Related papers: BioEM: GPU-accelerated computing of Bayesian infer…
Motivation: Structural heterogeneity in single-particle cryo-electron microscopy (cryo-EM) data represents a major challenge for high-resolution structure determination. Unsupervised classification may serve as the first step in the…
Background: The recent explosion of experimental techniques in single molecule biophysics has generated a variety of novel time series data requiring equally novel computational tools for analysis and inference. This article describes in…
Structural flexibility and/or dynamic interactions with other molecules is a critical aspect of protein function. CryoEM provides direct visualization of individual macromolecules sampling different conformational and compositional states.…
Cryo-electron microscopy (cryo-EM) is a technique for reconstructing the 3-dimensional (3D) structure of biomolecules (especially large protein complexes and molecular assemblies). As the resolution increases to the near-atomic scale,…
A single-particle cryo-electron microscopy (cryo-EM) measurement, called a micrograph, consists of multiple two-dimensional tomographic projections of a three-dimensional (3-D) molecular structure at unknown locations, taken under unknown…
Multiple kernel learning algorithms are proposed to combine kernels in order to obtain a better similarity measure or to integrate feature representations coming from different data sources. Most of the previous research on such methods is…
Bayesian spectral deconvolution provides a data-driven framework for mathematical model selection and parameter estimation from spectral data. Although highly versatile, it becomes computationally expensive as the number of model…
Cryo-electron microscopy (cryo-EM) is a powerful technique for determining high-resolution 3D biomolecular structures from imaging data. Its unique ability to capture structural variability has spurred the development of heterogeneous…
Single-particle cryo-electron microscopy (cryo-EM) has recently joined X-ray crystallography and NMR spectroscopy as a high-resolution structural method for biological macromolecules. Cryo-EM was selected by Nature Methods as Method of the…
In the next decade, the demands for computing in large scientific experiments are expected to grow tremendously. During the same time period, CPU performance increases will be limited. At the CERN Large Hadron Collider (LHC), these two…
Single-particle cryo-EM has transformed structural biology but still faces challenges in resolving conformational heterogeneity at atomic resolution. Existing cryo-EM heterogeneity analysis methods either lack atomic details or tend to…
Single-particle cryo-electron microscopy (cryo-EM) has become a cornerstone of structural biology, enabling near-atomic resolution analysis of macromolecules through advanced computational methods. However, the development of cryo-EM…
Cryo-Electron Microscopy (Cryo-EM) is a Nobel prize-winning technology for determining the 3D structure of particles at near-atomic resolution. A fundamental step in the recovering of the 3D single-particle structure is to align its 2D…
The reliability of cardiovascular computational models depends on the accurate solution of the hemodynamics, the realistic characterization of the hyperelastic and electric properties of the tissues along with the correct description of…
Analysis of brain imaging scans is critical to understanding the way the human brain functions, which can be leveraged to treat injuries and conditions that affect the quality of life for a significant portion of the human population. In…
The capacity to predict and control bioprocesses is perhaps one of the most important objectives of biotechnology. Computational simulation is an established methodology for the design and optimization of bioprocesses, where the finite…
Single-particle cryo-electron microscopy (cryo-EM) has become one of the mainstream structural biology techniques because of its ability to determine high-resolution structures of dynamic bio-molecules. However, cryo-EM data acquisition…
Single particle cryogenic electron microscopy (cryo-EM) is an imaging technique capable of recovering the high-resolution 3-D structure of biological macromolecules from many noisy and randomly oriented projection images. One notable…
We review the computation models for biofilm and bacteria cells, providing perspectives on biofilm's various properties and potential serving as engineering living materials (ELMs), considering the omnipresence of such biological matter.…
Empirical Dynamic Modeling (EDM) is a nonlinear time series causal inference framework. The latest implementation of EDM, cppEDM, has only been used for small datasets due to computational cost. With the growth of data collection…