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2020 – today
- 2024
[j72]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)- [j71]Yanli Wang, Jianlin Cheng:
HiCDiff: single-cell Hi-C data denoising with diffusion models. Briefings Bioinform. 25(4) (2024) - [j70]Alex Morehead, Jianlin Cheng:
Geometry-complete perceptron networks for 3D molecular graphs. Bioinform. 40(2) (2024) - [c27]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 - [i19]Alex Morehead, Nabin Giri, Jian Liu, Jianlin Cheng:
Deep Learning for Protein-Ligand Docking: Are We There Yet? CoRR abs/2405.14108 (2024) - [i18]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 abs/2406.13864 (2024) - 2023
- [j69]Chen Chen, Xiao Chen, Alex Morehead, Tianqi Wu, Jianlin Cheng:
3D-equivariant graph neural networks for protein model quality assessment. Bioinform. 39(1) (2023) - [j68]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) - [j67]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:
Predicted structural proteome of Sphagnum divinum and proteome-scale annotation. Bioinform. 39(8) (2023) - [j66]Yanli Wang, Zhiye Guo, Jianlin Cheng:
Single-cell Hi-C data enhancement with deep residual and generative adversarial networks. Bioinform. 39(8) (2023) - [j65]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): 308-317 (2023) - [j64]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): 318-325 (2023) - [j63]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): 62-69 (2023) - [j62]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): 42-91 (2023) - [c26]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: 1-8 - [c25]Alex Morehead, Watchanan Chantapakul, Jianlin Cheng:
Semi-Supervised Graph Learning Meets Dimensionality Reduction. ICMLA 2023: 2006-2013 - [i17]Alex Morehead, Jianlin Cheng:
Geometry-Complete Diffusion for 3D Molecule Generation. CoRR abs/2302.04313 (2023) - [i16]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 abs/2302.10907 (2023) - [i15]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 abs/2311.16140 (2023) - 2022
- [j61]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) - [j60]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): 1904-1910 (2022) - [j59]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): 92 (2022) - [j58]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): 283 (2022) - [j57]Xiao Chen, Jianlin Cheng:
DISTEMA: distance map-based estimation of single protein model accuracy with attentive 2D convolutional neural network. BMC Bioinform. 23-S(3): 141 (2022) - [c24]Alex Morehead, Chen Chen, Jianlin Cheng:
Geometric Transformers for Protein Interface Contact Prediction. ICLR 2022 - [c23]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: 1-6 - [i14]Alex Morehead, Watchanan Chantapakul, Jianlin Cheng:
Semi-Supervised Graph Learning Meets Dimensionality Reduction. CoRR abs/2203.12522 (2022) - [i13]Alex Morehead, Xiao Chen, Tianqi Wu, Jian Liu, Jianlin Cheng:
EGR: Equivariant Graph Refinement and Assessment of 3D Protein Complex Structures. CoRR abs/2205.10390 (2022) - [i12]Xiao Chen, Alex Morehead, Jian Liu, Jianlin Cheng:
DProQ: A Gated-Graph Transformer for Protein Complex Structure Assessment. CoRR abs/2205.10627 (2022) - [i11]Elham Soltanikazemi, Raj S. Roy, Farhan Quadir, Nabin Giri, Alex Morehead, Jianlin Cheng:
DRLComplex: Reconstruction of protein quaternary structures using deep reinforcement learning. CoRR abs/2205.13594 (2022) - [i10]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 abs/2206.01696 (2022) - [i9]Nabin Giri, Raj S. Roy, Jianlin Cheng:
Deep learning for reconstructing protein structures from cryo-EM density maps: recent advances and future directions. CoRR abs/2209.08171 (2022) - [i8]Alex Morehead, Jianlin Cheng:
Geometry-Complete Perceptron Networks for 3D Molecular Graphs. CoRR abs/2211.02504 (2022) - 2021
- [j56]Zhiye Guo, Tianqi Wu, Jian Liu, Jie Hou, Jianlin Cheng:
Improving deep learning-based protein distance prediction in CASP14. Bioinform. 37(19): 3190-3196 (2021) - [j55]Tianqi Wu, Zhiye Guo, Jie Hou, Jianlin Cheng:
DeepDist: real-value inter-residue distance prediction with deep residual convolutional network. BMC Bioinform. 22(1): 30 (2021) - [j54]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): 38 (2021) - [j53]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): 354 (2021) - [c22]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: 46-57 - [i7]Alex Morehead, Chen Chen, Ada Sedova, Jianlin Cheng:
DIPS-Plus: The Enhanced Database of Interacting Protein Structures for Interface Prediction. CoRR abs/2106.04362 (2021) - [i6]Alex Morehead, Chen Chen, Jianlin Cheng:
Geometric Transformers for Protein Interface Contact Prediction. CoRR abs/2110.02423 (2021) - 2020
- [j52]Meshal Alfarhood, Jianlin Cheng:
CATA++: A Collaborative Dual Attentive Autoencoder Method for Recommending Scientific Articles. IEEE Access 8: 183633-183648 (2020) - [j51]Tianqi Wu, Jie Hou, Badri Adhikari, Jianlin Cheng:
Analysis of several key factors influencing deep learning-based inter-residue contact prediction. Bioinform. 36(4): 1091-1098 (2020) - [j50]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): 509 (2020) - [j49]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-S(21): 534 (2020) - [c21]Xiao Chen, Nasrin Akhter, Zhiye Guo, Tianqi Wu, Jie Hou, Amarda Shehu, Jianlin Cheng:
Deep Ranking in Template-free Protein Structure Prediction. BCB 2020: 31:1-31:10 - [i5]Meshal Alfarhood, Jianlin Cheng:
CATA++: A Collaborative Dual Attentive Autoencoder Method for Recommending Scientific Articles. CoRR abs/2002.12277 (2020)
2010 – 2019
- 2019
- [j48]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): 787-797 (2019) - [j47]Tuan Trieu, Oluwatosin Oluwadare, Julia Wopata, Jianlin Cheng:
GenomeFlow: a comprehensive graphical tool for modeling and analyzing 3D genome structure. Bioinform. 35(8): 1416-1418 (2019) - [j46]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): 326:1-326:26 (2019) - [c20]Jianlin Cheng:
Introduction to 2019 ACM-BCB Highlights Session. BCB 2019: 548 - [c19]Jianlin Cheng:
Protein Tertiary Structure Modeling Driven by Deep Learning and Contact Distance Prediction in CASP13. BCB 2019: 551 - [c18]Meshal Alfarhood, Jianlin Cheng:
Collaborative Attentive Autoencoder for Scientific Article Recommendation. ICMLA 2019: 168-174 - 2018
- [j45]Jie Hou, Badri Adhikari, Jianlin Cheng:
DeepSF: deep convolutional neural network for mapping protein sequences to folds. Bioinform. 34(8): 1295-1303 (2018) - [j44]Badri Adhikari, Jie Hou, Jianlin Cheng:
DNCON2: improved protein contact prediction using two-level deep convolutional neural networks. Bioinform. 34(9): 1466-1472 (2018) - [j43]Badri Adhikari, Jianlin Cheng:
CONFOLD2: improved contact-driven ab initio protein structure modeling. BMC Bioinform. 19(1): 22:1-22:5 (2018) - [c17]Jie Hou, Badri Adhikari, Jianlin Cheng:
DeepSF: Deep Convolutional Neural Network for Mapping Protein Sequences to Folds. BCB 2018: 565 - [c16]Adil Al-Azzawi, Jade Hind, Jianlin Cheng:
Localized Deep-CNN Structure for Face Recognition. DeSE 2018: 52-57 - [c15]Adil Al-Azzawi, Hasanain Al-Sadr, Jianlin Cheng, Tony X. Han:
Localized Deep Norm-CNN Structure for Face Verification. ICMLA 2018: 8-15 - [c14]Meshal Alfarhood, Jianlin Cheng:
DeepHCF: A Deep Learning Based Hybrid Collaborative Filtering Approach for Recommendation Systems. ICMLA 2018: 89-96 - 2017
- [j42]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): 586-588 (2017) - [j41]Badri Adhikari, Jianlin Cheng:
Improved protein structure reconstruction using secondary structures, contacts at higher distance thresholds, and non-contacts. BMC Bioinform. 18(1): 380 (2017) - [j40]Haiou Li, Jie Hou, Badri Adhikari, Qiang Lyu, Jianlin Cheng:
Deep learning methods for protein torsion angle prediction. BMC Bioinform. 18(1): 417:1-417:13 (2017) - [j39]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): 480 (2017) - [c13]Tuan Trieu, Jianlin Cheng:
3D Genome Structure Modeling by Lorentzian Objective Function. BCB 2017: 641 - [i4]Jie Hou, Badri Adhikari, Jianlin Cheng:
DeepSF: deep convolutional neural network for mapping protein sequences to folds. CoRR abs/1706.01010 (2017) - 2016
- [j38]Tuan Trieu, Jianlin Cheng:
MOGEN: a tool for reconstructing 3D models of genomes from chromosomal conformation capturing data. Bioinform. 32(9): 1286-1292 (2016) - [j37]Debswapna Bhattacharya, Badri Adhikari, Jilong Li, Jianlin Cheng:
FRAGSION: ultra-fast protein fragment library generation by IOHMM sampling. Bioinform. 32(13): 2059-2061 (2016) - [j36]Debswapna Bhattacharya, Renzhi Cao, Jianlin Cheng:
UniCon3D: de novo protein structure prediction using united-residue conformational search via stepwise, probabilistic sampling. Bioinform. 32(18): 2791-2799 (2016) - [j35]Renzhi Cao, Debswapna Bhattacharya, Jie Hou, Jianlin Cheng:
DeepQA: improving the estimation of single protein model quality with deep belief networks. BMC Bioinform. 17: 495:1-495:9 (2016) - [j34]Badri Adhikari, Jackson Nowotny, Debswapna Bhattacharya, Jie Hou, Jianlin Cheng:
ConEVA: a toolbox for comprehensive assessment of protein contacts. BMC Bioinform. 17: 517:1-517:12 (2016) - [j33]Debswapna Bhattacharya, Jackson Nowotny, Renzhi Cao, Jianlin Cheng:
3Drefine: an interactive web server for efficient protein structure refinement. Nucleic Acids Res. 44(Webserver-Issue): W406-W409 (2016) - [c12]Rui Xie, Andrew Quitadamo, Jianlin Cheng, Xinghua Shi:
A predictive model of gene expression using a deep learning framework. BIBM 2016: 676-681 - [i3]Renzhi Cao, Taeho Jo, Jianlin Cheng:
Evaluation of Protein Structural Models Using Random Forests. CoRR abs/1602.04277 (2016) - [i2]Renzhi Cao, Debswapna Bhattacharya, Jie Hou, Jianlin Cheng:
DeepQA: Improving the estimation of single protein model quality with deep belief networks. CoRR abs/1607.04379 (2016) - 2015
- [j32]Renzhi Cao, Debswapna Bhattacharya, Badri Adhikari, Jilong Li, Jianlin Cheng:
Large-scale model quality assessment for improving protein tertiary structure prediction. Bioinform. 31(12): 116-123 (2015) - [j31]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: 337:1-337:11 (2015) - [j30]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: 338:1-338:19 (2015) - [j29]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: 5 (2015) - [j28]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): 103-112 (2015) - [c11]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: 535-536 - [c10]Jilong Li, Renzhi Cao, Jianlin Cheng:
MULTICOM: a large-scale conformation sampling and evaluation server for protein tertiary structure prediction. BCB 2015: 537 - 2014
- [j27]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: 120 (2014) - [j26]Xin Deng, Jianlin Cheng:
Enhancing HMM-based protein profile-profile alignment with structural features and evolutionary coupling information. BMC Bioinform. 15: 252 (2014) - [j25]Taeho Jo, Jianlin Cheng:
Improving protein fold recognition by random forest. BMC Bioinform. 15(S-11): S14 (2014) - 2013
- [j24]Jesse Eickholt, Jianlin Cheng:
DNdisorder: predicting protein disorder using boosting and deep networks. BMC Bioinform. 14: 88 (2013) - [j23]Mingzhu Zhu, Jeremy L. Dahmen, Gary Stacey, Jianlin Cheng:
Predicting gene regulatory networks of soybean nodulation from RNA-Seq transcriptome data. BMC Bioinform. 14: 278 (2013) - [j22]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): S12 (2013) - [j21]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): S3 (2013) - [c9]Debswapna Bhattacharya, Jianlin Cheng:
Protein Structure Refinement by Iterative Fragment Exchange. BCB 2013: 106 - [c8]Debswapna Bhattacharya, Jianlin Cheng:
Automated protein structure refinement using i3Drefine software and its assessment in CASP10. BCB 2013: 678 - 2012
- [j20]Jesse Eickholt, Jianlin Cheng:
Predicting protein residue-residue contacts using deep networks and boosting. Bioinform. 28(23): 3066-3072 (2012) - [j19]Jianlin Cheng, Jilong Li, Zheng Wang, Jesse Eickholt, Xin Deng:
The MULTICOM toolbox for protein structure prediction. BMC Bioinform. 13: 65 (2012) - [j18]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): S15 (2012) - [j17]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) - [c7]Jianhan Chen, Jianlin Cheng, A. Keith Dunker:
Session introduction. Pacific Symposium on Biocomputing 2012: 67-69 - 2011
- [j16]Zheng Wang, Jesse Eickholt, Jianlin Cheng:
APOLLO: a quality assessment service for single and multiple protein models. Bioinform. 27(12): 1715-1716 (2011) - [j15]Jesse Eickholt, Xin Deng, Jianlin Cheng:
DoBo: Protein domain boundary prediction by integrating evolutionary signals and machine learning. BMC Bioinform. 12: 43 (2011) - [j14]Xin Deng, Jianlin Cheng:
MSACompro: protein multiple sequence alignment using predicted secondary structure, solvent accessibility, and residue-residue contacts. BMC Bioinform. 12: 472 (2011) - [c6]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: 352-357 - 2010
- [j13]Zheng Wang, Jesse Eickholt, Jianlin Cheng:
MULTICOM: a multi-level combination approach to protein structure prediction and its assessments in CASP8. Bioinform. 26(7): 882-888 (2010) - [j12]Guan Ning Lin, Zheng Wang, Dong Xu, Jianlin Cheng:
SeqRate: sequence-based protein folding type classification and rates prediction. BMC Bioinform. 11(S-3): 1 (2010)
2000 – 2009
- 2009
- [j11]Xin Deng, Jesse Eickholt, Jianlin Cheng:
PreDisorder: ab initio sequence-based prediction of protein disordered regions. BMC Bioinform. 10: 436 (2009) - [j10]Allison N. Tegge, Zheng Wang, Jesse Eickholt, Jianlin Cheng:
NNcon: improved protein contact map prediction using 2D-recursive neural networks. Nucleic Acids Res. 37(Web-Server-Issue): 515-518 (2009) - [c5]Guan Ning Lin, Zheng Wang, Dong Xu, Jianlin Cheng:
Sequence-Based Prediction of Protein Folding Rates Using Contacts, Secondary Structures and Support Vector Machines. BIBM 2009: 3-8 - 2008
- [j9]Arlo Z. Randall, Jianlin Cheng, Michael J. Sweredoski, Pierre Baldi:
TMBpro: secondary structure, beta-contact and tertiary structure prediction of transmembrane beta-barrel proteins. Bioinform. 24(4): 513-520 (2008) - [c4]Jianlin Cheng, Zheng Wang, Gianluca Pollastri:
A neural network approach to ordinal regression. IJCNN 2008: 1279-1284 - 2007
- [j8]Jianlin Cheng, Pierre Baldi:
Improved residue contact prediction using support vector machines and a large feature set. BMC Bioinform. 8 (2007) - [j7]Jianlin Cheng:
DOMAC: an accurate, hybrid protein domain prediction server. Nucleic Acids Res. 35(Web-Server-Issue): 354-356 (2007) - [c3]Jianyong Dai, Jianlin Cheng:
HHMMVE: A Visual Editor for Profile Hidden Markov Model. BIOCOMP 2007: 591-597 - [i1]Jianlin Cheng:
A neural network approach to ordinal regression. CoRR abs/0704.1028 (2007) - 2006
- [j6]Jianlin Cheng, Pierre Baldi:
A machine learning information retrieval approach to protein fold recognition. Bioinform. 22(12): 1456-1463 (2006) - [j5]Jianlin Cheng, Michael J. Sweredoski, Pierre Baldi:
DOMpro: Protein Domain Prediction Using Profiles, Secondary Structure, Relative Solvent Accessibility, and Recursive Neural Networks. Data Min. Knowl. Discov. 13(1): 1-10 (2006) - [j4]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:
Functional Census of Mutation Sequence Spaces: The Example of p53 Cancer Rescue Mutants. IEEE ACM Trans. Comput. Biol. Bioinform. 3(2): 114-125 (2006) - 2005
- [j3]Jianlin Cheng, Michael J. Sweredoski, Pierre Baldi:
Accurate Prediction of Protein Disordered Regions by Mining Protein Structure Data. Data Min. Knowl. Discov. 11(3): 213-222 (2005) - [j2]Jianlin Cheng, Lucas Scharenbroich, Pierre Baldi, Eric Mjolsness:
Sigmoid: A Software Infrastructure for Pathway Bioinformatics and Systems Biology. IEEE Intell. Syst. 20(3): 68-75 (2005) - [j1]Jianlin Cheng, Arlo Z. Randall, Michael J. Sweredoski, Pierre Baldi:
SCRATCH: a protein structure and structural feature prediction server. Nucleic Acids Res. 33(Web-Server-Issue): 72-76 (2005) - [c2]Jianlin Cheng, Pierre Baldi:
Three-stage prediction of protein ?-sheets by neural networks, alignments and graph algorithms. ISMB (Supplement of Bioinformatics) 2005: 75-84 - 2004
- [c1]Pierre Baldi, Jianlin Cheng, Alessandro Vullo:
Large-Scale Prediction of Disulphide Bond Connectivity. NIPS 2004: 97-104
Coauthor Index
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Citation data
Add a list of citing articles from and to record detail pages.
load citations from opencitations.net
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OpenAlex data
Load additional information about publications from 
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last updated on 2024-10-07 21:16 CEST by the dblp team
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