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).

• Activating GCN2 and subsequently the Unfolded Protein Response with the small oral molecule NXP800 delays tumor growth in osteosarcoma.

  PMID 41644942 · PMC12895007 · Cell death discovery · 2026 · 7 claims · 13 setups

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  NXP800 decreases viability of osteosarcoma cell lines by blocking proliferation and inducing apoptosis

  mnng gcn2-gst nmri crystal clonogenic cycle

• Microbiota-derived IPA protects against colitis by regulating intestinal HMGCS2-mediated ketogenesis to facilitate mucosal healing.

  PMID 41651833 · PMC12988232 · Nature communications · 2026 · 8 claims · 8 setups

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  IPA is consistently depleted in IBD/colitis patients and in murine colitis models relative to healthy controls

  fecal c57bl germ-free mice quasi-targeted dss-induced tnbs-induced

• Prenatal and postnatal effects of gestational immune activation on synaptic and neurodevelopmental pathways via epigenetic mechanisms.

  PMID 41654489 · PMC12923905 · Translational psychiatry · 2026 · 7 claims · 6 setups

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  MIA induces enduring epigenetic reprogramming of gene regulatory networks in the developing brain that persists into adulthood

  sorted frontal rna-seq mia-responsive chip-seq rna-seq facs

• Haplotype-resolved chromosome-level genome assembly of an autohexaploid oil camellia tree Camellia osmantha.

  PMID 41663440 · PMC12996448 · Scientific data · 2026 · 8 claims · 8 setups

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  First haplotype-resolved chromosome-level genome assembly generated for a hexaploid oil camellia (C. osmantha 'Yidan')

  leaves fresh pacbio root pacbio hi-c whole-genome

• A Scalable Framework for Comprehensive Typing of Polymorphic Immune Genes from Long-Read Data.

  PMID 41669879 · PMC13088316 · Advanced science (Weinheim, Baden-Wurttemberg, Germany) · 2026 · 8 claims · 8 setups

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  SpecImmune is the first unified computational framework to simultaneously genotype HLA, KIR, IG, TCR, and CYP genes from long-read data.

  1kgp hprc hgsvc long-read targeted germline

• A chromosome-scale genome assembly of the striped fruit fly Zeugodacus scutellatus (Diptera: Tephritidae).

  PMID 41673002 · PMC13002913 · Scientific data · 2026 · 8 claims · 8 setups

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  A chromosome-scale genome assembly of Z. scutellata was generated using Illumina short reads, PacBio HiFi long reads, and Hi-C scaffolding

  scutellata single assembled whole-genome pacbio hi-c

• A phased, near-telomere-to-telomere chromosome-scale reference genome of the Moroccan argan tree.

  PMID 41673035 · PMC13002930 · Scientific data · 2026 · 8 claims · 7 setups

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  Generated a chromosome-scale, phased reference genome of Argania spinosa using PacBio HiFi long reads combined with Hi-C scaffolding

  argania pacbio assembled pacbio hi-c rna-seq

• Aerobicity stimulon in Escherichia coli revealed using multi-scale computational systems biology of respiratory variants.

  PMID 41675058 · PMC12886548 · iScience · 2026 · 8 claims · 7 setups

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  ETS variants with differing proton-pumping efficiencies achieve growth optimization on succinate and glycerol via adaptive laboratory evolution, analogous to prior glucose findings

  coli adaptive growth rate-yield

• A haplotype-complete chromosome-level assembly of octoploid Urochloa humidicola cv. Tully reveals multiple genomic compositions and evolutionary histories in the species.

  PMID 41678351 · PMC13042314 · G3 (Bethesda, Md.) · 2026 · 8 claims · 8 setups

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  A haplotype-complete, chromosome-level genome assembly of octoploid U. humidicola cv. Tully was generated from PacBio HiFi reads alone

  humidicola chromosomes urochloa additional pacbio busco proteome

• Chromosome-scale genome assembly and annotation of the two-spotted cricket Gryllus bimaculatus (Orthoptera: Gryllidae).

  PMID 41678355 · PMC13042277 · G3 (Bethesda, Md.) · 2026 · 8 claims · 8 setups

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  A chromosome-scale genome assembly of the white-eyed mutant G. bimaculatus strain was generated using ONT + PacBio HiFi long reads integrated with Hi-C data

  bimaculatus nanopore pacbio hi-c

• Identification and Validation of an Autophagy-Related Gene Signature for Prognostic Prediction and Immunotherapy Response in Esophageal Squamous Cell Carcinoma.

  PMID 41681864 · PMC12897147 · Cancers · 2026 · 8 claims · 8 setups

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  A 4-ARG prognostic model (NBEA, CLOCK, NLRX1, MAGEA3) built via stepwise multivariate Cox regression stratifies ESCC patients into high- and low-risk groups with significantly different survival.

  escc gse53625 gse160269 imvigor210 microarray univariate single-cell

• ATRX loss couples genome instability at a G-rich repeat to dysregulation of human alpha-globin expression.

  PMID 41688464 · PMC13018553 · Nature communications · 2026 · 8 claims · 8 setups

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  ATRX deficiency downregulates α-globin (HBM/HBA) selectively in a subset of cells that exhibit DNA damage, rather than uniformly across the population

  cd34+ single day hudep-2 crispr-cas9 cfu single-cell

• Oxaliplatin-induced cardiotoxicity in mice is connected to the changes in energy metabolism in the heart tissue.

  PMID 41689157 · PMC13005559 · Cardio-oncology (London, England) · 2026 · 8 claims · 7 setups

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  Chronic oxaliplatin treatment causes direct cardiotoxicity in mice, evidenced by ECG, histology, and RNA-seq changes.

  c57bl heart ecg histology heart

• PUM2 knockdown regulates the expression and alternative splicing of genes associated with myocardial fibrosis in H9C2 cells.

  PMID 41694110 · PMC12902810 · Experimental and therapeutic medicine · 2026 · 7 claims · 7 setups

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  PUM2 knockdown regulates the expression and alternative splicing of genes associated with myocardial fibrosis in H9C2 cells

  h9c2 rt-qpcr western counting

• TGFβ-activated PDHB promotes mitochondrial pyruvate metabolism and contributes to human endoderm differentiation via ATP-dependent BRG1.

  PMID 41702907 · PMC13022444 · Nature communications · 2026 · 8 claims · 8 setups

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  DE differentiation requires a TGFβ-driven metabolic switch characterized by reduced lactate production and enhanced TCA cycle activity/oxidative phosphorylation, mediated by PDHB

  escs crispr flow qrt-pcr

• An AIB1 isoform rewires glucocorticoid receptor signaling to promote TNBC progression.

  PMID 41704785 · PMC12907120 · iScience · 2026 · 8 claims · 10 setups

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  GR antagonists (RU486, relacorilant) inhibit AIB1Δ4-driven invasion of DCIS cells in 3D invasion assays, zebrafish extravasation, and mouse xenograft models

  dcis kdrl nod e0771 sphere rt-qpcr shrna

• Single-cell mapping of cholesterol metabolism reveals FDPS as a therapeutic vulnerability in hepatocellular carcinoma.

  PMID 41706364 · PMC12916967 · Cellular oncology (Dordrecht, Netherlands) · 2026 · 7 claims · 8 setups

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  Cholesterol metabolic activity is markedly elevated in HCC tumors and in immune checkpoint blockade (ICB) non-responders, with pronounced intratumoral heterogeneity across malignant cell subpopulations

  hcc tcga-lihc malignant hepa1-6 scrna-seq bulk hdwgcna

• Glutamine-mediated crosstalk between M2 macrophages and tumor cells via the SLC38A5/FOXM1/CNIH4 axis promotes oral squamous cell carcinoma progression.

  PMID 41715179 · PMC13020291 · Journal of translational medicine · 2026 · 8 claims · 8 setups

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  Glutamine secretion from M2 macrophages to tumor cells via SLC38A5 is the core mCCC pathway upregulated in metastatic OSCC lesions compared to primary lesions.

  oscc epithelial tcga-oscc hsc-3 scrna-seq hdwgcna bulk

• Isoform-specific single-cell perturb-seq reveals distinct functions of alternative promoters in drug response.

  PMID 41728950 · PMC12926921 · Nucleic acids research · 2026 · 5 claims · 8 setups

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  CRISPR-dCas9-based screens exhibit widespread promoter specificity, with untargeted promoters often showing compensatory upregulation to maintain overall gene expression

  mcf-7 rpe1 mcf-7-dcas9 tissue-wide isoform-specific reanalysis qrt-pcr

• Three-dimensional genome reorganization foreshadows zygotic genome activation in Drosophila.

  PMID 41735587 · PMC12987734 · Nature genetics · 2026 · 8 claims · 8 setups

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  Pico-C, a low-input Micro-C method, enables high-resolution, temporally resolved 3D genome mapping in early Drosophila embryos using as few as ~60,000 nuclei

  hand-staged early drosophila pico-c chip-seq atac-seq