Jianlin Cheng

Gianluca Pollastri, Jianlin Cheng, Zheng Wang, 2007, 2008 IEEE International Joint Conference on Neural Networks (IEEE World Congress on Computational Intelligence).

A Super-Clustering Approach for Fully Automated Single Particle Picking in Cryo-EM

Jianlin Cheng, Adil Al-Azzawi, John J Tanner, 2019, Genes.

Deep Learning to Predict Protein Backbone Structure from High-Resolution Cryo-EM Density Maps

Dong Si, Renzhi Cao, Jianlin Cheng, 2019, bioRxiv.

AutoCryoPicker: an unsupervised learning approach for fully automated single particle picking in Cryo-EM images

Jianlin Cheng, J. Tanner, Adil Al-Azzawi, 2019, bioRxiv.

Semi-Supervised Graph Learning Meets Dimensionality Reduction

Jianlin Cheng, Alex Morehead, Watchanan Chantapakul, 2022, ArXiv.

AutoCryoPicker: an unsupervised learning approach for fully automated single particle picking in Cryo-EM images

Jianlin Cheng, Adil Al-Azzawi, John J. Tanner, 2019, BMC Bioinformatics.

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

Jianlin Cheng, Adil Al-Azzawi, John J. Tanner, 2019, BMC Bioinformatics.

DNdisorder: predicting protein disorder using boosting and deep networks

Jianlin Cheng, Jesse Eickholt, Jianlin Cheng, 2013, BMC Bioinformatics.

PreDisorder: ab initio sequence-based prediction of protein disordered regions

Xin Deng, Jianlin Cheng, Jesse Eickholt, 2009, BMC Bioinformatics.

Localized Deep Norm-CNN Structure for Face Verification

Tony X. Han, Jianlin Cheng, Adil Al-Azzawi, 2018, 2018 17th IEEE International Conference on Machine Learning and Applications (ICMLA).

Localized Deep-CNN Structure for Face Recognition

Jianlin Cheng, Jade Hind, Adil Al-Azzawi, 2018, 2018 11th International Conference on Developments in eSystems Engineering (DeSE).

DeepHCF: A Deep Learning Based Hybrid Collaborative Filtering Approach for Recommendation Systems

Jianlin Cheng, Meshal Alfarhood, Jianlin Cheng, 2018, 2018 17th IEEE International Conference on Machine Learning and Applications (ICMLA).

A deep auto-encoder model for gene expression prediction

Xinghua Shi, Jianlin Cheng, Jia Wen, 2017, BMC Genomics.

Protein Residue Contacts and Prediction Methods.

Badri Adhikari, Jianlin Cheng, Jianlin Cheng, 2016, Methods in molecular biology.

FRAGSION: ultra-fast protein fragment library generation by IOHMM sampling

Jilong Li, Debswapna Bhattacharya, Badri Adhikari, 2016, Bioinform..

Inhibition of Hedgehog-Signaling Driven Genes in Prostate Cancer Cells by Sutherlandia frutescens Extract

Jianlin Cheng, D. Lubahn, Jilong Li, 2015, PloS one.

Protein disorder prediction at multiple levels of sensitivity and specificity

Jianlin Cheng, Jack Y. Yang, Joshua Hecker, 2008, BMC Genomics.

A large expert-curated cryo-EM image dataset for machine learning protein particle picking

Jianlin Cheng, Ashwin Dhakal, Rajan Gyawali, 2023, Scientific data.

Atomic protein structure refinement using all-atom graph representations and SE(3)-equivariant graph transformer

Jianlin Cheng, Tianqi Wu, Zhiye Guo, 2023, Bioinform..

Dosage-sensitive miRNAs trigger modulation of gene expression during genomic imbalance in maize

Jianlin Cheng, J. Birchler, Jie Hou, 2022, Nature Communications.

Geometry-Complete Diffusion for 3D Molecule Generation and Optimization

Jianlin Cheng, Alex Morehead, 2023, 2302.04313.

Assessment of predictions submitted for the CASP7 domain prediction category

David Kim, Keehyoung Joo, Jinwoo Lee, 2007, Proteins.

High-Performance Deep Learning Toolbox for Genome-Scale Prediction of Protein Structure and Function

Jianlin Cheng, Ada Sedova, Jeffrey Skolnick, 2021, Workshop on Machine Learning in High Performance Computing Environments.

Cryo2Struct : A Large Labeled Cryo-EM Density Map Dataset for AI-based Reconstruction of Protein Structures

Jianlin Cheng, Nabin Giri, 2023, bioRxiv.

A gated graph transformer for protein complex structure quality assessment and its performance in CASP15

Jianlin Cheng, Alex Morehead, Xiao Chen, 2023, bioRxiv.

DISTEMA: distance map-based estimation of single protein model accuracy with attentive 2D convolutional neural network

Jianlin Cheng, Xiao Chen, 2021, BMC Bioinformatics.

Protein model accuracy estimation empowered by deep learning and inter-residue distance prediction in CASP14

Jianlin Cheng, Jie Hou, Tianqi Wu, 2021, Scientific Reports.

Deep Ranking in Template-free Protein Structure Prediction

Nasrin Akhter, Amarda Shehu, Jianlin Cheng, 2020, BCB.

Reconstruction of metabolic pathways by combining probabilistic graphical model-based and knowledge-based methods

Qi Qi, Jilong Li, Jianlin Cheng, 2014, BMC Proceedings.

SeqRate: sequence-based protein folding type classification and rates prediction

Dong Xu, Jianlin Cheng, Guan Ning Lin, 2010, BMC Bioinformatics.

Does Concurrent Use of Some Botanicals Interfere with Treatment of Tuberculosis?

Jianlin Cheng, W. Folk, Hailong Song, 2016, NeuroMolecular Medicine.

Predicting gene regulatory networks of soybean nodulation from RNA-Seq transcriptome data

Jianlin Cheng, Mingzhu Zhu, G. Stacey, 2013, BMC Bioinformatics.

Gene Expression Prediction based on Deep Learning

Jianlin Cheng, Rui Xie, 2016 .

Deep learning methods for protein torsion angle prediction

Jie Hou, Badri Adhikari, Jianlin Cheng, 2017, BMC Bioinformatics.

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

Jianlin Cheng, Nabin Giri, 2022, bioRxiv.

Deep convolutional neural networks for predicting the quality of single protein structural models

Renzhi Cao, Jianlin Cheng, Jie Hou, 2019, bioRxiv.

Deciphering the association between gene function and spatial gene-gene interactions in 3D human genome conformation

Jianlin Cheng, Renzhi Cao, 2015, BMC Genomics.

SMISS: a protein function prediction server by integrating multiple sources

Renzhi Cao, Jianlin Cheng, Zhaolong Zhong, 2016, International Journal of Computational Intelligence in Bioinformatics and Systems Biology.

DeepGRN: prediction of transcription factor binding site across cell-types using attention-based deep neural networks

Jianlin Cheng, J. Birchler, Jie Hou, 2021, BMC Bioinformatics.

Single-cell Hi-C data enhancement with deep residual and generative adversarial networks

Jianlin Cheng, Zhiye Guo, Yanli Wang, 2023, Bioinformatics.

Four-Dimensional Chromosome Structure Prediction

Jianlin Cheng, M. Highsmith, 2021, International journal of molecular sciences.

Prediction of the 4D Chromosome Structure From Time-Series Hi-C Data

Jianlin Cheng, Max Highsmith, Jianlin Cheng, 2020, bioRxiv.

A maximum likelihood algorithm for reconstructing 3D structures of human chromosomes from chromosomal contact data

Jianlin Cheng, Oluwatosin Oluwadare, Yuxiang Zhang, 2018, BMC Genomics.

Chromosome3D: reconstructing three-dimensional chromosomal structures from Hi-C interaction frequency data using distance geometry simulated annealing

Jianlin Cheng, B. Adhikari, Tuan Trieu, 2016, BMC Genomics.

Iterative reconstruction of three-dimensional models of human chromosomes from chromosomal contact data

Jianlin Cheng, Renzhi Cao, Oluwatosin Oluwadare, 2015, BMC Bioinformatics.

Predicting Protein Model Quality from Sequence Alignments by Support Vector Machines

Jilong Li, Jianlin Cheng, Xin Deng, 2013, Journal of proteomics & bioinformatics.

CATA++: A Collaborative Dual Attentive Autoencoder Method for Recommending Scientific Articles

Jianlin Cheng, Meshal Alfarhood, Jianlin Cheng, 2020, IEEE Access.

A Contact-Assisted Approach to Protein Structure Structure Prediction and Its Assessment in CASP 10

Jianlin Cheng, Xin Deng, Jilong Li, 2013 .

Crystal structure of domain of unknown function 507 (DUF507) reveals a new protein fold

Jianlin Cheng, J. Tanner, Cole E McKay, 2023, Scientific reports.

Three-stage prediction of protein ?-sheets by neural networks, alignments and graph algorithms

Pierre Baldi, Jianlin Cheng, P. Baldi, 2005, ISMB.

The renoprotective effects of soy protein in the aging rat kidney.

Jianlin Cheng, B. Valliyodan, Jilong Li, 2020, Medical research archives.

Critical assessment of protein intrinsic disorder prediction

Silvio C. E. Tosatto, Marco Necci, Damiano Piovesan, 2020, Nature Methods.

A deep auto-encoder model for gene expression prediction

Xinghua Shi, Jianlin Cheng, Jia Wen, 2017, BMC Genomics.

PairedFB: a full hierarchical Bayesian model for paired RNA‐seq data with heterogeneous treatment effects

Chong He, Jie Hou, Jianlin Cheng, 2018, Bioinform..

TMBpro: secondary structure, beta-contact and tertiary structure prediction of transmembrane beta-barrel proteins

Pierre Baldi, Jianlin Cheng, Michael J. Sweredoski, 2008, Bioinform..

Deep Learning to Predict Protein Backbone Structure from High-Resolution Cryo-EM Density Maps

Dong Si, Renzhi Cao, Jianlin Cheng, 2020, Scientific Reports.

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

Jianlin Cheng, B. Tycko, Song Liu, 2023, Human molecular genetics.

A deep reinforcement learning approach to reconstructing quaternary structures of protein dimers through self-learning

Jianlin Cheng, Rajashree Roy, Elham Soltanikazemi, 2022, bioRxiv.

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

Jianlin Cheng, Frimpong Boadu, Hongyuan Cao, 2023, bioRxiv.

Hierarchical Reconstruction of High-Resolution 3D Models of Large Chromosomes

Jianlin Cheng, Tuan Trieu, Oluwatosin Oluwadare, 2019, Scientific Reports.

3D Genome Structure Modeling by Lorentzian Objective Function

Jianlin Cheng, Tuan Trieu, Jianlin Cheng, 2017, BCB.

SAXSDom: Modeling multidomain protein structures using small‐angle X‐ray scattering data

Badri Adhikari, Jianlin Cheng, Jie Hou, 2019, Proteins.

Exploring soybean metabolic pathways based on probabilistic graphical model and knowledge-based methods

Gary Stacey, Jie Hou, Jianlin Cheng, 2015, EURASIP J. Bioinform. Syst. Biol..

Predicting Protein-Ligand Binding Structure Using E(n) Equivariant Graph Neural Networks

Jianlin Cheng, Ashwin Dhakal, Rajan Gyawali, 2023, bioRxiv.

Root hair systems biology.

Jianlin Cheng, Dong Xu, G. Stacey, 2010, Trends in Plant Science.

An Improved Integration of Template-Based and Template-Free Protein Structure Modeling Methods and its Assessment in CASP11.

Jilong Li, Badri Adhikari, Jianlin Cheng, 2015, Protein and peptide letters.

WeFold: A coopetition for protein structure prediction

George A. Khoury, Adam K. Sieradzan, Tomasz K. Wirecki, 2014, Proteins.

Assessing Predicted Contacts for Building Protein Three-Dimensional Models.

Jianlin Cheng, Renzhi Cao, B. Adhikari, 2017, Methods in molecular biology.

Massive integration of diverse protein quality assessment methods to improve template based modeling in CASP11

Jilong Li, Renzhi Cao, Debswapna Bhattacharya, 2016, Proteins.

Large-scale model quality assessment for improving protein tertiary structure prediction

Jilong Li, Renzhi Cao, Debswapna Bhattacharya, 2015, Bioinform..

From Analysis of Ischemic Mouse Brain Proteome to Identification of Human Serum Clusterin as a Potential Biomarker for Severity of Acute Ischemic Stroke

Jiankun Cui, Jianlin Cheng, Jilong Li, 2018, Translational Stroke Research.

Predicted structural proteome of Sphagnum divinum and proteome-scale annotation

Jerry M. Parks, Russell B. Davidson, J. Skolnick, 2023, Bioinform..

Sigmoid: a software infrastructure for pathway bioinformatics and systems biology

Pierre Baldi, Eric Mjolsness, Jianlin Cheng, 2005, IEEE Intelligent Systems.

Accurate prediction of protein tertiary structural changes induced by single-site mutations with equivariant graph neural networks

Jianlin Cheng, Alex Morehead, Sajid Mahmud, 2023, bioRxiv.

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

Jianlin Cheng, Chen Chen, Tianqi Wu, 2023, bioRxiv.

Bioinformatics Original Paper a Machine Learning Information Retrieval Approach to Protein Fold Recognition

P. Baldi, Jianlin Cheng, 2022 .

Geometric Transformers for Protein Interface Contact Prediction

Jianlin Cheng, Alex Morehead, Chen Chen, 2021, ICLR.

DNpro: A Deep Learning Network Approach to Predicting Protein Stability Changes Induced by Single-Site Mutations

Xiao Zhou, Jianlin Cheng, Xiaoping Zhou, 2016 .

Structural bioinformatics A machine learning information retrieval approach to protein fold recognition

P. Baldi, Jianlin Cheng, 2006 .

Geometry-Complete Diffusion for 3D Molecule Generation

Jianlin Cheng, Alex Morehead, 2023, ArXiv.

A scalable and integrative system for pathway bioinformatics and systems biology.

Pierre Baldi, Eric Mjolsness, Jianlin Cheng, 2010, Advances in experimental medicine and biology.

4-28-2014 SMOQ : A Tool for Predicting the Absolute Residue-Specific Quality of a Single Protein Model with Support Vector Machine

Jianlin Cheng, Zheng Wang, Renzhi Cao, 2017 .

TAPIOCA: Topological Attention and Predictive Inference of Chromatin Arrangement Using Epigenetic Features

Jianlin Cheng, M. Highsmith, 2021, bioRxiv.

ClusterTAD: an unsupervised machine learning approach to detecting topologically associated domains of chromosomes from Hi-C data

Jianlin Cheng, Oluwatosin Oluwadare, 2017, BMC Bioinformatics.

CONFOLD: Residue‐residue contact‐guided ab initio protein folding

Jianlin Cheng, Renzhi Cao, B. Adhikari, 2015, Proteins.

The Aquila Digital Community The Aquila Digital Community

Silvio C. E. Tosatto, Karin M. Verspoor, David A. Lee, 2022 .

ConEVA: a toolbox for comprehensive assessment of protein contacts

Jie Hou, Debswapna Bhattacharya, Badri Adhikari, 2016, BMC Bioinformatics.

Integrated protein function prediction by mining function associations, sequences, and protein-protein and gene-gene interaction networks.

Jianlin Cheng, Renzhi Cao, 2016, Methods.

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

Jianlin Cheng, Chen Chen, Tianqi Wu, 2023, bioRxiv.

Geometry-Complete Diffusion for 3D Molecule Generation and Optimization

Jianlin Cheng, Alex Morehead, 2023, Communications chemistry.