Jing He - RankMe

55 papers B 2C 1Misc 1Journal 19Unranked 31

Year	Rank	Type	Title / Venue / Authors
2025	—	`conf`	Benchmarking and Improving Foundation Model Dietary Estimates from Meal Images. BCB Yongcheng Mu, Jiangwen Sun, Jing He
2025	—	`conf`	DeepSSETracer 2.0: Improved Deep Learning Model Performance for Protein Secondary Structure Segmentation from Cryo-EM Maps. BCB Companion Bryan Hawickhorst, Thu Nguyen, Willy Wriggers, Jiangwen Sun, Jing He
2024	—	`conf`	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) Thu Nguyen, Willy Wriggers, Jing He
2023	—	`conf`	AlphaFold2 Model Refinement Using Structure Decoys. BCB Maytha Alshammari, Jing He, Willy Wriggers
2023	—	`conf`	An Approach to Developing Benchmark Datasets for Protein Secondary Structure Segmentation from Cryo-EM Density Maps. BCB Thu Nguyen, Yongcheng Mu, Jiangwen Sun, Jing He
2022	—	`conf`	Refinement of AlphaFold2 Models against Experimental Cryo-EM Density Maps at 4-6Å Resolution. BIBM Maytha Alshammari, Jing He, Willy Wriggers
2022	—	`conf`	The Combined Focal Cross Entropy and Dice Loss Function for Segmentation of Protein Secondary Structures from Cryo-EM 3D Density maps. BIBM Yongcheng Mu, Jiangwen Sun, Jing He
2022	—	`conf`	Tracing Randomly Oriented Filaments in a Simulated Actin Network Tomogram. BIBM Salim Sazzed, Peter Scheible, Jing He, Willy Wriggers
2021	J	`jnl`	A Tool for Segmentation of Secondary Structures in 3D Cryo-EM Density Map Components Using Deep Convolutional Neural Networks. Frontiers Bioinform. Yongcheng Mu, Salim Sazzed, Maytha Alshammari, Jiangwen Sun, Jing He
2021	—	`conf`	TomoSim: Simulation of Filamentous Cryo-Electron Tomograms. BIBM Peter Scheible, Salim Sazzed, Jing He, Willy Wriggers
2021	—	`conf`	Tracing Filaments in Simulated 3D Cryo-Electron Tomography Maps Using a Fast Dynamic Programming Algorithm. BIBM Salim Sazzed, Peter Scheible, Jing He, Willy Wriggers
2020	J	`jnl`	Correction of Missing-Wedge Artifacts in Filamentous Tomograms by Template-Based Constrained Deconvolution. J. Chem. Inf. Model. Julio A. Kovacs, Junha Song, Manfred Auer, Jing He, Wade Hunter, Willy Wriggers
2020	J	`jnl`	Cylindrical Similarity Measurement for Helices in Medium-Resolution Cryo-Electron Microscopy Density Maps. J. Chem. Inf. Model. Salim Sazzed, Peter Scheible, Maytha Alshammari, Willy Wriggers, Jing He
2019	—	`conf`	A Histogram-based Outlier Profile for Atomic Structures Derived from Cryo-Electron Microscopy. BCB Lin Chen, Jing He
2018	—	`conf`	A Pattern Recognition Tool for Medium-Resolution Cryo-EM Density Maps and Low-Resolution Cryo-ET Density Maps. ISBRA Devin Haslam, Salim Sazzed, Willy Wriggers, Julio Kovcas, Junha Song, Manfred Auer, Jing He
2018	—	`conf`	Exploratory Studies Detecting Secondary Structures in Medium Resolution 3D Cryo-EM Images Using Deep Convolutional Neural Networks. BCB Devin Haslam, Tao Zeng, Rongjian Li, Jing He
2018	J	`jnl`	Quantification of Twist from the Central Lines of β-Strands. J. Comput. Biol. Tunazzina Islam, Michael Poteat, Jing He
2018	—	`conf`	Using Combined Features to Analyze Atomic Structures derived from Cryo-EM Density Maps. BCB Lin Chen, Jing He
2017	J	`jnl`	An Effective Computational Method Incorporating Multiple Secondary Structure Predictions in Topology Determination for Cryo-EM Images. IEEE ACM Trans. Comput. Biol. Bioinform. Abhishek Biswas, Desh Ranjan, Mohammad Zubair, Stephanie Zeil, Kamal Al-Nasr, Jing He
2017	—	`conf`	Analysis of ß-strand Twist from the 3-dimensional Image of a Protein. BCB Tunazzina Islam, Michael Poteat, Jing He
2017	J	`jnl`	Comparing an Atomic Model or Structure to a Corresponding Cryo-electron Microscopy Image at the Central Axis of a Helix. J. Comput. Biol. Stephanie Zeil, Julio A. Kovacs, Willy Wriggers, Jing He
2017	J	`jnl`	Preface: Selected Articles from 2015 Computational Structural Bioinformatics Workshop. J. Comput. Biol. Jing He, Nurit Haspel, Brian Chen
2016	—	`conf`	Challenges in matching secondary structures in cryo-EM: An exploration. BIBM Devin Haslam, Mohammad Zubair, Desh Ranjan, Abhishek Biswas, Jing He
2016	J	`jnl`	Constrained cyclic coordinate descent for cryo-EM images at medium resolutions: beyond the protein loop closure problem. Robotica Kamal Al-Nasr, Jing He
2016	—	`conf`	Deep convolutional neural networks for detecting secondary structures in protein density maps from cryo-electron microscopy. BIBM Rongjian Li, Dong Si, Tao Zeng, Shuiwang Ji, Jing He
2016	—	`conf`	Selecting near-native structures from decoys using maximal cliques. BIBM Jinyang Yan, Yonggang Lu, Jing He
2015	J	`jnl`	A Dynamic Programming Algorithm for Finding the Optimal Placement of a Secondary Structure Topology in Cryo-EM Data. J. Comput. Biol. Abhishek Biswas, Desh Ranjan, Mohammad Zubair, Jing He
2015	—	`conf`	A Novel Computational Method for Deriving Protein Secondary Structure Topologies Using Cryo-EM Density Maps and Multiple Secondary Structure Predictions. ISBRA Abhishek Biswas, Desh Ranjan, Mohammad Zubair, Jing He
2015	—	`conf`	Comparison of an atomic model and its cryo-EM image at the central axis of a helix. BIBM Jing He, Stephanie Zeil, Hussam Hallak, Kele McKaig, Julio A. Kovacs, Willy Wriggers
2015	—	`conf`	Deriving Protein Backbone Using Traces Extracted from Density Maps at Medium Resolutions. ISBRA Kamal Al-Nasr, Jing He
2015	—	`conf`	Detection of Secondary Structures from 3D Protein Images of Medium Resolutions and its Challenges. ICIG (2) Jing He, Dong Si, Maryam Arab
2015	J	`jnl`	The 7th Computational Structural Bioinformatics Workshop. J. Comput. Biol. Jing He, Amarda Shehu, Nurit Haspel, Brian Chen
2014	—	`conf`	Combining image processing and modeling to generate traces of beta-strands from cryo-EM density images of beta-barrels. EMBC Dong Si, Jing He
2014	—	`conf`	Construction of protein backbone pieces using segment-based FBCCD and Cryo-EM skeleton. BCB Kamal Al-Nasr, Jing He
2014	—	`conf`	Orientations of beta-strand traces and near maximum twist. BCB Dong Si, Jing He
2014	J	`jnl`	Solving the Secondary Structure MatchingProblem in Cryo-EM De Novo ModelingUsing a Constrained $K$-Shortest Path Graph Algorithm. IEEE ACM Trans. Comput. Biol. Bioinform. Kamal Al-Nasr, Desh Ranjan, Mohammad Zubair, Lin Chen, Jing He
2013	—	`conf`	A Constrained K-shortest Path Algorithm to Rank the Topologies of the Protein Secondary Structure Elements Detected in CryoEM Volume Maps. BCB Kamal Al-Nasr, Lin Chen, Desh Ranjan, Mohammad Zubair, Dong Si, Jing He
2013	—	`conf`	Beta-sheet Detection and Representation from Medium Resolution Cryo-EM Density Maps. BCB Dong Si, Jing He
2013	J	`jnl`	Intensity-Based Skeletonization of CryoEM Gray-Scale Images Using a True Segmentation-Free Algorithm. IEEE ACM Trans. Comput. Biol. Bioinform. Kamal Al-Nasr, Chunmei Liu, Mugizi Robert Rwebangira, Legand Burge, Jing He
2012	—	`conf`	Building the initial chain of the proteins through de novo modeling of the cryo-electron microscopy volume data at the medium resolutions. BCB Kamal Al-Nasr, Lin Chen, Dong Si, Desh Ranjan, Mohammad Zubair, Jing He
2012	—	`conf`	CryoEM skeleton length estimation using a decimated curve. BIBM Workshops Andrew McKnight, Kamal Al-Nasr, Dong Si, Andrey N. Chernikov, Nikos Chrisochoides, Jing He
2012	J	`jnl`	Improved Efficiency in Cryo-EM Secondary Structure Topology Determination from Inaccurate Data. J. Bioinform. Comput. Biol. Abhishek Biswas, Dong Si, Kamal Al-Nasr, Desh Ranjan, Mohammad Zubair, Jing He
2011	—	`conf`	A Constraint Dynamic Graph Approach to Identify the Secondary Structure Topology from cryoEM Density Data in Presence of Errors. BIBM Abhishek Biswas, Dong Si, Kamal Al-Nasr, Desh Ranjan, Mohammad Zubair, Jing He
2011	—	`conf`	A distance and orientation dependent potential energy function with cluster energy. BIBM Workshops Lin Chen, Jing He
2011	J	`jnl`	Ranking Valid Topologies of the Secondary Structure Elements Using a Constraint Graph. J. Bioinform. Comput. Biol. Kamal Al-Nasr, Desh Ranjan, Mohammad Zubair, Jing He
2010	J	`jnl`	Structure prediction for the helical skeletons detected from the low resolution protein density map. BMC Bioinform. Kamal Al-Nasr, Weitao Sun, Jing He
2009	J	`jnl`	An effective convergence independent loop closure method using Forward-Backward Cyclic Coordinate Descent. Int. J. Data Min. Bioinform. Kamal Al-Nasr, Jing He
2009	J	`jnl`	Reduction of the secondary structure topological space through direct estimation of the contact energy formed by the secondary structures. BMC Bioinform. Weitao Sun, Jing He
2008	J	`jnl`	Deriving Topology and Sequence Alignment for the Helix Skeleton in Low-Resolution protein Density Maps. J. Bioinform. Comput. Biol. Yonggang Lu, Jing He, Charlie E. M. Strauss
2007	J	`jnl`	A Constraint Logic Programming approach to associate 1D and 3D structural components for large protein complexes. Int. J. Data Min. Bioinform. Alessandro Dal Palù, Enrico Pontelli, Jing He, Yonggang Lu
2007	B	`conf`	Deriving Protein Structure Topology from the Helix Skeletion in Low Resolution Density Map using Rosetta. APBC Yonggang Lu, Jing He, Charlie E. M. Strauss
2006	Misc	`conf`	A constraint logic programming approach to 3D structure determination of large protein complexes. SAC Alessandro Dal Palù, Enrico Pontelli, Jing He, Yonggang Lu
2005	—	`ch.`	Using the Length Constraints of Helix to Evaluate protein secondary Structure Prediction for Helix. Advances in Bioinformatics and Its Applications Jing He, Yonggang Lu
2004	C	`conf`	A Parallel Algorithm for Helix Mapping Between 3D and 1D Protein Structure Using the Length Constraints. ISPA Jing He, Yonggang Lu, Enrico Pontelli
2004	B	`conf`	Detecting Local Symmetry Axis in 3-dimensional Virus Structures. APBC Jing He, Desh Ranjan, Wen Jiang, Wah Chiu, Michael F. Schmid