Selected Publications

Articles In Academic Journals

Year Title
2018 Quantification of Twist from the Central Lines of ?-StrandsJournal of Computational Biology. 114-120.
2018 Special Issue Preface: The 9th Computational Structural Bioinformatics WorkshopJournal of Computational Biology. 1-2.
2018 Tracing actin filament bundles in three-dimensional electron tomography density maps of hair cell stereociliaMolecules. 1-14.
2017 An effective computational method incorporating multiple secondary structure predictions in topology determination for cryo-EM imagesIEEE/ACM Transactions on Computational Biology and Bioinformatics. 578-586.
2017 Comparing an Atomic Model or Structure to a Corresponding Cryo-electron Microscopy Image at the Central Axis of a HelixJournal of Computational Biology. 52-67.
2015 A dynamic programming algorithm for finding the optimal placement of a secondary structure topology in Cryo-EM dataJournal of Computational Biology. 837-843.
2014 Solving the Secondary Structure Matching Problem in CryoEM De Novo Modeling using a Constrained K-shortest Path Graph AlgorithmIEEE/ACM Transactions on Computational Biology and Bioinformatics. 1.
2012 Improved efficiency in cryo-EM secondary structure topology determination from inaccurate dataJournal of bioinformatics and computational biology. 1242006.
2011 Ranking valid topologies of the secondary structure elements using a constraint graphJournal of bioinformatics and computational biology. 415-430.

Conference Papers

Year Title
2017 Analysis of ?-strand twist from the 3-dimensional image of a protein
2016 Challenges in matching secondary structures in cryo-EM: An exploration.  1714-1719.
2015 A novel computational method for deriving protein secondary structure topologies using Cryo-EM density maps and multiple secondary structure predictions.  60-71.
2013 A constrained k-shortest path algorithm to rank the topologies of the protein secondary structure elements detected in cryoem volume maps.  749.
2012 Building the initial chain of the proteins through de novo modeling of the cryo-electron microscopy volume data at the medium resolutions.  490-497.
2011 A Constraint Dynamic Graph Approach to Identify the Secondary Structure Topology from cryoEM Density Data in Presence of Errors.  160-163.
2010 Enumeration of the Geometrically Constrained Alignments of the Secondary Structures Using Constraint Graph
2004 Detecting local symmetry axis in 3-dimensional virus structures.  265-270.

Research Overview

  • -Development computational methods and tools ofr biological problems that involve molecular structures. The scholar's current work involves developing the simplified representations of 3-dimensional protein structure components to reduce the computation, developing the corresponding energyfunctions using statistical approaches, and improving the optimization process using the geometrical constraints computationally extracted from the protein density. The goal of my research is to contribute from the computer science point of view to the grand challenge of the protein folding problem.
  • Education And Training

  • Ph.D. in Structural & Computational Biology & Molecular Biophysics, Baylor College of Medicine 2001
  • M.S. in Applied Mathematics, New Mexico State University 1994
  • B.S. in Applied Mathematics, Jilin University 1990
  • Full Name

  • Jing He