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).

• Lorentz-regularized interpretable VAE for multi-scale single-cell transcriptomic and epigenomic embeddings.

  PMID 41555918 · PMC12812404 · Frontiers in genetics · 2025 · 7 claims · 5 setups

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  LiVAE, a dual-pathway VAE with Lorentzian geometric regularization between a primary Euclidean pathway and an information-bottleneck pathway, balances local fidelity with global topology coherence in single-cell embeddings

  single-cell same dapp1 benchmarking umap component-wise

• S3RL: Enhancing Spatial Single-Cell Transcriptomics With Separable Representation Learning.

  PMID 41556263 · PMC13042551 · Advanced science (Weinheim, Baden-Wurttemberg, Germany) · 2026 · 8 claims · 8 setups

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  S3RL is a separable representation learning framework that denoises sparse spatial transcriptomic data and enhances biologically relevant signals by integrating gene expression, spatial coordinates, and histological image features.

  dorsolateral dlpfc nanostring spatial cell-type multi-platform

• Redefinition of the toll-like receptor repertoire in Ciona robusta through genomic, structural, and expression analyses.

  PMID 41568004 · PMC12816324 · Frontiers in cellular and infection microbiology · 2025 · 8 claims · 8 setups

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  CiTLR13 is a redundant annotation of CiTLR1 (same genomic locus, >94% sequence identity), so it is not a distinct TLR gene

  ciona six lrr tlr blastp domain nucleotide

• Intestinal macrophages modulate synucleinopathy along the gut-brain axis.

  PMID 41606336 · PMC12960212 · Nature · 2026 · 8 claims · 8 setups

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  ME-Macs engulf misfolded, aggregated αS and modulate αS pathology and neurodegeneration in PD mouse models

  3kl sorted me-macs snca immunohistochemistry digital mass

• DHODH links mitochondrial bioenergetics, one-carbon metabolism, and DNA repair to sustain aggressive prostate adenocarcinoma.

  PMID 41612476 · PMC12930642 · Cell communication and signaling : CCS · 2026 · 8 claims · 8 setups

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  DHODH is markedly overexpressed in malignant prostate epithelial cells and abundant in tumors

  tcga-prad gse141445 22rv1 bulk single-cell lentiviral

• Functional correction and genome integrity with duplex base editing of β-thalassemic hematopoietic stem cells.

  PMID 41629994 · PMC12952134 · Genome biology · 2026 · 8 claims · 8 setups

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  Duplex base editing (2×BE) of BCL11A enhancer and HBG promoter produces significantly higher HbF and γ-globin induction than simplex BE or DSB-Cas9 editing

  β-thalassemic clones sanger ice targeted

• Tumour-brain crosstalk restrains cancer immunity via a sensory-sympathetic axis.

  PMID 41639447 · PMC12935554 · Nature · 2026 · 8 claims · 8 setups

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  Lung adenocarcinoma (LUAD) induces increased innervation and functional/transcriptional engagement of vagal sensory neurons (VSNs)

  kras-g12d tumour-bearing vagal npy2r-ires-cre whole-mount aav neurite

• 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

• Novel fatty acid metabolism-related molecular subtyping and prognostic signature for breast cancer.

  PMID 41674979 · PMC12885896 · Translational cancer research · 2026 · 8 claims · 8 setups

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  A FAM-related gene prognostic model (FAMGM) built using CoxBoost and random survival forest was identified as the optimal model among 101 machine learning combinations, based on highest average C-index across TCGA-BRCA and GSE96058 cohorts

  tcga-brca gse96058 brca breast bulk single-cell spatial

• Genome-wide association analyses highlight the role of the intestinal molecular environment in human gut microbiota variation.

  PMID 41688638 · PMC12987725 · Nature genetics · 2026 · 8 claims · 8 setups

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  Variants in the OR51E1–OR51E2 locus, encoding microbiome-derived fatty acid chemosensors expressed in enteroendocrine cells, are associated with gut microbial richness

  adults subset intestinal enteroendocrine genome-wide sanger single-cell

• pmid-41704762

  PMID 41704762 · PMC12907116 · 8 claims · 6 setups

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  Centenarian PBMCs exhibit a distinct, more functionally engaged chromatin accessibility landscape compared to controls and typical elderly individuals

  pbmcs atac-seq rna-seq cibersortx

• Characterizing Neutrophil Subtypes in Cancer Using scRNA Sequencing Demonstrates the Importance of IL1β/CXCR2 Axis in Generation of Metastasis-specific Neutrophils.

  PMID 38358352 · PMC10903300 · Cancer research communications · 2024 · 8 claims · 7 setups

  Has reproduction · 64

  Two main neutrophil subtypes exist in primary tumors: an activated subtype sharing transcriptomic signatures with healthy neutrophils, and a tumor-specific subtype.

  colorectal sorted integrated neutrophil scrna-seq bulk immunohistochemistry

• Social and ethical implications of genomics, race, ethnicity, and health inequities.

  PMID 19000599 · PMC2892396 · Seminars in oncology nursing · 2008 · 8 claims · 5 setups

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  Race and ethnicity are increasingly viewed as genetic surrogates for predicting disease risk and treatment response, though directly assessing genomic and environmental factors is more accurate.

  population prostate non-small-cell breast genome-wide gene somatic

• Robust characterization and interpretation of rare pathogenic cell populations from spatial omics using GARDEN.

  PMID 41547856 · PMC12917120 · Nature communications · 2026 · 8 claims · 8 setups

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  GARDEN identifies and characterizes rare pathogenic cell populations/regions in spatial omics by embedding graph-based dynamic attention into a spatially-aware graph fusion contrastive model

  breast anterior brain olfactory 10x starmap slide-seqv2

• CERTOMICS: trusted single-cell multiomics pipeline for high-resolution profiling of adoptive cellular immunotherapies.

  PMID 41741362 · PMC13008325 · Bioinformatics (Oxford, England) · 2026 · 8 claims · 2 setups

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  CERTOMICS is a Nextflow-based, CAR-aware pipeline for standardized single-cell multiomics profiling (GEX, V(D)J, ADT) of CAR-engineered cellular immunotherapies

  publicly multi-modal single-cell sequencing

• Single-cell RNA-sequencing of circulating tumour cells: A practical guide to workflow and translational applications.

  PMID 41053409 · PMC12500777 · Cancer metastasis reviews · 2025 · 8 claims · 8 setups

  Has reproduction

  A 12-step CTC-specific scRNA-seq workflow is proposed, spanning enrichment, single-cell sorting, sequencing, data pre-processing and downstream analysis, to overcome methodological inconsistencies in the field.

  ctcs pooled single neuroblastoma scrna-seq multi-omics

• Preparation of mouse pancreatic tumor for single-cell RNA sequencing and analysis of the data.

  PMID 34927097 · PMC8649395 · STAR protocols · 2021 · 6 claims · 7 setups

  Has reproduction · 50

  A combined mechanical and enzymatic dissociation protocol using the gentleMACS Dissociator yields a single-cell suspension from mouse pancreatic tumor tissue suitable for scRNA-seq while preserving cell characteristics

  pancreatic dissociated single-cell scrna-seq tumor dead red

• SMAC, a computational system to link literature, biomedical and expression data.

  PMID 31324861 · PMC6642118 · Scientific reports · 2019 · 8 claims · 8 setups

  Has reproduction · 50

  SMAC is a tool that extracts, prioritises, integrates and analyses biomedical and molecular data according to user-defined terms

  pubmed invasive geo genes semantic computational gene

• Developing a thyroid cancer differentiation state classification system using deep residual networks and metabolic signature profiling.

  PMID 40993300 · PMC12460824 · NPJ digital medicine · 2025 · 8 claims · 8 setups

  Has reproduction

  Metabolic status is closely tied to tumor differentiation state, with distinct metabolic reprogramming occurring during thyroid cancer dedifferentiation

  thyroid fuscc gse193581 aggregated untargeted whole-exome transcriptomics

• A robust approach to identifying tissue-specific gene expression regulatory variants using personalized human induced pluripotent stem cells.

  PMID 19911041 · PMC2766639 · PLoS genetics · 2009 · 8 claims · 7 setups

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  Padlock probes combined with high-throughput sequencing enable accurate, quantitative, low-bias digital RNA allelotyping of allele-specific expression

  genomic pgp1 skin fibroblasts padlock quantitative gene