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npj Systems Biology and Applications
Scopus
ISSN 2056-7189 · Nature Portfolio · 623 artikel di indeks
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Artikel Jurnal
Delaying cancer progression by integrating toxicity constraints in a model of adaptive therapy
Abstract Cancer therapies often fail when intolerable toxicity or drug-resistant cancer cells undermine otherwise effective treatment strategies. Over the past decade, adaptive therapy has emerged as a promising approach to postpone emergence of resistance by altering dose timing based on tumor…
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Dynamical network analysis reveals long-range residue couplings at the pMHC interface underlying enhanced immunogenicity
Abstract The interaction between a class I peptide-major histocompatibility complex (pMHC) and a T cell receptor (TCR) plays a central role in the elicitation of CD8+ T cell immune responses. As a result, considerable effort has been invested in understanding the structural, dynamic, and…
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Quantifying and comparing causal patterns in stochastic chemical reaction networks
Abstract Chemical reaction networks (CRNs) are broadly used to study biological systems via simulations. Gillespie’s Stochastic Simulation Algorithm (SSA) is commonly used to perform stochastic simulations with CRNs. Comparing two CRNs in such a setting relies on ad hoc signals obtained from the…
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Spatial FBA reveals heterogeneous Warburg niches in renal tumors and lactate consumption in colorectal cancer
Abstract To investigate how spatial constraints shape cancer metabolism, we devised the spatial Flux Balance Analysis (spFBA) framework for the enrichment of spatial transcriptomics data with relative estimates of metabolic fluxes. Applying spFBA to newly generated high-resolution datasets of…
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Computational approaches in chemical space exploration for carbon fixation pathways
Abstract Chemical space exploration is an important part of chemistry and biology, enabling the discovery and optimization of metabolic pathways, advancing synthetic metabolic functions, and understanding biochemical network evolution. We use a graph-based computational approach implemented in the…
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Mathematical modeling of combinatorial antigen targeting with multiple CAR T-cell products for glioblastoma treatment
Abstract Glioblastoma is a highly aggressive and difficult-to-treat brain cancer that resists conventional therapies. Recent advances in chimeric antigen receptor (CAR) T-cell therapy have shown promising potential for treating glioblastoma; however, achieving optimal efficacy remains challenging…
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Artikel Jurnal
Gene regulatory network transitions reveal the central transcription factors in lung adenocarcinoma progression
Abstract Transcription factors play a central role in cancer growth, progression, and metastasis, and contribute to intratumor phenotypic plasticity that enable drug tolerance and cancer relapse. Changes in the regulatory activities of transcription factors in cancer may not always be detected from…
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Simulation-based inference of cell migration dynamics in complex spatial environments
Abstract To assess cell migration in complex spatial environments, microfabricated chips, such as mazes and pillar forests, are routinely used to impose spatial and mechanical constraints, and cell trajectories are followed within these structures by advanced imaging techniques. In systems…
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Artikel Jurnal
Machine learning prediction for AML based on 3D genome selected circRNA
Abstract Acute myeloid leukemia (AML) is a clinically aggressive hematologic malignancy driven by complex genetic and epigenetic aberrations. Circular RNAs (circRNAs), characterized by covalently closed structures and exceptional stability, have emerged as promising diagnostic biomarkers. However…
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Modeling the microRNA regulation of TGF-β/SMAD signaling pathways for seizure control in temporal lobe epilepsy
Abstract Temporal lobe epilepsy (TLE) is the most prevalent type of focal epilepsy. Recent developments in sequencing, proteomics and network analysis tools provide new avenues for investigating potential molecular therapeutic targets. Both the TGF-β/SMAD signaling pathways and subsets of microRNAs…
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Cross-platform metabolomics imputation using importance-weighted autoencoders
Abstract Metabolomics data are often generated through different platforms and quantification methods which makes their synthesis and large-scale replication challenging. This study developed an ensemble of importance-weighted autoencoders to perform cross-platform metabolomics imputation between…
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Artikel Jurnal
Asthma-mediated control of optic glioma growth via T cell-microglia interactions: A mathematical model
Abstract Optic glioma, a slow-growing tumor, is associated with Neurofibromatosis type 1 (NF1) mutations and increased midkine (MDK) production. A connection between asthma and optic glioma has previously been observed, but the mechanisms are unclear. To elucidate the role of asthma in the…
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Mechanisms of rectified gap junctional coupling enhancing pacemaking activity of biologically engineered pacemaker cells
Abstract Bio-pacemakers offer a potential alternative to electronic devices, yet their stable implementation at cellular and tissue levels remains unresolved. In this computational study, we aimed to investigate possible effects of the electrotonic interaction between cardiac cells and the spatial…
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The future of mathematical oncology in the age of AI
Abstract This perspective article discusses emerging advances at the interface of mechanistic modeling and data-driven machine learning, highlighting opportunities for AI to accelerate discovery, improve predictive modeling, and enhance clinical decision-making. We address critical limitations of…
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Data driven network inference and longitudinal transcriptomics unveil dynamic regulation in Chronic Lymphocytic Leukaemia models
Abstract How do cancer cells respond to their environment, and what are the key regulators behind their behaviour? While immune cell reprogramming in the tumour microenvironment (TME) has been extensively studied, the dynamic regulatory changes within cancer cells in response to interactions with…
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Artikel Jurnal
Optimal control theory as a method for designing multidrug adaptive therapy regimens
Abstract Evolutionarily informed regimens offer new approaches that hope to combat the development of resistance during cancer treatment. These regimens are often complicated to design. In this work, we use optimal control theory (OCT) to guide the design of a two-drug adaptive therapy regimen. We…
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In silico modeling of anterior foregut endoderm differentiation towards lung epithelial progenitors
Abstract Directed differentiation of human induced pluripotent stem cells (iPSCs) into anterior foregut endoderm (AFE) and lung progenitors (LPs) has wide-ranging implications for lung developmental biology, disease modeling, and regenerative medicine. We expand on a previously developed…
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Association of copy number alterations with the immune transcriptomic landscape in cancer
Abstract Tumors with high copy number alteration (CNA) burden often respond poorly to immune checkpoint inhibitor therapy. However, how CNAs affect the anti-cancer immune response remains unclear. To address this, we set out to capture the transcriptional effects of CNAs and define a comprehensive…
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A powerful representation learning method for enhanced analysis of incomplete multi-omics data
Abstract Integrative analysis of multi-omics data provides a more comprehensive and nuanced view of a subject’s biological state. However, high-dimensionality and ubiquitous modality missingness present significant analytical challenges. Existing methods for incomplete multi-omics data are scarce…