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).

• Projecting contact matrices in 177 geographical regions: An update and comparison with empirical data for the COVID-19 era.

  PMID 34310590 · PMC8354454 · PLoS computational biology · 2021 · 7 claims · 6 setups

  Has reproduction · 98

  Updated synthetic contact matrices were generated for 177 geographical locations covering 97.2% of the world's population (up from 152 locations/95.9% in 2017).

  polymod geographical dhs locations bayesian synthetic household

• Hierarchical classification-based pan-cancer methylation analysis to classify primary cancer.

  PMID 38066424 · PMC10709847 · BMC bioinformatics · 2023 · 8 claims · 5 setups

  Has reproduction · 83

  CHCT, a hierarchical classification tool, splits classification of 30 cancer types into ten smaller subproblems using a two-tier architecture to classify primary cancer by methylation profile

  cancer clinical training independent methylation upgma random

• Zebrafish whole-adult-organism chemogenomics for large-scale predictive and discovery chemical biology.

  PMID 18618001 · PMC2442223 · PLoS genetics · 2008 · 8 claims · 6 setups

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  Zebrafish whole-adult-organism chemogenomics generates robust prediction models that discriminate P(H)AHs from ECs across independent experiments

  zebrafish computational seven consolidated whole-adult-organism supervised quantitative

• Expression genomics in breast cancer research: microarrays at the crossroads of biology and medicine.

  PMID 17397520 · PMC1868923 · Breast cancer research : BCR · 2007 · 8 claims · 8 setups

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  Genome-wide expression microarray studies reveal transcriptional networks/signatures that explain breast cancer biological and clinical heterogeneity

  breast early-stage diffuse dlbcl gene

• Multimodal data integration for biologically-relevant artificial intelligence to guide adjuvant chemotherapy in stage II colorectal cancer.

  PMID 40472802 · PMC12171563 · EBioMedicine · 2025 · 6 claims · 7 setups

  Has reproduction · 83

  AI-derived radiological clustering identifies stage II CRC patients with significantly different survival benefit from adjuvant chemotherapy

  stage patients tumour whole-tumour radiomics bulk cellular

• Tumor methionine metabolism drives T-cell exhaustion in hepatocellular carcinoma.

  PMID 33674593 · PMC7935900 · Nature communications · 2021 · 8 claims · 8 setups

  Has reproduction · 78

  A transcriptome-derived T-cell exhaustion score (ES) is prognostic for HCC patient survival independent of known clinical/molecular factors

  hcc-associated hcc malignant cd8+ single-cell bulk metabolomics

• Species-specific protein sequence and fold optimizations.

  PMID 12487631 · PMC139977 · BMC bioinformatics · 2002 · 7 claims · 7 setups

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  Environmental niche is a significant factor explaining variability in amino acid composition across 100 complete genomes

  predicted mean over orf principal hierarchical domain-based

• Inferring a spatial code of cell-cell interactions across a whole animal body.

  PMID 36395331 · PMC9714814 · PLoS computational biology · 2022 · 8 claims · 6 setups

  Has reproduction · 90

  cell2cell computes cell-cell interaction (CCI) potential using a novel modified Bray-Curtis score based on complementary coexpression of ligand-receptor pairs between cells

  elegans computational single-cell random genetic

• Discovering multiple transcripts of human hepatocytes using massively parallel signature sequencing (MPSS).

  PMID 17601345 · PMC1929076 · BMC genomics · 2007 · 8 claims · 8 setups

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  MPSS detected 10,279 UniGene clusters, representing 7,475 known genes, in human hepatocytes

  hepatocytes promoters genes hepatocyte mpss rt-pcr hierarchical

• Widespread dysregulation of MiRNAs by MYCN amplification and chromosomal imbalances in neuroblastoma: association of miRNA expression with survival.

  PMID 19924232 · PMC2773120 · PloS one · 2009 · 8 claims · 5 setups

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  37 miRNAs are significantly differentially expressed between MYCN-amplified (MNA) and non-MNA neuroblastoma tumors, suggesting direct or indirect regulation by MYCN

  neuroblastoma shep-tet21 stem-loop array tlda

• Discovery of molecular subtypes in leiomyosarcoma through integrative molecular profiling.

  PMID 19901961 · PMC2820592 · Oncogene · 2010 · 8 claims · 6 setups

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  Unsupervised gene expression clustering identifies 3 reproducible molecular subtypes of LMS (Group I/muscle-enriched, Group II, Group III)

  lms independent soft gene array immunohistochemistry

• High-resolution aCGH and expression profiling identifies a novel genomic subtype of ER negative breast cancer.

  PMID 17925008 · PMC2246289 · Genome biology · 2007 · 7 claims · 8 setups

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  A novel subtype of high-grade ER-negative breast cancer exists, characterized by a low genomic instability index (GII)

  breast computational array-cgh gene bac

• The DAVID Gene Functional Classification Tool: a novel biological module-centric algorithm to functionally analyze large gene lists.

  PMID 17784955 · PMC2375021 · Genome biology · 2007 · 8 claims · 6 setups

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  Gene-gene functional similarity can be measured using kappa statistics applied to a binary gene-annotation-term matrix built from 14 annotation categories.

  genome protein-protein genes artificial kappa clustering gene

• Defining human diabetic nephropathy on the molecular level: integration of transcriptomic profiles with biological knowledge.

  PMID 18704688 · PMC2597685 · Reviews in endocrine & metabolic disorders · 2008 · 8 claims · 8 setups

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  Genetic predisposition determines susceptibility and rate of progression to ESRD in diabetic patients, in addition to environmental factors

  kidney proximal pbmcs macrophages gene qrt-pcr immunohistochemistry

• Key regulatory molecules of cartilage destruction in rheumatoid arthritis: an in vitro study.

  PMID 18205922 · PMC2374452 · Arthritis research & therapy · 2008 · 7 claims · 4 setups

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  A standardized 3D in vitro alginate bead model of chondrocytes stimulated with synovial fibroblast supernatants can be used to profile RA-related cartilage destruction genes

  sv40 articular differentially antibody-based oligonucleotide real-time

• An integrative genomic and epigenomic approach for the study of transcriptional regulation.

  PMID 18365023 · PMC2266992 · PloS one · 2008 · 8 claims · 7 setups

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  Integrative analysis combining gene expression, DNA methylation, and H3K9 acetylation data reveals hundreds of additional differentially expressed genes missed by gene expression arrays alone

  aml computational help chip-chip gene

• Filling gaps in PPAR-alpha signaling through comparative nutrigenomics analysis.

  PMID 20003344 · PMC2801700 · BMC genomics · 2009 · 7 claims · 8 setups

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  Meta-analysis of 16 microarray datasets across human, mouse, rat and yeast identifies 164 genes (MDEGs) consistently differentially expressed in response to high fat diet or PPAR signaling perturbation.

  liver saccharomyces mdeg independent microarray transcription chromosomal