Jing He

发表

From Isotropic to Anisotropic Side Chain Representations: Comparison of Three Models for Residue Contact Estimation

Weitao Sun, Jing He, 2011, PloS one.

Understanding on the residue contact network using the log-normal cluster model and the multilevel wheel diagram.

Weitao Sun, Jing He, 2010, Biopolymers.

Combine Cryo-EM Density Map and Residue Contact for Protein Structure Prediction: A Case Study

Jing He, Maytha Alshammari, 2020, ACM-BCB ... ... : the ... ACM Conference on Bioinformatics, Computational Biology and Biomedicine. ACM Conference on Bioinformatics, Computational Biology and Biomedicine.

Modeling Beta-Traces for Beta-Barrels from Cryo-EM Density Maps

Dong Si, Jing He, Jing He, 2017, BioMed research international.

An Iterative Bézier Method for Fitting Beta-sheet Component of a Cryo-EM Density Map

Jing He, Michael Poteat, 2017, Molecular based mathematical biology.

Deep convolutional neural networks for detecting secondary structures in protein density maps from cryo-electron microscopy

Shuiwang Ji, Jing He, Rongjian Li, 2016, 2016 IEEE International Conference on Bioinformatics and Biomedicine (BIBM).

Tracing beta strands using StrandTwister from cryo-EM density maps at medium resolutions.

Dong Si, Jing He, Jing He, 2014, Structure.

Towards De Novo Folding of Protein Structures from Cryo-EM 3 D Images at Medium Resolutions

Jing He, Dong Si, 2014 .

Estimating loop length from CryoEM images at medium resolutions

Andrey N. Chernikov, Dong Si, Nikos Chrisochoides, 2013, BMC Structural Biology.

A machine learning approach for the identification of protein secondary structure elements from electron cryo-microscopy density maps.

Dong Si, Jing He, Shuiwang Ji, 2012, Biopolymers.

De novo protein structure modeling from cryoem data through a dynamic programming algorithm in the secondary structure topology graph

Jing He, Kamal Al Nasr, Jing He, 2012 .

Simulation of the Localized 3-dimensional Reconstruction for Electron Cryo-tomography

Jing He, O. Pakhomova, Dong Si, 2013 .

Estimating Lower Bounds on the Length of Protein Polymer Chain Segments using Robot Motion Planning

Jing He, N. Chrisochoides, Andrew McKnight, 2013 .

An Investigation of Atomic Structures Derived from X-ray Crystallography and Cryo-Electron Microscopy Using Distal Blocks of Side-Chains

Jing He, Lin Chen, Salim Sazzed, 2018, Molecules.

Preface: Selected Articles from 2015 Computational Structural Bioinformatics Workshop

Jing He, Brian Chen, Nurit Haspel, 2017, J. Comput. Biol..

A cryo-tomography-based volumetric model of the actin core of mouse vestibular hair cell stereocilia lacking plastin 1.

W. Wriggers, Jing He, J. Kovacs, 2020, Journal of structural biology.

Parallel Computing in Protein Structure Topology Determination

Weitao Sun, Jing He, Saeed Al-Haj, 2008 .

Native secondary structure topology has near minimum contact energy among all possible geometrically constrained topologies

Jing He, Weitao Sun, Weitao Sun, 2009, Proteins.

Refinement of AlphaFold2 models against experimental and hybrid cryo-EM density maps

W. Wriggers, Jing He, Maytha Alshammari, 2022, QRB Discovery.

Effect of sidechain anisotropy on residue contact determination

Weitao Sun, Jing He, 2009, 2009 IEEE International Conference on Bioinformatics and Biomedicine Workshop.

Outlier Profiles of Atomic Structures Derived from X-ray Crystallography and from Cryo-Electron Microscopy

Jing He, Lin Chen, 2020, Molecules.

Refinement of AlphaFold2 Models against Experimental Cryo-EM Density Maps at 4-6Å Resolution

W. Wriggers, Jing He, Maytha Alshammari, 2022, 2022 IEEE International Conference on Bioinformatics and Biomedicine (BIBM).

3D reconstruction from cryo-EM projection images using two spherical embeddings

Jing He, Y. Lu, Jiaxuan Liu, 2022, Communications Biology.

A Histogram-based Outlier Profile for Atomic Structures Derived from Cryo-Electron Microscopy

Jing He, Lin Chen, Jing He, 2019, BCB.

Using Combined Features to Analyze Atomic Structures derived from Cryo-EM Density Maps

Lin Chen, Jing He, Jing He, 2018, BCB.

Numerical geometry of map and model assessment.

Jing He, Willy Wriggers, W. Wriggers, 2015, Journal of structural biology.

A Constrained K-shortest Path Algorithm to Rank the Topologies of the Protein Secondary Structure Elements Detected in CryoEM Volume Maps

Desh Ranjan, Mohammad Zubair, Jing He, 2013, BCB.

Beta-sheet Detection and Representation from Medium Resolution Cryo-EM Density Maps

Dong Si, Jing He, Jing He, 2013, BCB.

Jing He, Willy Wriggers, Salim Sazzed, 2020, J. Chem. Inf. Model..

Constrained cyclic coordinate descent for cryo-EM images at medium resolutions: beyond the protein loop closure problem

Kamal Al-Nasr, Jing He, Jing He, 2016, Robotica.

Combining image processing and modeling to generate traces of beta-strands from cryo-EM density images of beta-barrels

Dong Si, Jing He, Jing He, 2014, 2014 36th Annual International Conference of the IEEE Engineering in Medicine and Biology Society.

Deriving Protein Backbone Using Traces Extracted from Density Maps at Medium Resolutions

Kamal Al-Nasr, Jing He, Jing He, 2015, ISBRA.

Intensity-Based Skeletonization of CryoEM Gray-Scale Images Using a True Segmentation-Free Algorithm

Legand Burge, Kamal Al-Nasr, Jing He, 2013, IEEE/ACM Transactions on Computational Biology and Bioinformatics.

Solving the Secondary Structure Matching Problem in Cryo-EM De Novo Modeling Using a Constrained $K$-Shortest Path Graph Algorithm

Desh Ranjan, Mohammad Zubair, Kamal Al-Nasr, 2014, IEEE/ACM Transactions on Computational Biology and Bioinformatics.

Ranking Valid Topologies of the Secondary Structure Elements Using a Constraint Graph

Desh Ranjan, Mohammad Zubair, Kamal Al-Nasr, 2011, J. Bioinform. Comput. Biol..

paghetti Tracer: A Framework for Tracing Semiregular Filamentous Densities in 3D Tomograms

W. Wriggers, Jing He, Salim Sazzed, 2022, Biomolecules.

Analysis of ß-strand Twist from the 3-dimensional Image of a Protein

Jing He, Tunazzina Islam, Michael Poteat, 2017, BCB.

A cryo-tomography-based volumetric model of the actin core of mouse vestibular hair cell stereocilia lacking plastin 1

Jing He, Julio A. Kovacs, Willy Wriggers, 2019, bioRxiv.

A Tool for Segmentation of Secondary Structures in 3D Cryo-EM Density Map Components Using Deep Convolutional Neural Networks

Jing He, Maytha Alshammari, Salim Sazzed, 2021, Frontiers in Bioinformatics.

Orientations of beta-strand traces and near maximum twist

Dong Si, Jing He, Jing He, 2014, BCB.

Improved Efficiency in Cryo-EM Secondary Structure Topology Determination from Inaccurate Data

Desh Ranjan, Mohammad Zubair, Abhishek Biswas, 2012, J. Bioinform. Comput. Biol..

Deriving Topology and Sequence Alignment for the Helix Skeleton in Low-Resolution protein Density Maps

Yonggang Lu, Jing He, Charlie E. M. Strauss, 2008, J. Bioinform. Comput. Biol..

Using Curriculum Learning in Pattern Recognition of 3-dimensional Cryo-electron Microscopy Density Maps

Jing He, Salim Sazzed, Yangmei Deng, 2020, ACM-BCB ... ... : the ... ACM Conference on Bioinformatics, Computational Biology and Biomedicine. ACM Conference on Bioinformatics, Computational Biology and Biomedicine.

Construction of protein backbone pieces using segment-based FBCCD and Cryo-EM skeleton

Kamal Al-Nasr, Jing He, Jing He, 2014, BCB.

An effective convergence independent loop closure method using Forward-Backward Cyclic Coordinate Descent

Kamal Al-Nasr, Jing He, Jing He, 2009, Int. J. Data Min. Bioinform..

An Effective Computational Method Incorporating Multiple Secondary Structure Predictions in Topology Determination for Cryo-EM Images

Desh Ranjan, Mohammad Zubair, Abhishek Biswas, 2017, IEEE/ACM Transactions on Computational Biology and Bioinformatics.

A Novel Computational Method for Deriving Protein Secondary Structure Topologies Using Cryo-EM Density Maps and Multiple Secondary Structure Predictions

Desh Ranjan, Mohammad Zubair, Abhishek Biswas, 2015, ISBRA.

Combining Cryo-EM Density Map and Residue Contact for Protein Secondary Structure Topologies

Jing He, Maytha Alshammari, 2021, Molecules.

Comparison of an atomic model and its cryo-EM image at the central axis of a helix

Jing He, Julio A. Kovacs, Willy Wriggers, 2015, 2015 IEEE International Conference on Bioinformatics and Biomedicine (BIBM).

Building the initial chain of the proteins through de novo modeling of the cryo-electron microscopy volume data at the medium resolutions

Desh Ranjan, Mohammad Zubair, Dong Si, 2012, BCB.

Comparing an Atomic Model or Structure to a Corresponding Cryo-electron Microscopy Image at the Central Axis of a Helix

Jing He, Julio A. Kovacs, Willy Wriggers, 2017, J. Comput. Biol..

IDENTIFICATION OF α-HELICES FROM LOW RESOLUTION PROTEIN DENSITY MAPS

Jing He, Enrico Pontelli, Yonggang Lu, 2006 .

Selecting near-native structures from decoys using maximal cliques

Yonggang Lu, Jing He, Jinyang Yan, 2016, 2016 IEEE International Conference on Bioinformatics and Biomedicine (BIBM).

A distance- and orientation-dependent energy function of amino acid key blocks.

Jing He, Lin Chen, 2014, Biopolymers.

A distance and orientation dependent potential energy function with cluster energy

Jing He, Lin Chen, Jing He, 2011, 2011 IEEE International Conference on Bioinformatics and Biomedicine Workshops (BIBMW).

Structure prediction for the helical skeletons detected from the low resolution protein density map

Kamal Al-Nasr, Jing He, Weitao Sun, 2010, BMC Bioinformatics.