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).

• Expression profiling of drug response--from genes to pathways.

  PMID 17117610 · PMC3181826 · Dialogues in clinical neuroscience · 2006 · 8 claims · 8 setups

  Full-text index only

  Understanding individual response to a drug (efficacy/tolerability) is the major bottleneck in current drug development and clinical trials.

  blastocyst skin specified cortex pathway two-color microarray

• Mutations in dnaA and a cryptic interaction site increase drug resistance in Mycobacterium tuberculosis.

  PMID 33253310 · PMC7738170 · PLoS pathogens · 2020 · 7 claims · 8 setups

  Has reproduction · 98

  Non-synonymous mutations in dnaA are statistically associated with drug resistance (INH, RIF, SM) in clinical M. tuberculosis strains across two independent GWAS cohorts (China and Vietnam)

  clinical dnaa isogenic h37rv genome-wide structural deep-sequencing

• Genomics: applications in mechanism elucidation.

  PMID 19166886 · PMC2698023 · Advanced drug delivery reviews · 2009 · 8 claims · 8 setups

  Full-text index only

  Genomic tools require no a priori knowledge of a compound's mode of action and can reveal biological pathways (metabolism, distribution, off-target effects) in addition to the precise mechanism of action.

  extract panel saccharomyces inbred affinity cytotoxicity genome-wide

• Malaria genomics meets drug-resistance phenotyping in the field.

  PMID 19664295 · PMC2745762 · Genome biology · 2009 · 8 claims · 8 setups

  Full-text index only

  Significantly longer parasite clearance times in Pailin (western Cambodia) versus Wang Pha (Thailand-Myanmar border) establish the presence of artemisinin resistance in western Cambodia.

  falciparum plasmodium drug clinical high-throughput

• Clinical and genotypic findings in HIV-infected patients with the K65R mutation failing first-line antiretroviral therapy in Nigeria.

  PMID 19644383 · PMC2815152 · Journal of acquired immune deficiency syndromes (1999) · 2009 · 8 claims · 3 setups

  Full-text index only

  K65R mutation is present in a substantial proportion (10.9%) of Nigerian patients failing first-line ART, including many with no prior tenofovir exposure

  plasma k65r-positive hiv-1 comparative clinical

• Enhancing chemotherapy response prediction via matched colorectal tumor-organoid gene expression analysis and network-based biomarker selection.

  PMID 39754813 · PMC11754497 · Translational oncology · 2025 · 6 claims · 8 setups

  Has reproduction · 78

  A consensus WGCNA approach combining matched tumor-organoid and independent organoid drug-response expression data identifies gene modules and hub genes predictive of 5-FU chemotherapy response

  colorectal matched combined expression microarray rna-seq consensus

• Artificial Intelligence Approach in Machine Learning-Based Modeling and Networking of the Coronavirus Pathogenesis Pathway.

  PMID 40699865 · PMC12191508 · Current issues in molecular biology · 2025 · 8 claims · 8 setups

  Has reproduction

  The coronavirus pathogenesis pathway is activated in SARS-CoV-2-infected iPSC-derived cardiac cells and in SARS-CoV/SARS-CoV-2-infected LUAD cells

  ace2-transfected calu-3 luad ipsc-derived ipa sequencing convolutional

• GoMiner: a resource for biological interpretation of genomic and proteomic data.

  PMID 12702209 · PMC154579 · Genome biology · 2003 · 8 claims · 4 setups

  Full-text index only

  GoMiner organizes 'interesting' gene lists (e.g., differentially expressed genes) into the Gene Ontology hierarchy for biological interpretation, displaying results as both a tree and a directed acyclic graph (DAG).

  du145 gene gominer cdna flow category

• A single-step sequencing method for the identification of Mycobacterium tuberculosis complex species.

  PMID 18618024 · PMC2453075 · PLoS neglected tropical diseases · 2008 · 7 claims · 8 setups

  Full-text index only

  ETR-D sequencing allows accurate, single-step identification of MTC species, circumventing the expensive polyphasic approach.

  mtc tuberculosis phenotypic pcr mptr

• Structure of protein interaction networks and their implications on drug design.

  PMID 19876376 · PMC2760708 · PLoS computational biology · 2009 · 8 claims · 6 setups

  Full-text index only

  Budding yeast and human PINs are scale-rich and configured as highly optimized tolerance (HOT) networks similar to Internet router-level topology, rather than scale-free networks formed by preferential attachment.

  budding pin yeast protein-protein graph-theoretic gene

• Therapy effect of either paclitaxel or cyclophosphamide combination treatment in patients with epithelial ovarian cancer and relation to TP53 gene status.

  PMID 9703286 · PMC2063030 · British journal of cancer · 1998 · 6 claims · 4 setups

  Full-text index only

  Paclitaxel/cisplatin therapy produces a higher positive response rate than cyclophosphamide/cisplatin therapy in advanced ovarian cancer

  patients frozen genomic clinically randomized rt-pcr temporal

• Pharmacogenomic biomarkers.

  PMID 12364812 · PMC3850811 · Disease markers · 2002 · 8 claims · 8 setups

  Full-text index only

  Development of a pharmacogenomic biomarker requires sequential steps: laboratory identification, retrospective confirmation in clinical samples, prospective clinical trial validation, and regulatory approval before patient stratification.

  populations population tumor breast genetic array immunohistochemistry

• Applications for protein sequence-function evolution data: mRNA/protein expression analysis and coding SNP scoring tools.

  PMID 16912992 · PMC1538848 · Nucleic acids research · 2006 · 7 claims · 8 setups

  Full-text index only

  PANTHER HMMs built from family/subfamily multiple sequence alignments can classify novel protein sequences into functional groups based on statistically significant HMM match scores

  input gene genome-wide genes sequence gene numerical

• 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

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

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

  Full-text index only

  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

• mitoXplorer, a visual data mining platform to systematically analyze and visualize mitochondrial expression dynamics and mutations.

  PMID 31799603 · PMC6954439 · Nucleic acids research · 2020 · 6 claims · 4 setups

  Has reproduction · 89

  mitoXplorer is a web-based visual data mining platform that integrates expression and mutation data of mito-genes with a manually curated mitochondrial interactome of ~1200 genes grouped into 38 mitochondrial processes across four model species including human

  rpe-1 trisomic rpe bulk proteomics metabolic

• RummaGEO: Automatic mining of human and mouse gene sets from GEO.

  PMID 39569206 · PMC11573963 · Patterns (New York, N.Y.) · 2024 · 8 claims · 7 setups

  Has reproduction · 63

  RummaGEO is a gene expression signature search engine built from automatically mined human and mouse RNA-seq perturbation studies in GEO

  genes rummageo rummageo-derived leiden bulk gene leiden

• Integrated multi-omics analysis combined with clinical validation reveals that HLA-DRB5 and ODAPH are causal risk genes for keratoconus.

  PMID 41803193 · PMC13179358 · Scientific reports · 2026 · 7 claims · 8 setups

  Has reproduction · 64

  HLA-DRB5 and ODAPH are causal risk genes for keratoconus, supported by SMR and Bayesian colocalization (HLA-DRB5 PP4=0.844, SMR p=0.001, OR=1.768; ODAPH PP4=1.0, SMR p=0.013, OR=202.851).

  corneal gwas string bulk summary-data two-sample

• From Pasteur to genomics: progress and challenges in infectious diseases.

  PMID 15516917 · PMC7096024 · Nature medicine · 2004 · 8 claims · 8 setups

  Full-text index only

  Genomic sequencing has revealed the blueprint of most pathogens, enabling new diagnostics, therapeutics and vaccines including for previously uncultivable agents.

  bacterial neisseria sars hiv-infected whole-genome reverse nucleic

• Variants in the vitamin D receptor gene and asthma.

  PMID 15651992 · PMC546000 · BMC genetics · 2005 · 8 claims · 6 setups

  Full-text index only

  VDR gene variants are candidate risk factors for asthma/allergy because vitamin D effects are mediated through the VDR and VDR maps to the 12q asthma linkage region

  individuals children parents transmission bronchial pulmonary