Normal view
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cs.AI, q-bio.NC updates on arXiv.org
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PPGFlowECG: Latent Rectified Flow with Cross-Modal Encoding for PPG-Guided ECG Generation and Cardiovascular Disease Detection
arXiv:2509.19774v2 Announce Type: replace-cross Abstract: Electrocardiography (ECG) is the clinical gold standard for cardiovascular disease (CVD) assessment, yet continuous monitoring is constrained by the need for dedicated hardware and trained personnel. Photoplethysmography (PPG) is ubiquitous in wearable devices and readily scalable, but it lacks electrophysiological specificity, limiting diagnostic reliability. While generative methods aim to translate PPG into clinically useful ECG signa
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npj Digital Medicine
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A machine learning-derived polygenic risk score reveals that healthy lifestyle counteracts obesity-related mortality
npj Digital Medicine, Published online: 06 January 2026; doi:10.1038/s41746-025-02314-6A machine learning-derived polygenic risk score reveals that healthy lifestyle counteracts obesity-related mortality
A machine learning-derived polygenic risk score reveals that healthy lifestyle counteracts obesity-related mortality
npj Digital Medicine, Published online: 06 January 2026; doi:10.1038/s41746-025-02314-6
A machine learning-derived polygenic risk score reveals that healthy lifestyle counteracts obesity-related mortality-
cs.AI, q-bio.NC updates on arXiv.org
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WisPaper: Your AI Scholar Search Engine
arXiv:2512.06879v1 Announce Type: cross Abstract: Researchers struggle to efficiently locate and manage relevant literature within the exponentially growing body of scientific publications. We present \textsc{WisPaper}, an intelligent academic retrieval and literature management platform that addresses this challenge through three integrated capabilities: (1) \textit{Scholar Search}, featuring both quick keyword-based and deep agentic search modes for efficient paper discovery; (2) \textit{Libr
WisPaper: Your AI Scholar Search Engine
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cs.AI, q-bio.NC updates on arXiv.org
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MirrorMind: Empowering OmniScientist with the Expert Perspectives and Collective Knowledge of Human Scientists
arXiv:2511.16997v1 Announce Type: new Abstract: The emergence of AI Scientists has demonstrated remarkable potential in automating scientific research. However, current approaches largely conceptualize scientific discovery as a solitary optimization or search process, overlooking that knowledge production is inherently a social and historical endeavor. Human scientific insight stems from two distinct yet interconnected sources. First is the individual cognitive trajectory, where a researcher's
MirrorMind: Empowering OmniScientist with the Expert Perspectives and Collective Knowledge of Human Scientists
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cs.AI, q-bio.NC updates on arXiv.org
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Multimodal 3D Genome Pre-training
arXiv:2504.09060v2 Announce Type: replace-cross Abstract: Deep learning techniques have driven significant progress in various analytical tasks within 3D genomics in computational biology. However, a holistic understanding of 3D genomics knowledge remains underexplored. Here, we propose MIX-HIC, the first multimodal foundation model of 3D genome that integrates both 3D genome structure and epigenomic tracks, which obtains unified and comprehensive semantics. For accurate heterogeneous semantic
Multimodal 3D Genome Pre-training
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Omics In Lung
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Circulating Plasma Proteins as Biomarkers for Immunotherapy Toxicity: Insights from Proteome-Wide Mendelian Randomization and Bioinformatics Analysis
Biomedicines. 2025 Jul 14;13(7):1717. doi: 10.3390/biomedicines13071717.ABSTRACTBackground: Immune checkpoint inhibitors (ICIs) have transformed cancer treatment, yet severe immune-related adverse events (irAEs) often necessitate immunotherapy discontinuation and cause life-threatening complications. Circulating plasma proteins, dynamically accessible and functionally linked to immunity, may predict and offer novel targets for irAEs. Methods: Leveraging multi-omics integration, we conducted bidi
Circulating Plasma Proteins as Biomarkers for Immunotherapy Toxicity: Insights from Proteome-Wide Mendelian Randomization and Bioinformatics Analysis
Biomedicines. 2025 Jul 14;13(7):1717. doi: 10.3390/biomedicines13071717.
ABSTRACT
Background: Immune checkpoint inhibitors (ICIs) have transformed cancer treatment, yet severe immune-related adverse events (irAEs) often necessitate immunotherapy discontinuation and cause life-threatening complications. Circulating plasma proteins, dynamically accessible and functionally linked to immunity, may predict and offer novel targets for irAEs. Methods: Leveraging multi-omics integration, we conducted bidirectional two-sample Mendelian randomization (MR) using protein quantitative trait loci (pQTLs) from 4998 plasma proteins and genome-wide association data of irAE phenotypes. A causal inference framework combining colocalization analysis, multivariable MR (MVMR) adjusting for body mass index (BMI) confounding, and mediation MR elucidated BMI-independent pathways. Systems biology approaches including tissue-specific expression profiling, pathway enrichment, and protein interaction network analysis revealed spatial and functional drivers of irAE pathogenesis. Results: Proteome-wide MR mapping identified eight plasma proteins (CCL20, CSF1, CXCL9, CD40, TGFβ1, CLSTN2, TNFSF12, TGFα) causally associated with all-grade irAEs, and five (CCL20, CCL25, CXCL10, ADA, TGFα) with high-grade irAEs. Colocalization prioritized CD40/TNFSF12 (all-grade) and ADA/CCL25 (high-grade) as therapeutic targets (PPH4 > 0.7). CXCL9/TNFSF12 (all-grade) and CCL25 (high-grade) exerted BMI-independent effects, suggesting intrinsic immune dysregulation mechanisms. Tissue-specific gene expression patterns, CSF1, TGFβ1 in lung, TNFSF12 in the ileum may explain organ-specific irAE vulnerabilities. High-grade irAEs correlated with compartmentalized immune dysregulation and IL-17/immunodeficiency pathway activation. Conclusions: This study establishes the causal atlas of plasma proteins in irAE pathogenesis, bridging biomarker discovery with actionable therapeutic targets. These advances align with next-generation immunotherapy goals: maximizing efficacy while taming the immune storm.
PMID:40722787 | PMC:PMC12293052 | DOI:10.3390/biomedicines13071717
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Nature - Issue - nature.com science feeds
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The Somatic Mosaicism across Human Tissues Network
Nature, Published online: 02 July 2025; doi:10.1038/s41586-025-09096-7The Somatic Mosaicism across Human Tissues Network aims to create a reference catalogue of somatic mosaicism across different tissues and cells within individuals.
The Somatic Mosaicism across Human Tissues Network
Nature, Published online: 02 July 2025; doi:10.1038/s41586-025-09096-7
The Somatic Mosaicism across Human Tissues Network aims to create a reference catalogue of somatic mosaicism across different tissues and cells within individuals.-
Cell
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Extrachromosomal DNA replication and maintenance couple with DNA damage pathway in tumors
This study demonstrates that extrachromosomal DNA (ecDNA) replication induces DNA double-strand breaks and activates the DNA damage response (DDR). The DDR pathways, such as alt-NHEJ, are critical for ecDNA maintenance in tumor cells. Mechanistic insights into ecDNA replication and maintenance unveil a therapeutic approach for treating tumors harboring ecDNA.
Extrachromosomal DNA replication and maintenance couple with DNA damage pathway in tumors
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Omics in Hepatocellular
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Integrative multi-omics analysis reveals a novel subtype of hepatocellular carcinoma with biological and clinical relevance
Front Immunol. 2024 Dec 6;15:1517312. doi: 10.3389/fimmu.2024.1517312. eCollection 2024.ABSTRACTBACKGROUND: Hepatocellular carcinoma (HCC) is a highly heterogeneous tumor, and the development of accurate predictive models for prognosis and drug sensitivity remains challenging.METHODS: We integrated laboratory data and public cohorts to conduct a multi-omics analysis of HCC, which included bulk RNA sequencing, proteomic analysis, single-cell RNA sequencing (scRNA-seq), spatial transcriptomics seq
Integrative multi-omics analysis reveals a novel subtype of hepatocellular carcinoma with biological and clinical relevance
Front Immunol. 2024 Dec 6;15:1517312. doi: 10.3389/fimmu.2024.1517312. eCollection 2024.
ABSTRACT
BACKGROUND: Hepatocellular carcinoma (HCC) is a highly heterogeneous tumor, and the development of accurate predictive models for prognosis and drug sensitivity remains challenging.
METHODS: We integrated laboratory data and public cohorts to conduct a multi-omics analysis of HCC, which included bulk RNA sequencing, proteomic analysis, single-cell RNA sequencing (scRNA-seq), spatial transcriptomics sequencing (ST-seq), and genome sequencing. We constructed a tumor purity (TP) and tumor microenvironment (TME) prognostic risk model. Proteomic analysis validated the TP-TME-related signatures. Joint analysis of scRNA-seq and ST-seq revealed characteristic clusters associated with TP high-risk subtypes, and immunohistochemistry confirmed the expression of key genes. We conducted functional enrichment analysis, transcription factor activity inference, cell-cell interaction, drug efficacy analysis, and mutation information analysis to identify a novel subtype of HCC.
RESULTS: Our analyses constructed a robust HCC prognostic risk prediction model. The patients with TP-TME high-risk subtypes predominantly exhibit hypoxia and activation of the Wnt/beta-catenin, Notch, and TGF-beta signaling pathways. Furthermore, we identified a novel subtype, XPO1+Epithelial. This subtype expresses signatures of the TP risk subtype and aligns with the biological behavior of high-risk patients. Additional analyses revealed that XPO1+Epithelial is influenced primarily by fibroblasts via ligand-receptor interactions, such as FN1-(ITGAV+ITGB1), and constitute a significant component of the TP-TME subtype. Moreover, XPO1+Epithelial interact with monocytes/macrophages, T/NK cells, and endothelial cells through ligand-receptor pairs, including MIF-(CD74+CXCR4), MIF-(CD74+CD44), and VEGFA-VEGFR1R2, respectively, thereby promoting the recruitment of immune-suppressive cells and angiogenesis. The ST-seq cohort treated with Tyrosine Kinase Inhibitors (TKIs) and Programmed Cell Death Protein 1 (PD-1) presented elevated levels of TP and TME risk subtype signature genes, as well as XPO1+Epithelial, T-cell, and endothelial cell infiltration in the treatment response group. Drug sensitivity analyses indicated that TP-TME high-risk subtypes, including sorafenib and pembrolizumab, were associated with sensitivity to multiple drugs. Further exploratory analyses revealed that CTLA4, PDCD1, and the cancer antigens MSLN, MUC1, EPCAM, and PROM1 presented significantly increase expression levels in the high-risk subtype group.
CONCLUSIONS: This study constructed a robust prognostic model for HCC and identified novel subgroups at the single-cell level, potentially assisting in the assessment of prognostic risk for HCC patients and facilitating personalized drug therapy.
PMID:39712016 | PMC:PMC11659151 | DOI:10.3389/fimmu.2024.1517312
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Cell
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A multi-tissue metabolome atlas of primate pregnancy
A multi-tissue metabolome atlas of 23 maternal tissues from pregnant monkeys revealed dynamic metabolic coupling, core pathways, and a multitude of pregnancy-adaptive metabolites during normal primate pregnancy, with implications for female health.
A multi-tissue metabolome atlas of primate pregnancy
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Nature Biotechnology - Issue - nature.com science feeds
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Mosaic integration and knowledge transfer of single-cell multimodal data with MIDAS
Nature Biotechnology, Published online: 23 January 2024; doi:10.1038/s41587-023-02040-ySingle-cell, multiomic datasets are integrated using dimensionality reduction, imputation and batch correction.
Mosaic integration and knowledge transfer of single-cell multimodal data with MIDAS
Nature Biotechnology, Published online: 23 January 2024; doi:10.1038/s41587-023-02040-y
Single-cell, multiomic datasets are integrated using dimensionality reduction, imputation and batch correction.-
Nature - Issue - nature.com science feeds
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Scientific discovery in the age of artificial intelligence
Nature, Published online: 02 August 2023; doi:10.1038/s41586-023-06221-2The advances in artificial intelligence over the past decade are examined, with a discussion on how artificial intelligence systems can aid the scientific process and the central issues that remain despite advances.
Scientific discovery in the age of artificial intelligence
Nature, Published online: 02 August 2023; doi:10.1038/s41586-023-06221-2
The advances in artificial intelligence over the past decade are examined, with a discussion on how artificial intelligence systems can aid the scientific process and the central issues that remain despite advances.-
Nature Biotechnology - Issue - nature.com science feeds
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De novo detection of somatic mutations in high-throughput single-cell profiling data sets
Nature Biotechnology, Published online: 06 July 2023; doi:10.1038/s41587-023-01863-zSComatic identifies somatic mutations from scRNA-seq and scATAC data without a matched reference sample.
De novo detection of somatic mutations in high-throughput single-cell profiling data sets
Nature Biotechnology, Published online: 06 July 2023; doi:10.1038/s41587-023-01863-z
SComatic identifies somatic mutations from scRNA-seq and scATAC data without a matched reference sample.