Cheng, Jianlin

A large-scale evaluation of computational protein function prediction

Radivojac, P., Clark, W. T., Oron, T. R., Schnoes, A. M., Wittkop, T., Sokolov, A., Graim, K., Funk, C., Verspoor, K., Ben-Hur, A., et al. (2013) · Nature Methods

Bioinformatics and Genomic NetworksMachine Learning in Bioinformatics

Cited by 1,028

The CAFA challenge reports improved protein function prediction and new functional annotations for hundreds of genes through experimental screens

Zhou, N., Jiang, Y., Bergquist, T. R., Lee, A. J., Kacsoh, B. Z., Crocker, A. W., Lewis, K. A., Georghiou, G., Nguyen, H. N., Hamid, M. N., et al. (2019) · Genome Biology

Bioinformatics and Genomic NetworksGenomics and Phylogenetic Studies

Cited by 452

Efficient Acceleration of Deep Learning Inference on Resource-Constrained Edge Devices: A Review

Shuvo, M. M. H., Islam, S. K., Cheng, J., & Morshed, B. I. (2023) · Proceedings of the IEEE

Advanced Neural Network ApplicationsIoT and Edge/Fog Computing

Cited by 436

Critical assessment of protein intrinsic disorder prediction

Necci, M., Piovesan, D., Predictors, C., Hoque, M. T., Walsh, I., Iqbal, S., Vendruscolo, M., Sormanni, P., Wang, C., Raimondi, D., et al. (2021) · Nature Methods

Protein Structure and DynamicsMachine Learning in Bioinformatics

Cited by 343

Bioinformatics Methods for Mass Spectrometry-Based Proteomics Data Analysis

Chen, C., Hou, J., Tanner, J. J., & Cheng, J. (2020) · International Journal of Molecular Sciences

Advanced Proteomics Techniques and ApplicationsBioinformatics and Genomic Networks

Cited by 280

Blind prediction of homo- and hetero-protein complexes: the CASP13-CAPRI experiment

Lensink, M. F., Brysbaert, G., Nadzirin, N., Velankar, S., Chaleil, R. A. G., Gerguri, T., Bates, P. A., Laine, E., Carbone, A., Grudinin, S., et al. (2019) · Proteins Structure Function and Bioinformatics

Protein Structure and DynamicsEnzyme Structure and Function

Cited by 122

Enhancing AlphaFold-Multimer-based Protein Complex Structure Prediction with MULTICOM in CASP15

Liu, J., Guo, Z., Wu, T., Roy, R. S., Quadir, F., Chen, C., & Cheng, J. (2023) · Communications Biology

Protein Structure and DynamicsEnzyme Structure and Function

Cited by 86

Enhancing alphafold-multimer-based protein complex structure prediction with MULTICOM in CASP15

Liu, J., Guo, Z., Wu, T., Roy, R. S., Quadir, F., Chen, C., & Cheng, J. (2023) · Communications Biology

Protein Structure and DynamicsEnzyme Structure and Function

Cited by 86

Combining protein sequences and structures with transformers and equivariant graph neural networks to predict protein function

Boadu, F., Cao, H., & Cheng, J. (2023) · Bioinformatics

Machine Learning in BioinformaticsProtein Structure and Dynamics

Cited by 81

DeepCryoPicker: fully automated deep neural network for single protein particle picking in cryo-EM

Al-Azzawi, A., Ouadou, A., Max, H., Duan, Y., Tanner, J. J., & Cheng, J. (2020) · BMC Bioinformatics

Advanced Electron Microscopy Techniques and ApplicationsCell Image Analysis Techniques

Cited by 74

Deep learning for reconstructing protein structures from cryo-EM density maps: Recent advances and future directions

Giri, N., Roy, R. S., & Cheng, J. (2023) · Current Opinion in Structural Biology

Advanced Electron Microscopy Techniques and ApplicationsProtein Structure and Dynamics

Cited by 59

Prediction of inter-chain distance maps of protein complexes with 2D attention-based deep neural networks

Guo, Z., Liu, J., Skolnick, J., & Cheng, J. (2022) · Nature Communications

Protein Structure and DynamicsMachine Learning in Bioinformatics

Cited by 58

Prediction of inter-chain distance maps of protein complexes with 2D attention-based deep neural networks

Guo, Z., Liu, J., Skolnick, J., & Cheng, J. (2022) · Nature Communications

Protein Structure and DynamicsMachine Learning in Bioinformatics

Cited by 57

Deep learning methods for protein function prediction

Boadu, F., Lee, A., & Cheng, J. (2025) · PROTEOMICS

Machine Learning in BioinformaticsBioinformatics and Genomic Networks

Cited by 53

De Novo Atomic Protein Structure Modeling for Cryo-EM Density Maps Using 3D Transformer and Hidden Markov Model

Giri, N., & Cheng, J. (2024) · Nature Communications

Advanced Electron Microscopy Techniques and ApplicationsProtein Structure and Dynamics

Cited by 47

A deep dilated convolutional residual network for predicting interchain contacts of protein homodimers

Roy, R. S., Quadir, F., Soltanikazemi, E., & Cheng, J. (2021) · Bioinformatics

Protein Structure and DynamicsMachine Learning in Bioinformatics

Cited by 45

A deep dilated convolutional residual network for predicting interchain contacts of protein homodimers

Roy, R. S., Quadir, F., Soltanikazemi, E., & Cheng, J. (2022) · Bioinformatics

Protein Structure and DynamicsMachine Learning in Bioinformatics

Cited by 45

Combination of deep neural network with attention mechanism enhances the explainability of protein contact prediction

Chen, C., Wu, T., Guo, Z., & Cheng, J. (2021) · Proteins: Structure, Function, and Bioinformatics

Protein Structure and DynamicsMachine Learning in Bioinformatics

Cited by 44

3D-equivariant graph neural networks for protein model quality assessment

Chen, C., Chen, X., Morehead, A., Wu, T., & Cheng, J. (2023) · Bioinformatics

Protein Structure and DynamicsEnzyme Structure and Function

Cited by 33

Improving protein tertiary structure prediction by deep learning and distance prediction in CASP14

Liu, J., Wu, T., Guo, Z., Hou, J., & Cheng, J. (2022) · Proteins: Structure, Function, and Bioinformatics

Protein Structure and DynamicsEnzyme Structure and Function

Cited by 32

Improving AlphaFold2-based Protein Tertiary Structure Prediction with MULTICOM in CASP15

Liu, J., Guo, Z., Wu, T., Roy, R. S., Chen, C., & Cheng, J. (2023) · Communications Chemistry

Protein Structure and DynamicsEnzyme Structure and Function

Cited by 31

Improving AlphaFold2-based protein tertiary structure prediction with MULTICOM in CASP15

Liu, J., Guo, Z., Wu, T., Roy, R. S., Chen, C., & Cheng, J. (2023) · Communications Chemistry

Protein Structure and DynamicsEnzyme Structure and Function

Cited by 31

Improving Protein-Ligand Interaction Modeling with cryo-EM Data, Templates, and Deep Learning in 2021 Ligand Model Challenge

Giri, N., & Cheng, J. (2022) · Biomolecules

Advanced Electron Microscopy Techniques and ApplicationsProtein Structure and Dynamics

Cited by 28

Dissection of a down syndrome-associated trisomy to separate the gene dosage-dependent and -independent effects of an extra chromosome

Xing, Z., Li, Y., Cortes-Gomez, E., Jiang, X., Gao, S., Pao, A., Shan, J., Song, Y., Perez, A., Yu, T., et al. (2023) · Human Molecular Genetics

Down syndrome and intellectual disability researchGenomic variations and chromosomal abnormalities

Cited by 23