudotime

• Boosting the detection of enhancer-promoter loops via normalization methods for chromatin interaction data.

  PMID 41633996 · PMC12976324 · Nature communications · 2026 · 8 claims · 8 setups

  Full-text index only

  ICE and KR matrix balancing normalization methods over-correct and attenuate low-frequency enhancer-promoter loop signals despite preserving structural (CTCF-mediated) loops

  gm12878 embryonic mescs hi-c chip-seq chia-pet

• PHScaffolding: a hypergraph clustering and dual-weight integration strategy for scaffolding with Pore-C reads.

  PMID 41569288 · PMC12825295 · Briefings in bioinformatics · 2026 · 7 claims · 6 setups

  Full-text index only

  PHScaffolding builds a weighted hypergraph from Pore-C read-to-contig alignments, with hyperedges representing multi-way contig interactions and weighted by the geometric mean of per-contig alignment lengths

  hg002 gm12878 arabidopsis contig pore-c genome hypergraph

• Bayesian estimates of linkage disequilibrium.

  PMID 17592642 · PMC1924864 · BMC genetics · 2007 · 8 claims · 3 setups

  Full-text index only

  The MLE of D' is biased toward disequilibrium, with the bias particularly severe in small samples (<100 subjects) and rare alleles (MAF<0.05)

  simulated genotype pairwise computer genotype bayesian

• Physical and nutrient stimuli differentially modulate gut motility patterns, gut transit rate, and transcriptome in an agastric fish, the ballan wrasse.

  PMID 33571240 · PMC7877642 · PloS one · 2021 · 8 claims · 2 setups

  Full-text index only

  Intestinal stretch generated by inert cellulose causes faster evacuation of digesta from the anterior intestine than digestible protein and lipid

  intestine bulbous time-lapse sequencing

• Compensatory mutations cause excess of antagonistic epistasis in RNA secondary structure folding.

  PMID 12590655 · PMC149451 · BMC evolutionary biology · 2003 · 6 claims · 1 setups

  Full-text index only

  RNA secondary structure folding shows a clear prevalence of antagonistic epistasis (β < 1) among reference sequences

  randomly