Systems biology
View article: Revealing global stoichiometry conservation architecture in cells from Raman spectral patterns
Revealing global stoichiometry conservation architecture in cells from Raman spectral patterns Open
Cells can adapt to various environments by changing their biomolecular profiles while maintaining physiological homeostasis. What organizational principles in cells enable the simultaneous realization of adaptability and homeostasis? To ad…
View article: Genome–epigenome crosstalk in T-cell lymphomas: from maps to mechanisms
Genome–epigenome crosstalk in T-cell lymphomas: from maps to mechanisms Open
T-cell lymphomas are clinically and biologically heterogeneous malignancies that comprise ~ 10% of non-Hodgkin lymphomas. Outcomes with first-line chemotherapy remain poor. Over the past decade, integrative genomic and epigenomic studies h…
View article: Deep Generative AI for Multi-Target Therapeutic Design: Toward Self-Improving Drug Discovery Framework
Deep Generative AI for Multi-Target Therapeutic Design: Toward Self-Improving Drug Discovery Framework Open
Multi-target drug design represents a paradigm shift in tackling the complexity and heterogeneity of diseases such as cancer. Conventional single-target therapies frequently face limitations due to network redundancy, pathway compensation,…
View article: Rules of life at the interface of calcium signaling and mechanobiology
Rules of life at the interface of calcium signaling and mechanobiology Open
Living systems process a broad range of internal and external stimuli, respond to environmental constraints, and adapt to various conditions through tight coordination between signaling networks and cellular mechanics. Among these, calcium…
View article: Scientific achievements of the Department of Molecular Biology in understanding stress-dependent mechanisms of glioma growth
Scientific achievements of the Department of Molecular Biology in understanding stress-dependent mechanisms of glioma growth Open
Since 2005, the Department of Molecular Biology has initiated research aimed at solving key problems in biochemistry and molecular biology, with an emphasis on elucidating the molecular basis of malignant tumor growth and the mechanisms of…
View article: PULSAR: a Foundation Model for Multi-scale and Multicellular Biology
PULSAR: a Foundation Model for Multi-scale and Multicellular Biology Open
Biology emerges from interactions across physical scales, where molecular interactions drive cellular states, which in turn orchestrate multicellular tissue functions that collectively define health and disease. However, current computatio…
View article: Transcriptomic profiling of DYT-TOR1A patients-derived iPSC reveals dysregulation in extracellular matrix, lipid metabolism, and Chr22q11.23
Transcriptomic profiling of DYT-TOR1A patients-derived iPSC reveals dysregulation in extracellular matrix, lipid metabolism, and Chr22q11.23 Open
View article: Temperature changes are signaled in cyanobacteria through the PipX interaction network
Temperature changes are signaled in cyanobacteria through the PipX interaction network Open
Cyanobacteria perform oxygenic photosynthesis and have evolved sophisticated mechanisms to adapt their metabolism to challenging environmental changes. Despite their ecological and biotechnological importance, many regulatory proteins are …
View article: NEURO-Restore: Convergent Computational and Mathematical Validation of Multi-Target Neuroinflammatory Modulation in Alzheimer's Disease—Independent Pathways to 31-40× Therapeutic Superiority
NEURO-Restore: Convergent Computational and Mathematical Validation of Multi-Target Neuroinflammatory Modulation in Alzheimer's Disease—Independent Pathways to 31-40× Therapeutic Superiority Open
This submission presents NEURO-Restore v3.0, a novel multi-target therapeutic formulation for Alzheimer's disease (AD) with projected 31-40× superiority over current FDA-approved treatments. The work establishes convergent validation throu…
View article: Characterizing heterogeneous cis-regulatory elements in gene regulatory programs associated with breast cancer
Characterizing heterogeneous cis-regulatory elements in gene regulatory programs associated with breast cancer Open
View article: Cut or bind? Antigen-specific processing mechanisms define CD4+ T cell immunodominant epitopes for SARS-CoV-2 S and N proteins
Cut or bind? Antigen-specific processing mechanisms define CD4+ T cell immunodominant epitopes for SARS-CoV-2 S and N proteins Open
Background CD4⁺ T cell responses are key to adaptive immunity, yet the mechanisms underlying peptide selection and immunodominance across MHC class II variants in humans remain poorly defined. Two non-mutually exclusive models — First Bind…
View article: Molecular mechanisms of gut microbiota dysbiosis and metabolites in Alzheimer’s disease pathogenesis: implications for precision therapeutics
Molecular mechanisms of gut microbiota dysbiosis and metabolites in Alzheimer’s disease pathogenesis: implications for precision therapeutics Open
Alzheimer’s disease (AD) originates from both central and peripheral pathways. The gut microbiota is a clear risk factor. In AD, microbiota imbalances drive immune system activation, disrupt protective barriers, and alter neuromodulatory s…
View article: Emerging role of histone and non-histone lactylation in metabolic reprogramming of female-specific malignancies
Emerging role of histone and non-histone lactylation in metabolic reprogramming of female-specific malignancies Open
Lysine lactylation (Klac), a recently characterized post-translational modification, has emerged as a critical epigenetic regulator in female-prevalent malignancies including breast, ovarian, cervical, and endometrial cancers. Emerging evi…
View article: A Multiscale Integrated Approach to the Study of the Nervous System in Health and Disease
A Multiscale Integrated Approach to the Study of the Nervous System in Health and Disease Open
The study of the nervous system in health and disease presents an extraordinary scientific challenge, one deeply rooted in the intrinsic complexity of brain structure and function across multiple scales of biological organization. The nerv…
View article: Omics-based insights into skin ulcerative disease in sea cucumbers: a systematic review
Omics-based insights into skin ulcerative disease in sea cucumbers: a systematic review Open
Skin ulcerative disease (SUD) in sea cucumbers poses a significant threat to marine biodiversity, aquaculture sustainability, and ecosystem health. Characterized by localized lesions that can progress to extensive tissue necrosis, SUD aris…
View article: SIRT6 in Cancer: Mechanistic Insights into Its Dual Roles in Cancer Biology and Implications for Precision Therapeutic Development
SIRT6 in Cancer: Mechanistic Insights into Its Dual Roles in Cancer Biology and Implications for Precision Therapeutic Development Open
Sirtuin 6 (SIRT6), a (Nicotinamide adenine dinucleotide) NAD+-dependent deacylase and mono- (adenosine diphosphate) ADP-ribosyltransferase, is increasingly recognized as a pivotal regulator of genomic stability, metabolic reprogramming, an…
View article: Differential protein expression and enriched pathways in pediatric sepsis: identification of novel brain-associated biomarkers revealed through proteomic profiling
Differential protein expression and enriched pathways in pediatric sepsis: identification of novel brain-associated biomarkers revealed through proteomic profiling Open
View article: Decoding non-coding SNPs: systems genomics modelling dissects the heterogeneity of IBD
Decoding non-coding SNPs: systems genomics modelling dissects the heterogeneity of IBD Open
Genome-wide association studies have identified numerous susceptibility loci in complex diseases, such as chronic immune-mediated inflammatory disorders (IMIDs), yet their impact on pathomechanisms remains poorly understood. Low effect siz…
View article: Toward a Regulatory Framework for Platform Immuno-Oncology: A Systems and Risk-Modeling Approach
Toward a Regulatory Framework for Platform Immuno-Oncology: A Systems and Risk-Modeling Approach Open
Modern cancer immunotherapies increasingly rely on multi-component platforms that integrate cytokine agonists, innate and adaptive immune activation, tumor antigen targeting, and microenvironment remodeling. These systems function not as i…
View article: DiCoLo: Integration-free and cluster-free detection of localized differential gene co-expression in single-cell data
DiCoLo: Integration-free and cluster-free detection of localized differential gene co-expression in single-cell data Open
Detecting changes in gene coordination patterns between biological conditions and identifying the cell populations in which these changes occur are key challenges in single-cell analysis. Existing approaches often compare gene co-expressio…
View article: A comprehensive view of aluminum stress in Oryza sativa from a systems biology perspective
A comprehensive view of aluminum stress in Oryza sativa from a systems biology perspective Open
View article: Multi-Pathway Mechanisms of Engeletin in Ischemic Stroke: A Comprehensive Study Based on Network Pharmacology, Machine Learning, and Immune Infiltration Analysis
Multi-Pathway Mechanisms of Engeletin in Ischemic Stroke: A Comprehensive Study Based on Network Pharmacology, Machine Learning, and Immune Infiltration Analysis Open
Ischemic stroke (IS) is a leading cause of mortality and long-term disability, underpinned by complex molecular mechanisms, such as oxidative stress, neuroinflammation, and apoptosis. The flavonoid Engeletin exhibits promising neuroprotect…
View article: Exploring the mechanism of Si Miao Yong An decoction in treating radiation enteritis based on network pharmacology and molecular docking
Exploring the mechanism of Si Miao Yong An decoction in treating radiation enteritis based on network pharmacology and molecular docking Open
Objective: To explore the active components, key targets, and mechanisms of Si Miao Yong An Decoction in the treatment of radiation enteritis based on network pharmacology and molecular docking. Methods: The TCMSP and UniProt databases wer…
View article: Artificial Intelligence Driven Innovation: Advancing Mesenchymal Stem Cell Therapies and Intelligent Biomaterials for Regenerative Medicine
Artificial Intelligence Driven Innovation: Advancing Mesenchymal Stem Cell Therapies and Intelligent Biomaterials for Regenerative Medicine Open
Artificial intelligence (AI) is revolutionizing regenerative medicine, particularly in advancing mesenchymal stem cell (MSC) therapies and smart biomaterials. This review highlights AI’s role in two core areas: First, at the biological lev…
View article: AI-Guided Discovery of Universal Cancer Convergence Pathways and Multi-Target Therapeutic Interventions
AI-Guided Discovery of Universal Cancer Convergence Pathways and Multi-Target Therapeutic Interventions Open
This computational framework presents ONCO-RESTORE v2.0, a comprehensive AI-guided approach to identifying universal cancer convergence pathways and designing multi-target therapeutic interventions. Background:Cancer remains the second-lea…
View article: A Hybrid Modeling Framework for Predictive Digital Twins of CHO Cell Culture
A Hybrid Modeling Framework for Predictive Digital Twins of CHO Cell Culture Open
Digital twins of mammalian cell cultures hold great potential for predictive bioprocess modeling, yet their development is challenged by the nonlinear dynamics and metabolic complexity of these systems. We present a hybrid computational fr…
View article: Survival strategies of mycoplasmas: the critical role of post-translational modifications
Survival strategies of mycoplasmas: the critical role of post-translational modifications Open
Mycoplasmas are unique prokaryotic pathogens distinguished by their lack of a cell wall. These microorganisms are widespread in nature and can cause severe infections, leading to substantial tissue damage. Recent advances in mycoplasmology…
View article: Engineering metabolic regulation for random environments: best compromises between enzyme cost and homeostasis
Engineering metabolic regulation for random environments: best compromises between enzyme cost and homeostasis Open
The metabolic fluxes in cells are regulated by metabolites that bind to enzymes and modulate their activities. Metabolites can stabilize their own concentrations by exerting a negative feedback on their production pathways. Although metabo…
View article: Exploring therapeutic mechanism of Fuzhenghefuzhiyang Formula in psoriasis: inflammation and metabolism regulation
Exploring therapeutic mechanism of Fuzhenghefuzhiyang Formula in psoriasis: inflammation and metabolism regulation Open
Background Psoriasis is a long-term, immune-mediated inflammatory disorder of the skin, affecting about 2-3% of the global population with rising prevalence rates. Clinical practice has demonstrated that Fuzhenghefuzhiyang formula (FZHFZY)…
View article: Mechano-chemical modeling of glia initiated secondary injury of neurons under mechanical load
Mechano-chemical modeling of glia initiated secondary injury of neurons under mechanical load Open
Traumatic Brain Injury (TBI) results from an impact or concussion to the head with the injury being specifically characterized through pathological degradation at various biological length scales. Following injury, various mechanical model…