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).

• Multi-organ expression profiling uncovers a gene module in coronary artery disease involving transendothelial migration of leukocytes and LIM domain binding 2: the Stockholm Atherosclerosis Gene Expression (STAGE) study.

  PMID 19997623 · PMC2780352 · PLoS genetics · 2009 · 8 claims · 6 setups

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  Functionally associated gene modules, not individual genes, underlie CAD development and can be identified via multi-organ expression clustering

  liver atherosclerotic 128-gene independent two-way gene bioinformatic

• The genome of Brugia malayi - all worms are not created equal.

  PMID 18952001 · PMC2668601 · Parasitology international · 2009 · 8 claims · 8 setups

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  Comparative genome analysis shows conserved long-range synteny but divergent local gene order between B. malayi and C. elegans, reflecting distinct evolutionary trajectories of parasitic and free-living lineages.

  malayi elegans wbm-infected filarial whole-genome genome-wide comparative

• 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

• An artificial intelligence optimized hepatic differentiation unveils NR5A2 and AP-1 transcriptional regulation in hepatic maturation.

  PMID 41962865 · PMC13185932 · The Journal of biological chemistry · 2026 · 7 claims · 8 setups

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  A CNN-based AI algorithm trained on bright-field images of hepatic progenitor cells (HPCs) accurately predicts successful vs. failed differentiation without immunostaining or lineage tracing

  hpsc-derived hlcs cnn-based qpcr flow

• Heterochronic transcription factor expression drives cone-dominant retina development in 13-lined ground squirrels.

  PMID 41649260 · PMC12880807 · eLife · 2026 · 8 claims · 8 setups

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  13LGS cone photoreceptors arise from both early-stage and late-stage neurogenic progenitors, unlike mice where cones arise only from early-stage progenitors

  13-lined retina 13lgs retinal single-cell scrna-seq chromvar

• Comprehensive analyses of telomerase component DKC1 and its association with clinical, molecular and immune landscapes in uterine corpus endometrial carcinoma.

  PMID 40458122 · PMC12127311 · Frontiers in cell and developmental biology · 2025 · 8 claims · 8 setups

  Has reproduction · 71

  DKC1 mRNA and protein expression are significantly upregulated in UCEC tumors compared with non-tumorous endometrial tissue

  ucec ishikawa rna-seq proteomics immunohistochemistry

• Dysregulated expression of cell cycle regulators CDC20, PLK1, BUB1, CDC45, CDCA5 in pancreatic ductal adenocarcinoma.

  PMID 41699006 · PMC13002898 · Scientific reports · 2026 · 8 claims · 8 setups

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  CDC20, PLK1, BUB1, CDC45, and CDCA5 are concordantly identified as hub genes across seven NCBI-GEO datasets and the Pakistani RNA-seq dataset

  pakistani pdac overlapping tcga-paad bulk functional protein-protein

• Genomic and proteomic approaches for studying human cancer: prospects for true patient-tailored therapy.

  PMID 15601541 · PMC3525069 · Human genomics · 2004 · 8 claims · 6 setups

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  DNA microarray gene expression profiling generates robust molecular classifications for many tumour types (brain, breast, colon, gastric, kidney, leukaemia, lymphoma, lung, melanoma, ovary, prostate, etc.)

  breast sars serum tumour microarray custom mass

• 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

• Diapause vs. reproductive programs: transcriptional phenotypes in a keystone copepod.

  PMID 33782539 · PMC8007741 · Communications biology · 2021 · 8 claims · 7 setups

  Has reproduction · 57

  t-SNE clustering of all-gene expression data groups field-collected (diapause program) samples into one cluster while early and late culture (reproductive program) samples separate into two distinct phenotypes

  calanus same 11k degs bulk dimensionality differential

• Mammary cell gene expression atlas links epithelial cell remodeling events to breast carcinogenesis.

  PMID 34079055 · PMC8172904 · Communications biology · 2021 · 8 claims · 8 setups

  Has reproduction · 96

  Integration of five mouse scRNAseq datasets reveals a trifurcating lineage trajectory originating from embryonic mammary stem cells (MaSCs) that differentiates into three epithelial lineages (Basal, L-Alv, L-Hor) via unipotent progenitor clusters

  mammary surgically normal single-cell whole-mount integration

• A Meta-Analysis of Wolbachia Transcriptomics Reveals a Stage-Specific Wolbachia Transcriptional Response Shared Across Different Hosts.

  PMID 32718933 · PMC7467002 · G3 (Bethesda, Md.) · 2020 · 7 claims · 7 setups

  Has reproduction · 89

  There is a general lack of global gene regulation across re-analyzed Wolbachia transcriptomes, with the exception of a weak transcriptional response upregulating ribosomal proteins in early larval stages.

  onchocerca dirofilaria wolbachia drosophila rna-seq functional

• Evolutionary innovation within conserved gene regulatory networks underlying biomineralized skeletons in Bilateria.

  PMID 41556888 · PMC12862220 · Molecular biology and evolution · 2026 · 8 claims · 6 setups

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  A biphasic regulatory program orchestrates larval and adult shell formation in Crassostrea nippona, involving coordinated activity of ancient transcription factors and dynamic chromatin remodeling

  crassostrea iso-seq rna-seq atac-seq

• Gene regulatory network transitions reveal the central transcription factors in lung adenocarcinoma progression.

  PMID 41559111 · PMC12873405 · NPJ systems biology and applications · 2026 · 7 claims · 8 setups

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  NR2F1 is a central transcription factor in LUAD progression, identified independently through GRN architecture transitions and gene regulation dynamics analysis

  luad epithelial myeloid nr2f1 single-cell gene binding

• Pseudotimecascade Visualizes Gene Expression Cascade in Pseudotime Analysis.

  PMID 41939293 · PMC13047748 · Computational and structural biotechnology journal · 2026 · 8 claims · 6 setups

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  Pseudotimecascade jointly analyzes multiple genes to uncover their relative temporal ordering and stage-specific activation patterns along pseudotime.

  bone genes same scrna-seq single-sample gene

• A transcriptome sequence dataset characterizing eggs, nymphs and adults of Oxycarenus hyalinipennis, the cotton seed bug.

  PMID 41717652 · PMC12915258 · Data in brief · 2026 · 8 claims · 8 setups

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  This dataset provides the first transcriptomic resources for the invasive pest Oxycarenus hyalinipennis

  whole-insect cross assembled global rna-seq differential sequence

• Identification and analysis of genes associated with epithelial ovarian cancer by integrated bioinformatics methods.

  PMID 34143800 · PMC8213194 · PloS one · 2021 · 8 claims · 7 setups

  Has reproduction · 75

  306 overlapping DEGs (265 up-regulated, 41 down-regulated) were identified from three independent GEO microarray datasets comparing EOC and adjacent normal ovarian tissue

  eoc analysis overlapping pubmed microarray kegg protein-protein

• Spatial transcriptomics reveals the molecular signatures of prodromal and advanced α-synucleinopathy.

  PMID 41736854 · PMC12927100 · iScience · 2026 · 7 claims · 6 setups

  Has reproduction · 70

  Early-stage (prodromal) aSyn pathology in M83+/+ mouse brainstem is associated with upregulation of ATP/energy metabolism pathways (glycolysis, oxidative phosphorylation, fatty acid metabolism)

  sagittal st-derived spatial immunofluorescence cell-cell

• Daily temperature cycles promote alternative splicing of RNAs encoding SR45a, a splicing regulator in maize.

  PMID 33705553 · PMC8195531 · Plant physiology · 2021 · 8 claims · 4 setups

  Has reproduction · 76

  Increasing maximum daily temperature (MDT) elevates the frequency of alternative splicing in maize leaves, particularly intron retention (IR) and exon skipping (ES).

  maize rna-seq gene differential

• Developmental stage dominates cell-type identity and reveals a chromatin regulatory function for Rad50 in Drosophila.

  PMID 41978263 · PMC13076223 · Nucleic acids research · 2026 · 8 claims · 8 setups

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  Developmental stage is a stronger determinant of transcriptional identity than cell type across Drosophila neurons, glia, and hemocytes

  neurons cns e16 salivary bulk atac-seq western