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).

• PanglaoDB: a web server for exploration of mouse and human single-cell RNA sequencing data.

  PMID 30951143 · PMC6450036 · Database : the journal of biological databases and curation · 2019 · 7 claims · 7 setups

  Has reproduction · 80

  PanglaoDB is a web server providing pre-processed and pre-computed analyses of published mouse and human scRNA-seq experiments through a user-friendly interface.

  randomly single-cell single scrna-seq cell-type orthogonal

• 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

• Phosphorylation states of cell cycle and DNA repair proteins can be altered by the nsSNPs.

  PMID 16111488 · PMC1208866 · BMC cancer · 2005 · 8 claims · 4 setups

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  15 of 89 nsSNPs (16.9%) studied were predicted to abolish or create phosphorylation sites in 14 of 32 proteins (44.0%)

  orthologues repair case-control phosphorylation cross-species database

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

  PMID 32155147 · PMC7138332 · PLoS biology · 2020 · 8 claims · 7 setups

  Has reproduction · 90

  Replacing Scc1 with Rec8 in mitosis impairs sister chromosome cohesion, advances the timing of genome replication, and reduces reproductive fitness by 45%

  saccharomyces cerevisiae competitive live-cell flow

• Tumor and Immune Dynamics Following Sequential CDK4/6 and PD-1 Inhibition: Results from a Phase 2 Study in Dedifferentiated Liposarcoma.

  PMID 41325133 · PMC13037771 · Cancer research communications · 2026 · 7 claims · 4 setups

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  A palbociclib lead-in prior to retifanlimab produced a high rate of immune-related adverse events, leading to halted enrollment.

  tumor peripheral patients single-cell high-parameter clinical

• A tumor-intrinsic WNT-inhibitory NOTUM program drives immune resistance in microsatellite stable colorectal cancer.

  PMID 42097145 · PMC13198260 · Cell reports. Medicine · 2026 · 8 claims · 7 setups

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  A distinct NOTUM/NKD1/APCDD1-high, WNT-inhibitory cancer cell population (WICC) emerges predominantly in advanced-stage MSS CRC

  crc patient-derived ibd mmr-proficient single-cell cell-cycle patient-level

• 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

• GRIP-Lung: Generative Model of Response to Drug-Induced Perturbation in Lung Cancer.

  PMID 41977443 · PMC13072768 · International journal of molecular sciences · 2026 · 8 claims · 7 setups

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  GRIP-Lung, a GAN framework embedding cell-line identity and drug conditions, predicts drug-induced gene expression profiles in lung cancer cell lines

  lung nsclc a549 nci-60 bulk five-fold differential

• MECP2 mutations rewire human ESC fate and bias cortical lineage commitment.

  PMID 42030940 · PMC13163216 · Stem cell reports · 2026 · 8 claims · 8 setups

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  MECP2 mutations induce an early naïve-like transcriptional drift in human ESCs, marked by upregulation of ZFP42/REX1 and other naïve-enriched markers

  isogenic undifferentiated 3-month bulk bulk single-cell single-nucleus

• 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

• The Cohesin Ring Uses Its Hinge to Organize DNA Using Non-topological as well as Topological Mechanisms.

  PMID 29754816 · PMC6371919 · Cell · 2018 · 8 claims · 7 setups

  Has reproduction · 80

  Co-entrapment of sister DNAs inside cohesin rings (CDs) correlates perfectly with sister chromatid cohesion across multiple cell-cycle stages and mutants

  cerevisiae smc1 minichromosome gel calibrated

• CDKN2A and CDK4 mutation analysis in Italian melanoma-prone families: functional characterization of a novel CDKN2A germ line mutation.

  PMID 11556834 · PMC2375081 · British journal of cancer · 2001 · 7 claims · 6 setups

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  Germ line CDKN2A mutations were found in 5 of 15 (33.3%) Italian melanoma-prone families, including one novel mutation (P48T) and three known pathogenic mutations (R24P, G101W, N71S)

  genomic radiolabelled tig-er u2os sscp protein-protein retroviral

• Sequencing the regulatory genome.

  PMID 18598374 · PMC2481419 · Genome biology · 2008 · 8 claims · 8 setups

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  Nuclear-lamina-associated domains (LADs) define chromatin regions with distinct transcriptional characteristics (fewer, lower-expressed genes, low RNA Pol II occupancy, H3K27me3-enriched borders)

  interphase nine beta-globin drosophila nuclear digital chip

• 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

• MEIOC prevents continued mitotic cycling and promotes meiotic entry during mouse oogenesis.

  PMID 41287933 · PMC12848572 · Development (Cambridge, England) · 2026 · 8 claims · 4 setups

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  MEIOC prevents continued mitotic cycling in preleptotene oocytes prior to meiotic entry

  e16.5 e14.5 ovarian edu bulk single-cell

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

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

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  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

• Characterization of genome-wide p53-binding sites upon stress response.

  PMID 18474530 · PMC2441782 · Nucleic acids research · 2008 · 7 claims · 7 setups

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  Genome-wide ChIP-on-chip identified 1546 high-confidence p53-binding sites upon Actinomycin D treatment in U2OS cells

  u2os saos-2 chip-on-chip chip-qpcr western

• 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

• mtDNA G10398A variant in African-American women with breast cancer provides resistance to apoptosis and promotes metastasis in mice.

  PMID 19763141 · PMC2909846 · Journal of human genetics · 2009 · 8 claims · 8 setups

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  The G10398A cybrid shows slower proliferation and delayed cell cycle progression (G1 accumulation, decreased G2/M) compared to wild-type G10398 cybrid

  blood mitochondria g10398a cybrid pcr cybrid spectrophotometric

• 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