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).

Publications 1.3k Datasets 392.5k Experiments 23

System / cell line: model ✕ Assay: transfer ✕ Clear

scMILD: Single-cell multiple instance learning for sample classification and associated subpopulation discovery.

PMID 41907409 · PMC13019583 · iScience · 2026 · 8 claims · 8 setups

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scMILD identifies condition-associated cells using only sample-level labels via a dual-branch MIL architecture with a shared encoder

simulated lupus covid-19 ulcerative simulated mixture scrna-seq
PAH-former: Transfer learning for efficient discovery of pulmonary arterial hypertension-associated genes.

PMID 41790620 · PMC12965534 · PloS one · 2026 · 7 claims · 7 setups

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PAH-former, a Geneformer model fine-tuned on public PAH scRNA-seq data, can perform in silico perturbation to identify and rank candidate PAH disease-associated genes

pah scrna-seq pah-former candidate scrna-seq transfer perturbation
Artificial Intelligence Approach in Machine Learning-Based Modeling and Networking of the Coronavirus Pathogenesis Pathway.

PMID 40699865 · PMC12191508 · Current issues in molecular biology · 2025 · 8 claims · 8 setups

Has reproduction

The coronavirus pathogenesis pathway is activated in SARS-CoV-2-infected iPSC-derived cardiac cells and in SARS-CoV/SARS-CoV-2-infected LUAD cells

ace2-transfected calu-3 luad ipsc-derived ipa sequencing convolutional
scXDR: drug response prediction across single-cell datasets via heterogeneous network transfer learning.

PMID 41507436 · PMC12859067 · Communications biology · 2026 · 7 claims · 7 setups

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scXDR outperforms seven methods that transfer drug response information from bulk RNA-seq to single-cell data, across all four evaluated scenarios

single-cell scrna-seq scxdr gse117872 heterogeneous benchmarking type
CellPolaris: Transfer Learning for Gene Regulatory Network Construction to Guide Cell State Transitions.

PMID 41498638 · PMC12948241 · Advanced science (Weinheim, Baden-Wurttemberg, Germany) · 2026 · 8 claims · 8 setups

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CellPolaris is a unified computational framework performing TF-centered GRN construction, master TF identification, and TF perturbation simulation

bulk previously round paired transfer-learning cross-species
CD69 regulates the tissue dynamics of epigenetically imprinted memory CD4(+) T cells.

PMID 41950321 · PMC13060599 · Science advances · 2026 · 8 claims · 8 setups

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CD69 is essential for tissue retention of CD4+ TRM cells in inflamed lungs, in both allergic (HDM/OVA) and infectious (BCG) models

ova-specific lung thy1.1+ peripheral adoptive flow parabiosis
The transcription factor EHF promotes the maturation and immunosuppression of conventional dendritic cells.

PMID 41730908 · PMC13039115 · Nature communications · 2026 · 8 claims · 8 setups

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EHF orchestrates an immunosuppressive maturation program in cDC1s and cDC2s downstream of TLR7/8/9 sensing of self-nucleic acids

ehf facs-sorted dss-induced lethal cd4+
CLAMP: predicting specific protein-mediated chromatin loops in diverse species with a chromatin accessibility language model.

PMID 41555433 · PMC12903630 · Genome biology · 2026 · 8 claims · 8 setups

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CLAMP, a chromatin-accessibility language model, predicts protein-mediated chromatin loops across 10 species, 18 proteins, and 24 cell types with superior performance versus existing methods.

species gm12878 types chromatin cross-protein cross-cell-type
Proceedings of the First International Conference on Phylogenomics. March 15-19, 2006. Quebec, Canada.

PMID 17288567 · PMC1796603 · BMC evolutionary biology · 2007 · 8 claims · 8 setups

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Gene tree parsimony applied to EST data with widespread gene duplication can infer an organismal phylogeny in excellent agreement with the expected angiosperm phylogeny.

angiosperms animal oryza proteobacteria gene site-heterogeneous codon
mitoXplorer, a visual data mining platform to systematically analyze and visualize mitochondrial expression dynamics and mutations.

PMID 31799603 · PMC6954439 · Nucleic acids research · 2020 · 5 claims · 5 setups

Has reproduction · 89

mitoXplorer integrates transcriptome, proteome, and mutation data with a manually curated mitochondrial interactome of ~1200 genes grouped into 38 mitochondrial processes across four model species.

rpe-1 trisomic rpe yeast bulk proteomics mitotracker
Intrinsic suppression of type I interferon production underlies the therapeutic efficacy of IL-15-producing natural killer cells in B-cell acute lymphoblastic leukemia.

PMID 37217248 · PMC10231005 · Journal for immunotherapy of cancer · 2023 · 8 claims · 8 setups

Has reproduction · 76

High expression of IFN-I signaling/response genes (IFNAR1, IFNAR2, STAT1, MX1, OAS1) predicts favorable relapse-free survival in B-ALL patients

cog b-all eμ-myc crispra gene-expression-based flow mass
Protein ranking by semi-supervised network propagation.

PMID 16723003 · PMC1810311 · BMC bioinformatics · 2006 · 8 claims · 5 setups

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RankProp, a diffusion-based network propagation algorithm on a PSI-BLAST-derived protein similarity network, significantly outperforms local search methods (BLAST/PSI-BLAST) at detecting remote homologs.

scop similarity same psi-blast rankprop probabilistic
The ubiquitin ligase KLHL6 drives resistance to CD8(+) T cell dysfunction.

PMID 41535474 · PMC12979199 · Nature · 2026 · 8 claims · 8 setups

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KLHL6 is a dual-negative regulator of both T cell exhaustion and mitochondrial dysfunction

cd8+ cas9+ sgklhl6-transduced klhl6 bulk pooled flow
TOPK Suppresses the CD8(+) T Cell Antitumor Immunity via Modulation of IRF5 Expression.

PMID 41868885 · PMC13003159 · Cancer communications (London, England) · 2026 · 8 claims · 8 setups

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A TOPK+ subset of tumor-infiltrating CD8+ T cells exists in melanoma at higher frequency than in normal lymph nodes and shows suppressed cytotoxic/cytokine programs.

tumor-infiltrating melanoma b16-f10 unspecified scrna-seq flow multiplex
Loss of CD4(+) T cell-intrinsic arginase 1 accelerates Th1 response kinetics and reduces lung pathology during influenza infection.

PMID 37572656 · PMC10576612 · Immunity · 2023 · 8 claims · 8 setups

Has reproduction · 68

Arg1 is highly and specifically induced in lung CD4+ T cells during in vivo influenza infection

flow-sort-purified lung cd4+ congenically rna-seq flow expression
Widespread nitrous oxide undersaturation in farm waterbodies creates an unexpected greenhouse gas sink.

PMID 31036633 · PMC6525509 · Proceedings of the National Academy of Sciences of the United States of America · 2019 · 8 claims · 7 setups

Has reproduction · 87

The majority (67%) of small agricultural reservoirs surveyed were undersaturated in N2O and thus acted as atmospheric N2O sinks despite being highly eutrophic and N-rich

small same reservoir dissolved water physical
Metabolic syndrome: from epidemiology to systems biology.

PMID 18852695 · PMC2829312 · Nature reviews. Genetics · 2008 · 8 claims · 8 setups

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MetSyn component traits (obesity, insulin resistance, dyslipidaemia, hypertension) exhibit causal interactions and common etiologies rather than being independent conditions

populations rats adipose four genome-wide linkage gene
Babelomics: advanced functional profiling of transcriptomics, proteomics and genomics experiments.

PMID 18515841 · PMC2447758 · Nucleic acids research · 2008 · 8 claims · 5 setups

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Babelomics is a web suite offering both conventional functional enrichment methods and more advanced gene set analysis (GSA) methods, a combination offered by only one other tool (FuncAssociate) among competitors.

user-supplied ranked gene fasta-formatted functional gene novo
Annexin A13 Protects Against Acute Kidney Injury by Inactivating TGF-β/Smad3 Signaling.

PMID 41486854 · PMC12915081 · Advanced science (Weinheim, Baden-Wurttemberg, Germany) · 2026 · 8 claims · 8 setups

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ANXA13 is selectively downregulated in the kidneys of AKI patients and IRI- or cisplatin-induced AKI mice, primarily in proximal tubular cells

kidney aki renal hek293t rna-seq immunohistochemistry serum
CCL3+ Neutrophil Signature Predicts Response to Neoadjuvant Toripalimab plus Chemotherapy in Patients with Hypopharyngeal Squamous Cell Carcinoma: A Phase II Trial.

PMID 41817286 · PMC13223550 · Clinical cancer research : an official journal of the American Association for Cancer Research · 2026 · 7 claims · 8 setups

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A proinflammatory, CCL3-high neutrophil subset (Neu_CCL3) is significantly enriched in the pretreatment tumor microenvironment of patients who respond to nCIT.

pretreatment microarray cohorts moc1 single-cell bulk immunohistochemistry

Experiments

scMILD: Single-cell multiple instance learning for sample classification and associated subpopulation discovery.

PAH-former: Transfer learning for efficient discovery of pulmonary arterial hypertension-associated genes.

Artificial Intelligence Approach in Machine Learning-Based Modeling and Networking of the Coronavirus Pathogenesis Pathway.

scXDR: drug response prediction across single-cell datasets via heterogeneous network transfer learning.

CellPolaris: Transfer Learning for Gene Regulatory Network Construction to Guide Cell State Transitions.

CD69 regulates the tissue dynamics of epigenetically imprinted memory CD4(+) T cells.

The transcription factor EHF promotes the maturation and immunosuppression of conventional dendritic cells.

CLAMP: predicting specific protein-mediated chromatin loops in diverse species with a chromatin accessibility language model.

Proceedings of the First International Conference on Phylogenomics. March 15-19, 2006. Quebec, Canada.

mitoXplorer, a visual data mining platform to systematically analyze and visualize mitochondrial expression dynamics and mutations.

Intrinsic suppression of type I interferon production underlies the therapeutic efficacy of IL-15-producing natural killer cells in B-cell acute lymphoblastic leukemia.

Protein ranking by semi-supervised network propagation.

The ubiquitin ligase KLHL6 drives resistance to CD8(+) T cell dysfunction.

TOPK Suppresses the CD8(+) T Cell Antitumor Immunity via Modulation of IRF5 Expression.

Loss of CD4(+) T cell-intrinsic arginase 1 accelerates Th1 response kinetics and reduces lung pathology during influenza infection.

Widespread nitrous oxide undersaturation in farm waterbodies creates an unexpected greenhouse gas sink.

Metabolic syndrome: from epidemiology to systems biology.

Babelomics: advanced functional profiling of transcriptomics, proteomics and genomics experiments.

Annexin A13 Protects Against Acute Kidney Injury by Inactivating TGF-β/Smad3 Signaling.

CCL3+ Neutrophil Signature Predicts Response to Neoadjuvant Toripalimab plus Chemotherapy in Patients with Hypopharyngeal Squamous Cell Carcinoma: A Phase II Trial.