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 polyploid phasing from low-depth progeny samples.

  PMID 35692633 · PMC9184567 · iScience · 2022 · 8 claims · 7 setups

  Has reproduction · 73

  WH-PPG phases polyploid parental samples by scoring informative variant pairs with a Bayesian log-likelihood model of progeny allele depths, clustering alleles by co-occurrence likelihood, and assigning clusters to haplotypes via interval scheduling

  solanum illumina pacbio wh-ppg

• Development of an integrated genome informatics, data management and workflow infrastructure: a toolbox for the study of complex disease genetics.

  PMID 15601538 · PMC3525068 · Human genomics · 2004 · 8 claims · 8 setups

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  An integrated system combining Ensembl, ACeDB, Gbrowse and custom relational databases provides a scalable genome informatics and workflow infrastructure for complex disease gene discovery.

  pcr candidate embl clinical snp manual homology

• Statistical learning of peptide retention behavior in chromatographic separations: a new kernel-based approach for computational proteomics.

  PMID 18053132 · PMC2254445 · BMC bioinformatics · 2007 · 6 claims · 5 setups

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  The paired oligo-border kernel (POBK) combined with SVMs predicts peptide adsorption/elution in SAX-SPE and retention time in IP-RP-HPLC more accurately than existing methods.

  peptides peptide sax-spe ip-rp-hplc cross-run

• Genomic variation in myeloma: design, content, and initial application of the Bank On A Cure SNP Panel to detect associations with progression-free survival.

  PMID 18778477 · PMC2553089 · BMC medicine · 2008 · 7 claims · 7 setups

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  A custom BOAC SNP panel of 3404 SNPs in 983 genes was developed using the Affymetrix GeneChip Targeted Genotyping Platform, focused on non-synonymous coding SNPs and regulatory-region SNPs in candidate genes.

  coriell myeloma duplicate snp targeted genotyping machine

• Complete genome sequence of Treponema pallidum ssp. pallidum strain SS14 determined with oligonucleotide arrays.

  PMID 18482458 · PMC2408589 · BMC microbiology · 2008 · 8 claims · 6 setups

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  CGS combined with targeted DDT sequencing and whole genome fingerprinting (WGF) can accurately determine a treponemal genome sequence using only three arrays, at accuracy comparable to or better than finished DDT sequencing

  treponema pcr-amplified ss14 pcr comparative dideoxy-terminator genome

• Quantitative analysis of age specific variation in the abundance of human female parotid salivary proteins.

  PMID 19764810 · PMC2834885 · Journal of proteome research · 2009 · 7 claims · 5 setups

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  Protein expression in human female parotid saliva is age-dependent, with distinct protein sets differentially abundant between young and older healthy women

  pooled hcic trypsin-digested normalized hydrophobic sds-page mudpit

• Genomic signatures of migratory preference and historical whaling in eastern South Pacific humpback whales.

  PMID 41986456 · PMC13161203 · Communications biology · 2026 · 7 claims · 8 setups

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  Nuclear genomic data show no clear population structure among feeding grounds, indicating panmixia despite divergent migratory destinations

  megaptera same unrelated regional whole-genome relatedness population

• Genomic analysis of the Ixworth chicken: insights into a local dual-purpose breed.

  PMID 41814148 · PMC13064311 · BMC genomics · 2026 · 6 claims · 8 setups

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  The Ixworth chicken is genetically distinct from red junglefowl, commercial broilers, and commercial layers.

  ixworth six pairwise whole-genome variant principal

• Discovering and protecting cryptic biodiversity: A case study of a previously undescribed, vulnerable bird species in Japan.

  PMID 41852645 · PMC12993812 · PNAS nexus · 2026 · 8 claims · 8 setups

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  The Tokara Islands population is a cryptic species new to science, morphologically similar to but genetically distinct from Ijima's Leaf Warbler on the Izu Islands

  museum ijimae phylloscopidae genome-wide morphometric bioacoustic whole-genome

• Full-length 16S rRNA nanopore sequencing enables species resolution of Fusobacterium associated with colorectal cancer.

  PMID 41963777 · PMC13078227 · Gut microbes · 2026 · 8 claims · 7 setups

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  Full-length 16S rRNA ONT sequencing combined with custom demultiplexing (nanoMux) enables robust species-level discrimination within the Fusobacterium genus

  gtdb rrndb zymobiomics host-bacteria ani phylogenetic 16s

• Rapid identification of microbial pathogens and antimicrobial resistance from bloodstream infections using long-read sequencing.

  PMID 42274466 · PMC13256323 · Microbial genomics · 2026 · 8 claims · 8 setups

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  A novel ONT long-read sequencing laboratory and bioinformatic workflow rapidly identifies bacterial and fungal organisms and AMR determinants from positive blood cultures

  positive matching pure ont long-read short-read maldi-tof

• iS2C2: a cointelligent platform for mechanistic discovery of disease cellular crosstalk.

  PMID 42108258 · PMC13158306 · Signal transduction and targeted therapy · 2026 · 8 claims · 5 setups

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  iS2C2 integrates the S2C2 cell-cell communication algorithm with LLMs to generate biologically interpretable hypotheses from scRNA-seq and spatial transcriptomics data

  single-cell algorithm domain scrna-seq single-cell perturbation llm-based

• SGCRNA: spectral clustering-guided co-expression network analysis without scale-free constraints for multi-omic data.

  PMID 41615289 · PMC12856952 · Briefings in bioinformatics · 2026 · 8 claims · 8 setups

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  WGCNA's reliance on a scale-free topology assumption is problematic because real co-expression networks do not consistently exhibit scale-free properties

  gse114007 gse261545 dryad.37pvmcvsg prjna762466 bulk spatial merfish

• Genomic data sampling and its effect on classification performance assessment.

  PMID 12553886 · PMC149349 · BMC bioinformatics · 2003 · 8 claims · 3 setups

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  Cross-validation, leave-one-out, and bootstrap are designed to reduce bias and variance in accuracy estimation from small samples.

  leukemia srbct splice-junction supervised

• PedGenie: an analysis approach for genetic association testing in extended pedigrees and genealogies of arbitrary size.

  PMID 16620382 · PMC1459209 · BMC bioinformatics · 2006 · 7 claims · 3 setups

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  PedGenie is a valid, flexible statistical tool for genetic association analysis in pedigrees of arbitrary size and structure using Monte Carlo significance testing

  simulated gaw12 breast monte pedigree-based genetic

• DNA sequencing: bench to bedside and beyond.

  PMID 17855400 · PMC2094077 · Nucleic acids research · 2007 · 8 claims · 7 setups

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  DNA sequencing methods derived from Sanger's 1977 dideoxy method have dominated sequencing for 30 years despite being only incrementally refined.

  bacteriophage double-stranded single-stranded cloned plus maxam-gilbert dideoxy

• Integration of text- and data-mining using ontologies successfully selects disease gene candidates.

  PMID 15767279 · PMC1065256 · Nucleic acids research · 2005 · 7 claims · 6 setups

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  Integrating eVOC anatomical ontology-based text-mining of PubMed abstracts with data-mining of gene expression annotation successfully selects and prioritizes candidate disease genes

  biomedical refseq training independent text-mining data-mining candidate

• Protective effect of KCNH2 single nucleotide polymorphism K897T in LQTS families and identification of novel KCNQ1 and KCNH2 mutations.

  PMID 18808722 · PMC2570672 · BMC medical genetics · 2008 · 8 claims · 7 setups

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  LQTS-associated mutations were identified in 8 of 112 families studied

  large lqts family mutation linkage direct single-strand

• Human synthetic lethal inference as potential anti-cancer target gene detection.

  PMID 20015360 · PMC2804737 · BMC systems biology · 2009 · 7 claims · 8 setups

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  Targeting the synthetic lethal partner of a gene mutated in cancer selectively damages tumor cells while sparing healthy cells, offering a rationale for anti-cancer drug design

  saccharomyces sapiens ihsln genes database phylogenetic gene

• A re-annotation pipeline for Illumina BeadArrays: improving the interpretation of gene expression data.

  PMID 19923232 · PMC2817484 · Nucleic acids research · 2010 · 8 claims · 7 setups

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  A Perl-based pipeline that BLASTs/BLATs Illumina probe sequences against genomes and transcript databases (RefSeq, UCSC Known Genes, UniGene/GenBank, Ensembl) can classify probes by quality grade (Perfect/Good/Bad/No match) and is applicable across 8 BeadArray platforms and other array types

  maqc hepatocytes japanese illeum microarray dasl sequence