Detecting Local Symmetry Axis in 3-dimensional Virus Structures. - Jing He 002; Desh Ranjan; Wen Jiang; Wah Chiu; Michael F. Schmid (APBC, 2004)

A Parallel Algorithm for Helix Mapping Between 3D and 1D Protein Structure Using the Length Constraints. - Jing He 002; Yonggang Lu; Enrico Pontelli (ISPA, 2004)

Using the Length Constraints of Helix to Evaluate protein secondary Structure Prediction for Helix. - Jing He 002; Yonggang Lu (Advances in Bioinformatics and Its Applications, 2005)

A constraint logic programming approach to 3D structure determination of large protein complexes. - Alessandro Dal Palù; Enrico Pontelli; Jing He 002; Yonggang Lu (SAC, 2006)

Deriving Protein Structure Topology from the Helix Skeletion in Low Resolution Density Map using Rosetta. - Yonggang Lu; Jing He 002; Charlie E. M. Strauss (APBC, 2007)

A Constraint Logic Programming approach to associate 1D and 3D structural components for large protein complexes. - Alessandro Dal Palù; Enrico Pontelli; Jing He 002; Yonggang Lu (Int. J. Data Min. Bioinform., 2007)

Deriving Topology and Sequence Alignment for the Helix Skeleton in Low-Resolution protein Density Maps. - Yonggang Lu; Jing He 002; Charlie E. M. Strauss (J. Bioinform. Comput. Biol., 2008)

Reduction of the secondary structure topological space through direct estimation of the contact energy formed by the secondary structures. - Weitao Sun; Jing He 002 (BMC Bioinform., 2009)

An effective convergence independent loop closure method using Forward-Backward Cyclic Coordinate Descent. - Kamal Al-Nasr; Jing He 002 (Int. J. Data Min. Bioinform., 2009)

Structure prediction for the helical skeletons detected from the low resolution protein density map. - Kamal Al-Nasr; Weitao Sun; Jing He 002 (BMC Bioinform., 2010)

A Constraint Dynamic Graph Approach to Identify the Secondary Structure Topology from cryoEM Density Data in Presence of Errors. - Abhishek Biswas; Dong Si; Kamal Al-Nasr; Desh Ranjan; Mohammad Zubair; Jing He 002 (BIBM, 2011)

A distance and orientation dependent potential energy function with cluster energy. - Lin Chen 007; Jing He 002 (BIBM Workshops, 2011)

Ranking Valid Topologies of the Secondary Structure Elements Using a Constraint Graph. - Kamal Al-Nasr; Desh Ranjan; Mohammad Zubair; Jing He 002 (J. Bioinform. Comput. Biol., 2011)

Building the initial chain of the proteins through de novo modeling of the cryo-electron microscopy volume data at the medium resolutions. - Kamal Al-Nasr; Lin Chen 007; Dong Si; Desh Ranjan; Mohammad Zubair; Jing He 002 (BCB, 2012)

CryoEM skeleton length estimation using a decimated curve. - Andrew McKnight; Kamal Al-Nasr; Dong Si; Andrey N. Chernikov; Nikos Chrisochoides; Jing He 002 (BIBM Workshops, 2012)

Improved Efficiency in Cryo-EM Secondary Structure Topology Determination from Inaccurate Data. - Abhishek Biswas; Dong Si; Kamal Al-Nasr; Desh Ranjan; Mohammad Zubair; Jing He 002 (J. Bioinform. Comput. Biol., 2012)

A Constrained K-shortest Path Algorithm to Rank the Topologies of the Protein Secondary Structure Elements Detected in CryoEM Volume Maps. - Kamal Al-Nasr; Lin Chen 007; Desh Ranjan; Mohammad Zubair; Dong Si; Jing He 002 (BCB, 2013)

Beta-sheet Detection and Representation from Medium Resolution Cryo-EM Density Maps. - Dong Si; Jing He 002 (BCB, 2013)

Intensity-Based Skeletonization of CryoEM Gray-Scale Images Using a True Segmentation-Free Algorithm. - Kamal Al-Nasr; Chunmei Liu; Mugizi Robert Rwebangira; Legand Burge; Jing He 002 (IEEE ACM Trans. Comput. Biol. Bioinform., 2013)

Construction of protein backbone pieces using segment-based FBCCD and Cryo-EM skeleton. - Kamal Al-Nasr; Jing He 002 (BCB, 2014)

Orientations of beta-strand traces and near maximum twist. - Dong Si; Jing He 002 (BCB, 2014)

Combining image processing and modeling to generate traces of beta-strands from cryo-EM density images of beta-barrels. - Dong Si; Jing He 002 (EMBC, 2014)

Solving the Secondary Structure MatchingProblem in Cryo-EM De Novo ModelingUsing a Constrained $K$-Shortest Path Graph Algorithm. - Kamal Al-Nasr; Desh Ranjan; Mohammad Zubair; Lin Chen 007; Jing He 002 (IEEE ACM Trans. Comput. Biol. Bioinform., 2014)

Comparison of an atomic model and its cryo-EM image at the central axis of a helix. - Jing He 002; Stephanie Zeil; Hussam Hallak; Kele McKaig; Julio A. Kovacs; Willy Wriggers (BIBM, 2015)

Detection of Secondary Structures from 3D Protein Images of Medium Resolutions and its Challenges. - Jing He 002; Dong Si; Maryam Arab (ICIG (2), 2015)

Deriving Protein Backbone Using Traces Extracted from Density Maps at Medium Resolutions. - Kamal Al-Nasr; Jing He 002 (ISBRA, 2015)

A Novel Computational Method for Deriving Protein Secondary Structure Topologies Using Cryo-EM Density Maps and Multiple Secondary Structure Predictions. - Abhishek Biswas; Desh Ranjan; Mohammad Zubair; Jing He 002 (ISBRA, 2015)

A Dynamic Programming Algorithm for Finding the Optimal Placement of a Secondary Structure Topology in Cryo-EM Data. - Abhishek Biswas; Desh Ranjan; Mohammad Zubair; Jing He 002 (J. Comput. Biol., 2015)

The 7th Computational Structural Bioinformatics Workshop. - Jing He 002; Amarda Shehu; Nurit Haspel; Brian Chen (J. Comput. Biol., 2015)

Challenges in matching secondary structures in cryo-EM: An exploration. - Devin Haslam; Mohammad Zubair; Desh Ranjan; Abhishek Biswas; Jing He 002 (BIBM, 2016)

Deep convolutional neural networks for detecting secondary structures in protein density maps from cryo-electron microscopy. - Rongjian Li; Dong Si; Tao Zeng; Shuiwang Ji; Jing He 002 (BIBM, 2016)

Selecting near-native structures from decoys using maximal cliques. - Jinyang Yan; Yonggang Lu; Jing He 002 (BIBM, 2016)

Constrained cyclic coordinate descent for cryo-EM images at medium resolutions: beyond the protein loop closure problem. - Kamal Al-Nasr; Jing He 002 (Robotica, 2016)

Analysis of ß-strand Twist from the 3-dimensional Image of a Protein. - Tunazzina Islam; Michael Poteat; Jing He 002 (BCB, 2017)

Preface: Selected Articles from 2015 Computational Structural Bioinformatics Workshop. - Jing He 002; Nurit Haspel; Brian Chen (J. Comput. Biol., 2017)

Comparing an Atomic Model or Structure to a Corresponding Cryo-electron Microscopy Image at the Central Axis of a Helix. - Stephanie Zeil; Julio A. Kovacs; Willy Wriggers; Jing He 002 (J. Comput. Biol., 2017)

An Effective Computational Method Incorporating Multiple Secondary Structure Predictions in Topology Determination for Cryo-EM Images. - Abhishek Biswas; Desh Ranjan; Mohammad Zubair; Stephanie Zeil; Kamal Al-Nasr; Jing He 002 (IEEE ACM Trans. Comput. Biol. Bioinform., 2017)

Using Combined Features to Analyze Atomic Structures derived from Cryo-EM Density Maps. - Lin Chen 007; Jing He 002 (BCB, 2018)

Exploratory Studies Detecting Secondary Structures in Medium Resolution 3D Cryo-EM Images Using Deep Convolutional Neural Networks. - Devin Haslam; Tao Zeng; Rongjian Li; Jing He 002 (BCB, 2018)

A Pattern Recognition Tool for Medium-Resolution Cryo-EM Density Maps and Low-Resolution Cryo-ET Density Maps. - Devin Haslam; Salim Sazzed; Willy Wriggers; Julio Kovcas; Junha Song; Manfred Auer; Jing He 002 (ISBRA, 2018)

Special IssuePreface: The 9th Computational Structural Bioinformatics Workshop. - Jing He 002; Kamal Al-Nasr; Weitao Sun; Yonggang Lu (J. Comput. Biol., 2018)

Quantification of Twist from the Central Lines of β-Strands. - Tunazzina Islam; Michael Poteat; Jing He 002 (J. Comput. Biol., 2018)

A Histogram-based Outlier Profile for Atomic Structures Derived from Cryo-Electron Microscopy. - Lin Chen 007; Jing He 002 (BCB, 2019)

Correction of Missing-Wedge Artifacts in Filamentous Tomograms by Template-Based Constrained Deconvolution. - Julio A. Kovacs; Junha Song; Manfred Auer; Jing He 002; Wade Hunter; Willy Wriggers (J. Chem. Inf. Model., 2020)

Cylindrical Similarity Measurement for Helices in Medium-Resolution Cryo-Electron Microscopy Density Maps. - Salim Sazzed; Peter Scheible; Maytha Alshammari; Willy Wriggers; Jing He 002 (J. Chem. Inf. Model., 2020)

Tracing Filaments in Simulated 3D Cryo-Electron Tomography Maps Using a Fast Dynamic Programming Algorithm. - Salim Sazzed; Peter Scheible; Jing He 002; Willy Wriggers (BIBM, 2021)

TomoSim: Simulation of Filamentous Cryo-Electron Tomograms. - Peter Scheible; Salim Sazzed; Jing He 002; Willy Wriggers (BIBM, 2021)

A Tool for Segmentation of Secondary Structures in 3D Cryo-EM Density Map Components Using Deep Convolutional Neural Networks. - Yongcheng Mu; Salim Sazzed; Maytha Alshammari; Jiangwen Sun; Jing He 002 (Frontiers Bioinform., 2021)

Refinement of AlphaFold2 Models against Experimental Cryo-EM Density Maps at 4-6Å Resolution. - Maytha Alshammari; Jing He 002; Willy Wriggers (BIBM, 2022)

The Combined Focal Cross Entropy and Dice Loss Function for Segmentation of Protein Secondary Structures from Cryo-EM 3D Density maps. - Yongcheng Mu; Jiangwen Sun; Jing He 002 (BIBM, 2022)

Tracing Randomly Oriented Filaments in a Simulated Actin Network Tomogram. - Salim Sazzed; Peter Scheible; Jing He 002; Willy Wriggers (BIBM, 2022)

AlphaFold2 Model Refinement Using Structure Decoys. - Maytha Alshammari; Jing He 002; Willy Wriggers (BCB, 2023)

An Approach to Developing Benchmark Datasets for Protein Secondary Structure Segmentation from Cryo-EM Density Maps. - Thu Nguyen; Yongcheng Mu; Jiangwen Sun; Jing He 002 (BCB, 2023)

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. - Thu Nguyen; Willy Wriggers; Jing He 002 (ISBRA (3), 2024)