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).

• Enhanced microRNA accumulation and gene silencing efficiency through optimized precursor base pairing.

  PMID 41505763 · PMC12782649 · The Plant journal : for cell and molecular biology · 2026 · 7 claims · 6 setups

  Has reproduction · 87

  Introducing a G–C pair immediately upstream of the mature amiRNA (A18G substitution) markedly enhances amiRNA accumulation and gene silencing efficiency in shc precursors.

  nicotiana arabidopsis a18g-modified srna quantitative chlorophyll

• What have we learned from the congenital myasthenic syndromes.

  PMID 19688192 · PMC3050586 · Journal of molecular neuroscience : MN · 2010 · 8 claims · 8 setups

  Full-text index only

  CMS have been traced to mutations in at least 11 disease genes encoding proteins at the neuromuscular junction

  endplate endplates cos bacterially electron intracellular density

• Altered spin state equilibrium in the T309V mutant of cytochrome P450 2D6: a spectroscopic and computational study.

  PMID 17318599 · PMC1915625 · Journal of biological inorganic chemistry : JBIC : a publication of the Society of Biological Inorganic Chemistry · 2007 · 7 claims · 7 setups

  Full-text index only

  The T309V mutation shifts the CYP2D6 heme spin equilibrium toward the six-coordinate low-spin (6cLS) state, decreasing the five-coordinate high-spin (5cHS) fraction relative to wild type.

  recombinant cyp2d6 computational resonance uv-vis sds-page

• Digital sorting of complex tissues for cell type-specific gene expression profiles.

  PMID 23497278 · PMC3626856 · BMC bioinformatics · 2013 · 8 claims · 8 setups

  Has reproduction · 85

  The Digital Sorting Algorithm (DSA) deconvolves mixed tissue expression into cell type-specific profiles using only marker genes, without requiring prior knowledge of cell type frequencies or in vitro pure-cell profiles.

  liver im-9 immune deconvolved microarray simulation roc

• 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

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  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

• FEM: mining biological meaning from cell level in single-cell RNA sequencing data.

  PMID 34909283 · PMC8641482 · PeerJ · 2021 · 7 claims · 5 setups

  Has reproduction · 75

  The FEM algorithm converts each cell's gene expression matrix (GEM) into a functional expression matrix by applying Fisher's exact test enrichment per cell and per gene set, then encoding adjusted p-values as information content.

  peripheral pancreas liver pbmc scrna-seq differential dimensionality

• Estimating and Correcting for Off-Target Cellular Contamination in Brain Cell Type Specific RNA-Seq Data.

  PMID 33746712 · PMC7966716 · Frontiers in molecular neuroscience · 2021 · 6 claims · 7 setups

  Has reproduction · 50

  A computational method using high-quality scRNA-seq reference data can estimate per-sample, per-cell-type off-target contamination coefficients in sctRNA-seq datasets.

  brain cortex allen lcm-seq lcm-seq scrna-seq marker

• Differentiation status determines the effects of IFNγ on the expression of PD-L1 and immunomodulatory genes in melanoma.

  PMID 39736644 · PMC11687009 · Cell communication and signaling : CCS · 2024 · 6 claims · 8 setups

  Has reproduction · 61

  Dedifferentiation via MITF knockdown renders 624Mel melanoma cells hypersensitive to IFNγ, causing non-additive (synergistic) upregulation of IFNγ-induced immunoregulatory genes.

  624mel yumm1.7 wild-type qpcr bulk luminex

• Gene-Expression Profiling Suggests Impaired Signaling via the Interferon Pathway in Cstb-/- Microglia.

  PMID 27355630 · PMC4927094 · PloS one · 2016 · 8 claims · 8 setups

  Has reproduction · 54

  In Cstb-/- microglia, 184 genes were differentially expressed relative to control, of which 33 were identified by both microarray and RNA-seq.

  analysis microarray rna-seq quantitative

• Involvement of HTLV-I Tax and CREB in aneuploidy: a bioinformatics approach.

  PMID 16822311 · PMC1553470 · Retrovirology · 2006 · 8 claims · 6 setups

  Full-text index only

  CTLL cells stably expressing wild-type Tax (CTLL/WT) show higher aneuploidy than a CREB-transactivation-deficient Tax clone (CTLL/703)

  ctll gene promoter metaphase microarray bioinformatics

• Cancer biomarker AKR1B10 and carbonyl metabolism.

  PMID 19028477 · PMC6193474 · Chemico-biological interactions · 2009 · 8 claims · 6 setups

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  AKR1B10 reduces the anticancer drug daunorubicin to daunorubicinol, decreasing its chemotherapeutic effectiveness

  recombinant fenofibrate enzyme sds-page x-ray

• Evolutionary repair: Changes in multiple functional modules allow meiotic cohesin to support mitosis.

  PMID 32155147 · PMC7138332 · PLoS biology · 2020 · 8 claims · 8 setups

  Has reproduction · 90

  Replacing the mitotic kleisin Scc1 with the meiotic kleisin Rec8 impairs sister chromosome cohesion, advances genome replication timing, and reduces reproductive fitness by 45%.

  cerevisiae parallel evolved rec8-expressing competitive experimental whole-genome

• Metabolic reprogramming and prognostic insights in molecular landscapes driven by glycolysis in ovarian cancer.

  PMID 40707588 · PMC12290113 · Scientific reports · 2025 · 7 claims · 8 setups

  Has reproduction · 77

  457 differentially expressed GRGs were identified between OC and normal ovarian tissue, of which 30 were significantly associated with prognosis

  tcga-oc tcga-oc-gse26193 ov_gse154600 iose-80 bulk univariate copy

• Caloric Restriction Reprograms Adipose Tissues in Rhesus Monkeys.

  PMID 41042069 · PMC12686577 · Aging cell · 2025 · 8 claims · 8 setups

  Has reproduction · 66

  At baseline, SAT and VAT transcriptomes are highly similar, with only ~1% of genes (30 genes, adjusted p<0.05) differentially expressed between depots in Controls

  subcutaneous sat rhesus bulk gsea xcell

• L2L: a simple tool for discovering the hidden significance in microarray expression data.

  PMID 16168088 · PMC1242216 · Genome biology · 2005 · 8 claims · 4 setups

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  L2L systematically compares a user's differentially expressed gene list against a database of published differentially expressed gene lists to find statistically significant overlaps and generate hypotheses about shared mechanisms

  mammalian user-supplied diabetic uniprot compiled l2l re-analysis

• Computational approaches for predicting the biological effect of p53 missense mutations: a comparison of three sequence analysis based methods.

  PMID 16522644 · PMC1390679 · Nucleic acids research · 2006 · 7 claims · 6 setups

  Full-text index only

  Align-GVGD predicts loss of transactivation activity with high specificity (~88%) but lower sensitivity (67.9-71.2%) for neutral mutants

  p53 tp53 yeast-based sequence align-gvgd

• A modular analysis framework for blood genomics studies: application to systemic lupus erythematosus.

  PMID 18631455 · PMC2727981 · Immunity · 2008 · 7 claims · 8 setups

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  Transcriptional modules constructed from coordinately expressed genes across 8 diseases form stable, biologically coherent functional units

  pbmc genes monocytes original microarray literature stimulation

• DiRE: identifying distant regulatory elements of co-expressed genes.

  PMID 18487623 · PMC2447744 · Nucleic acids research · 2008 · 8 claims · 4 setups

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  DiRE predicts distant regulatory elements by combining gene co-expression data, comparative genomics and TFBS profiles to determine TFBS-association signatures

  liver myod transgenic microarray tfbs enhancer

• Exploring the prognostic and diagnostic value of lactylation-related genes in sepsis.

  PMID 39367086 · PMC11452377 · Scientific reports · 2024 · 8 claims · 7 setups

  Has reproduction · 73

  Intersecting sepsis-associated differentially expressed genes with a curated list of 332 lactylation genes yields 55 sepsis-related lactylation genes.

  peripheral overlapping geo pbmcs bulk kegg protein-protein

• Vascular adhesion protein-1 defines a unique subpopulation of human hematopoietic stem cells and regulates their proliferation.

  PMID 34719737 · PMC8629906 · Cellular and molecular life sciences : CMLS · 2021 · 7 claims · 8 setups

  Has reproduction · 50

  VAP-1 is expressed on a subset of human HSC and on bone marrow vasculature, forming a hematogenic niche.

  facs-sorted sorted cd34+ bulk single-cell flow