Related papers: Sparse approximations of protein structure from no…
The observations in many applications consist of counts of discrete events, such as photons hitting a dector, which cannot be effectively modeled using an additive bounded or Gaussian noise model, and instead require a Poisson noise model.…
Cryo-electron microscopy provides 2-D projection images of the 3-D electron scattering intensity of many instances of the particle under study (e.g., a virus). Both symmetry (rotational point groups) and heterogeneity are important aspects…
This paper introduces a new shape-based image reconstruction technique applicable to a large class of imaging problems formulated in a variational sense. Given a collection of shape priors (a shape dictionary), we define our problem as…
Understanding complex biological macromolecules, especially proteins, is vital for grasping their diverse chemical functions with direct impact in biology and pharmacology. While techniques like X-ray crystallography and cryo-electron…
Resolving the structural variability of proteins is often key to understanding the structure-function relationship of those macromolecular machines. Single particle analysis using Cryogenic electron microscopy (CryoEM), combined with…
Proteins are essential for maintaining life. For example, knowing the structure of a protein, cell regulatory mechanisms of organisms can be modeled, supporting the development of disease treatments or the understanding of relationships…
Structure determination is key to understanding protein function at a molecular level. Whilst significant advances have been made in predicting structure and function from amino acid sequence, researchers must still rely on expensive,…
The ability to computationally generate novel yet physically foldable protein structures could lead to new biological discoveries and new treatments targeting yet incurable diseases. Despite recent advances in protein structure prediction,…
We develop a novel method for detection of signals and reconstruction of images in the presence of random noise. The method uses results from percolation theory. We specifically address the problem of detection of multiple objects of…
We present a geometry-aware method for heterogeneous single-particle cryogenic electron microscopy (cryo-EM) reconstruction that predicts atomic backbone conformations. To incorporate protein-structure priors, we represent the backbone as a…
Single-particle electron cryomicroscopy is an essential tool for high-resolution 3D reconstruction of proteins and other biological macromolecules. An important challenge in cryo-EM is the reconstruction of non-rigid molecules with parts…
Protein structure prediction models are now capable of generating accurate 3D structural hypotheses from sequence alone. However, they routinely fail to capture the conformational diversity of dynamic biomolecular complexes, often requiring…
Predicting protein structure from amino acid sequence is one of the most important unsolved problems of molecular biology and biophysics.Not only would a successful prediction algorithm be a tremendous advance in the understanding of the…
The problem of reconstructing and identifying intracellular protein signaling and biochemical networks is of critical importance in biology today. We sought to develop a mathematical approach to this problem using, as a test case, one of…
Single particle reconstruction has recently emerged in 3D fluorescence microscopy as a powerful technique to improve the axial resolution and the degree of fluorescent labeling. It is based on the reconstruction of an average volume of a…
Electron tomography (ET) has become a standard technique for 3D characterization of materials at the nano-scale. Traditional reconstruction algorithms such as weighted back projection suffer from disruptive artifacts with insufficient…
Proteins are miniature machines whose function depends on their three-dimensional (3D) structure. Determining this structure computationally remains an unsolved grand challenge. A major bottleneck involves selecting the most accurate…
Modern technology for producing extremely bright and coherent X-ray laser pulses provides the possibility to acquire a large number of diffraction patterns from individual biological nanoparticles, including proteins, viruses, and DNA.…
Single particle cryo-electron microscopy (EM) is an increasingly popular method for determining the 3-D structure of macromolecules from noisy 2-D images of single macromolecules whose orientations and positions are random and unknown. One…
We introduce a new methodology 'charcoal' for estimating the location of sparse changes in high-dimensional linear regression coefficients, without assuming that those coefficients are individually sparse. The procedure works by…