Jianlin Cheng

ORCID

Publication Activity (10 Years)

Years Active: 2004-2024
Publications (10 Years): 74

Top Venues

Publications

Alex Morehead, Jianlin Cheng
Geometry-complete perceptron networks for 3D molecular graphs. Bioinform. 40 (2) (2024)
Alex Morehead, Nabin Giri, Jian Liu, Jianlin Cheng
Deep Learning for Protein-Ligand Docking: Are We There Yet? CoRR (2024)
Yanli Wang, Jianlin Cheng
HiCDiff: single-cell Hi-C data denoising with diffusion models. Briefings Bioinform. 25 (4) (2024)
Rajan Gyawali, Ashwin Dhakal, Liguo Wang, Jianlin Cheng
CryoSegNet: accurate cryo-EM protein particle picking by integrating the foundational AI image segmentation model and attention-gated U-Net. Briefings Bioinform. 25 (4) (2024)
Arian R. Jamasb, Alex Morehead, Chaitanya K. Joshi, Zuobai Zhang, Kieran Didi, Simon V. Mathis, Charles Harris, Jian Tang, Jianlin Cheng, Pietro Lio, Tom L. Blundell
Evaluating representation learning on the protein structure universe. CoRR (2024)
Arian Rokkum Jamasb, Alex Morehead, Chaitanya K. Joshi, Zuobai Zhang, Kieran Didi, Simon V. Mathis, Charles Harris, Jian Tang, Jianlin Cheng, Pietro Lio, Tom L. Blundell
Evaluating Representation Learning on the Protein Structure Universe. ICLR (2024)
Alex Morehead, Watchanan Chantapakul, Jianlin Cheng
Semi-Supervised Graph Learning Meets Dimensionality Reduction. ICMLA (2023)
Chen Chen, Xiao Chen, Alex Morehead, Tianqi Wu, Jianlin Cheng
3D-equivariant graph neural networks for protein model quality assessment. Bioinform. 39 (1) (2023)
Frimpong Boadu, Hongyuan Cao, Jianlin Cheng
Combining protein sequences and structures with transformers and equivariant graph neural networks to predict protein function. Bioinform. 39 (Supplement-1) (2023)
Russell B. Davidson, Mark Coletti, Mu Gao, Bryan Piatkowski, Avinash Sreedasyam, Farhan Quadir, David J. Weston, Jeremy Schmutz, Jianlin Cheng, Jeffrey Skolnick, Jerry M. Parks, Ada Sedova
and proteome-scale annotation. Bioinform. 39 (8) (2023)
Alessio Del Conte, Adel Bouhraoua, Mahta Mehdiabadi, Damiano Clementel, Alexander Miguel Monzon, Alex S. Holehouse, Daniel A. Griffith, Ryan J. Emenecker, Ashwini Patil, Ronesh Sharma, Tatsuhiko Tsunoda, Alok Sharma, Yi Jun Tang, Bin Liu, Claudio Mirabello, Björn Wallner, Burkhard Rost, Dagmar Ilzhöfer, Maria Littmann, Michael Heinzinger, Lea I M. Krautheimer, Michael Bernhofer, Liam J. McGuffin, Isabelle Callebaut, Tristan Bitard Feildel, Jian Liu, Jianlin Cheng, Zhiye Guo, Jinbo Xu, Sheng Wang, Nawar Malhis, Jörg Gsponer, Chol-Song Kim, Kun-Sop Han, Myong-Chol Ma, Lukasz A. Kurgan, Sina Ghadermarzi, Akila Katuwawala, Bi Zhao, Zhenling Peng, Zhonghua Wu, Gang Hu, Kui Wang, Md. Tamjidul Hoque, Md Wasi Ul Kabir, Michele Vendruscolo, Pietro Sormanni, Min Li, Fuhao Zhang, Pengzhen Jia, Yida Wang, Michail Yu. Lobanov, Oxana V. Galzitskaya, Wim F. Vranken, Adrián Díaz, Thomas Litfin, Yaoqi Zhou, Jack Hanson, Kuldip K. Paliwal, Zsuzsanna Dosztányi, Gábor Erdös, Silvio C. E. Tosatto, Damiano Piovesan
CAID prediction portal: a comprehensive service for predicting intrinsic disorder and binding regions in proteins. Nucleic Acids Res. 51 (W1) (2023)
Xiao Chen, Alex Morehead, Jian Liu, Jianlin Cheng
A gated graph transformer for protein complex structure quality assessment and its performance in CASP15. Bioinform. 39 (Supplement-1) (2023)
Prasad Calyam, Mayank Kejriwal, Praveen Rao, Jianlin Cheng, Weichao Wang, Linquan Bai, V. Sriram Siddhardh Nadendla, Sanjay Madria, Sajal K. Das, Rohit Chadha, Khaza Anuarul Hoque, Kannappan Palaniappan, Kiran Neupane, Roshan Lal Neupane, Sankeerth Gandhari, Mukesh Singhal, Lotfi Ben Othmane, Meng Yu, Vijay Anand, Bharat K. Bhargava, Brett Robertson, Kerk F. Kee, Patrice Buzzanell, Natalie A. Bolton, Harsh Taneja
Towards a Domain-Agnostic Knowledge Graph-as-a-Service Infrastructure for Active Cyber Defense with Intelligent Agents. AIPR (2023)
Alex Morehead, Jianlin Cheng
Geometry-Complete Diffusion for 3D Molecule Generation. CoRR (2023)
Yanli Wang, Zhiye Guo, Jianlin Cheng
Single-cell Hi-C data enhancement with deep residual and generative adversarial networks. Bioinform. 39 (8) (2023)
Fei He, Zhiyuan Yang, Mingyue Gao, Biplab Poudel, Newgin Sam Ebin Sam Dhas, Rajan Gyawali, Ashwin Dhakal, Jianlin Cheng, Dong Xu
Adapting Segment Anything Model (SAM) through Prompt-based Learning for Enhanced Protein Identification in Cryo-EM Micrographs. CoRR (2023)
Tianqi Wu, Zhiye Guo, Jianlin Cheng
Atomic protein structure refinement using all-atom graph representations and SE(3)-equivariant graph transformer. Bioinform. 39 (5) (2023)
Zhiye Guo, Jian Liu, Yanli Wang, Mengrui Chen, Duolin Wang, Dong Xu, Jianlin Cheng
Diffusion Models in Bioinformatics: A New Wave of Deep Learning Revolution in Action. CoRR (2023)
Md Maruf Hossain Shuvo, Syed Kamrul Islam, Jianlin Cheng, Bashir I. Morshed
Efficient Acceleration of Deep Learning Inference on Resource-Constrained Edge Devices: A Review. Proc. IEEE 111 (1) (2023)
Alex Morehead, Watchanan Chantapakul, Jianlin Cheng
Semi-Supervised Graph Learning Meets Dimensionality Reduction. CoRR (2022)
Sajid Mahmud, Zhiye Guo, Farhan Quadir, Jian Liu, Jianlin Cheng
Multi-head attention-based U-Nets for predicting protein domain boundaries using 1D sequence features and 2D distance maps. BMC Bioinform. 23 (1) (2022)
Xiao Chen, Jianlin Cheng
DISTEMA: distance map-based estimation of single protein model accuracy with attentive 2D convolutional neural network. BMC Bioinform. (3) (2022)
Alex Morehead, Jianlin Cheng
Geometry-Complete Perceptron Networks for 3D Molecular Graphs. CoRR (2022)
Xiao Chen, Alex Morehead, Jian Liu, Jianlin Cheng
DProQ: A Gated-Graph Transformer for Protein Complex Structure Assessment. CoRR (2022)
Ashwin Dhakal, Cole McKay, John J. Tanner, Jianlin Cheng
Artificial intelligence in the prediction of protein-ligand interactions: recent advances and future directions. Briefings Bioinform. 23 (1) (2022)
Elham Soltanikazemi, Raj S. Roy, Farhan Quadir, Nabin Giri, Alex Morehead, Jianlin Cheng
DRLComplex: Reconstruction of protein quaternary structures using deep reinforcement learning. CoRR (2022)
Sajid Mahmud, Elham Soltanikazemi, Frimpong Boadu, Ashwin Dhakal, Jianlin Cheng
Deep Learning Prediction of Severe Health Risks for Pediatric COVID-19 Patients with a Large Feature Set in 2021 BARDA Data Challenge. CoRR (2022)
Md Maruf Hossain Shuvo, Nafis Ahmed, Humayera Islam, Khuder Alaboud, Jianlin Cheng, Abu Saleh Mohammad Mosa, Syed Kamrul Islam
Machine Learning Embedded Smartphone Application for Early-Stage Diabetes Risk Assessment. MeMeA (2022)
Alex Morehead, Xiao Chen, Tianqi Wu, Jian Liu, Jianlin Cheng
EGR: Equivariant Graph Refinement and Assessment of 3D Protein Complex Structures. CoRR (2022)
Alex Morehead, Chen Chen, Jianlin Cheng
Geometric Transformers for Protein Interface Contact Prediction. ICLR (2022)
Nabin Giri, Raj S. Roy, Jianlin Cheng
Deep learning for reconstructing protein structures from cryo-EM density maps: recent advances and future directions. CoRR (2022)
Raj S. Roy, Farhan Quadir, Elham Soltanikazemi, Jianlin Cheng
A deep dilated convolutional residual network for predicting interchain contacts of protein homodimers. Bioinform. 38 (7) (2022)
Adil Al-Azzawi, Anes Ouadou, Ye Duan, Jianlin Cheng
Correction to: Auto3DCryoMap: an automated particle alignment approach for 3D cryo-EM density map reconstruction. BMC Bioinform. 23 (1) (2022)
Mu Gao, Peik Lund-Andersen, Alex Morehead, Sajid Mahmud, Chen Chen, Xiao Chen, Nabin Giri, Raj S. Roy, Farhan Quadir, T. Chad Effler, Ryan Prout, Subil Abraham, Wael R. Elwasif, Nicholas Quentin Haas, Jeffrey Skolnick, Jianlin Cheng, Ada Sedova
High-Performance Deep Learning Toolbox for Genome-Scale Prediction of Protein Structure and Function. MLHPC@SC (2021)
Tianqi Wu, Zhiye Guo, Jie Hou, Jianlin Cheng
DeepDist: real-value inter-residue distance prediction with deep residual convolutional network. BMC Bioinform. 22 (1) (2021)
Alex Morehead, Chen Chen, Ada Sedova, Jianlin Cheng
DIPS-Plus: The Enhanced Database of Interacting Protein Structures for Interface Prediction. CoRR (2021)
Tianqi Wu, Zhiye Guo, Jie Hou, Jianlin Cheng
Correction to: DeepDist: real‑value inter‑residue distance prediction with deep residual convolutional network. BMC Bioinform. 22 (1) (2021)
Alex Morehead, Chen Chen, Jianlin Cheng
Geometric Transformers for Protein Interface Contact Prediction. CoRR (2021)
Chen Chen, Jie Hou, Xiaowen Shi, Hua Yang, James A. Birchler, Jianlin Cheng
DeepGRN: prediction of transcription factor binding site across cell-types using attention-based deep neural networks. BMC Bioinform. 22 (1) (2021)
Zhiye Guo, Tianqi Wu, Jian Liu, Jie Hou, Jianlin Cheng
Improving deep learning-based protein distance prediction in CASP14. Bioinform. 37 (19) (2021)
Adil Al-Azzawi, Anes Ouadou, Highsmith Max, Ye Duan, John J. Tanner, Jianlin Cheng
DeepCryoPicker: fully automated deep neural network for single protein particle picking in cryo-EM. BMC Bioinform. 21 (1) (2020)
Xiao Chen, Nasrin Akhter, Zhiye Guo, Tianqi Wu, Jie Hou, Amarda Shehu, Jianlin Cheng
Deep Ranking in Template-free Protein Structure Prediction. BCB (2020)
Meshal Alfarhood, Jianlin Cheng
CATA++: A Collaborative Dual Attentive Autoencoder Method for Recommending Scientific Articles. CoRR (2020)
Tianqi Wu, Jie Hou, Badri Adhikari, Jianlin Cheng
Analysis of several key factors influencing deep learning-based inter-residue contact prediction. Bioinform. 36 (4) (2020)
Adil Al-Azzawi, Anes Ouadou, Ye Duan, Jianlin Cheng
Auto3DCryoMap: an automated particle alignment approach for 3D cryo-EM density map reconstruction. BMC Bioinform. (21) (2020)
Meshal Alfarhood, Jianlin Cheng
CATA++: A Collaborative Dual Attentive Autoencoder Method for Recommending Scientific Articles. IEEE Access 8 (2020)
Tuan Trieu, Oluwatosin Oluwadare, Julia Wopata, Jianlin Cheng
GenomeFlow: a comprehensive graphical tool for modeling and analyzing 3D genome structure. Bioinform. 35 (8) (2019)
Meshal Alfarhood, Jianlin Cheng
Collaborative Attentive Autoencoder for Scientific Article Recommendation. ICMLA (2019)
Yuanyuan Bian, Chong He, Jie Hou, Jianlin Cheng, Jing Qiu
PairedFB: a full hierarchical Bayesian model for paired RNA-seq data with heterogeneous treatment effects. Bioinform. 35 (5) (2019)
Jianlin Cheng
Protein Tertiary Structure Modeling Driven by Deep Learning and Contact Distance Prediction in CASP13. BCB (2019)
Jianlin Cheng
Introduction to 2019 ACM-BCB Highlights Session. BCB (2019)
Adil Al-Azzawi, Anes Ouadou, John J. Tanner, Jianlin Cheng
AutoCryoPicker: an unsupervised learning approach for fully automated single particle picking in Cryo-EM images. BMC Bioinform. 20 (1) (2019)
Adil Al-Azzawi, Jade Hind, Jianlin Cheng
Localized Deep-CNN Structure for Face Recognition. DeSE (2018)
Jie Hou, Badri Adhikari, Jianlin Cheng
DeepSF: Deep Convolutional Neural Network for Mapping Protein Sequences to Folds. BCB (2018)
Adil Al-Azzawi, Hasanain Al-Sadr, Jianlin Cheng, Tony X. Han
Localized Deep Norm-CNN Structure for Face Verification. ICMLA (2018)
Badri Adhikari, Jie Hou, Jianlin Cheng
DNCON2: improved protein contact prediction using two-level deep convolutional neural networks. Bioinform. 34 (9) (2018)
Badri Adhikari, Jianlin Cheng
CONFOLD2: improved contact-driven ab initio protein structure modeling. BMC Bioinform. 19 (1) (2018)
Meshal Alfarhood, Jianlin Cheng
DeepHCF: A Deep Learning Based Hybrid Collaborative Filtering Approach for Recommendation Systems. ICMLA (2018)
Jie Hou, Badri Adhikari, Jianlin Cheng
DeepSF: deep convolutional neural network for mapping protein sequences to folds. Bioinform. 34 (8) (2018)
Renzhi Cao, Badri Adhikari, Debswapna Bhattacharya, Miao Sun, Jie Hou, Jianlin Cheng
QAcon: single model quality assessment using protein structural and contact information with machine learning techniques. Bioinform. 33 (4) (2017)
Haiou Li, Jie Hou, Badri Adhikari, Qiang Lyu, Jianlin Cheng
Deep learning methods for protein torsion angle prediction. BMC Bioinform. 18 (1) (2017)
Jie Hou, Badri Adhikari, Jianlin Cheng
DeepSF: deep convolutional neural network for mapping protein sequences to folds. CoRR (2017)
Badri Adhikari, Jianlin Cheng
Improved protein structure reconstruction using secondary structures, contacts at higher distance thresholds, and non-contacts. BMC Bioinform. 18 (1) (2017)
Tuan Trieu, Jianlin Cheng
3D Genome Structure Modeling by Lorentzian Objective Function. BCB (2017)
Oluwatosin Oluwadare, Jianlin Cheng
ClusterTAD: an unsupervised machine learning approach to detecting topologically associated domains of chromosomes from Hi-C data. BMC Bioinform. 18 (1) (2017)
Debswapna Bhattacharya, Renzhi Cao, Jianlin Cheng
protein structure prediction using united-residue conformational search via stepwise, probabilistic sampling. Bioinform. 32 (18) (2016)
Renzhi Cao, Debswapna Bhattacharya, Jie Hou, Jianlin Cheng
DeepQA: Improving the estimation of single protein model quality with deep belief networks. CoRR (2016)
Renzhi Cao, Debswapna Bhattacharya, Jie Hou, Jianlin Cheng
DeepQA: improving the estimation of single protein model quality with deep belief networks. BMC Bioinform. 17 (2016)
Renzhi Cao, Taeho Jo, Jianlin Cheng
Evaluation of Protein Structural Models Using Random Forests. CoRR (2016)
Debswapna Bhattacharya, Jackson Nowotny, Renzhi Cao, Jianlin Cheng
3Drefine: an interactive web server for efficient protein structure refinement. Nucleic Acids Res. 44 (Webserver-Issue) (2016)
Tuan Trieu, Jianlin Cheng
MOGEN: a tool for reconstructing 3D models of genomes from chromosomal conformation capturing data. Bioinform. 32 (9) (2016)
Debswapna Bhattacharya, Badri Adhikari, Jilong Li, Jianlin Cheng
FRAGSION: ultra-fast protein fragment library generation by IOHMM sampling. Bioinform. 32 (13) (2016)
Badri Adhikari, Jackson Nowotny, Debswapna Bhattacharya, Jie Hou, Jianlin Cheng
ConEVA: a toolbox for comprehensive assessment of protein contacts. BMC Bioinform. 17 (2016)
Rui Xie, Andrew Quitadamo, Jianlin Cheng, Xinghua Shi
A predictive model of gene expression using a deep learning framework. BIBM (2016)
Jilong Li, Jie Hou, Lin Sun, Jordan Maximillian Wilkins, Yuan Lu, Chad E. Niederhuth, Benjamin Ryan Merideth, Thomas P. Mawhinney, Valeri V. Mossine, Michael Greenlief, John C. Walker, William R. Folk, Mark Hannink, Dennis B. Lubahn, James A. Birchler, Jianlin Cheng
From gigabyte to kilobyte: a bioinformatics protocol for mining large RNA-Seq transcriptomics data. BCB (2015)
Jie Hou, Gary Stacey, Jianlin Cheng
Exploring soybean metabolic pathways based on probabilistic graphical model and knowledge-based methods. EURASIP J. Bioinform. Syst. Biol. 2015 (2015)
Renzhi Cao, Debswapna Bhattacharya, Badri Adhikari, Jilong Li, Jianlin Cheng
Large-scale model quality assessment for improving protein tertiary structure prediction. Bioinform. 31 (12) (2015)
Jilong Li, Renzhi Cao, Jianlin Cheng
A large-scale conformation sampling and evaluation server for protein tertiary structure prediction and its assessment in CASP11. BMC Bioinform. 16 (2015)
Jackson Nowotny, Sharif Ahmed, Lingfei Xu, Oluwatosin Oluwadare, Hannah Chen, Noelan Hensley, Tuan Trieu, Renzhi Cao, Jianlin Cheng
Iterative reconstruction of three-dimensional models of human chromosomes from chromosomal contact data. BMC Bioinform. 16 (2015)
Jilong Li, Renzhi Cao, Jianlin Cheng
MULTICOM: a large-scale conformation sampling and evaluation server for protein tertiary structure prediction. BCB (2015)
Matt Spencer, Jesse Eickholt, Jianlin Cheng
A Deep Learning Network Approach to ab initio Protein Secondary Structure Prediction. IEEE ACM Trans. Comput. Biol. Bioinform. 12 (1) (2015)
Xin Deng, Jianlin Cheng
Enhancing HMM-based protein profile-profile alignment with structural features and evolutionary coupling information. BMC Bioinform. 15 (2014)
Renzhi Cao, Zheng Wang, Yiheng Wang, Jianlin Cheng
SMOQ: a tool for predicting the absolute residue-specific quality of a single protein model with support vector machines. BMC Bioinform. 15 (2014)
Taeho Jo, Jianlin Cheng
Improving protein fold recognition by random forest. BMC Bioinform. 15 (S-11) (2014)
Jesse Eickholt, Jianlin Cheng
A study and benchmark of DNcon: a method for protein residue-residue contact prediction using deep networks. BMC Bioinform. 14 (S-14) (2013)
Debswapna Bhattacharya, Jianlin Cheng
Protein Structure Refinement by Iterative Fragment Exchange. BCB (2013)
Jesse Eickholt, Jianlin Cheng
DNdisorder: predicting protein disorder using boosting and deep networks. BMC Bioinform. 14 (2013)
Mingzhu Zhu, Jeremy L. Dahmen, Gary Stacey, Jianlin Cheng
Predicting gene regulatory networks of soybean nodulation from RNA-Seq transcriptome data. BMC Bioinform. 14 (2013)
Zheng Wang, Renzhi Cao, Jianlin Cheng
Three-Level Prediction of Protein Function by Combining Profile-Sequence Search, Profile-Profile Search, and Domain Co-Occurrence Networks. BMC Bioinform. 14 (S-3) (2013)
Debswapna Bhattacharya, Jianlin Cheng
Automated protein structure refinement using i3Drefine software and its assessment in CASP10. BCB (2013)
Trupti Joshi, Kapil Patil, Michael R. Fitzpatrick, D. Franklin Levi, Qiuming Yao, Jeffrey R. Cook, Zheng Wang, Marc Libault, Laurent Brechenmacher, Babu Valliyodan, Xiaolei Wu, Jianlin Cheng, Gary Stacey, Henry T. Nguyen, Dong Xu
Soybean Knowledge Base (SoyKB): a web resource for soybean translational genomics. BMC Genom. 13 (S-1) (2012)
Jesse Eickholt, Jianlin Cheng
Predicting protein residue-residue contacts using deep networks and boosting. Bioinform. 28 (23) (2012)
Jianlin Cheng, Jesse Eickholt, Zheng Wang, Xin Deng
Recursive protein Modeling: a Divide and Conquer Strategy for protein Structure Prediction and its Case Study in CASP9. J. Bioinform. Comput. Biol. 10 (3) (2012)
Jianhan Chen, Jianlin Cheng, A. Keith Dunker
Session introduction. Pacific Symposium on Biocomputing (2012)
Jianlin Cheng, Jilong Li, Zheng Wang, Jesse Eickholt, Xin Deng
The MULTICOM toolbox for protein structure prediction. BMC Bioinform. 13 (2012)
Zheng Wang, Jesse Eickholt, Jianlin Cheng
APOLLO: a quality assessment service for single and multiple protein models. Bioinform. 27 (12) (2011)
Xin Deng, Jianlin Cheng
MSACompro: protein multiple sequence alignment using predicted secondary structure, solvent accessibility, and residue-residue contacts. BMC Bioinform. 12 (2011)
Jesse Eickholt, Xin Deng, Jianlin Cheng
DoBo: Protein domain boundary prediction by integrating evolutionary signals and machine learning. BMC Bioinform. 12 (2011)
Jianlin Cheng, Zheng Wang, Jesse Eickholt, Xin Deng
Recursive protein modeling: A divide and conquer strategy for protein structure prediction and its case study in CASP9. BIBM Workshops (2011)
Guan Ning Lin, Zheng Wang, Dong Xu, Jianlin Cheng
SeqRate: sequence-based protein folding type classification and rates prediction. BMC Bioinform. 11 (S-3) (2010)

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Publication Activity (10 Years)

Top Topics

Top Venues

Jianlin Cheng