Jing He

Publication Activity (10 Years)

Years Active: 2004-2024
Publications (10 Years): 31

Top Topics

Gel Electrophoresis

Electron Microscopy

Convolutional Neural Networks

Secondary Structure

Top Venues

J. Comput. Biol.

Publications

Thu Nguyen, Willy Wriggers, Jing He
A Data Set of Paired Structural Segments Between Protein Data Bank and AlphaFold DB for Medium-Resolution Cryo-EM Density Maps: A Gap in Overall Structural Quality. ISBRA (3) (2024)
Maytha Alshammari, Jing He, Willy Wriggers
AlphaFold2 Model Refinement Using Structure Decoys. BCB (2023)
Thu Nguyen, Yongcheng Mu, Jiangwen Sun, Jing He
An Approach to Developing Benchmark Datasets for Protein Secondary Structure Segmentation from Cryo-EM Density Maps. BCB (2023)
Maytha Alshammari, Jing He, Willy Wriggers
Refinement of AlphaFold2 Models against Experimental Cryo-EM Density Maps at 4-6Å Resolution. BIBM (2022)
Salim Sazzed, Peter Scheible, Jing He, Willy Wriggers
Tracing Randomly Oriented Filaments in a Simulated Actin Network Tomogram. BIBM (2022)
Yongcheng Mu, Jiangwen Sun, Jing He
The Combined Focal Cross Entropy and Dice Loss Function for Segmentation of Protein Secondary Structures from Cryo-EM 3D Density maps. BIBM (2022)
Peter Scheible, Salim Sazzed, Jing He, Willy Wriggers
TomoSim: Simulation of Filamentous Cryo-Electron Tomograms. BIBM (2021)
Yongcheng Mu, Salim Sazzed, Maytha Alshammari, Jiangwen Sun, Jing He
A Tool for Segmentation of Secondary Structures in 3D Cryo-EM Density Map Components Using Deep Convolutional Neural Networks. Frontiers Bioinform. 1 (2021)
Salim Sazzed, Peter Scheible, Jing He, Willy Wriggers
Tracing Filaments in Simulated 3D Cryo-Electron Tomography Maps Using a Fast Dynamic Programming Algorithm. BIBM (2021)
Salim Sazzed, Peter Scheible, Maytha Alshammari, Willy Wriggers, Jing He
Cylindrical Similarity Measurement for Helices in Medium-Resolution Cryo-Electron Microscopy Density Maps. J. Chem. Inf. Model. 60 (5) (2020)
Julio A. Kovacs, Junha Song, Manfred Auer, Jing He, Wade Hunter, Willy Wriggers
Correction of Missing-Wedge Artifacts in Filamentous Tomograms by Template-Based Constrained Deconvolution. J. Chem. Inf. Model. 60 (5) (2020)
Lin Chen, Jing He
A Histogram-based Outlier Profile for Atomic Structures Derived from Cryo-Electron Microscopy. BCB (2019)
Lin Chen, Jing He
Using Combined Features to Analyze Atomic Structures derived from Cryo-EM Density Maps. BCB (2018)
Devin Haslam, Tao Zeng, Rongjian Li, Jing He
Exploratory Studies Detecting Secondary Structures in Medium Resolution 3D Cryo-EM Images Using Deep Convolutional Neural Networks. BCB (2018)
Jing He, Kamal Al-Nasr, Weitao Sun, Yonggang Lu
Preface: The 9th Computational Structural Bioinformatics Workshop. J. Comput. Biol. 25 (1) (2018)
Devin Haslam, Salim Sazzed, Willy Wriggers, Julio Kovcas, Junha Song, Manfred Auer, Jing He
A Pattern Recognition Tool for Medium-Resolution Cryo-EM Density Maps and Low-Resolution Cryo-ET Density Maps. ISBRA (2018)
Tunazzina Islam, Michael Poteat, Jing He
Quantification of Twist from the Central Lines of β-Strands. J. Comput. Biol. 25 (1) (2018)
Abhishek Biswas, Desh Ranjan, Mohammad Zubair, Stephanie Zeil, Kamal Al-Nasr, Jing He
An Effective Computational Method Incorporating Multiple Secondary Structure Predictions in Topology Determination for Cryo-EM Images. IEEE ACM Trans. Comput. Biol. Bioinform. 14 (3) (2017)
Tunazzina Islam, Michael Poteat, Jing He
Analysis of ß-strand Twist from the 3-dimensional Image of a Protein. BCB (2017)
Stephanie Zeil, Julio A. Kovacs, Willy Wriggers, Jing He
Comparing an Atomic Model or Structure to a Corresponding Cryo-electron Microscopy Image at the Central Axis of a Helix. J. Comput. Biol. 24 (1) (2017)
Jing He, Nurit Haspel, Brian Chen
Preface: Selected Articles from 2015 Computational Structural Bioinformatics Workshop. J. Comput. Biol. 24 (1) (2017)
Devin Haslam, Mohammad Zubair, Desh Ranjan, Abhishek Biswas, Jing He
Challenges in matching secondary structures in cryo-EM: An exploration. BIBM (2016)
Rongjian Li, Dong Si, Tao Zeng, Shuiwang Ji, Jing He
Deep convolutional neural networks for detecting secondary structures in protein density maps from cryo-electron microscopy. BIBM (2016)
Jinyang Yan, Yonggang Lu, Jing He
Selecting near-native structures from decoys using maximal cliques. BIBM (2016)
Kamal Al-Nasr, Jing He
Constrained cyclic coordinate descent for cryo-EM images at medium resolutions: beyond the protein loop closure problem. Robotica 34 (8) (2016)
Abhishek Biswas, Desh Ranjan, Mohammad Zubair, Jing He
A Dynamic Programming Algorithm for Finding the Optimal Placement of a Secondary Structure Topology in Cryo-EM Data. J. Comput. Biol. 22 (9) (2015)
Jing He, Amarda Shehu, Nurit Haspel, Brian Chen
The 7th Computational Structural Bioinformatics Workshop. J. Comput. Biol. 22 (9) (2015)
Jing He, Dong Si, Maryam Arab
Detection of Secondary Structures from 3D Protein Images of Medium Resolutions and its Challenges. ICIG (2) (2015)
Jing He, Stephanie Zeil, Hussam Hallak, Kele McKaig, Julio A. Kovacs, Willy Wriggers
Comparison of an atomic model and its cryo-EM image at the central axis of a helix. BIBM (2015)
Abhishek Biswas, Desh Ranjan, Mohammad Zubair, Jing He
A Novel Computational Method for Deriving Protein Secondary Structure Topologies Using Cryo-EM Density Maps and Multiple Secondary Structure Predictions. ISBRA (2015)
Kamal Al-Nasr, Jing He
Deriving Protein Backbone Using Traces Extracted from Density Maps at Medium Resolutions. ISBRA (2015)
Dong Si, Jing He
Orientations of beta-strand traces and near maximum twist. BCB (2014)
Dong Si, Jing He
Combining image processing and modeling to generate traces of beta-strands from cryo-EM density images of beta-barrels. EMBC (2014)
Kamal Al-Nasr, Desh Ranjan, Mohammad Zubair, Lin Chen, Jing He
Solving the Secondary Structure MatchingProblem in Cryo-EM De Novo ModelingUsing a Constrained $K$-Shortest Path Graph Algorithm. IEEE ACM Trans. Comput. Biol. Bioinform. 11 (2) (2014)
Kamal Al-Nasr, Jing He
Construction of protein backbone pieces using segment-based FBCCD and Cryo-EM skeleton. BCB (2014)
Kamal Al-Nasr, Chunmei Liu, Mugizi Robert Rwebangira, Legand Burge, Jing He
Intensity-Based Skeletonization of CryoEM Gray-Scale Images Using a True Segmentation-Free Algorithm. IEEE ACM Trans. Comput. Biol. Bioinform. 10 (5) (2013)
Dong Si, Jing He
Beta-sheet Detection and Representation from Medium Resolution Cryo-EM Density Maps. BCB (2013)
Kamal Al-Nasr, Lin Chen, Desh Ranjan, Mohammad Zubair, Dong Si, Jing He
A Constrained K-shortest Path Algorithm to Rank the Topologies of the Protein Secondary Structure Elements Detected in CryoEM Volume Maps. BCB (2013)
Abhishek Biswas, Dong Si, Kamal Al-Nasr, Desh Ranjan, Mohammad Zubair, Jing He
Improved Efficiency in Cryo-EM Secondary Structure Topology Determination from Inaccurate Data. J. Bioinform. Comput. Biol. 10 (3) (2012)
Andrew McKnight, Kamal Al-Nasr, Dong Si, Andrey N. Chernikov, Nikos Chrisochoides, Jing He
CryoEM skeleton length estimation using a decimated curve. BIBM Workshops (2012)
Kamal Al-Nasr, Lin Chen, Dong Si, Desh Ranjan, Mohammad Zubair, Jing He
Building the initial chain of the proteins through de novo modeling of the cryo-electron microscopy volume data at the medium resolutions. BCB (2012)
Abhishek Biswas, Dong Si, Kamal Al-Nasr, Desh Ranjan, Mohammad Zubair, Jing He
A Constraint Dynamic Graph Approach to Identify the Secondary Structure Topology from cryoEM Density Data in Presence of Errors. BIBM (2011)
Lin Chen, Jing He
A distance and orientation dependent potential energy function with cluster energy. BIBM Workshops (2011)
Kamal Al-Nasr, Desh Ranjan, Mohammad Zubair, Jing He
Ranking Valid Topologies of the Secondary Structure Elements Using a Constraint Graph. J. Bioinform. Comput. Biol. 9 (3) (2011)
Kamal Al-Nasr, Weitao Sun, Jing He
Structure prediction for the helical skeletons detected from the low resolution protein density map. BMC Bioinform. 11 (S-1) (2010)
Weitao Sun, Jing He
Reduction of the secondary structure topological space through direct estimation of the contact energy formed by the secondary structures. BMC Bioinform. 10 (S-1) (2009)
Kamal Al-Nasr, Jing He
An effective convergence independent loop closure method using Forward-Backward Cyclic Coordinate Descent. Int. J. Data Min. Bioinform. 3 (3) (2009)
Yonggang Lu, Jing He, Charlie E. M. Strauss
Deriving Topology and Sequence Alignment for the Helix Skeleton in Low-Resolution protein Density Maps. J. Bioinform. Comput. Biol. 6 (1) (2008)
Yonggang Lu, Jing He, Charlie E. M. Strauss
Deriving Protein Structure Topology from the Helix Skeletion in Low Resolution Density Map using Rosetta. APBC (2007)
Alessandro Dal Palù, Enrico Pontelli, Jing He, Yonggang Lu
A Constraint Logic Programming approach to associate 1D and 3D structural components for large protein complexes. Int. J. Data Min. Bioinform. 1 (4) (2007)
Alessandro Dal Palù, Enrico Pontelli, Jing He, Yonggang Lu
A constraint logic programming approach to 3D structure determination of large protein complexes. SAC (2006)
Jing He, Yonggang Lu, Enrico Pontelli
A Parallel Algorithm for Helix Mapping Between 3D and 1D Protein Structure Using the Length Constraints. ISPA (2004)
Jing He, Desh Ranjan, Wen Jiang, Wah Chiu, Michael F. Schmid
Detecting Local Symmetry Axis in 3-dimensional Virus Structures. APBC (2004)