Peer review journal publication

(available at Google scholar / PubMed)

23. Matthew Conover, Max Staples, Dong Si, Miao Sun, Renzhi Cao*. AngularQA: Protein Model QualityAssessment with LSTM Networks. Computational and Mathematical Biophysics 7, no. 1 (2019): 1-9. 2019. [at Computational and Mathematical Biophysics]

22. Stephenson, N., E. Shane, J. Chase, J. Rowland, D. Ries, N. Justice, J. Zhang, L. Chan, Renzhi Cao*. Survey of Machine Learning Techniques in Drug Discovery. Current drug metabolism (2018). [at Curr Drug Metab] Impact factor: 2.655.

21. John Smith, Matthew Conover, Natalie Stephenson, Jesse Eickholt, Dong Si, Miao Sun, Renzhi Cao *. TopQA: A Topological Representation for Single-Model Protein Quality Assessment with Machine Learning. International Journal of Computational Biology and Drug Design, 2018. Accepted.

20. Keasar Chen, Liam J. McGuffin, Björn Wallner, ...,R. Cao, etc. An analysis and evaluation of the WeFold collaborative for protein structure prediction and its pipelines in CASP11 and CASP12. Scientific reports 8, no. 1 (2018): 9939. [at Scientific Report] Impact factor: 4.122.

19. R. Cao, C. Freitas, L. Chan, M. Sun, H. Jiang, Z. Chen. ProLanGO: Protein Function Prediction Using Neural Machine Translation Based on a Recurrent Neural Network Molecules, doi:10.3390/molecules22101732, 2017. [at Molecules] Impact factor: 2.861.

18. R. Cao, B. Adhikari, D. Bhattacharya, M. Sun, J. Hou, J. Cheng. QAcon: single model quality assessment using protein structural and contact information with machine learning techniques. Bioinformatics (2016): btw694.[at Bioinformatics] , Impact factor: 5.766.

17. R. Cao, D. Bhattacharya, J. Hou, J. Cheng. DeepQA: improving the estimation of single protein model quality with deep belief networks. BMC bioinformatics 17.1 (2016): 495. [at BMC Bioinformatics] , [software download],Impact factor: 2.435.

-------------------------------------------------------------- Before join PLU at 2016 --------------------------------------------------------------

16. Y. Jiang, ... R. Cao, ..., etc. An expanded evaluation of protein function prediction methods shows an improvement in accuracy. Genome Biology201617:184 DOI: 10.1186/s13059-016-1037-6, 2016. [at Genome Biology] , Impact factor: 11.313.

15. D. Bhattacharya, R. Cao, J. Cheng. UniCon3D: de novo protein structure prediction using united-residue conformational search via stepwise, probabilistic sampling, accepted by Bioinformatics, 2016. [at Bioinformatics] , [Web server], Impact factor: 5.766.

14. D. Bhattacharya, J. Nowotny, R. Cao, J. Cheng. 3Drefine: An Interactive Web Server for Efficient Protein Structure Refinement. Nucleic Acids Research, doi: 10.1093/nar/gkw336, 2016. [at Nucleic Acids Research] , [Web server], Impact factor: 9.112.

13. R. Cao, J. Cheng. Protein single-model quality assessment by feature-based probability density functions. Scientific Reports, doi:10.1038/srep23990, 2016. [at Scientific Report] [at Web Server], [software download]. Impact factor: 5.578.

12. J. Nowotny, A. Wells, O. Oluwadare, L. Xu, R. Cao, T. Trieu, C. He, J. Cheng. GMOL: an interactive tool for 3D genome structure visualization. Scientific Reports, doi:10.1038/srep20802, 2016. [at Scientific Report] Impact factor: 5.578.

11. J. Nowotny, S. Ahmed, L. Xu, O. Oluwadare, H. Chen, N. Hensley, T. Trieu, R. Cao, J. Cheng. Iterative reconstruction of three-dimensional models of human chromosomes from chromosomal contact data. BMC bioinformatics, 16(1):338, 2015. [at BMC bioinformatics website]. Impact factor: 2.58.

10.R. Cao, J. Cheng. Deciphering the association between gene function and spatial gene-gene interactions in 3D human genome conformation. BMC Genomics, 16:880, 2015 [at BMC genomics website]. Impact factor: 3.99.

9. J. Li,R. Cao, J. Cheng. A large-scale conformation sampling and evaluation server for protein tertiary structure prediction and its assessment in CASP11. BMC bioinformatics, 2015 [at BMC bioinformatics website]. Impact factor: 2.58.

8.R. Cao, Bhattacharya, B. Adhikari, J. Li, J. Cheng. Massive integration of diverse protein quality assessment methods to improve template based modeling in CASP11 Proteins, 2015.[at Proteins website]. Impact factor: 2.63.

7.R. Cao, J. Cheng. Integrated protein function prediction by mining function associations, sequences, and protein-protein and gene-gene interaction networks. Methods, 2015 [at Methods website]. Impact factor: 3.65.

6.B. Adhikari, D. Bhattacharya, R. Cao, J. Cheng. CONFOLD: Residue-Residue Contact-guided ab initio Protein Folding Proteins. 83(8):1436-1439, 2015. [at proteins website]. Impact factor: 2.63.

5.R. Cao, Bhattacharya, B. Adhikari, J. Li, J. Cheng. Large-Scale Model Quality Asessment for Improving Protein Tertiary Structure Prediction. 23rd International Conference on Intelligent Systems for Molecular Biology (ISMB), Bioinformatics. 31(12):i116-i123, 2015.[at Bioinformatics website], [Web server]. Impact factor: 4.98.

4.R. Cao, Z. Wang, Y. Wang, J. Cheng. SMOQ: a tool for predicting the absolute residue-specific quality of a single protein model with support vector machines. BMC Bioinformatics, 15:120, 2014.[at BMC Bioinformatics's website]. Impact factor: 2.58.

3.R. Cao, Z. Wang, J. Cheng. Designing and evaluating the MULTICOM protein local and global model quality prediction methods in the CASP10 experiment. BMC Structural Biology, 14:13, 2014. [at BMC Structural Biology's website]. Impact factor: 1.18.

2. Z. Wang, R. Cao, K. Taylor, A. Briley, C. Caldwell, J. Cheng. The Properties of Genome Conformation and Spatial Gene Interaction and Regulation Networks of Normal and Malignant Human Cell Types. PLoS ONE. 8(3):e58793, 2013. [At PLOS ONE website]. Impact factor: 3.23.

1. Z. Wang, R. Cao, J. Cheng. Three-Level Prediction of Protein Function by Combining Profile-Sequence Search, Profile-Profile Search, and Domain Co-occurrence Networks. BMC Bioinformatics. 14(Suppl 3):S3, 2013. [At BMC bioinformatics website]. Impact factor: 2.58.

Conferences

6. Nathan Kosylo, John Smith, Matthew Conover, Leong Chan, Hongtao Zhang, Hanfei Mei, R. Cao *. Artificial Intelligence on Job-hopping Forecasting: AI on Job-hopping. In 2018 Portland International Conference on Management of Engineering and Technology (PICMET), pp. 1-5. IEEE, 2018. [at PICMET website].

5. Jingjing Yang, R. Cao, Dong Si. EMNets: A Convolutional Autoencoder for Protein Surface Retrieval Based on Cryo-Electron Microscopy Imaging. In Proceedings of the 2018 ACM International Conference on Bioinformatics, Computational Biology, and Health Informatics, pp. 639-644. ACM, 2018. [at ACM].

4.R. Cao, J. Hou, T. Jo, J. Cheng. Evaluation of Protein Structural Models Using Random Forests. Accepted, 2017. [BICOB website].

3.R. Cao, Bhattacharya, B. Adhikari, J. Li, J. Cheng. Large-Scale Model Quality Asessment for Improving Protein Tertiary Structure Prediction. 23rd International Conference on Intelligent Systems for Molecular Biology (ISMB), Bioinformatics. 31(12):i116-i123, 2015.[at Bioinformatics website].

2. Xingfu Wang, Renzhi Cao, Qiuyuan Huang, Zineng Ke,Zhiqiang Liu. "A Novel Anchor-free Position Algorithm Based on Cluster Technique" .2010 2nd International Conference on Software Technology and Engineering. ICSTE 2010. San Juan, Puerto Rico, USA. October 3-5, 2010.IEEE Catalog Number: CFP1030L-PRT. ISBN: 978-1-4244-8665-6. http://www.icste.org/index.htm.

1. Haiqing Jiang, Renzhi Cao, Xingfu Wang.   "Apply Modified Method of Nonlinear Optimization toImprove Localization accuracy in WSN".   The 5th International Conference on Wireless Communications Networking and Mobile Computing, WiCOM 2009 , Sept. 24-26, 2009, Beijing.(INDEX Accession number: 20100112610590)ISBN-13: 9781424436934

Patents

2. Xingfu Wang, Renzhi Cao, Lei Qian, Yan Xiong. Sensor Localization Method. Public Number: CN101820676A

1.Xingfu Wang, Lei Qian, Renzhi Cao. Tolerant Majority-Colluding Attacks for Secure Localization in Wireless Sensor Networks. Public Number: CN101820618A

 

Invited book chapter

Jilong Li, Debswapna Bhattacharya, Renzhi Cao, Badri Adhikari, Xin Deng, Jesse Eickholt, Jianlin Cheng. Renzhi Cao. "The MULTICOM Protein Tertiary Structure Prediction System" Online link.Methods in Molecular Biology, Springer, Vol. 1137, 3rd ed. isbn: 978-1-4939-0366-5, doi:10.1007/978-1-4939-0366-5_3. 2014

 

Badri Adhikari, Debswapna Bhattacharya, Renzhi Cao, Jianlin Cheng. "Assessing predicted contacts for building protein three-dimensional models".Methods in Molecular Biology, Springer, 2016

 

Oral presentation

10. Renzhi Cao, How machines learn like human. Tech talk presentation, 1/10/2017 at Morken 216. Flyer

9. Renzhi Cao, Single-model quality assessment using protein structural and contact information with machine learning techniques. The 13th MidSouth Computational Biology and Bioinformatics Conference (MCBIOS). Oral presentation. 2016. PDF slides

8. Renzhi Cao, D. Bhattacharya, B. Adhikari, J. Li, J. Cheng. Large-Scale Model Quality Asessment for Improving Protein Tertiary Structure Prediction. The 23rd International Conference on Intelligent Systems for Molecular Biology (ISMB), Dublin, Ireland, 2015.

7. Renzhi Cao 2015 Life Science Center Week. Poster [website]

6. Renzhi Cao, Debswapna Bhattacharya, Jilong Li, Badri Adhikari, Jianlin Cheng. MULTICOM: large scale model quality assessment and mining techniques for human protein tertiary structure prediction. 11th Community Wide Experiment on the Critical Assessment of Techniques for Protein Structure Prediction (CASP11) conference 2014. Poster presentation.

5. Jilong Li, Renzhi Cao, Jianlin Cheng. A Conformation Ensemble Approach to Protein Tertiary Structure Prediction by MULTICOM-CLUSTER. CASP11 conference 2014. Poster presentation.

4. Renzhi Cao. Protein quality assessment. PhD qualify examination. University of missouri, columbia. Oral presentation. [slides]

3. Renzhi Cao, Jianlin Cheng. Protein model quality assessment by MULTICOM server prediction. Midsouth Computational Biology and Bioinformatics Society. MCBIOS conference 2013. Oral presentation.

2. Zheng Wang, Renzhi Cao, Kristen Taylor, Aaron Briley, Charles Caldwell, Jianlin Cheng. THE PROPERTIES OF HUMAN GENOME CONFORMATION AND SPATIAL GENE INTERACTION AND REGULATION NETWORKS. At Pacific Symposium on Biocomputing (PSB 2013) Poster Presentation.

1. Renzhi Cao, Zheng Wang, Jilong Li, Jianlin Cheng.Protein Model Quality Prediction by MULTICOM Servers. At Pacific Symposium on Biocomputing (PSB 2013) Poster Presentation.