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 115

Assay: stress ✕ Clear

The role of proteomics in depression research.

PMID 19997739 · PMC2940035 · European archives of psychiatry and clinical neuroscience · 2010 · 8 claims · 8 setups

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Proteomics offers a complementary, functional-endpoint approach that can elucidate MDD pathophysiological mechanisms and biomarkers beyond transcriptomic/targeted studies

postmortem schizophrenia frontal hypothalamus gel shotgun proteome
Protein kinase A-dependent biophysical phenotype for V227F-KCNJ2 mutation in catecholaminergic polymorphic ventricular tachycardia.

PMID 19843922 · PMC2766080 · Circulation. Arrhythmia and electrophysiology · 2009 · 7 claims · 7 setups

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Homomeric Kir2.1-V227F channels have significantly reduced I K1 (inward reduced ~40%; outward reduced 85-99% at -40 to -60mV) compared to WT

cos-1 kir2.1 32-year-old whole-cell site-directed clinical
Neuroplasticity, psychosocial genomics, and the biopsychosocial paradigm in the 21st century.

PMID 19728478 · PMC2933650 · Health & social work · 2009 · 8 claims · 8 setups

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Recent neuroplasticity and psychosocial genomics research validates and elaborates Engel's biopsychosocial paradigm by revealing mechanisms linking psychosocial experience to neurobiology.

experienced long-term ocd women structural eeg attentional
Negative emotionality: monoamine oxidase B gene variants modulate personality traits in healthy humans.

PMID 19657584 · PMC3653168 · Journal of neural transmission (Vienna, Austria : 1996) · 2009 · 7 claims · 7 setups

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MAOB SNPs rs10521432 and rs6651806 are significantly associated with Negative Emotionality in healthy volunteers

healthy genotype maoa snp multidimensional profile
Elevated phenylacetylglutamine caused by gut dysbiosis associated with type 2 diabetes increases neutrophil extracellular traps formation and exacerbates brain infarction.

PMID 40471587 · PMC12599254 · Clinical science (London, England : 1979) · 2025 · 7 claims · 8 setups

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Plasma PAGln levels are significantly higher in ischemic stroke patients with T2D than in those without T2D

fecal plasma sprague-dawley cerebral 16s metagenome targeted
Deleterious Effects of SARS-CoV-2 Infection on Human Pancreatic Cells.

PMID 34282405 · PMC8285288 · Frontiers in cellular and infection microbiology · 2021 · 8 claims · 7 setups

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iPSC-derived pancreatic endocrine and exocrine (acinar/ductal) cultures express ACE2 and TMPRSS2, enabling SARS-CoV-2 entry

ipsc-derived post-mortem vero-e6 immunofluorescence sars-cov-2 rt-qpcr
Automated mapping of DNA replication fork progression in human cells with ForkML.

PMID 41577668 · PMC12932727 · Nature communications · 2026 · 8 claims · 8 setups

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ForkML uses double BrdU pulse-labelling and nanopore sequencing with a machine-learning fork detection/orientation pipeline to automatically map thousands of individual replication fork velocities.

hct116 hela bj-htert cerevisiae nanopore gloe-seq mass
Gut microbiome signatures associated with depression and obesity.

PMID 41615149 · PMC13011431 · mSystems · 2026 · 8 claims · 4 setups

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Taxonomic gut microbiome profiles classify depressed vs non-depressed subjects with a balanced accuracy of 0.90 using machine learning

stool subjects shotgun alpha machine
CTCF/cohesin-binding sites are susceptible to replication-associated DNA damage and genomic instability in cancer cells.

PMID 41630911 · PMC12860730 · iScience · 2026 · 8 claims · 8 setups

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CTCF and cohesin (RAD21) remain co-bound to DNA throughout interphase, including during the S (replication) phase, in HeLa cells

hela tumors flow chromatin frap
Nanopore long-read-only genome assembly of clinical Enterobacterales isolates is complete and accurate.

PMID 41758556 · PMC12948150 · Microbial genomics · 2026 · 8 claims · 8 setups

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Autocycler (consensus long-read-only assembler) circularised the most chromosomes, 95% (87/92), significantly more than Unicycler, Unicycler bold, Flye and Hybracter (hybrid)

clinical enterobacterales assembled assembler-polisher nanopore illumina comparative
Vitamin C Conditioning Generates Tumor-Targeting CAR T Cells with Superior Cytotoxicity and Fitness in a Posttransplant Lymphoproliferative Disorder Tumor Model.

PMID 41416402 · PMC13136873 · Molecular cancer therapeutics · 2026 · 8 claims · 8 setups

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VitC conditioning enhances transduction efficiency and proliferative capacity, yielding a higher yield of CD4+ and CD8+ CAR19-Ts

cd3+ je6-1 car19-ts coculture flow nf-κb cytotoxicity
Chromosome-scale genome assembly for yellow wood sorrel, Oxalis stricta.

PMID 41482730 · PMC12958822 · G3 (Bethesda, Md.) · 2026 · 8 claims · 8 setups

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O. stricta genome assembly is chromosome-scale, 436 Mb, spanning 12 chromosomes across 2 subgenomes

stricta long-read short-read hi-c
Ex Vivo Immuno-Oncology Platform Reveals Spatial T-cell Infiltration Patterns Linked to ATR Inhibition Responses in High-Grade Serous Ovarian Cancer.

PMID 41563843 · PMC7618831 · Cancer immunology research · 2026 · 8 claims · 8 setups

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iPDCs cultured on human omentum gel (OmGel) recapitulate tumor genomic and histologic characteristics while retaining intratumoral immune cells

formalin-fixed blood dissociated ipdcs histopathology whole-exome flow
Large-scale multi-omics unveils host-microbiome interactions driving root development and nitrogen acquisition.

PMID 41634153 · PMC12929062 · Nature plants · 2026 · 8 claims · 8 setups

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Multi-omics integration of root transcriptome, rhizosphere 16S microbiome and root/shoot ionome across 175 B. napus accessions at two field sites links host gene expression to microbiome assembly and nutrient traits

lateral rhizosphere shoot napus sequencing 16s ionomic
Genome-wide discovery and phenotyping of non-coding transcripts in A. fumigatus reveals lncRNAs with a role in antifungal drug sensitivity.

PMID 41673015 · PMC12921299 · Nature communications · 2026 · 7 claims · 8 setups

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Genome-wide pipeline generated a manually curated database of 1089 novel lncRNAs from 2388 candidate loci in A. fumigatus

fumigatus distinct non-fumigatus niger rna-seq comparative qrt-pcr
SiCmiR Atlas: Single-Cell miRNA Landscape Reveals Hub-miRNA and Network Signatures in Human Cancers.

PMID 41691474 · PMC13042402 · Advanced science (Weinheim, Baden-Wurttemberg, Germany) · 2026 · 8 claims · 8 setups

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SiCmiR, a two-layer neural network, predicts mature miRNA expression profiles from only 977 LINCS L1000 landmark genes

tcga k562 pancreatic acth-secreting paired bulk scrna-seq-based
Bacterial reporter-paired scRNA sequencing reveals cross talk between zinc starvation and zinc toxicity in macrophage antibacterial defense.

PMID 41802048 · PMC12993976 · Proceedings of the National Academy of Sciences of the United States of America · 2026 · 8 claims · 8 setups

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Macrophages starve intracellular E. coli of zinc to sensitize them to subsequent zinc toxicity, coupling zinc starvation and zinc toxicity in a single antimicrobial response

monocyte-derived hmdm zntr-dual macrophages confocal high-throughput flow
T cell-intrinsic VISTA expression promotes resistance to CTLA-4 blockade by restricting CD8+ T cell responses.

PMID 41837284 · PMC12987620 · The Journal of clinical investigation · 2026 · 8 claims · 8 setups

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Loss of T cell-intrinsic VISTA enhances early priming and short-term expansion of CD8+ T cells but this initial advantage fails to confer durable tumor control

tumor vsir cell-specific myeloid-specific flow adoptive peptide
Systematic background selection with BasCoD enhances contrastive dimension reduction in single cell genomics.

PMID 41844632 · PMC13144610 · Nature communications · 2026 · 8 claims · 7 setups

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BasCoD is a statistical testing framework using spectral subspace inclusion theory to evaluate whether a candidate background dataset is suitable for contrastive dimension reduction of a target dataset

ts65dn ipscs k562 intestinal contrastive population-scale perturb-seq
Single-Cell RNA Analysis of Murine Osteosarcoma Uncovers Skp2 Function in Metastasis, Genomic Instability, and Immune Activation and Reveals Additional Target Pathways.

PMID 41877584 · PMC13103941 · Cancer research communications · 2026 · 8 claims · 6 setups

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Skp2 KO improves survival, drives apoptosis, and induces antitumor immunity in Rb1/Trp53-deficient murine osteosarcoma

tumors same osteosarcoma skp2 scrna-seq mutation copy-number

Experiments

The role of proteomics in depression research.

Protein kinase A-dependent biophysical phenotype for V227F-KCNJ2 mutation in catecholaminergic polymorphic ventricular tachycardia.

Neuroplasticity, psychosocial genomics, and the biopsychosocial paradigm in the 21st century.

Negative emotionality: monoamine oxidase B gene variants modulate personality traits in healthy humans.

Elevated phenylacetylglutamine caused by gut dysbiosis associated with type 2 diabetes increases neutrophil extracellular traps formation and exacerbates brain infarction.

Deleterious Effects of SARS-CoV-2 Infection on Human Pancreatic Cells.

Automated mapping of DNA replication fork progression in human cells with ForkML.

Gut microbiome signatures associated with depression and obesity.

CTCF/cohesin-binding sites are susceptible to replication-associated DNA damage and genomic instability in cancer cells.

Nanopore long-read-only genome assembly of clinical Enterobacterales isolates is complete and accurate.

Vitamin C Conditioning Generates Tumor-Targeting CAR T Cells with Superior Cytotoxicity and Fitness in a Posttransplant Lymphoproliferative Disorder Tumor Model.

Chromosome-scale genome assembly for yellow wood sorrel, Oxalis stricta.

Ex Vivo Immuno-Oncology Platform Reveals Spatial T-cell Infiltration Patterns Linked to ATR Inhibition Responses in High-Grade Serous Ovarian Cancer.

Large-scale multi-omics unveils host-microbiome interactions driving root development and nitrogen acquisition.

Genome-wide discovery and phenotyping of non-coding transcripts in A. fumigatus reveals lncRNAs with a role in antifungal drug sensitivity.

SiCmiR Atlas: Single-Cell miRNA Landscape Reveals Hub-miRNA and Network Signatures in Human Cancers.

Bacterial reporter-paired scRNA sequencing reveals cross talk between zinc starvation and zinc toxicity in macrophage antibacterial defense.

T cell-intrinsic VISTA expression promotes resistance to CTLA-4 blockade by restricting CD8+ T cell responses.

Systematic background selection with BasCoD enhances contrastive dimension reduction in single cell genomics.

Single-Cell RNA Analysis of Murine Osteosarcoma Uncovers Skp2 Function in Metastasis, Genomic Instability, and Immune Activation and Reveals Additional Target Pathways.