Jianlin Cheng

134 papers A* 2B 1C 5Misc 1Journal 106Unranked 18
YearRankTypeTitle / Venue / Authors
2026 J jnl
GRNFormer: accurate gene regulatory network inference using graph transformer.
Bioinform.
Akshata Hegde, Jianlin Cheng
2025 J jnl
Artificial intelligence in cryo-EM protein particle picking: recent advances and remaining challenges.
Briefings Bioinform.
Ashwin Dhakal, Rajan Gyawali, Liguo Wang, Jianlin Cheng
2025 J jnl
CryoTEN: efficiently enhancing cryo-EM density maps using transformers.
Bioinform.
Joel Selvaraj, Liguo Wang, Jianlin Cheng
2025 J jnl
FlowDock: Geometric flow matching for generative protein-ligand docking and affinity prediction.
Bioinform.
Alex Morehead, Jianlin Cheng
2025 J jnl
Guest Editorial for Special Section on ACM BCB 2023.
IEEE Trans. Comput. Biol. Bioinform.
Jianlin Cheng, Jing He, Mehmet Koyutürk
2025 J jnl
HalluMat: Detecting Hallucinations in LLM-Generated Materials Science Content Through Multi-Stage Verification.
CoRR
Bhanu Prakash Vangala, Sajid Mahmud, Pawan Neupane, Joel Selvaraj, Jianlin Cheng
2025 J jnl
MPBind: a multitask protein binding site predictor using protein language models and equivariant GNNs.
Bioinform.
Yanli Wang, Frimpong Boadu, Jianlin Cheng
2025 J jnl
Machine Learning Methods for Gene Regulatory Network Inference.
CoRR
Akshata Hegde, Tom Nguyen, Jianlin Cheng
2025 J jnl
Machine learning methods for gene regulatory network inference.
Briefings Bioinform.
Akshata Hegde, Tom Nguyen, Jianlin Cheng
2025 J jnl
MegaFold: System-Level Optimizations for Accelerating Protein Structure Prediction Models.
CoRR
Hoa La, Ahan Gupta, Alex Morehead, Jianlin Cheng, Minjia Zhang
2025 J jnl
PSBench: a large-scale benchmark for estimating the accuracy of protein complex structural models.
CoRR
Pawan Neupane, Jian Liu, Jianlin Cheng
2024 J jnl
CryoSegNet: accurate cryo-EM protein particle picking by integrating the foundational AI image segmentation model and attention-gated U-Net.
Briefings Bioinform.
Rajan Gyawali, Ashwin Dhakal, Liguo Wang, Jianlin Cheng
2024 J jnl
CryoTransformer: a transformer model for picking protein particles from cryo-EM micrographs.
Bioinform.
Ashwin Dhakal, Rajan Gyawali, Liguo Wang, Jianlin Cheng
2024 J jnl
Deep Learning for Protein-Ligand Docking: Are We There Yet?
CoRR
Alex Morehead, Nabin Giri, Jian Liu, Jianlin Cheng
2024 J jnl
Denoising Long-Tail Augmented Contrastive Network for Multi-Behavior Recommendation.
IEEE Access
Jinle He, Chengyong Yang, Jiayi Liu, Jianlin Cheng
2024 A* conf
Evaluating Representation Learning on the Protein Structure Universe.
ICLR
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
2024 J jnl
Evaluating representation learning on the protein structure universe.
CoRR
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
2024 J jnl
FlowDock: Geometric Flow Matching for Generative Protein-Ligand Docking and Affinity Prediction.
CoRR
Alex Morehead, Jianlin Cheng
2024 J jnl
Geometry-complete perceptron networks for 3D molecular graphs.
Bioinform.
Alex Morehead, Jianlin Cheng
2024 J jnl
HiCDiff: single-cell Hi-C data denoising with diffusion models.
Briefings Bioinform.
Yanli Wang, Jianlin Cheng
2024 — ed.
IEEE International Conference on Bioinformatics and Biomedicine, BIBM 2024, Lisbon, Portugal, December 3-6, 2024
BIBM
Mario Cannataro, Huiru Jane Zheng, Lin Gao, Jianlin Cheng, João Luís de Miranda, Ester Zumpano, Xiaohua Hu, Young-Rae Cho, Taesung Park
2023 J jnl
3D-equivariant graph neural networks for protein model quality assessment.
Bioinform.
Chen Chen, Xiao Chen, Alex Morehead, Tianqi Wu, Jianlin Cheng
2023 J jnl
A gated graph transformer for protein complex structure quality assessment and its performance in CASP15.
Bioinform.
Xiao Chen, Alex Morehead, Jian Liu, Jianlin Cheng
2023 J jnl
Adapting Segment Anything Model (SAM) through Prompt-based Learning for Enhanced Protein Identification in Cryo-EM Micrographs.
CoRR
Fei He, Zhiyuan Yang, Mingyue Gao, Biplab Poudel, Newgin Sam Ebin Sam Dhas, Rajan Gyawali, Ashwin Dhakal, Jianlin Cheng, Dong Xu
2023 J jnl
Atomic protein structure refinement using all-atom graph representations and SE(3)-equivariant graph transformer.
Bioinform.
Tianqi Wu, Zhiye Guo, Jianlin Cheng
2023 J jnl
CAID prediction portal: a comprehensive service for predicting intrinsic disorder and binding regions in proteins.
Nucleic Acids Res.
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
2023 J jnl
Combining protein sequences and structures with transformers and equivariant graph neural networks to predict protein function.
Bioinform.
Frimpong Boadu, Hongyuan Cao, Jianlin Cheng
2023 J jnl
Diffusion Models in Bioinformatics: A New Wave of Deep Learning Revolution in Action.
CoRR
Zhiye Guo, Jian Liu, Yanli Wang, Mengrui Chen, Duolin Wang, Dong Xu, Jianlin Cheng
2023 J jnl
Efficient Acceleration of Deep Learning Inference on Resource-Constrained Edge Devices: A Review.
Proc. IEEE
Md Maruf Hossain Shuvo, Syed Kamrul Islam, Jianlin Cheng, Bashir I. Morshed
2023 J jnl
Geometry-Complete Diffusion for 3D Molecule Generation.
CoRR
Alex Morehead, Jianlin Cheng
2023 J jnl
Predicted structural proteome of
Bioinform.
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
2023 C conf
Semi-Supervised Graph Learning Meets Dimensionality Reduction.
ICMLA
Alex Morehead, Watchanan Chantapakul, Jianlin Cheng
2023 J jnl
Single-cell Hi-C data enhancement with deep residual and generative adversarial networks.
Bioinform.
Yanli Wang, Zhiye Guo, Jianlin Cheng
2023 — conf
Towards a Domain-Agnostic Knowledge Graph-as-a-Service Infrastructure for Active Cyber Defense with Intelligent Agents.
AIPR
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
2022 J jnl
A deep dilated convolutional residual network for predicting interchain contacts of protein homodimers.
Bioinform.
Raj S. Roy, Farhan Quadir, Elham Soltanikazemi, Jianlin Cheng
2022 J jnl
Artificial intelligence in the prediction of protein-ligand interactions: recent advances and future directions.
Briefings Bioinform.
Ashwin Dhakal, Cole McKay, John J. Tanner, Jianlin Cheng
2022 J jnl
Correction to: Auto3DCryoMap: an automated particle alignment approach for 3D cryo-EM density map reconstruction.
BMC Bioinform.
Adil Al-Azzawi, Anes Ouadou, Ye Duan, Jianlin Cheng
2022 J jnl
DISTEMA: distance map-based estimation of single protein model accuracy with attentive 2D convolutional neural network.
BMC Bioinform.
Xiao Chen, Jianlin Cheng
2022 J jnl
DProQ: A Gated-Graph Transformer for Protein Complex Structure Assessment.
CoRR
Xiao Chen, Alex Morehead, Jian Liu, Jianlin Cheng
2022 J jnl
DRLComplex: Reconstruction of protein quaternary structures using deep reinforcement learning.
CoRR
Elham Soltanikazemi, Raj S. Roy, Farhan Quadir, Nabin Giri, Alex Morehead, Jianlin Cheng
2022 J jnl
Deep Learning Prediction of Severe Health Risks for Pediatric COVID-19 Patients with a Large Feature Set in 2021 BARDA Data Challenge.
CoRR
Sajid Mahmud, Elham Soltanikazemi, Frimpong Boadu, Ashwin Dhakal, Jianlin Cheng
2022 J jnl
Deep learning for reconstructing protein structures from cryo-EM density maps: recent advances and future directions.
CoRR
Nabin Giri, Raj S. Roy, Jianlin Cheng
2022 J jnl
EGR: Equivariant Graph Refinement and Assessment of 3D Protein Complex Structures.
CoRR
Alex Morehead, Xiao Chen, Tianqi Wu, Jian Liu, Jianlin Cheng
2022 A* conf
Geometric Transformers for Protein Interface Contact Prediction.
ICLR
Alex Morehead, Chen Chen, Jianlin Cheng
2022 J jnl
Geometry-Complete Perceptron Networks for 3D Molecular Graphs.
CoRR
Alex Morehead, Jianlin Cheng
2022 — conf
Machine Learning Embedded Smartphone Application for Early-Stage Diabetes Risk Assessment.
MeMeA
Md Maruf Hossain Shuvo, Nafis Ahmed, Humayera Islam, Khuder Alaboud, Jianlin Cheng, Abu Saleh Mohammad Mosa, Syed Kamrul Islam
2022 J jnl
Multi-head attention-based U-Nets for predicting protein domain boundaries using 1D sequence features and 2D distance maps.
BMC Bioinform.
Sajid Mahmud, Zhiye Guo, Farhan Quadir, Jian Liu, Jianlin Cheng
2022 J jnl
Semi-Supervised Graph Learning Meets Dimensionality Reduction.
CoRR
Alex Morehead, Watchanan Chantapakul, Jianlin Cheng
2021 J jnl
Correction to: DeepDist: real‑value inter‑residue distance prediction with deep residual convolutional network.
BMC Bioinform.
Tianqi Wu, Zhiye Guo, Jie Hou, Jianlin Cheng
2021 J jnl
DIPS-Plus: The Enhanced Database of Interacting Protein Structures for Interface Prediction.
CoRR
Alex Morehead, Chen Chen, Ada Sedova, Jianlin Cheng
2021 J jnl
DeepDist: real-value inter-residue distance prediction with deep residual convolutional network.
BMC Bioinform.
Tianqi Wu, Zhiye Guo, Jie Hou, Jianlin Cheng
2021 J jnl
DeepGRN: prediction of transcription factor binding site across cell-types using attention-based deep neural networks.
BMC Bioinform.
Chen Chen, Jie Hou, Xiaowen Shi, Hua Yang, James A. Birchler, Jianlin Cheng
2021 J jnl
GNET2: an R package for constructing gene regulatory networks from transcriptomic data.
Bioinform.
Chen Chen, Jie Hou, Xiaowen Shi, Hua Yang, James A. Birchler, Jianlin Cheng
2021 J jnl
Geometric Transformers for Protein Interface Contact Prediction.
CoRR
Alex Morehead, Chen Chen, Jianlin Cheng
2021 — conf
High-Performance Deep Learning Toolbox for Genome-Scale Prediction of Protein Structure and Function.
MLHPC@SC
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
2021 J jnl
Improving deep learning-based protein distance prediction in CASP14.
Bioinform.
Zhiye Guo, Tianqi Wu, Jian Liu, Jie Hou, Jianlin Cheng
2020 J jnl
Analysis of several key factors influencing deep learning-based inter-residue contact prediction.
Bioinform.
Tianqi Wu, Jie Hou, Badri Adhikari, Jianlin Cheng
2020 J jnl
Auto3DCryoMap: an automated particle alignment approach for 3D cryo-EM density map reconstruction.
BMC Bioinform.
Adil Al-Azzawi, Anes Ouadou, Ye Duan, Jianlin Cheng
2020 J jnl
CATA++: A Collaborative Dual Attentive Autoencoder Method for Recommending Scientific Articles.
IEEE Access
Meshal Alfarhood, Jianlin Cheng
2020 J jnl
CATA++: A Collaborative Dual Attentive Autoencoder Method for Recommending Scientific Articles.
CoRR
Meshal Alfarhood, Jianlin Cheng
2020 — conf
Deep Ranking in Template-free Protein Structure Prediction.
BCB
Xiao Chen, Nasrin Akhter, Zhiye Guo, Tianqi Wu, Jie Hou, Amarda Shehu, Jianlin Cheng
2020 J jnl
DeepCryoPicker: fully automated deep neural network for single protein particle picking in cryo-EM.
BMC Bioinform.
Adil Al-Azzawi, Anes Ouadou, Highsmith Max, Ye Duan, John J. Tanner, Jianlin Cheng
2019 J jnl
AutoCryoPicker: an unsupervised learning approach for fully automated single particle picking in Cryo-EM images.
BMC Bioinform.
Adil Al-Azzawi, Anes Ouadou, John J. Tanner, Jianlin Cheng
2019 C conf
Collaborative Attentive Autoencoder for Scientific Article Recommendation.
ICMLA
Meshal Alfarhood, Jianlin Cheng
2019 J jnl
GenomeFlow: a comprehensive graphical tool for modeling and analyzing 3D genome structure.
Bioinform.
Tuan Trieu, Oluwatosin Oluwadare, Julia Wopata, Jianlin Cheng
2019 — conf
Introduction to 2019 ACM-BCB Highlights Session.
BCB
Jianlin Cheng
2019 J jnl
PairedFB: a full hierarchical Bayesian model for paired RNA-seq data with heterogeneous treatment effects.
Bioinform.
Yuanyuan Bian, Chong He, Jie Hou, Jianlin Cheng, Jing Qiu
2019 — conf
Protein Tertiary Structure Modeling Driven by Deep Learning and Contact Distance Prediction in CASP13.
BCB
Jianlin Cheng
2018 J jnl
CONFOLD2: improved contact-driven ab initio protein structure modeling.
BMC Bioinform.
Badri Adhikari, Jianlin Cheng
2018 J jnl
DNCON2: improved protein contact prediction using two-level deep convolutional neural networks.
Bioinform.
Badri Adhikari, Jie Hou, Jianlin Cheng
2018 C conf
DeepHCF: A Deep Learning Based Hybrid Collaborative Filtering Approach for Recommendation Systems.
ICMLA
Meshal Alfarhood, Jianlin Cheng
2018 — conf
DeepSF: Deep Convolutional Neural Network for Mapping Protein Sequences to Folds.
BCB
Jie Hou, Badri Adhikari, Jianlin Cheng
2018 J jnl
DeepSF: deep convolutional neural network for mapping protein sequences to folds.
Bioinform.
Jie Hou, Badri Adhikari, Jianlin Cheng
2018 C conf
Localized Deep Norm-CNN Structure for Face Verification.
ICMLA
Adil Al-Azzawi, Hasanain Al-Sadr, Jianlin Cheng, Tony X. Han
2018 C conf
Localized Deep-CNN Structure for Face Recognition.
DeSE
Adil Al-Azzawi, Jade Hind, Jianlin Cheng
2017 — conf
3D Genome Structure Modeling by Lorentzian Objective Function.
BCB
Tuan Trieu, Jianlin Cheng
2017 J jnl
ClusterTAD: an unsupervised machine learning approach to detecting topologically associated domains of chromosomes from Hi-C data.
BMC Bioinform.
Oluwatosin Oluwadare, Jianlin Cheng
2017 J jnl
Deep learning methods for protein torsion angle prediction.
BMC Bioinform.
Haiou Li, Jie Hou, Badri Adhikari, Qiang Lyu, Jianlin Cheng
2017 J jnl
DeepSF: deep convolutional neural network for mapping protein sequences to folds.
CoRR
Jie Hou, Badri Adhikari, Jianlin Cheng
2017 J jnl
Improved protein structure reconstruction using secondary structures, contacts at higher distance thresholds, and non-contacts.
BMC Bioinform.
Badri Adhikari, Jianlin Cheng
2017 J jnl
QAcon: single model quality assessment using protein structural and contact information with machine learning techniques.
Bioinform.
Renzhi Cao, Badri Adhikari, Debswapna Bhattacharya, Miao Sun, Jie Hou, Jianlin Cheng
2016 J jnl
3Drefine: an interactive web server for efficient protein structure refinement.
Nucleic Acids Res.
Debswapna Bhattacharya, Jackson Nowotny, Renzhi Cao, Jianlin Cheng
2016 — conf
A predictive model of gene expression using a deep learning framework.
BIBM
Rui Xie, Andrew Quitadamo, Jianlin Cheng, Xinghua Shi
2016 J jnl
ConEVA: a toolbox for comprehensive assessment of protein contacts.
BMC Bioinform.
Badri Adhikari, Jackson Nowotny, Debswapna Bhattacharya, Jie Hou, Jianlin Cheng
2016 J jnl
DeepQA: Improving the estimation of single protein model quality with deep belief networks.
CoRR
Renzhi Cao, Debswapna Bhattacharya, Jie Hou, Jianlin Cheng
2016 J jnl
DeepQA: improving the estimation of single protein model quality with deep belief networks.
BMC Bioinform.
Renzhi Cao, Debswapna Bhattacharya, Jie Hou, Jianlin Cheng
2016 J jnl
Evaluation of Protein Structural Models Using Random Forests.
CoRR
Renzhi Cao, Taeho Jo, Jianlin Cheng
2016 J jnl
FRAGSION: ultra-fast protein fragment library generation by IOHMM sampling.
Bioinform.
Debswapna Bhattacharya, Badri Adhikari, Jilong Li, Jianlin Cheng
2016 J jnl
MOGEN: a tool for reconstructing 3D models of genomes from chromosomal conformation capturing data.
Bioinform.
Tuan Trieu, Jianlin Cheng
2016 J jnl
UniCon3D:
Bioinform.
Debswapna Bhattacharya, Renzhi Cao, Jianlin Cheng
2015 J jnl
A Deep Learning Network Approach to ab initio Protein Secondary Structure Prediction.
IEEE ACM Trans. Comput. Biol. Bioinform.
Matt Spencer, Jesse Eickholt, Jianlin Cheng
2015 J jnl
A large-scale conformation sampling and evaluation server for protein tertiary structure prediction and its assessment in CASP11.
BMC Bioinform.
Jilong Li, Renzhi Cao, Jianlin Cheng
2015 J jnl
Exploring soybean metabolic pathways based on probabilistic graphical model and knowledge-based methods.
EURASIP J. Bioinform. Syst. Biol.
Jie Hou, Gary Stacey, Jianlin Cheng
2015 — conf
From gigabyte to kilobyte: a bioinformatics protocol for mining large RNA-Seq transcriptomics data.
BCB
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
2015 J jnl
Iterative reconstruction of three-dimensional models of human chromosomes from chromosomal contact data.
BMC Bioinform.
Jackson Nowotny, Sharif Ahmed, Lingfei Xu, Oluwatosin Oluwadare, Hannah Chen, Noelan Hensley, Tuan Trieu, Renzhi Cao, Jianlin Cheng
2015 J jnl
Large-scale model quality assessment for improving protein tertiary structure prediction.
Bioinform.
Renzhi Cao, Debswapna Bhattacharya, Badri Adhikari, Jilong Li, Jianlin Cheng
2015 — conf
MULTICOM: a large-scale conformation sampling and evaluation server for protein tertiary structure prediction.
BCB
Jilong Li, Renzhi Cao, Jianlin Cheng
2014 J jnl
Enhancing HMM-based protein profile-profile alignment with structural features and evolutionary coupling information.
BMC Bioinform.
Xin Deng, Jianlin Cheng
2014 J jnl
Improving protein fold recognition by random forest.
BMC Bioinform.
Taeho Jo, Jianlin Cheng
2014 J jnl
SMOQ: a tool for predicting the absolute residue-specific quality of a single protein model with support vector machines.
BMC Bioinform.
Renzhi Cao, Zheng Wang, Yiheng Wang, Jianlin Cheng
2013 J jnl
A study and benchmark of DNcon: a method for protein residue-residue contact prediction using deep networks.
BMC Bioinform.
Jesse Eickholt, Jianlin Cheng
2013 — conf
Automated protein structure refinement using i3Drefine software and its assessment in CASP10.
BCB
Debswapna Bhattacharya, Jianlin Cheng
2013 J jnl
DNdisorder: predicting protein disorder using boosting and deep networks.
BMC Bioinform.
Jesse Eickholt, Jianlin Cheng
2013 J jnl
Predicting gene regulatory networks of soybean nodulation from RNA-Seq transcriptome data.
BMC Bioinform.
Mingzhu Zhu, Jeremy L. Dahmen, Gary Stacey, Jianlin Cheng
2013 — conf
Protein Structure Refinement by Iterative Fragment Exchange.
BCB
Debswapna Bhattacharya, Jianlin Cheng
2013 J jnl
Three-Level Prediction of Protein Function by Combining Profile-Sequence Search, Profile-Profile Search, and Domain Co-Occurrence Networks.
BMC Bioinform.
Zheng Wang, Renzhi Cao, Jianlin Cheng
2012 J jnl
Predicting protein residue-residue contacts using deep networks and boosting.
Bioinform.
Jesse Eickholt, Jianlin Cheng
2012 J jnl
Recursive protein Modeling: a Divide and Conquer Strategy for protein Structure Prediction and its Case Study in CASP9.
J. Bioinform. Comput. Biol.
Jianlin Cheng, Jesse Eickholt, Zheng Wang, Xin Deng
2012 Misc conf
Session introduction.
Pacific Symposium on Biocomputing
Jianhan Chen, Jianlin Cheng, A. Keith Dunker
2012 J jnl
Soybean Knowledge Base (SoyKB): a web resource for soybean translational genomics.
BMC Genom.
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
2012 J jnl
The MULTICOM toolbox for protein structure prediction.
BMC Bioinform.
Jianlin Cheng, Jilong Li, Zheng Wang, Jesse Eickholt, Xin Deng
2011 J jnl
APOLLO: a quality assessment service for single and multiple protein models.
Bioinform.
Zheng Wang, Jesse Eickholt, Jianlin Cheng
2011 J jnl
DoBo: Protein domain boundary prediction by integrating evolutionary signals and machine learning.
BMC Bioinform.
Jesse Eickholt, Xin Deng, Jianlin Cheng
2011 J jnl
MSACompro: protein multiple sequence alignment using predicted secondary structure, solvent accessibility, and residue-residue contacts.
BMC Bioinform.
Xin Deng, Jianlin Cheng
2011 — conf
Recursive protein modeling: A divide and conquer strategy for protein structure prediction and its case study in CASP9.
BIBM Workshops
Jianlin Cheng, Zheng Wang, Jesse Eickholt, Xin Deng
2010 J jnl
MULTICOM: a multi-level combination approach to protein structure prediction and its assessments in CASP8.
Bioinform.
Zheng Wang, Jesse Eickholt, Jianlin Cheng
2010 J jnl
SeqRate: sequence-based protein folding type classification and rates prediction.
BMC Bioinform.
Guan Ning Lin, Zheng Wang, Dong Xu, Jianlin Cheng
2009 J jnl
NNcon: improved protein contact map prediction using 2D-recursive neural networks.
Nucleic Acids Res.
Allison N. Tegge, Zheng Wang, Jesse Eickholt, Jianlin Cheng
2009 J jnl
PreDisorder: ab initio sequence-based prediction of protein disordered regions.
BMC Bioinform.
Xin Deng, Jesse Eickholt, Jianlin Cheng
2009 — conf
Sequence-Based Prediction of Protein Folding Rates Using Contacts, Secondary Structures and Support Vector Machines.
BIBM
Guan Ning Lin, Zheng Wang, Dong Xu, Jianlin Cheng
2008 B conf
A neural network approach to ordinal regression.
IJCNN
Jianlin Cheng, Zheng Wang, Gianluca Pollastri
2008 J jnl
TMBpro: secondary structure, beta-contact and tertiary structure prediction of transmembrane beta-barrel proteins.
Bioinform.
Arlo Z. Randall, Jianlin Cheng, Michael J. Sweredoski, Pierre Baldi
2007 J jnl
A neural network approach to ordinal regression
CoRR
Jianlin Cheng
2007 J jnl
DOMAC: an accurate, hybrid protein domain prediction server.
Nucleic Acids Res.
Jianlin Cheng
2007 — conf
HHMMVE: A Visual Editor for Profile Hidden Markov Model.
BIOCOMP
Jianyong Dai, Jianlin Cheng
2007 J jnl
Improved residue contact prediction using support vector machines and a large feature set.
BMC Bioinform.
Jianlin Cheng, Pierre Baldi
2006 J jnl
A machine learning information retrieval approach to protein fold recognition.
Bioinform.
Jianlin Cheng, Pierre Baldi
2006 J jnl
DOMpro: Protein Domain Prediction Using Profiles, Secondary Structure, Relative Solvent Accessibility, and Recursive Neural Networks.
Data Min. Knowl. Discov.
Jianlin Cheng, Michael J. Sweredoski, Pierre Baldi
2006 J jnl
Functional Census of Mutation Sequence Spaces: The Example of p53 Cancer Rescue Mutants.
IEEE ACM Trans. Comput. Biol. Bioinform.
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, Pierre Baldi, Rainer K. Brachmann, Richard H. Lathrop
2005 J jnl
Accurate Prediction of Protein Disordered Regions by Mining Protein Structure Data.
Data Min. Knowl. Discov.
Jianlin Cheng, Michael J. Sweredoski, Pierre Baldi
2005 J jnl
SCRATCH: a protein structure and structural feature prediction server.
Nucleic Acids Res.
Jianlin Cheng, Arlo Z. Randall, Michael J. Sweredoski, Pierre Baldi
2005 J jnl
Sigmoid: A Software Infrastructure for Pathway Bioinformatics and Systems Biology.
IEEE Intell. Syst.
Jianlin Cheng, Lucas Scharenbroich, Pierre Baldi, Eric Mjolsness
2005 — conf
Three-stage prediction of protein ?-sheets by neural networks, alignments and graph algorithms.
ISMB (Supplement of Bioinformatics)
Jianlin Cheng, Pierre Baldi
2004 — conf
Large-Scale Prediction of Disulphide Bond Connectivity.
NIPS
Pierre Baldi, Jianlin Cheng, Alessandro Vullo