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 metadata approach for clinical data management in translational genomics studies in breast cancer.

  PMID 19948017 · PMC3225860 · BMC medical genomics · 2009 · 8 claims · 5 setups

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  A metadata/CDE-based approach using CancerGrid's semantic web tools enables automatic integration of heterogeneous clinical datasets without loss of original detail

  clinical breast metadata estrogen her2

• The landscape of responses to neoadjuvant immunotherapy in resectable Kirsten rat sarcoma viral oncogene homolog-mutant lung adenocarcinoma: Clinical heterogeneity and correlative immunologic analysis.

  PMID 42011021 · PMC13096693 · Clinical and translational medicine · 2026 · 6 claims · 8 setups

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  KRAS-mutant LUAD patients show significantly poorer pathological response and inferior long-term survival after neoadjuvant immunotherapy compared to KRAS-wildtype patients

  resected resectable epithelial cd4t_treg_tnfrsf4 scrna-seq retrospective cnv

• 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

• rMAP 2.0: a modular, reproducible, and scalable WDL-Cromwell-Docker workflow for genomic analysis of ESKAPEE pathogens.

  PMID 41782684 · PMC12955837 · Bioinformatics advances · 2026 · 8 claims · 8 setups

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  rMAP 2.0 standardizes end-to-end bacterial WGS analysis (QC, trimming, assembly, annotation, AMR/virulence/mobile-element profiling, sequence typing, pangenome inference, phylogenetics) via containerized WDL/Cromwell execution

  enterobacterales illumina aeruginosa pneumoniae whole-genome wgs amr

• Bridging cancer cell-intrinsic driver genes and -extrinsic cell-cell communication with Driver2Comm.

  PMID 41701761 · PMC12928580 · PLoS computational biology · 2026 · 8 claims · 5 setups

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  Driver2Comm is a computational framework that identifies intrinsic-extrinsic (IE) pathways functionally connecting cancer cell driver genes with their associated CCC signatures in the TME using single-cell transcriptomics data.

  pdac genes tcga single-cell copy fisher's

• QuantiSNP: an Objective Bayes Hidden-Markov Model to detect and accurately map copy number variation using SNP genotyping data.

  PMID 17341461 · PMC1874617 · Nucleic acids research · 2007 · 8 claims · 7 setups

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  QuantiSNP (OB-HMM) provides probabilistic quantification of copy number states and significantly improves accuracy of segmental aneuploidy identification and breakpoint mapping relative to existing tools (BeadStudio/Illumina)

  genomic same pseudo-normal artificially snp fish molecular

• Highlights of international conference of immunogenomics and immunomics, October 8-12, 2006 Budapest, Hungary.

  PMID 17470366 · PMC7130317 · Cellular immunology · 2006 · 8 claims · 8 setups

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  An 'immunological constant of rejection' involving interferon-stimulated genes (ISGs) and innate immune effector functions (IEF) underlies diverse immune-mediated tissue destruction processes (allograft rejection, cancer rejection, autoimmunity, infection)

  hla-b44 plasma macrophages complement proteomics shotgun cap

• Ensembl 2013.

  PMID 23203987 · PMC3531136 · Nucleic acids research · 2013 · 8 claims · 8 setups

  Has reproduction · 85

  Ensembl (http://www.ensembl.org) provides genome information for sequenced chordate genomes, currently supporting 70 species with a focus on human, mouse, zebrafish and rat.

  genome species supported variants evidence-based rna-seq chip-seq