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 1.2k

Assay: enrichment ✕ Clear

Stenotrophomonas maltophilia Bloodstream Infection Outbreak in Acute Care Hospital, California, USA, 2022-2023(1).

PMID 41863496 · PMC13016006 · Emerging infectious diseases · 2026 · 8 claims · 5 setups

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13 S. maltophilia bloodstream infections occurred among ICU patients from May 2022–September 2023, with whole-genome sequencing showing the isolates were highly related (ST239).

hospitalized clinical water hospital matched whole-genome environmental
Integration of a neuronal RNAseq dataset with the draft Gryllus bimaculatus transcriptome refines gene predictions and highlights potential systematic response to injury.

PMID 42054377 · PMC13127959 · PloS one · 2026 · 8 claims · 7 setups

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Integrating prothoracic ganglion RNAseq data with the draft genome refines gene predictions, adding 3,868 novel genes and 9,172 new transcript isoforms (including non-coding transcripts)

bimaculatus prothoracic differentially gbig rna-seq genome differential
Gene Expression Patterns Regulating Peanut Reproductive Phenology.

PMID 42099581 · PMC13147162 · Plant direct · 2026 · 8 claims · 6 setups

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Overall gene expression was distinct between Tifrunner and GT-C20 in both leaf and shoot tip tissues

leaf deseq2 shoot gene bulk differential principal
Transcriptional landscape of repetitive elements in normal and cancer human cells.

PMID 25012247 · PMC4122776 · BMC genomics · 2014 · 8 claims · 8 setups

Has reproduction · 76

RepEnrich, a computational method that uses all mapping reads (uniquely mapping plus multi-mapping reads assigned to repetitive element subfamily assemblies/pseudogenomes), quantifies genome-wide repetitive element enrichment

chromosomes lines imr-90 prostate simulated pol chip-seq
DNA methylation biomarkers-based pan-cancer classifier: predictive modeling for cancer classification.

PMID 42152108 · PMC13185202 · Genome medicine · 2026 · 8 claims · 5 setups

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Relatively simple ML models (logistic regression) outperform complex algorithms such as deep neural networks for methylation-based cancer classification

validation cns healthy genes methylation copy-number gene-set
Characterizing Response to PARP Inhibitor Treatment Combinations in Advanced Prostate Cancer.

PMID 42193276 · PMC13203762 · Biomedicines · 2026 · 8 claims · 8 setups

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PARPi + ARPi combinations are effective in ARPi-sensitive (C4-2B) and ARPi-resistant (AbiR, MDVR) prostate cancer models, but provide the greatest benefit in ARPi-sensitive cells

c4-2b cck-8 morphology western
Hybrid sequencing reveals incompleteness of the H37Rv reference genome and highlights lineage-specific genomic divergence in Mycobacterium tuberculosis.

PMID 42224013 · PMC13225438 · Microbial genomics · 2026 · 8 claims · 6 setups

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The H37Rv_ref reference genome, sequenced in 1998 with early technology, is incomplete relative to modern hybrid-sequenced assemblies

tuberculosis h37rv_cn a2018772 publicly hybrid comparative functional
Mouse placentae generated by in vitro fertilization exhibit altered gene expression, activated hypoxia responses, and reduced fitness†.

PMID 40874534 · PMC12808545 · Biology of reproduction · 2026 · 6 claims · 6 setups

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IVF-conceived mouse placentae exhibit global and cell type–specific gene expression differences compared to FB placentae

e12.5 differentially trophoblast placenta single-nucleus pseudobulk pathway
B-lineage commitment is dependent on a reversible epigenetic switch.

PMID 41266087 · PMC12863259 · Genes & development · 2026 · 8 claims · 8 setups

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B-lymphoid commitment is mediated by a transcription factor-dose-dependent epigenetic switch that suppresses inherent T-lineage potential in early lymphoid progenitors

bone expanded pax5 ebf1 combined atac-seq chip-seq
Single-Cell Lineage Tracing Uncovers Resistance Signatures and Sensitizing Strategies to FLT3 Inhibitors in Acute Myeloid Leukemia.

PMID 41270153 · PMC7618455 · Cancer research · 2026 · 8 claims · 8 setups

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ReSisTrace single-cell lineage tracing identifies pre-resistant and pre-sensitive cell states to FLT3 inhibitors midostaurin and quizartinib in FLT3-ITD-positive MOLM-13 AML cells before treatment

molm-13 aml-pdx1 single-cell lineage gene
Longitudinal Profiling of Tumor and Immune Compartments Uncovers Patterns of Dysregulation and Associations with Response in Multiple Myeloma.

PMID 41364805 · PMC13012255 · Blood cancer discovery · 2026 · 7 claims · 8 setups

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IFN-γ signaling after autologous stem cell transplant (ASCT) is associated with markers of impaired CD8+ T-cell memory phenotype

cd138neg cd138pos bone cd8+ single-cell bulk whole-genome
Berberine suppresses colon inflammation via integrated modulation of host metabolism, microbial ecology, and innate immune signaling.

PMID 41356191 · PMC12680593 · Theranostics · 2026 · 6 claims · 8 setups

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Berberine enhances energy metabolism (oxidative phosphorylation, ATP biosynthesis, fatty acid metabolism) in intestinal epithelial cells of DSS-induced mice, preserving normal physiological function

colon feces serum dss-induced single-cell targeted 16s
Comparative Transcriptomic Profiling Identifies IL-1β as a Non-Canonical Driver of Human Dendritic Cell Maturation.

PMID 41472934 · PMC12745711 · Iranian journal of biotechnology · 2026 · 8 claims · 7 setups

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IL-1β can substitute for PAMPs in inducing DC maturation via a non-canonical pathway distinct from classical TLR-mediated activation

monocyte-derived dendritic bulk principal pathway
Mechanical compression induces neuronal apoptosis, reduces synaptic activity, and promotes glial neuroinflammation in mice and humans.

PMID 41481451 · PMC12773780 · Proceedings of the National Academy of Sciences of the United States of America · 2026 · 8 claims · 8 setups

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Chronic mechanical compression (0.14 kPa) directly induces neuronal apoptosis in human iPSC-derived neurons cocultured with murine glia

ipsc-derived gfp-expressing mglia astrocytes hoechst gfp+ immunofluorescence
Alternative splicing dynamics during human cardiac development in vivo and in vitro.

PMID 41483812 · PMC12925949 · Stem cell reports · 2026 · 8 claims · 8 setups

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iPSC-CMs globally resemble prenatal cardiac cells at both the transcriptional and splicing levels

ipsc-cms heart bulk ipsc-cm immunofluorescence single-cell bulk
Advancing Prognosis Prediction and Immunotherapy Efficacy in Lung Adenocarcinoma Through Machine Learning: Novel Insights From Anoikis Regulator Patterns in Single-Cell Multiomics.

PMID 41488744 · PMC12764181 · International journal of genomics · 2026 · 8 claims · 8 setups

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Epithelial and endothelial cells show the highest anoikis-enriched scores among LUAD TME cell types, with AT2-like Epi being the most anoikis-related epithelial subpopulation.

luad pan-cancer tumor scrna-seq spatial bulk
Deep-learning prediction of gene expression from personal genomes.

PMID 41495833 · PMC12869966 · Genome biology · 2026 · 8 claims · 8 setups

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Fine-tuning Enformer on paired personal WGS and RNA-seq data (Variformer) corrects Enformer's failure to predict inter-individual gene expression differences across held-out people.

gtex rosmap same monocyte paired mutagenesis chromhmm
Unraveling the Causal Linkages of RBP7 and SCGB3A1 on Pelvic Organ Prolapse: Multifaceted Insights From Genome-Wide Mendelian Randomization, Single-Cell RNA Analysis, and Network Pharmacology.

PMID 41497737 · PMC12765987 · BioMed research international · 2026 · 8 claims · 7 setups

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High RBP7 expression causally increases POP risk

vaginal gwas rbp7 key single-cell mendelian protein-protein
A machine learning-defined cellular senescence signature systematically enhances prognostication and guides immunotherapy strategies for the treatment of gliomas.

PMID 41501133 · PMC12886967 · NPJ precision oncology · 2026 · 8 claims · 8 setups

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CSRGPS is a robust, machine-learning-derived prognostic signature that outperforms existing glioma prognostic models across multiple cohorts

tcga-gbm glioma meta consensus wgcna machine
TEAD4 and RXRA Regulate the Function of Nucleus Pulposus Cells in Intervertebral Disc Degeneration Via the TNF-α/NF-κB Pathway: An Integrated Analysis of Single-Cell RNA-Seq, Bulk RNA-Seq, and In Vitro Validation.

PMID 41511606 · PMC12995935 · Applied biochemistry and biotechnology · 2026 · 8 claims · 8 setups

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TEAD4 and RXRA play critical roles in IDD progression, likely regulating NP cell behavior and ECM metabolism via the TNF-α/NF-κB pathway

differential il-1β-induced scrna-seq bulk gsea

Experiments

Stenotrophomonas maltophilia Bloodstream Infection Outbreak in Acute Care Hospital, California, USA, 2022-2023(1).

Integration of a neuronal RNAseq dataset with the draft Gryllus bimaculatus transcriptome refines gene predictions and highlights potential systematic response to injury.

Gene Expression Patterns Regulating Peanut Reproductive Phenology.

Transcriptional landscape of repetitive elements in normal and cancer human cells.

DNA methylation biomarkers-based pan-cancer classifier: predictive modeling for cancer classification.

Characterizing Response to PARP Inhibitor Treatment Combinations in Advanced Prostate Cancer.

Hybrid sequencing reveals incompleteness of the H37Rv reference genome and highlights lineage-specific genomic divergence in Mycobacterium tuberculosis.

Mouse placentae generated by in vitro fertilization exhibit altered gene expression, activated hypoxia responses, and reduced fitness†.

B-lineage commitment is dependent on a reversible epigenetic switch.

Single-Cell Lineage Tracing Uncovers Resistance Signatures and Sensitizing Strategies to FLT3 Inhibitors in Acute Myeloid Leukemia.

Longitudinal Profiling of Tumor and Immune Compartments Uncovers Patterns of Dysregulation and Associations with Response in Multiple Myeloma.

Berberine suppresses colon inflammation via integrated modulation of host metabolism, microbial ecology, and innate immune signaling.

Comparative Transcriptomic Profiling Identifies IL-1β as a Non-Canonical Driver of Human Dendritic Cell Maturation.

Mechanical compression induces neuronal apoptosis, reduces synaptic activity, and promotes glial neuroinflammation in mice and humans.

Alternative splicing dynamics during human cardiac development in vivo and in vitro.

Advancing Prognosis Prediction and Immunotherapy Efficacy in Lung Adenocarcinoma Through Machine Learning: Novel Insights From Anoikis Regulator Patterns in Single-Cell Multiomics.

Deep-learning prediction of gene expression from personal genomes.

Unraveling the Causal Linkages of RBP7 and SCGB3A1 on Pelvic Organ Prolapse: Multifaceted Insights From Genome-Wide Mendelian Randomization, Single-Cell RNA Analysis, and Network Pharmacology.

A machine learning-defined cellular senescence signature systematically enhances prognostication and guides immunotherapy strategies for the treatment of gliomas.

TEAD4 and RXRA Regulate the Function of Nucleus Pulposus Cells in Intervertebral Disc Degeneration Via the TNF-α/NF-κB Pathway: An Integrated Analysis of Single-Cell RNA-Seq, Bulk RNA-Seq, and In Vitro Validation.