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).

• Independent component analysis reveals new and biologically significant structures in micro array data.

  PMID 16762055 · PMC1557674 · BMC bioinformatics · 2006 · 7 claims · 8 setups

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  ICA applied to three microarray datasets reveals many biologically significant components, including low-ranking ones not obvious by rank alone

  acute serum-stimulated head aml microarray clust term

• DNA bar coding and pyrosequencing to identify rare HIV drug resistance mutations.

  PMID 17576693 · PMC1934997 · Nucleic acids research · 2007 · 6 claims · 7 setups

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  DNA bar coding combined with pyrosequencing allows parallel, deep characterization of drug resistance mutations across many HIV populations in a single experiment

  hiv pooled plasma pyrosequencing conventional rt-pcr

• Synonymous substitution rates predict HIV disease progression as a result of underlying replication dynamics.

  PMID 17305421 · PMC1797821 · PLoS computational biology · 2007 · 8 claims · 8 setups

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  The synonymous substitution rate (dS) of HIV env is strongly correlated with disease progression parameters (progression time, CD4+ decline rate, viral load increase rate), unlike the nonsynonymous rate (dN).

  longitudinal backbone env intra-patient relaxed-clock correlation site-to-site

• Advances in breast cancer: pathways to personalized medicine.

  PMID 19088015 · PMC4535810 · Clinical cancer research : an official journal of the American Association for Cancer Research · 2008 · 8 claims · 8 setups

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  Germline BRCA1/BRCA2 mutations are strong predictors of breast and ovarian cancer, conferring a 40-80% lifetime risk of breast cancer

  population-based women breast high-risk germline genome-wide microarray

• Short-term genome evolution of Listeria monocytogenes in a non-controlled environment.

  PMID 19014550 · PMC2642827 · BMC genomics · 2008 · 6 claims · 6 setups

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  The 2000 listeriosis outbreak was likely caused by an L. monocytogenes strain that persisted in the food processing facility for at least 12 years since 1988

  monocytogenes additional food j774 whole-genome comparative pcr

• SIGMA2: a system for the integrative genomic multi-dimensional analysis of cancer genomes, epigenomes, and transcriptomes.

  PMID 18840289 · PMC2571113 · BMC bioinformatics · 2008 · 8 claims · 6 setups

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  SIGMA2 is a Java-based software system that integrates and visualizes genomic, epigenomic, and transcriptomic cancer data.

  single hcc2218 nsclc array gene multi-omics

• Proteomics as a method for early detection of cancer: a review of proteomics, exhaled breath condensate, and lung cancer screening.

  PMID 18095050 · PMC2150625 · Journal of general internal medicine · 2008 · 8 claims · 7 setups

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  Protein expression is closely aligned with cellular activity, unlike genomic changes which may have no functional significance

  serum resected plasma lower microarray two-dimensional proteomic

• Proteomic profiling in ovarian cancer.

  PMID 19955909 · PMC7319026 · International journal of gynecological cancer : official journal of the International Gynecological Cancer Society · 2009 · 8 claims · 6 setups

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  No validated or cost-efficient screening program exists for ovarian cancer; physical exam, CA125, and transvaginal ultrasound lack sufficient sensitivity/specificity for early-stage detection.

  serum tumor rolling mass microarray

• Profiling critical cancer gene mutations in clinical tumor samples.

  PMID 19924296 · PMC2774511 · PloS one · 2009 · 7 claims · 4 setups

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  OncoMap, a panel of ~400 mass-spectrometric genotyping assays targeting 33 cancer genes, enables robust mutation profiling of clinical fresh-frozen and FFPE tumor DNA.

  clinical fresh same pediatric mass sanger barcoded

• Unique clinicopathologic features characterize ALK-rearranged lung adenocarcinoma in the western population.

  PMID 19671850 · PMC2865649 · Clinical cancer research : an official journal of the American Association for Cancer Research · 2009 · 8 claims · 6 setups

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  20 of 358 (5.6%) lung adenocarcinomas from Western institutions harbored ALK rearrangements

  formalin-fixed lung sections poorly fluorescent immunohistochemistry mutational

• Relation of candidate genes that encode for endothelial function to migraine and stroke: the Stroke Prevention in Young Women study.

  PMID 19661472 · PMC2753702 · Stroke · 2009 · 8 claims · 6 setups

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  EDN SNP rs1800542 is associated with increased ischemic stroke risk in Caucasian women

  international spyw candidate haplotype population

• Divergent clonal evolution and tumor microenvironment remodeling shape gastric cancer peritoneal metastasis.

  PMID 41882239 · PMC13181027 · Communications biology · 2026 · 8 claims · 7 setups

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  Substantial intra-patient heterogeneity exists between GCPM and primary tumors at both genetic and functional (transcriptomic) levels

  gastric wgs paired genes whole-genome whole-transcriptome mutational

• Inherited resilience to clonal hematopoiesis by modifying stem cell RNA regulation.

  PMID 41477881 · PMC12850507 · Science (New York, N.Y.) · 2026 · 8 claims · 8 setups

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  A haplotype at the 17q22 locus, tagged by the noncoding variant rs17834140-T, is a causal protective variant against CHIP and myeloid malignancies

  population hspcs cd34+cd45ra-cd90+ heterozygous gwas atac-seq crispr

• Integrating single-cell and bulk transcriptomes identifies B cell features associated with neoadjuvant chemoradiotherapy sensitivity in rectal cancer.

  PMID 41484196 · PMC12800305 · Scientific reports · 2026 · 8 claims · 8 setups

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  A B cell subpopulation co-expressing HLA-DRB5, HLA-DQA2, HLA-DQB1, CD74, and ACTG1 is significantly associated with favorable nCRT response in rectal cancer

  larc scrna-seq scissor+ single-cell bulk pseudotime

• A cellular epigenetic classification system for glioblastoma.

  PMID 41499453 · PMC13128495 · Neuro-oncology · 2026 · 8 claims · 8 setups

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  ITHresolveGBM, a hierarchical two-step NMF method, deconvolutes bulk GBM DNA methylation profiles into three non-malignant (immune, glial, neuronal) and three malignant components

  gbm healthy pseudo-bulk tcga illumina single-cell deconvolution

• Evaluating deconvolution methods using real bulk RNA-expression data for robust prognostic insights across cancer types.

  PMID 41566530 · PMC12906006 · Genome biology · 2026 · 7 claims · 6 setups

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  Pseudobulk and real bulk RNA-seq deconvolution performance differ significantly, and method ranking consistency is lower between pseudobulk and real bulk than within either data type alone

  breast real colon tcga paired pseudobulk bulk

• Single-cell sequencing analysis and machine learning model reveal aberrant TIM-3 expression in microglia during Alzheimer's disease progression.

  PMID 41580850 · PMC12911240 · Journal of translational medicine · 2026 · 7 claims · 8 setups

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  A TIM-3+ microglial subset drives AD pathogenesis through a dual mechanism: sustained neuroinflammation via TNF-α/NF-κB and IL-6/JAK/STAT3 signaling, and impaired amyloid-β clearance linked to PI3K-AKT and FcγR pathways

  brain overlapping transcriptomic patients single-cell bulk kegg

• Mosaic partial epidermal reprogramming remodels neighbors and niches to refine skin homeostasis and repair.

  PMID 41617708 · PMC12960685 · Nature communications · 2026 · 8 claims · 8 setups

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  A genetically engineered mouse model (Krt14-CreER; LSL-rtTA-EGFP; TetO-OSKM-mCherry, 'Epi-iOSKM') enables transient, reversible, mosaic OSKM expression in interfollicular epidermal cells without inducing pluripotency or teratoma risk

  epidermis sorted epidermal ife immunostaining single-cell pseudotime

• Dynamic regulation of spermatogenesis and hybrid sterility revealed by single-cell analysis in yak and cattle.

  PMID 41622528 · PMC12916010 · Molecular biology and evolution · 2026 · 7 claims · 8 setups

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  Cattle and yak testes contain seven types of spermatogonia, ten spermatocyte subtypes, and ten spermatid types with largely conserved transcriptional programs governing spermatogenic fate transitions.

  testicular spermatocytes spermatids bc1 single-cell chromosome hematoxylin

• Therapeutic synergies that overcome carboplatin resistance in triple-negative breast cancer.

  PMID 41630032 · PMC13037280 · Journal of experimental & clinical cancer research : CR · 2026 · 8 claims · 8 setups

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  Four isogenic carboplatin-resistant (CR) PDX pairs (WHIM30, BCM-2147, BCM-3887, BCM-7482) were generated via serial in vivo carboplatin exposure to model acquired resistance in TNBC

  isogenic pdx ffpe carboplatin-resistant bulk single-cell nuclear