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).

• MUUMI: an R package for statistical and network-based meta-analysis for multi-omics data integration.

  PMID 41634555 · PMC12955011 · BMC bioinformatics · 2026 · 8 claims · 5 setups

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  MUUMI unifies statistical meta-analysis and network-based omics data integration within a single analytical R package framework

  lung integrated ranked thp-1 sequencing microarray statistical

• Integration of aged brain multi-omics reveals cross-system mechanisms underlying Alzheimer's disease heterogeneity.

  PMID 41950003 · PMC13244359 · Cell reports · 2026 · 8 claims · 7 setups

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  Multi-omics factor analysis (MOFA) integrating seven omics views from 1,358 ROS/MAP participants identifies cross-omics biological factors relating to AD phenotypes.

  dorsolateral brain postmortem cortex h3k9ac bulk proteomics

• Nonsense-mediated mRNA decay inhibition reshapes the cancer immunopeptidome.

  PMID 41956098 · PMC7619149 · Immunity · 2026 · 8 claims · 8 setups

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  Reduced NMD activity (lower NMD score) predicts improved CPI response across >1,000 patients, independent of TMB or tumor type

  tcga a375 reporter patient-derived multi-omics crispr-cas9 sirna

• Radiogenomics predicts immune microenvironment heterogeneity and response to combination immunotherapy in hepatocellular carcinoma.

  PMID 41555384 · PMC12895822 · Journal of translational medicine · 2026 · 8 claims · 8 setups

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  A parsimonious 2-gene immune-related signature (IRS = 0.425×KPNA2 + 0.302×SMG5) is significantly associated with immune heterogeneity and response to ICI plus anti-angiogenic combination therapy in HCC

  hcc gse202642 paired hcc-derived bulk single-cell immunohistochemistry

• Multiomic analysis of malignant pleural mesothelioma identifies molecular axes and specialized tumor profiles driving intertumor heterogeneity.

  PMID 36928603 · PMC10101853 · Nature genetics · 2023 · 8 claims · 6 setups

  Has reproduction · 80

  The WHO histopathological classification of MPM accounts for only up to ~10% of interpatient molecular differences

  mpm mesomics whole-genome bulk methylation

• Immune profiling in a living human recipient of a gene-edited pig kidney.

  PMID 41507576 · PMC12823403 · Nature medicine · 2026 · 8 claims · 8 setups

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  Xenograft experienced early T cell-mediated rejection (Banff grade 2A) within 1 week post-transplant despite profound circulating T cell depletion, likely driven by subtherapeutic immunosuppression and residual CD8+ T cells in lymph nodes.

  xenotransplant recipient kidney integrative single-cell flow

• A multi-omics features-based approach integrating immunogenicity and inflammation enhances immunotherapy benefit in clear cell renal cell carcinoma.

  PMID 41640425 · PMC12864441 · Frontiers in cell and developmental biology · 2025 · 7 claims · 8 setups

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  The TIs-ML multi-omics model predicts ICB response/survival in ccRCC with superior accuracy (AUC > 0.997) compared to single biomarkers like PD-L1 and TMB

  autoimmune igan scrna-seq bulk bulk scrna-seq scissor-based

• A cross-scale multimodal framework identifies clinically actionable immunotherapy biomarkers in melanoma through bulk to single-cell and spatial transcriptomics integration.

  PMID 41840725 · PMC13104449 · Human genomics · 2026 · 7 claims · 8 setups

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  Multi-omics consensus clustering (MOVICS) identifies two distinct SKCM molecular subtypes, CS1 and CS2

  tcga-skcm meta-geo gtex melanoma multi-omics bulk transcriptome-wide

• Multi-omics feature engineering driven by biomedical foundation models improves drug response prediction for inflammatory bowel disease patients.

  PMID 41844950 · PMC13129071 · Scientific reports · 2026 · 8 claims · 7 setups

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  FM (MAMMAL)-derived drug-target binding affinity (BA) inference can be used to rank/select biologically relevant protein targets and their associated genes/SNPs for a drug of interest without knowledge of protein structure or active sites

  reference top surgical snp-mutated inference gene genomic

• Discovery of key regulators in classical monocyte phenotypes linked to COVID-19 severity using single-cell multi-omics sequencing.

  PMID 41732268 · PMC12925236 · iScience · 2026 · 8 claims · 8 setups

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  Two severity-associated classical monocyte (cMono) subtypes, IL7R+ and CD163+, exist with distinct transcriptional and epigenetic landscapes.

  pbmcs pbmc classical cmono single-nucleus differential multimodal

• GAMMI: graph-guided contrastive and adversarial integration of single-cell and spatial multi-omics data.

  PMID 42108634 · PMC13158126 · Briefings in bioinformatics · 2026 · 6 claims · 5 setups

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  GAMMI consistently outperforms state-of-the-art integration methods (GLUE, Harmony, MIDAS, scMoMaT) in biological conservation and batch correction across five mosaic single-cell multi-omics benchmarks

  pbmc postmortem gse138852 gammi-derived multi-omics scrna-seq differential

• Integrated Analysis of Transcriptome and Metabolome Reveals Metabolite Biosynthesis in Pigmented Potatoes.

  PMID 41898740 · PMC13026113 · International journal of molecular sciences · 2026 · 7 claims · 7 setups

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  Pigmented potato cultivars (DG26, DJ247) accumulate higher levels of flavonoids and linoleic acid derivatives than the white-fleshed cultivar (AG594)

  potato bioinformatic untargeted rna-seq rt-qpcr

• Predicting enhancer-gene links from single-cell multi-omics data by integrating prior Hi-C information.

  PMID 42100854 · PMC13229940 · Nucleic acids research · 2026 · 8 claims · 6 setups

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  SCEG-HiC, a weighted graphical lasso (wglasso) method, predicts enhancer-gene links from single-cell multi-omics data by integrating bulk average Hi-C as a prior penalty matrix

  specified covid-19 scatac scatac-seq bulk

• A unified framework for correcting batch effects and integrating multi-omics data.

  PMID 41786846 · PMC13079841 · Scientific reports · 2026 · 7 claims · 6 setups

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  MoDAmix, a four-stage domain adaptation framework (pre-training, single-omics adversarial adaptation, multi-omics adversarial alignment, semi-supervised class alignment), unifies batch correction across multiple omics layers.

  brain aml same single-cell bulk k-means

• MultiPert: An adversarial alignment and dual attention framework for single-cell multi-omics perturbation prediction.

  PMID 41811907 · PMC12998955 · PLoS computational biology · 2026 · 8 claims · 7 setups

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  MultiPert reliably predicts both perturbed gene expression and protein abundance profiles from single-cell multi-omics data

  thp-1 kidney gse156478 computational zinb-vae autoencoder eccite-seq

• Lactate and histone H3K18 lactylation are associated with metabolic control of gene expression in the retina.

  PMID 41950290 · PMC13095125 · PLoS genetics · 2026 · 8 claims · 8 setups

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  Enhanced ATP production during mouse retinal development is achieved primarily through an increase in glycolysis rather than mitochondrial respiration.

  retina histones histone retinal seahorse lactate-glo ldh

• Benchmarking LLM-based agents for single-cell omics analysis.

  PMID 41742311 · PMC13064268 · Genome biology · 2026 · 8 claims · 8 setups

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  Introduces a comprehensive benchmarking evaluation system comprising an open-source agent platform, 18 evaluation metrics across four dimensions, and 50 real-world single-cell omics tasks

  agent single-cell spatial scatac-seq llm-agent scrna-seq spatial

• RNA structure maps across mammalian cellular compartments.

  PMID 30886404 · PMC6640855 · Nature structural & molecular biology · 2019 · 8 claims · 6 setups

  Has reproduction · 45

  icSHAPE can map RNA secondary structure in vivo across three subcellular compartments (chromatin, nucleoplasm, cytoplasm) in both human and mouse cells

  v6.5 naked fractionated icshape rt-qpcr western

• Critical evaluation of drug response prediction models with DrEval.

  PMID 42120410 · PMC13168506 · Nature communications · 2026 · 8 claims · 6 setups

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  DrEval is a living open-source benchmarking pipeline for unbiased, biologically meaningful evaluation of cancer drug response prediction models, integrating standardized preprocessing, hyperparameter tuning, statistically rigorous evaluation, cross-study benchmarks, and ablation studies.

  ctrpv2 ccle beataml2 pdx_bruna viability drug pdx