Large-Scale Prediction of Disulphide Bond Connectivity. - Pierre Baldi; Jianlin Cheng; Alessandro Vullo (NIPS, 2004)

Three-stage prediction of protein ?-sheets by neural networks, alignments and graph algorithms. - Jianlin Cheng; Pierre Baldi (ISMB (Supplement of Bioinformatics), 2005)

Accurate Prediction of Protein Disordered Regions by Mining Protein Structure Data. - Jianlin Cheng; Michael J. Sweredoski; Pierre Baldi (Data Min. Knowl. Discov., 2005)

Sigmoid: A Software Infrastructure for Pathway Bioinformatics and Systems Biology. - Jianlin Cheng; Lucas Scharenbroich; Pierre Baldi; Eric Mjolsness (IEEE Intell. Syst., 2005)

SCRATCH: a protein structure and structural feature prediction server. - Jianlin Cheng; Arlo Z. Randall; Michael J. Sweredoski; Pierre Baldi (Nucleic Acids Res., 2005)

A machine learning information retrieval approach to protein fold recognition. - Jianlin Cheng; Pierre Baldi (Bioinform., 2006)

DOMpro: Protein Domain Prediction Using Profiles, Secondary Structure, Relative Solvent Accessibility, and Recursive Neural Networks. - Jianlin Cheng; Michael J. Sweredoski; Pierre Baldi (Data Min. Knowl. Discov., 2006)

Functional Census of Mutation Sequence Spaces: The Example of p53 Cancer Rescue Mutants. - Samuel A. Danziger; Sanjay Joshua Swamidass; Jue Zeng; Lawrence R. Dearth; Qiang Lu; Jonathan H. Chen; Jianlin Cheng; Vinh P. Hoang; Hiroto Saigo; Ray Luo 001; Pierre Baldi; Rainer K. Brachmann; et al. (IEEE ACM Trans. Comput. Biol. Bioinform., 2006)

HHMMVE: A Visual Editor for Profile Hidden Markov Model. - Jianyong Dai; Jianlin Cheng (BIOCOMP, 2007)

Improved residue contact prediction using support vector machines and a large feature set. - Jianlin Cheng; Pierre Baldi (BMC Bioinform., 2007)

A neural network approach to ordinal regression - Jianlin Cheng (CoRR, 2007)

DOMAC: an accurate, hybrid protein domain prediction server. - Jianlin Cheng (Nucleic Acids Res., 2007)

A neural network approach to ordinal regression. - Jianlin Cheng; Zheng Wang 025; Gianluca Pollastri (IJCNN, 2008)

TMBpro: secondary structure, beta-contact and tertiary structure prediction of transmembrane beta-barrel proteins. - Arlo Z. Randall; Jianlin Cheng; Michael J. Sweredoski; Pierre Baldi (Bioinform., 2008)

Sequence-Based Prediction of Protein Folding Rates Using Contacts, Secondary Structures and Support Vector Machines. - Guan Ning Lin; Zheng Wang 025; Dong Xu 002; Jianlin Cheng (BIBM, 2009)

PreDisorder: ab initio sequence-based prediction of protein disordered regions. - Xin Deng; Jesse Eickholt; Jianlin Cheng (BMC Bioinform., 2009)

NNcon: improved protein contact map prediction using 2D-recursive neural networks. - Allison N. Tegge; Zheng Wang 019; Jesse Eickholt; Jianlin Cheng (Nucleic Acids Res., 2009)

MULTICOM: a multi-level combination approach to protein structure prediction and its assessments in CASP8. - Zheng Wang 019; Jesse Eickholt; Jianlin Cheng (Bioinform., 2010)

SeqRate: sequence-based protein folding type classification and rates prediction. - Guan Ning Lin; Zheng Wang 025; Dong Xu 002; Jianlin Cheng (BMC Bioinform., 2010)

Recursive protein modeling: A divide and conquer strategy for protein structure prediction and its case study in CASP9. - Jianlin Cheng; Zheng Wang 019; Jesse Eickholt; Xin Deng (BIBM Workshops, 2011)

APOLLO: a quality assessment service for single and multiple protein models. - Zheng Wang 019; Jesse Eickholt; Jianlin Cheng (Bioinform., 2011)

MSACompro: protein multiple sequence alignment using predicted secondary structure, solvent accessibility, and residue-residue contacts. - Xin Deng; Jianlin Cheng (BMC Bioinform., 2011)

DoBo: Protein domain boundary prediction by integrating evolutionary signals and machine learning. - Jesse Eickholt; Xin Deng; Jianlin Cheng (BMC Bioinform., 2011)

Session introduction. - Jianhan Chen; Jianlin Cheng; A. Keith Dunker (Pacific Symposium on Biocomputing, 2012)

Predicting protein residue-residue contacts using deep networks and boosting. - Jesse Eickholt; Jianlin Cheng (Bioinform., 2012)

The MULTICOM toolbox for protein structure prediction. - Jianlin Cheng; Jilong Li; Zheng Wang 019; Jesse Eickholt; Xin Deng (BMC Bioinform., 2012)

Soybean Knowledge Base (SoyKB): a web resource for soybean translational genomics. - Trupti Joshi; Kapil Patil; Michael R. Fitzpatrick; D. Franklin Levi; Qiuming Yao; Jeffrey R. Cook; Zheng Wang 019; Marc Libault; Laurent Brechenmacher; Babu Valliyodan; Xiaolei Wu; Jianlin Cheng; et al. (BMC Genom., 2012)

Protein Structure Refinement by Iterative Fragment Exchange. - Debswapna Bhattacharya; Jianlin Cheng (BCB, 2013)

Automated protein structure refinement using i3Drefine software and its assessment in CASP10. - Debswapna Bhattacharya; Jianlin Cheng (BCB, 2013)

DNdisorder: predicting protein disorder using boosting and deep networks. - Jesse Eickholt; Jianlin Cheng (BMC Bioinform., 2013)

A study and benchmark of DNcon: a method for protein residue-residue contact prediction using deep networks. - Jesse Eickholt; Jianlin Cheng (BMC Bioinform., 2013)

Three-Level Prediction of Protein Function by Combining Profile-Sequence Search, Profile-Profile Search, and Domain Co-Occurrence Networks. - Zheng Wang 025; Renzhi Cao; Jianlin Cheng (BMC Bioinform., 2013)

Predicting gene regulatory networks of soybean nodulation from RNA-Seq transcriptome data. - Mingzhu Zhu; Jeremy L. Dahmen; Gary Stacey; Jianlin Cheng (BMC Bioinform., 2013)

SMOQ: a tool for predicting the absolute residue-specific quality of a single protein model with support vector machines. - Renzhi Cao; Zheng Wang 025; Yiheng Wang; Jianlin Cheng (BMC Bioinform., 2014)

Enhancing HMM-based protein profile-profile alignment with structural features and evolutionary coupling information. - Xin Deng; Jianlin Cheng (BMC Bioinform., 2014)

Improving protein fold recognition by random forest. - Taeho Jo 002; Jianlin Cheng (BMC Bioinform., 2014)

MULTICOM: a large-scale conformation sampling and evaluation server for protein tertiary structure prediction. - Jilong Li; Renzhi Cao; Jianlin Cheng (BCB, 2015)

From gigabyte to kilobyte: a bioinformatics protocol for mining large RNA-Seq transcriptomics data. - Jilong Li; Jie Hou 001; 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; et al. (BCB, 2015)

Large-scale model quality assessment for improving protein tertiary structure prediction. - Renzhi Cao; Debswapna Bhattacharya; Badri Adhikari; Jilong Li; Jianlin Cheng (Bioinform., 2015)

A large-scale conformation sampling and evaluation server for protein tertiary structure prediction and its assessment in CASP11. - Jilong Li; Renzhi Cao; Jianlin Cheng (BMC Bioinform., 2015)

Iterative reconstruction of three-dimensional models of human chromosomes from chromosomal contact data. - Jackson Nowotny; Sharif Ahmed; Lingfei Xu; Oluwatosin Oluwadare; Hannah Chen 002; Noelan Hensley; Tuan Trieu; Renzhi Cao; Jianlin Cheng (BMC Bioinform., 2015)

Exploring soybean metabolic pathways based on probabilistic graphical model and knowledge-based methods. - Jie Hou 001; Gary Stacey; Jianlin Cheng (EURASIP J. Bioinform. Syst. Biol., 2015)

A Deep Learning Network Approach to ab initio Protein Secondary Structure Prediction. - Matt Spencer; Jesse Eickholt; Jianlin Cheng (IEEE ACM Trans. Comput. Biol. Bioinform., 2015)

A predictive model of gene expression using a deep learning framework. - Rui Xie; Andrew Quitadamo; Jianlin Cheng; Xinghua Shi (BIBM, 2016)

FRAGSION: ultra-fast protein fragment library generation by IOHMM sampling. - Debswapna Bhattacharya; Badri Adhikari; Jilong Li; Jianlin Cheng (Bioinform., 2016)

UniCon3D: de novo protein structure prediction using united-residue conformational search via stepwise, probabilistic sampling. - Debswapna Bhattacharya; Renzhi Cao; Jianlin Cheng (Bioinform., 2016)

MOGEN: a tool for reconstructing 3D models of genomes from chromosomal conformation capturing data. - Tuan Trieu; Jianlin Cheng (Bioinform., 2016)

ConEVA: a toolbox for comprehensive assessment of protein contacts. - Badri Adhikari; Jackson Nowotny; Debswapna Bhattacharya; Jie Hou 001; Jianlin Cheng (BMC Bioinform., 2016)

DeepQA: improving the estimation of single protein model quality with deep belief networks. - Renzhi Cao; Debswapna Bhattacharya; Jie Hou 001; Jianlin Cheng (BMC Bioinform., 2016)

Evaluation of Protein Structural Models Using Random Forests. - Renzhi Cao; Taeho Jo 002; Jianlin Cheng (CoRR, 2016)

3Drefine: an interactive web server for efficient protein structure refinement. - Debswapna Bhattacharya; Jackson Nowotny; Renzhi Cao; Jianlin Cheng (Nucleic Acids Res., 2016)

3D Genome Structure Modeling by Lorentzian Objective Function. - Tuan Trieu; Jianlin Cheng (BCB, 2017)

QAcon: single model quality assessment using protein structural and contact information with machine learning techniques. - Renzhi Cao; Badri Adhikari; Debswapna Bhattacharya; Miao Sun; Jie Hou 001; Jianlin Cheng (Bioinform., 2017)

Improved protein structure reconstruction using secondary structures, contacts at higher distance thresholds, and non-contacts. - Badri Adhikari; Jianlin Cheng (BMC Bioinform., 2017)

Deep learning methods for protein torsion angle prediction. - Haiou Li; Jie Hou 001; Badri Adhikari; Qiang Lyu; Jianlin Cheng (BMC Bioinform., 2017)

ClusterTAD: an unsupervised machine learning approach to detecting topologically associated domains of chromosomes from Hi-C data. - Oluwatosin Oluwadare; Jianlin Cheng (BMC Bioinform., 2017)

DeepSF: Deep Convolutional Neural Network for Mapping Protein Sequences to Folds. - Jie Hou 001; Badri Adhikari; Jianlin Cheng (BCB, 2018)

Localized Deep-CNN Structure for Face Recognition. - Adil Al-Azzawi; Jade Hind; Jianlin Cheng (DeSE, 2018)

Localized Deep Norm-CNN Structure for Face Verification. - Adil Al-Azzawi; Hasanain Al-Sadr; Jianlin Cheng; Tony X. Han (ICMLA, 2018)

DeepHCF: A Deep Learning Based Hybrid Collaborative Filtering Approach for Recommendation Systems. - Meshal Alfarhood; Jianlin Cheng (ICMLA, 2018)

DNCON2: improved protein contact prediction using two-level deep convolutional neural networks. - Badri Adhikari; Jie Hou 001; Jianlin Cheng (Bioinform., 2018)

CONFOLD2: improved contact-driven ab initio protein structure modeling. - Badri Adhikari; Jianlin Cheng (BMC Bioinform., 2018)

Introduction to 2019 ACM-BCB Highlights Session. - Jianlin Cheng (BCB, 2019)

Protein Tertiary Structure Modeling Driven by Deep Learning and Contact Distance Prediction in CASP13. - Jianlin Cheng (BCB, 2019)

Collaborative Attentive Autoencoder for Scientific Article Recommendation. - Meshal Alfarhood; Jianlin Cheng (ICMLA, 2019)

PairedFB: a full hierarchical Bayesian model for paired RNA-seq data with heterogeneous treatment effects. - Yuanyuan Bian; Chong He; Jie Hou 001; Jianlin Cheng; Jing Qiu (Bioinform., 2019)

GenomeFlow: a comprehensive graphical tool for modeling and analyzing 3D genome structure. - Tuan Trieu; Oluwatosin Oluwadare; Julia Wopata; Jianlin Cheng (Bioinform., 2019)

AutoCryoPicker: an unsupervised learning approach for fully automated single particle picking in Cryo-EM images. - Adil Al-Azzawi; Anes Ouadou; John J. Tanner; Jianlin Cheng (BMC Bioinform., 2019)

Deep Ranking in Template-free Protein Structure Prediction. - Xiao Chen; Nasrin Akhter; Zhiye Guo; Tianqi Wu; Jie Hou 001; Amarda Shehu; Jianlin Cheng (BCB, 2020)

CATA++: A Collaborative Dual Attentive Autoencoder Method for Recommending Scientific Articles. - Meshal Alfarhood; Jianlin Cheng (IEEE Access, 2020)

Analysis of several key factors influencing deep learning-based inter-residue contact prediction. - Tianqi Wu; Jie Hou 001; Badri Adhikari; Jianlin Cheng (Bioinform., 2020)

Auto3DCryoMap: an automated particle alignment approach for 3D cryo-EM density map reconstruction. - Adil Al-Azzawi; Anes Ouadou; Ye Duan; Jianlin Cheng (BMC Bioinform., 2020)

DeepCryoPicker: fully automated deep neural network for single protein particle picking in cryo-EM. - Adil Al-Azzawi; Anes Ouadou; Highsmith Max; Ye Duan; John J. Tanner; Jianlin Cheng (BMC Bioinform., 2020)

High-Performance Deep Learning Toolbox for Genome-Scale Prediction of Protein Structure and Function. - Mu Gao; Peik Lund-Andersen; Alex Morehead; Sajid Mahmud; Chen Chen 130; Xiao Chen; Nabin Giri; Raj S. Roy; Farhan Quadir; T. Chad Effler; Ryan Prout; Subil Abraham; et al. (MLHPC@SC, 2021)

Improving deep learning-based protein distance prediction in CASP14. - Zhiye Guo; Tianqi Wu; Jian Liu; Jie Hou 001; Jianlin Cheng (Bioinform., 2021)

DeepGRN: prediction of transcription factor binding site across cell-types using attention-based deep neural networks. - Chen Chen 130; Jie Hou 001; Xiaowen Shi; Hua Yang; James A. Birchler; Jianlin Cheng (BMC Bioinform., 2021)

DeepDist: real-value inter-residue distance prediction with deep residual convolutional network. - Tianqi Wu; Zhiye Guo; Jie Hou 001; Jianlin Cheng (BMC Bioinform., 2021)

Correction to: DeepDist: real‑value inter‑residue distance prediction with deep residual convolutional network. - Tianqi Wu; Zhiye Guo; Jie Hou 001; Jianlin Cheng (BMC Bioinform., 2021)

DIPS-Plus: The Enhanced Database of Interacting Protein Structures for Interface Prediction. - Alex Morehead; Chen Chen 130; Ada Sedova; Jianlin Cheng (CoRR, 2021)

DIPS-Plus: The Enhanced Database of Interacting Protein Structures for Interface Prediction. - Alex Morehead; Chen Chen 130; Ada Sedova; Jianlin Cheng (Zenodo, 2021)

DIPS-Plus: The Enhanced Database of Interacting Protein Structures for Interface Prediction. - Alex Morehead; Chen Chen 130; Ada Sedova; Jianlin Cheng (Zenodo, 2021)

Replication Data for: Geometric Transformers for Protein Interface Contact Prediction. - Alex Morehead; Chen Chen 130; Jianlin Cheng (Zenodo, 2021)

Replication Data for: Geometric Transformers for Protein Interface Contact Prediction. - Alex Morehead; Chen Chen 130; Jianlin Cheng (Zenodo, 2021)

Geometric Transformers for Protein Interface Contact Prediction. - Alex Morehead; Chen Chen 130; Jianlin Cheng (ICLR, 2022)

Machine Learning Embedded Smartphone Application for Early-Stage Diabetes Risk Assessment. - Md Maruf Hossain Shuvo; Nafis Ahmed; Humayera Islam; Khuder Alaboud; Jianlin Cheng; Abu Saleh Mohammad Mosa; Syed Kamrul Islam (MeMeA, 2022)

Artificial intelligence in the prediction of protein-ligand interactions: recent advances and future directions. - Ashwin Dhakal; Cole McKay; John J. Tanner; Jianlin Cheng (Briefings Bioinform., 2022)

A deep dilated convolutional residual network for predicting interchain contacts of protein homodimers. - Raj S. Roy; Farhan Quadir; Elham Soltanikazemi; Jianlin Cheng (Bioinform., 2022)

Correction to: Auto3DCryoMap: an automated particle alignment approach for 3D cryo-EM density map reconstruction. - Adil Al-Azzawi; Anes Ouadou; Ye Duan; Jianlin Cheng (BMC Bioinform., 2022)

DISTEMA: distance map-based estimation of single protein model accuracy with attentive 2D convolutional neural network. - Xiao Chen; Jianlin Cheng (BMC Bioinform., 2022)

Multi-head attention-based U-Nets for predicting protein domain boundaries using 1D sequence features and 2D distance maps. - Sajid Mahmud; Zhiye Guo; Farhan Quadir; Jian Liu; Jianlin Cheng (BMC Bioinform., 2022)

EGR: Equivariant Graph Refinement and Assessment of 3D Protein Complex Structures. - Alex Morehead; Xiao Chen; Tianqi Wu; Jian Liu; Jianlin Cheng (CoRR, 2022)

DProQ: A Gated-Graph Transformer for Protein Complex Structure Assessment. - Xiao Chen; Alex Morehead; Jian Liu; Jianlin Cheng (CoRR, 2022)

DRLComplex: Reconstruction of protein quaternary structures using deep reinforcement learning. - Elham Soltanikazemi; Raj S. Roy; Farhan Quadir; Nabin Giri; Alex Morehead; Jianlin Cheng (CoRR, 2022)

Deep Learning Prediction of Severe Health Risks for Pediatric COVID-19 Patients with a Large Feature Set in 2021 BARDA Data Challenge. - Sajid Mahmud; Elham Soltanikazemi; Frimpong Boadu; Ashwin Dhakal; Jianlin Cheng (CoRR, 2022)

Deep learning for reconstructing protein structures from cryo-EM density maps: recent advances and future directions. - Nabin Giri; Raj S. Roy; Jianlin Cheng (CoRR, 2022)

Replication Data for: Geometric Transformers for Protein Interface Contact Prediction. - Alex Morehead; Chen Chen 130; Jianlin Cheng (Zenodo, 2022)

Replication Data for: Geometric Transformers for Protein Interface Contact Prediction. - Alex Morehead; Chen Chen 130; Jianlin Cheng (Zenodo, 2022)

Towards a Domain-Agnostic Knowledge Graph-as-a-Service Infrastructure for Active Cyber Defense with Intelligent Agents. - Prasad Calyam; Mayank Kejriwal; Praveen Rao 001; Jianlin Cheng; Weichao Wang; Linquan Bai; V. Sriram Siddhardh Nadendla; Sanjay Madria; Sajal K. Das 001; Rohit Chadha; Khaza Anuarul Hoque; Kannappan Palaniappan; et al. (AIPR, 2023)

Semi-Supervised Graph Learning Meets Dimensionality Reduction. - Alex Morehead; Watchanan Chantapakul; Jianlin Cheng (ICMLA, 2023)

Combining protein sequences and structures with transformers and equivariant graph neural networks to predict protein function. - Frimpong Boadu; Hongyuan Cao; Jianlin Cheng (Bioinform., 2023)

A gated graph transformer for protein complex structure quality assessment and its performance in CASP15. - Xiao Chen; Alex Morehead; Jian Liu; Jianlin Cheng (Bioinform., 2023)

Geometry-Complete Diffusion for 3D Molecule Generation. - Alex Morehead; Jianlin Cheng (CoRR, 2023)

Diffusion Models in Bioinformatics: A New Wave of Deep Learning Revolution in Action. - Zhiye Guo; Jian Liu; Yanli Wang; Mengrui Chen; Duolin Wang; Dong Xu; Jianlin Cheng (CoRR, 2023)

Adapting Segment Anything Model (SAM) through Prompt-based Learning for Enhanced Protein Identification in Cryo-EM Micrographs. - Fei He; Zhiyuan Yang; Mingyue Gao; Biplab Poudel; Newgin Sam Ebin Sam Dhas; Rajan Gyawali; Ashwin Dhakal; Jianlin Cheng; Dong Xu 002 (CoRR, 2023)

Efficient Acceleration of Deep Learning Inference on Resource-Constrained Edge Devices: A Review. - Md Maruf Hossain Shuvo; Syed Kamrul Islam; Jianlin Cheng; Bashir I. Morshed (Proc. IEEE, 2023)

3D-equivariant graph neural networks for protein model quality assessment. - Chen Chen 130; Xiao Chen; Alex Morehead; Tianqi Wu; Jianlin Cheng (Bioinform., 2023)

Atomic protein structure refinement using all-atom graph representations and SE(3)-equivariant graph transformer. - Tianqi Wu; Zhiye Guo; Jianlin Cheng (Bioinform., 2023)

DIPS-Plus: The Enhanced Database of Interacting Protein Structures for Interface Prediction (Supplementary Data). - Alex Morehead; Chen Chen 130; Ada Sedova; Jianlin Cheng (Zenodo, 2023)

DIPS-Plus: The Enhanced Database of Interacting Protein Structures for Interface Prediction (Supplementary Data). - Alex Morehead; Chen Chen 130; Ada Sedova; Jianlin Cheng (Zenodo, 2023)

CAID prediction portal: a comprehensive service for predicting intrinsic disorder and binding regions in proteins. - 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; et al. (Nucleic Acids Res., 2023)

Predicted structural proteome of Sphagnum divinum and proteome-scale annotation. - 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 (Bioinform., 2023)

Single-cell Hi-C data enhancement with deep residual and generative adversarial networks. - Yanli Wang; Zhiye Guo; Jianlin Cheng (Bioinform., 2023)

Evaluating Representation Learning on the Protein Structure Universe. - Arian Rokkum Jamasb; Alex Morehead; Chaitanya K. Joshi; Zuobai Zhang; Kieran Didi; Simon V. Mathis; Charles Harris; Jian Tang 005; Jianlin Cheng; Pietro Lio; Tom L. Blundell (ICLR, 2024)

Denoising Long-Tail Augmented Contrastive Network for Multi-Behavior Recommendation. - Jinle He; Chengyong Yang; Jiayi Liu; Jianlin Cheng (IEEE Access, 2024)

Artificial intelligence in cryo-EM protein particle picking: recent advances and remaining challenges. - Ashwin Dhakal; Rajan Gyawali; Liguo Wang; Jianlin Cheng (Briefings Bioinform., 2024)

CryoSegNet: accurate cryo-EM protein particle picking by integrating the foundational AI image segmentation model and attention-gated U-Net. - Rajan Gyawali; Ashwin Dhakal; Liguo Wang; Jianlin Cheng (Briefings Bioinform., 2024)

HiCDiff: single-cell Hi-C data denoising with diffusion models. - Yanli Wang; Jianlin Cheng (Briefings Bioinform., 2024)

Deep Learning for Protein-Ligand Docking: Are We There Yet? - Alex Morehead; Nabin Giri; Jian Liu; Jianlin Cheng (CoRR, 2024)

FlowDock: Geometric Flow Matching for Generative Protein-Ligand Docking and Affinity Prediction. - Alex Morehead; Jianlin Cheng (CoRR, 2024)

Geometry-complete perceptron networks for 3D molecular graphs. - Alex Morehead; Jianlin Cheng (Bioinform., 2024)

Machine Learning Methods for Gene Regulatory Network Inference. - Akshata Hegde; Tom Nguyen; Jianlin Cheng (CoRR, 2025)

PSBench: a large-scale benchmark for estimating the accuracy of protein complex structural models. - Pawan Neupane; Jian Liu; Jianlin Cheng (CoRR, 2025)

MegaFold: System-Level Optimizations for Accelerating Protein Structure Prediction Models. - Hoa La; Ahan Gupta; Alex Morehead; Jianlin Cheng; Minjia Zhang (CoRR, 2025)