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).

• Cell-type- and chromosome-specific chromatin landscapes and DNA replication programs of Drosophila testis tumor stem cell-like cells.

  PMID 41371963 · PMC12758400 · Genome research · 2026 · 8 claims · 6 setups

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  GSC-like and CySC-like cells isolated from upd tumor testes are transcriptionally comparable to wild-type GSC/early-spermatogonia and CySC clusters, respectively

  upd gsc-like wild-type scrna-seq differential gene

• Genome-wide analysis of the H3K4 histone demethylase RBP2 reveals a transcriptional program controlling differentiation.

  PMID 18722178 · PMC3003864 · Molecular cell · 2008 · 7 claims · 8 setups

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  RBP2 target promoters separate into two functionally distinct classes: differentiation-independent genes (mitochondrial function, RNA/DNA metabolism) and differentiation-dependent genes (cell cycle)

  u937 saos-2 chip-chip chip-on-chip gene

• CYCLONET--an integrated database on cell cycle regulation and carcinogenesis.

  PMID 17202170 · PMC1899094 · Nucleic acids research · 2007 · 7 claims · 4 setups

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  Cyclonet is a web-based integrated database combining 'omics' and chemoinformatics data on mammalian cell cycle regulation in normal and pathological (cancer) states, built on a systems biology approach.

  breast commercial vertebrate genes cdna activity computational

• FLASH-MM: fast and scalable single-cell differential expression analysis using linear mixed-effects models.

  PMID 41644528 · PMC12982622 · Nature communications · 2026 · 8 claims · 6 setups

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  FLASH-MM produces LMM parameter estimates identical to lmer (lme4) up to the sixth decimal place while being 50- to 140-fold faster as sample size increases from 20,000 to 120,000 cells

  simulated same healthy female-biased simulated comparative single-cell

• Whither genomics?

  PMID 11104516 · PMC138820 · Genome biology · 2000 · 8 claims · 8 setups

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  Genomics is both a science (understanding genome structure/evolution) and a tool (learning gene function) that collects comprehensive data on all genes, in contrast to genetics which studies a few genes controlling a phenotype

  mammalian budding yeast general expression genome-wide synthetic

• Therapeutic Stress-Induced Remodeling of Transposable Elements and TE-Gene Chimeras in KYSE150 Esophageal Squamous Cell Carcinoma Cells.

  PMID 42074115 · PMC13116134 · International journal of molecular sciences · 2026 · 8 claims · 8 setups

  Has reproduction · 67

  Combined 125I radiation and carfilzomib treatment causes structured, non-random remodeling of the TE transcriptome in KYSE150 ESCC cells.

  kyse150 bulk rna-seq-based differential

• RUVBL1 and RUVBL2 are druggable MYC effector regulators in neuroblastoma cells.

  PMID 41940329 · PMC13049659 · iScience · 2026 · 8 claims · 8 setups

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  RUVBL1 and RUVBL2 target gene sets are significantly depleted in MYCN-driven NB mouse tumors treated with ATR inhibitors (elimusertib, ceralasertib)

  th-mycn neuroblastoma clb-bar clb-ga rna-seq gene western

• Epigenetic profiling of hematopoietic stem cells from male mice identifies KDR and PU.1 as regulators of aging transcriptome and caloric restriction response.

  PMID 41720793 · PMC13035812 · Nature communications · 2026 · 8 claims · 8 setups

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  Lifelong CR reduces white blood cell production and shifts hematopoiesis toward myeloid and thrombo-erythroid lineages while suppressing lymphoid output

  peripheral sorted young aged complete flow bulk

• A genome-wide siRNA screen reveals diverse cellular processes and pathways that mediate genome stability.

  PMID 19647519 · PMC2772893 · Molecular cell · 2009 · 8 claims · 6 setups

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  A genome-wide siRNA screen in HeLa cells using γH2AX as a readout identifies genes whose knockdown elevates DNA damage/genome instability

  hela candidate screen genome-wide propidium sirna

• Mutually exclusive teams-like patterns of gene regulation characterize phenotypic heterogeneity along the noradrenergic-mesenchymal axis in neuroblastoma.

  PMID 38230570 · PMC10795782 · Cancer biology & therapy · 2024 · 8 claims · 6 setups

  Has reproduction · 87

  NOR-specific and MES-specific gene expression patterns are largely mutually exclusive, exhibiting a teams-like behavior across multiple bulk NB transcriptomic datasets

  lines bulk single-cell housekeeping bulk pca single-sample

• Targeting TPX2-dependent lineage plasticity by CDK4/6 inhibition reverses therapy resistance in neuroendocrine bladder carcinoma.

  PMID 41923619 · PMC13130694 · Cell reports. Medicine · 2026 · 8 claims · 8 setups

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  A 315-gene 'NE-like signature' (NE-like Sig), derived from the WGCNA MEmidnightblue module, marks a lineage-plasticity-associated transcriptional program distinct from canonical NE differentiation.

  cases in-house bladder nebc wgcna single-cell spatial

• Transcription network construction for large-scale microarray datasets using a high-performance computing approach.

  PMID 18366618 · PMC2386070 · BMC genomics · 2008 · 8 claims · 7 setups

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  RMT removes the random noise component of the gene expression correlation matrix by testing its eigenvalue statistics against a null hypothesis derived from a truly random correlation matrix

  yeast liver eight-node microarray k-means hybrid

• Mitochondrial DNA methylation predicts immunotherapy response and prognosis in lung adenocarcinoma: evidence from scRNA-Seq and machine learning.

  PMID 41663976 · PMC12997902 · BMC cancer · 2026 · 8 claims · 8 setups

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  Differentially expressed MTDM-related genes (DEMTDMRGs) are significantly enriched in cell cycle regulation, ferroptosis, and ABC transporter pathways

  luad demtdmrgs gse131907 wgcna kegg univariate

• Assembly of Macromolecular Complexes in the Whole-Cell Model of a Minimal Cell.

  PMID 41427637 · PMC12794154 · The journal of physical chemistry. B · 2026 · 8 claims · 6 setups

  Has reproduction · 67

  Assembly pathways for 21 unique macromolecular complexes (RNAP, ribosome, degradosome, ATP synthase, ABC transporters, etc.) were incorporated into the existing Syn3A whole-cell model

  jcvi-syn3a coli syn3a simulated hybrid ribosome atp

• Transcriptional readthrough precedes alternative splicing programs triggered in CML cells by imatinib.

  PMID 41860998 · PMC13004010 · Science advances · 2026 · 8 claims · 6 setups

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  Imatinib treatment induces transcriptional readthrough in K562 CML cells within 1 hour, before detectable gene expression or alternative splicing changes

  k562 imatinib-resistant long-read short-read rt-qpcr

• A choreography of centrosomal mRNAs reveals a conserved localization mechanism involving active polysome transport.

  PMID 33649340 · PMC7921559 · Nature communications · 2021 · 7 claims · 8 setups

  Has reproduction · 96

  A systematic HT-smFISH screen of centrosomal protein-coding genes identifies a total of eight human mRNAs (PCNT, CEP350, BICD2, NIN, CCDC88C, ASPM, NUMA1, HMMR) that localize to centrosomes.

  hela hela-centrin1-gfp aspm high-throughput low-throughput time-lapse

• Error-pooling-based statistical methods for identifying novel temporal replication profiles of human chromosomes observed by DNA tiling arrays.

  PMID 17430969 · PMC1888820 · Nucleic acids research · 2007 · 8 claims · 4 setups

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  Developed an LPE-based error-pooling and weighted ANOVA modeling approach for statistical analysis of high-density tiling array data

  cell-cycle-synchronized hela computational differentially tiling cdna statistical

• Genomic and proteomic profiling of oxidative stress response in human diploid fibroblasts.

  PMID 18654835 · PMC4973579 · Biogerontology · 2009 · 8 claims · 7 setups

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  Treatment of HCA3 human diploid fibroblasts with a mild dose of H2O2 (600 μM) induces premature senescence without killing the cells.

  hca3 differentially mudpit cdna semi-quantitative

• Single cell snapshot analyses under proper representation reveal that epithelial-mesenchymal transition couples at G1 and G2/M.

  PMID 41611829 · PMC12894973 · Communications biology · 2026 · 7 claims · 8 setups

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  TGF-β induced EMT in MCF10A cells follows two broad paths that arise from coupling between cell cycle and EMT at either the G1 or G2/M phase

  mcf10a scrna-seq vector pseudotime

• Impact of enteric neuronal loss on intestinal cell composition.

  PMID 42063560 · PMC13127327 · iScience · 2026 · 8 claims · 7 setups

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  ENS loss in ret mutant zebrafish alters the non-neuronal composition of the intestine, with increased immune cells and shifts in epithelial and ECM-producing populations

  intestine ens immune phox2bb single-cell scrna-seq whole-mount