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).

• Characterizing Neutrophil Subtypes in Cancer Using scRNA Sequencing Demonstrates the Importance of IL1β/CXCR2 Axis in Generation of Metastasis-specific Neutrophils.

  PMID 38358352 · PMC10903300 · Cancer research communications · 2024 · 8 claims · 7 setups

  Has reproduction · 64

  Two main neutrophil subtypes exist in primary tumors: an activated subtype sharing transcriptomic signatures with healthy neutrophils, and a tumor-specific subtype.

  colorectal sorted integrated neutrophil scrna-seq bulk immunohistochemistry

• Unveiling prognostics biomarkers of tyrosine metabolism reprogramming in liver cancer by cross-platform gene expression analyses.

  PMID 32542016 · PMC7295234 · PloS one · 2020 · 7 claims · 8 setups

  Has reproduction · 51

  Five tyrosine catabolic enzymes (TAT, HPD, HGD, GSTZ1, FAH) are downregulated in HCC compared to normal liver at mRNA and/or protein level

  oncomine tcga-lihc gse89377 hcc pan-cancer bulk microarray

• In vivo structural characterization of the SARS-CoV-2 RNA genome identifies host proteins vulnerable to repurposed drugs.

  PMID 33636127 · PMC7871767 · Cell · 2021 · 8 claims · 8 setups

  Has reproduction · 95

  icSHAPE was used to determine the in vivo and in vitro structural landscape of the SARS-CoV-2 RNA genome in infected Huh7.5.1 cells, plus UTR structures of six other coronaviruses

  huh7.5.1 sars-cov-2 utrs 18s icshape structure deep-learning

• Mitotic checkpoint protein hsMAD2 as a marker predicting liver metastasis of human gastric cancers.

  PMID 11572763 · PMC5926839 · Japanese journal of cancer research : Gann · 2001 · 8 claims · 4 setups

  Full-text index only

  No mutations were found in the coding sequence of the hsMAD2 gene in 32 primary gastric cancers

  gastric cancer formalin-fixed near-diploid pcr semi-quantitative immunohistochemistry

• Lack of mutation at codon 531 of SRC in advanced colorectal cancers from Italian patients.

  PMID 11161376 · PMC2363715 · British journal of cancer · 2001 · 6 claims · 4 setups

  Full-text index only

  No SRC codon 531 mutation was detected in any of 155 Italian colorectal cancer cases (171 tissue specimens, primary tumours and liver metastases)

  colorectal liver scalar subset pcr-rflp direct

• Fucosylated glycoproteins as markers of liver disease.

  PMID 19126969 · PMC3827789 · Disease markers · 2008 · 8 claims · 6 setups

  Full-text index only

  Core alpha 1,6-linked fucosylation of AFP (AFP-L3) is increased in HCC and is a more specific marker of HCC than total AFP

  afp pooled larger igg lectin fucose-specific immunoblot

• Raf-1 activation disrupts its binding to keratins during cell stress.

  PMID 15314064 · PMC2172217 · The Journal of cell biology · 2004 · 8 claims · 8 setups

  Full-text index only

  Raf-1 kinase associates directly with keratin K8 (not K18), independent of Raf kinase activity and independent of Ras-Raf interaction

  ht29 transgenic bhk-21 bhk co-immunoprecipitation co-transfection oxidative

• Proteomics of the lysosome.

  PMID 18977398 · PMC2684028 · Biochimica et biophysica acta · 2009 · 8 claims · 8 setups

  Full-text index only

  The mammalian lysosome has been shown to contain ~60 soluble luminal proteins and ~25 transmembrane proteins

  liver placenta brain conditioned lc-ms n-terminal man6-p

• Computationally scalable regression modeling for ultrahigh-dimensional omics data with ParProx.

  PMID 34254998 · PMC8575036 · Briefings in bioinformatics · 2021 · 6 claims · 4 setups

  Has reproduction · 79

  ParProx implements latent group lasso penalized regression (overlapping and non-overlapping groups) for survival (Cox) and classification (logistic) analysis of omics data.

  tcga breast liver simulated cox logistic simulation

• Implementing the reuse of public DIA proteomics datasets: from the PRIDE database to Expression Atlas.

  PMID 35701420 · PMC9197839 · Scientific data · 2022 · 8 claims · 5 setups

  Has reproduction · 50

  An open, containerised, Nextflow-orchestrated reanalysis pipeline combining metadata annotation, SWATH-MS analysis, statistical analysis, and Expression Atlas integration was developed for public DIA data.

  pooled datasets pxd014194 technical swath-ms dda-based differential

• Expression in human prostate of drug- and carcinogen-metabolizing enzymes: association with prostate cancer risk.

  PMID 9823980 · PMC2063181 · British journal of cancer · 1998 · 7 claims · 5 setups

  Full-text index only

  CYP2D6, CYP3A, and an N-acetyltransferase enzyme activity are functionally expressed in human prostate tissue

  peripheral prostate genomic allele-specific enzymatic determination

• Differential diagnosis between chronic pancreatitis and pancreatic cancer: value of the detection of KRAS2 mutations in circulating DNA.

  PMID 12189555 · PMC2376157 · British journal of cancer · 2002 · 8 claims · 4 setups

  Full-text index only

  KRAS2 mutations are significantly more frequent in serum DNA of pancreatic cancer patients than chronic pancreatitis controls

  serum serum-extracted allele-specific fluorimetric immunoassay

• KEGG spider: interpretation of genomics data in the context of the global gene metabolic network.

  PMID 19094223 · PMC2646283 · Genome biology · 2008 · 8 claims · 8 setups

  Full-text index only

  KEGG spider, using a global 'pathway-free' metabolic network framework, provides deeper insight into metabolism variations than existing enrichment-based methods.

  diffuse-type liver renal anaplastic differential proteomic proteomics

• A compatible exon-exon junction database for the identification of exon skipping events using tandem mass spectrum data.

  PMID 19087293 · PMC2636810 · BMC bioinformatics · 2008 · 6 claims · 6 setups

  Full-text index only

  A theoretical exon-exon junction protein database accounting for all in-phase (frame-preserving) exon combinations can be built from the Ensembl Core Database using Perl/Bioperl/MySQL/Ensembl API.

  ensembl liver candidate same database tandem decoy

• Identification of genes associated with multiple cancers via integrative analysis.

  PMID 19919702 · PMC2785840 · BMC genomics · 2009 · 8 claims · 8 setups

  Full-text index only

  Mc.TGD (Multi-cancer Threshold Gradient Descent) is the first regularized approach to conduct two-dimensional selection of genes with joint effects on cancer development across multiple cancers.

  breast kidney liver lung gene wilcoxon

• PRLTS gene alterations in human prostate cancer.

  PMID 9197531 · PMC5921422 · Japanese journal of cancer research : Gann · 1997 · 5 claims · 3 setups

  Full-text index only

  LOH at the PRLTS gene locus is a relatively common abnormality in prostate cancer

  tumor metastatic loh pcr-sscp sequencing

• Indoleamine 2, 3-Dioxygenase 1 and CD8 Expression Profiling Revealed an Immunological Subtype of Colon Cancer With a Poor Prognosis.

  PMID 33425745 · PMC7793995 · Frontiers in oncology · 2020 · 8 claims · 8 setups

  Has reproduction · 48

  A colon cancer subtype with CD8Ahigh IDO1high tumors shows the worst survival despite high CD8 T cell infiltrates

  tcga-coad ncbi-geo tisidb gepia rna-seq tumor-infiltrating gene

• Wx: a neural network-based feature selection algorithm for transcriptomic data.

  PMID 31324856 · PMC6642261 · Scientific reports · 2019 · 8 claims · 8 setups

  Has reproduction · 50

  The Wx algorithm ranks genes using a DI score reflecting each gene's classification power for distinguishing two groups.

  tcga gse72056 gse40419 gse103322 bulk single-cell rna-seq

• Smart spatial omics (S2-omics) optimizes region of interest selection to capture molecular heterogeneity in diverse tissues.

  PMID 41298871 · PMC12662399 · Nature cell biology · 2025 · 7 claims · 6 setups

  Has reproduction · 100

  S2-omics is an end-to-end workflow that automatically selects ROIs from H&E histology images to maximize molecular information content for spatial omics profiling.

  gastric colorectal additional breast xenium visium histology

• 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