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BaNDyT: Bayesian Network Modeling of Molecular Dynamics Trajectories.
J Chem Inf Model
January 2025
Department of Computational and Quantitative Medicine, Beckman Research Institute of the City of Hope, 1218 S 5th Ave, Monrovia, California 91016, United States.
Bayesian network modeling (BN modeling, or BNM) is an interpretable machine learning method for constructing probabilistic graphical models from the data. In recent years, it has been extensively applied to diverse types of biomedical data sets. Concurrently, our ability to perform long-time scale molecular dynamics (MD) simulations on proteins and other materials has increased exponentially.
View Article and Find Full Text PDFQuantum materials governed by emergent topological fermions have become a cornerstone of physics. Dirac fermions in graphene form the basis for moiré quantum matter and Dirac fermions in magnetic topological insulators enabled the discovery of the quantum anomalous Hall (QAH) effect. By contrast, there are few materials whose electromagnetic response is dominated by emergent Weyl fermions.
View Article and Find Full Text PDFMultiscale footprints reveal the organization of cis-regulatory elements.
Nature
January 2025
Gene Regulation Observatory, Broad Institute of MIT and Harvard, Cambridge, MA, USA.
Cis-regulatory elements (CREs) control gene expression and are dynamic in their structure and function, reflecting changes in the composition of diverse effector proteins over time. However, methods for measuring the organization of effector proteins at CREs across the genome are limited, hampering efforts to connect CRE structure to their function in cell fate and disease. Here we developed PRINT, a computational method that identifies footprints of DNA-protein interactions from bulk and single-cell chromatin accessibility data across multiple scales of protein size.
View Article and Find Full Text PDFMulti-dimensional bio mass cytometry: simultaneous analysis of cytoplasmic proteins and metabolites on single cells.
Chem Sci
January 2025
Beijing National Laboratory for Molecular Sciences, Key Laboratory of Bioorganic Chemistry and Molecular Engineering of Ministry of Education, College of Chemistry and Molecular Engineering, Peking University Beijing 100871 China
Single-cell multi-dimensional analysis enables more profound biological insight, providing a comprehensive understanding of cell physiological processes. Due to limited cellular contents, the lack of protein and metabolite amplification ability, and the complex cytoplasmic environment, the simultaneous analysis of intracellular proteins and metabolites remains challenging. Herein, we proposed a multi-dimensional bio mass cytometry platform characterized by protein signal conversion and amplification through an orthogonal exogenous enzymatic reaction.
View Article and Find Full Text PDFDrought-Induced Weakening of Temperature Control on Ecosystem Carbon Uptake Across Northern Lands.
Glob Chang Biol
January 2025
Key Laboratory of Lake and Watershed Science for Water Security, Nanjing Institute of Geography and Limnology, Chinese Academy of Sciences, Nanjing, China.
Rapid warming in northern lands has led to increased ecosystem carbon uptake. It remains unclear, however, whether and how the beneficial effects of warming on carbon uptake will continue with climate change. Moreover, the role played by water stress in temperature control on ecosystem carbon uptake remains highly uncertain.
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