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).

• Decision forest analysis of 61 single nucleotide polymorphisms in a case-control study of esophageal cancer; a novel method.

  PMID 16026601 · PMC1637030 · BMC bioinformatics · 2005 · 8 claims · 2 setups

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  DF-SNPs, a novel adaptation of the Decision Forest method, can classify esophageal cancer cases vs. controls based on SNP genotype data with high concordance, sensitivity, and specificity.

  genomic snp high-throughput decision

• Multilocus sequence typing of Cronobacter sakazakii and Cronobacter malonaticus reveals stable clonal structures with clinical significance which do not correlate with biotypes.

  PMID 19852808 · PMC2770063 · BMC microbiology · 2009 · 8 claims · 6 setups

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  A seven-locus MLST scheme (atpD, fusA, glnS, gltB, gyrB, infB, pps) reliably identifies and discriminates C. sakazakii and C. malonaticus strains

  sakazakii cronobacter sequenced multilocus biotyping phylogenetic

• 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

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  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

• Genomic expression during human myelopoiesis.

  PMID 17683550 · PMC2045681 · BMC genomics · 2007 · 8 claims · 5 setups

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  An integrated myelopoiesis expression dataset of 9,425 genes, each mapped to a unique genomic position, was generated from 24 microarray experiments across 8 myeloid cell types.

  myeloid same cd34+ gene microarray unsupervised sam

• Coxiella burnetii genotyping.

  PMID 16102309 · PMC3320512 · Emerging infectious diseases · 2005 · 8 claims · 5 setups

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  Multispacer sequence typing (MST) is the first reliable method for typing Coxiella burnetii isolates

  coxiella burnetii matrix sequence pcr molecular pcr-based

• MLST clustering of Campylobacter jejuni isolates from patients with gastroenteritis, reactive arthritis and Guillain-Barré syndrome.

  PMID 19702866 · PMC3985121 · Journal of applied microbiology · 2010 · 8 claims · 4 setups

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  Danish C. jejuni isolates from gastroenteritis, RA and GBS patients are highly genetically diverse, comprising 51 STs within 18 clonal complexes among 122 isolates.

  campylobacter concatenated clonal multilocus upgma clonalframe

• A DNA microarray survey of gene expression in normal human tissues.

  PMID 15774023 · PMC1088941 · Genome biology · 2005 · 6 claims · 6 setups

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  Unsupervised hierarchical clustering of gene expression groups normal tissue samples largely according to anatomic location, cellular composition, or physiologic function.

  normal common computational each two-color comparative unsupervised

• Relationships between emm and multilocus sequence types within a global collection of Streptococcus pyogenes.

  PMID 18405369 · PMC2359762 · BMC microbiology · 2008 · 8 claims · 5 setups

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  emm type is often a poor marker for clonal genetic background across the global S. pyogenes collection

  streptococcus pyogenes emm values multilocus emm comparative

• SeqBuster, a bioinformatic tool for the processing and analysis of small RNAs datasets, reveals ubiquitous miRNA modifications in human embryonic cells.

  PMID 20008100 · PMC2836562 · Nucleic acids research · 2010 · 8 claims · 6 setups

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  SeqBuster is a versatile web-based and stand-alone bioinformatic toolkit for processing and analyzing large-scale small RNA deep sequencing datasets.

  embryonic hesc small sequence adapter

• A global database for modeling tumor-immune cell communication.

  PMID 37438390 · PMC10338499 · Scientific data · 2023 · 7 claims · 6 setups

  Has reproduction · 66

  TICCom integrates 739 experimentally-validated or manually-curated TIC interactions collected from more than 3,000 literatures

  pubmed scrna-seq tcga basal manual scrna-seq bulk

• CLEAN: CLustering Enrichment ANalysis.

  PMID 19640299 · PMC2734555 · BMC bioinformatics · 2009 · 8 claims · 4 setups

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  The gene-specific CLEAN score improves reproducibility of cluster analysis conclusions across independent datasets compared to the traditional cluster-wide score (cwCLEAN).

  four breast combined hierarchical cluster csimm-based

• Directionality of point mutation and 5-methylcytosine deamination rates in the chimpanzee genome.

  PMID 17166280 · PMC1764022 · BMC genomics · 2006 · 8 claims · 6 setups

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  C→T (G→A) changes occur most frequently among nucleotide substitutions in the chimpanzee genome

  chimpanzee intergenic genome-wide chi-square nucleotide-content

• Phylogenetic analysis of mRNA polyadenylation sites reveals a role of transposable elements in evolution of the 3'-end of genes.

  PMID 18757892 · PMC2553571 · Nucleic acids research · 2008 · 8 claims · 6 setups

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  3'-most (L type) poly(A) sites are more conserved than upstream F/M type sites, while intronic (C/H type) sites are the least conserved

  consensus poly comparative transposable

• Atlas of nascent RNA transcripts reveals tissue-specific enhancer to gene linkages.

  PMID 40281430 · PMC12032694 · BMC genomics · 2025 · 7 claims · 8 setups

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  A large repository of nascent run-on RNA-seq samples (DBNascent) was assembled and uniformly processed to identify sites of bidirectional transcription genome-wide.

  bidirectional across high-quality nascent comparative eqtl

• Single-Cell Transcriptomic Landscape of Right-Sided Colon Cancer Reveals Cellular and Molecular Features of Metastatic Potential.

  PMID 41898210 · PMC13024220 · Biomedicines · 2026 · 8 claims · 6 setups

  Has reproduction · 71

  RCC_LM tumors exhibit higher genomic instability (CNV score) than RCC_noM tumors

  right-sided malignant epithelial types scrna-seq copy trajectory

• Recurrent KRAS codon 146 mutations in human colorectal cancer.

  PMID 16969076 · PMC2714972 · Cancer biology & therapy · 2006 · 8 claims · 8 setups

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  KRAS A146 missense mutations are a recurrent, previously unrecognized class of somatic mutation in colorectal cancer

  colorectal sporadic familial cancer pcr direct chi-squared