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).

• Advances in genomic and pharmacokinetic profiling for clinical stratification of metastatic breast cancer.

  PMID 41369820 · PMC12799884 · Discover oncology · 2025 · 8 claims · 8 setups

  Has reproduction · 59

  Key genes AR, AKT1, UBC, CDH1, SMAD3, ROR1, and ROR2 are associated with chemotherapy resistance and poor prognosis in metastatic breast cancer

  breast tcga-brca geo gse40622 gene pan-cancer differential

• Prospects of telomere-to-telomere assembly in barley: Analysis of sequence gaps in the MorexV3 reference genome.

  PMID 35338551 · PMC9241371 · Plant biotechnology journal · 2022 · 7 claims · 8 setups

  Has reproduction · 71

  Almost all centromeric sequences and 45S ribosomal DNA repeat arrays are absent from the MorexV3 pseudomolecules

  barley optical chip-seq k-mer

• Systematic analysis of human kinase genes: a large number of genes and alternative splicing events result in functional and structural diversity.

  PMID 16351747 · PMC1866387 · BMC bioinformatics · 2005 · 8 claims · 7 setups

  Full-text index only

  Systematic in silico search identified 5 novel human kinase genes (on chromosomes 1, 11, 13, 15, 16) and 1 pseudogene (chromosome X) absent from KinBase

  genome genomic kinase psi-blast comparative genscan

• Satellog: a database for the identification and prioritization of satellite repeats in disease association studies.

  PMID 15949044 · PMC1181805 · BMC bioinformatics · 2005 · 7 claims · 6 setups

  Full-text index only

  Satellog is a database cataloging all pure 1-16 unit satellite repeats in the human genome with supplementary polymorphism, gene-location, and expression data for prioritizing repeats in disease-association studies.

  reference unigene ensembl normal tandem polymorphism gene

• Speeding disease gene discovery by sequence based candidate prioritization.

  PMID 15766383 · PMC1274252 · BMC bioinformatics · 2005 · 7 claims · 8 setups

  Full-text index only

  Disease genes (OMIM) differ significantly from non-disease genes in sequence-based features including gene/cDNA/protein size, exon number, homolog conservation, secretion signal, 3' UTR length, CpG islands, and distance to nearest gene.

  ensembl training same hgmd comparative machine tenfold

• Heterogeneous genomic molecular clocks in primates.

  PMID 17029560 · PMC1592237 · PLoS genetics · 2006 · 7 claims · 7 setups

  Full-text index only

  Non-CpG site substitutions show clear generation-time dependency, consistent with a replication-error origin

  baboon chimpanzee same human-chimpanzee relative phylogenetic four-species

• Bayesian prediction of microbial oxygen requirement.

  PMID 26913185 · PMC4743139 · F1000Research · 2013 · 7 claims · 8 setups

  Has reproduction · 76

  A naive Bayesian classifier based on presence/absence of class-associated Pfam-A domains can distinguish three oxygen requirement classes (aerobe, anaerobe, facultative anaerobe) from genome sequence, unlike prior studies that only made pairwise distinctions.

  bacterial selected predicted pfam-a genome gene domain

• Analysis of nucleotide diversity of NAT2 coding region reveals homogeneity across Native American populations and high intra-population diversity.

  PMID 16847467 · PMC3099416 · The pharmacogenomics journal · 2007 · 8 claims · 6 setups

  Full-text index only

  NAT2 variants are homogeneously distributed across native populations of the American continent

  chromosomes same inferred american pcr statistical haplotype

• Interactome networks: the state of the science.

  PMID 16515723 · PMC1431712 · Genome biology · 2006 · 8 claims · 8 setups

  Full-text index only

  Spastin interacts with CHMP1B, an ESCRT-III-associated protein, supporting a role for spastin in intracellular membrane trafficking relevant to hereditary spastic paraplegia

  genes tnfα orf proteins yeast tandem interference

• GLIDA: GPCR--ligand database for chemical genomics drug discovery--database and tools update.

  PMID 17986454 · PMC2238933 · Nucleic acids research · 2008 · 7 claims · 5 setups

  Full-text index only

  GLIDA is a public relational database integrating biological information on GPCRs with chemical information on their ligands and their binding interactions.

  ligand gpcr glida principal sequence gene

• FatiGO +: a functional profiling tool for genomic data. Integration of functional annotation, regulatory motifs and interaction data with microarray experiments.

  PMID 17478504 · PMC1933151 · Nucleic acids research · 2007 · 8 claims · 8 setups

  Full-text index only

  FatiGO+ is a web-based tool for functional profiling of genome-scale experiments that integrates functional annotation, regulatory motifs and interaction data

  user-supplied gene predicted interactome gene kegg transcription

• Animal models of gene-nutrient interactions.

  PMID 19037208 · PMC2703433 · Obesity (Silver Spring, Md.) · 2008 · 8 claims · 5 setups

  Full-text index only

  Mice and rats are well-suited models for human food selection because they share food preferences with humans and are supported by extensive genetic tools (sequenced genome, inbred strains, gene targeting, Cre-lox).

  interbred inbred pubmed genome qtl strain bibliometric

• Evolutionary modeling of rate shifts reveals specificity determinants in HIV-1 subtypes.

  PMID 18989394 · PMC2566816 · PLoS computational biology · 2008 · 7 claims · 4 setups

  Full-text index only

  A novel Bayesian method, RASER, can detect site-specific evolutionary rate shifts and the lineages in which they occurred without pre-specifying candidate lineages.

  hiv-1 simulated bayesian simulation structural

• Novel transglutaminase-1 mutations and genotype-phenotype investigations of 104 patients with autosomal recessive congenital ichthyosis in the USA.

  PMID 18948357 · PMC3044481 · Journal of medical genetics · 2009 · 8 claims · 6 setups

  Full-text index only

  TGM1 germline mutations were identified in 55% (57/104) of patients with ARCI

  arci unrelated dog direct sequence blast

• Cancer screening: a mathematical model relating secreted blood biomarker levels to tumor sizes.

  PMID 18715113 · PMC2517618 · PLoS medicine · 2008 · 8 claims · 4 setups

  Full-text index only

  A linear one-compartment mathematical model can relate secreted blood tumor biomarker levels to tumor burden/size at steady state

  ovarian serum model culture clinical mathematical

• Genotypic analysis of two hypervariable human cytomegalovirus genes.

  PMID 18649324 · PMC2658010 · Journal of medical virology · 2008 · 8 claims · 8 setups

  Full-text index only

  UL146 sequences from 184 samples fall into the same 14 genotypes (G1-G14) previously defined, with no new genotypes found.

  hcmv clinical pcr ul146 pcr nested molecular

• When does a protein become an allergen? Searching for a dynamic definition based on most advanced technology tools.

  PMID 18477011 · PMC2607534 · Clinical and experimental allergy : journal of the British Society for Allergy and Clinical Immunology · 2008 · 7 claims · 8 setups

  Full-text index only

  IgE-binding is not an intrinsic property of a protein but the result of an interaction between two molecules (antigen and IgE), so a molecule can only be classified relative to demonstrated IgE binding.

  subjects allergic serum allergenic double-blind skin serum

• Mapping proteins to disease terminologies: from UniProt to MeSH.

  PMID 18460185 · PMC2367626 · BMC bioinformatics · 2008 · 8 claims · 7 setups

  Full-text index only

  Developed a three-step procedure (disease name extraction, exact matching, partial/similarity-based matching) to map UniProtKB/Swiss-Prot disease names to MeSH terms

  randomly swiss-prot uniprotkb mesh manual exact partial

• An efficient method for the prediction of deleterious multiple-point mutations in the secondary structure of RNAs using suboptimal folding solutions.

  PMID 18445289 · PMC2386494 · BMC bioinformatics · 2008 · 8 claims · 6 setups

  Full-text index only

  Using RNAsubopt suboptimal solutions computed once for the wild-type sequence, specific multiple-point mutations likely to cause conformational rearrangement can be selected without brute-force enumeration.

  example hepatitis minimum suboptimal multiple-point

• A hierarchical and modular approach to the discovery of robust associations in genome-wide association studies from pooled DNA samples.

  PMID 18194558 · PMC2248205 · BMC genetics · 2008 · 8 claims · 5 setups

  Full-text index only

  A hierarchical/modular approach integrating quality control, LD, physical distance, and gene ontology identifies authentic associations among those found by statistical tests in pooled DNA GWAS

  pooled sickle centenarian snp pooled gene