MLEG Publications


Zheng Xiong, Yinyan He, Jason Hattric-Simpers, Jianjun Hu (2017) Automated Phase Segmentation for large-Scale X-ray Diffration Data using Graph-based Phase Segmentation (GPhase) Algorithm. ACS Combinatorial Sciences. DOI: 10.1021/acscombsci.6b00121
Shaoboli, Zheng Xiong, Jianjun Hu (2017) Inferring Phase Diagrams from X-ray Diffraction data with large background signals using Graph Segmentation Algorithm (BGPhase). Submited. 2017
Emrah Atilgan, Jianjun Hu (2017) First-Principle based Computational Doping of SrTiO3 Using Combinatorial Genetic Algorithms. Bulletin of Materials Science. (Accepted) 2017
Shaobo Li, Jason Jie HU, Yuxin Cui, Jianjun Hu (2017) Convolutional Neural Networks for Patent Classification. Information Processing and Management. (in revision)
related USPTO-2M benchmark patent classification dataset (Download)
ShaoboLi,Weixing Chen, Jianjun Hu,"ASPIE: a Framework for Active Sensing and Processing of Complex Events in the Internet of Manufacturing Things". Submitted (2017)
Xuemei Chen,Chenglong Zhang, Shaobo Li, Jianjun Hu, "Fusion Model of Rolling Bear Fault Diagnosis Based on LVQ Neural Network and Decision Tree", submitted (2017)
Qin Li, Anhong Zhang, Yang Wu, Shaobo Li, Jianjun Hu, "Analysis of season-based variable admission ticket pricing models based on online reviews of tourism websites", submitted (2017)


Yuxin Cui, Jianjun Hu (2016) Self-adjusting Nuclei Segmentation (SANS) of Hematoxylin-Eosin Stained Histopathological Breast Cancer Images. in Proceeding of 2016 IEEE International Conference on Bioinformatics and Biomedicine (BIBM)
Zhonghao Liu, Jianjun Hu, "Geometry based general prediction model of protein-peptide binding affinities", 2016 IEEE International Conference on Bioinformatics and Biomedicine (BIBM), vol. 00, no. , pp. 1590-1597, 2016, doi:10.1109/BIBM.2016.7822757
Jonathan Kenneth Bunn, Jianjun Hu, Jason R. Hattrick-Simpers (2016) Semi-Supervised Approach to Phase Identification from Combinatorial Sample Diffraction Patterns, JOM, pp doi:10.1007/s11837-016-2033-8. p1-10 2016
Jason Hattrick-Simpers, J.K.Bunn, Jianjun Hu (2016) Using Semi-Supervised Machine Learning to Map the Phase Diagrams of Open Materials Data Sets. in Proceeding of 2016 Annual Meeting of AIChE,San Francisco, CA
Eric Chen, Jianjun Hu (2016) Computational Identification of Phosphorylation Sites around Nuclear Localization Signal Sequence Reveals New Insight into Genes Associated with Human Diseases. Journal of Bioinformatics and proteomics Review. Rev 3(1):1- 4. 2016


Z. Liu, and J. Hu, Mislocalization-related disease gene discovery using gene expression based computational protein localization prediction. Methods. v93. p119-127. 2015
Jonathan Kenneth Bunn, Shizhong Han, Yan Tong, Yan Zhang, Jianjun Hu, and Jason Ryan Hattrick-Simpers. “Generalized Machine Learning Algorithm for Automatic Phase Attribution in High-throughput Experimental Studies,” Journal of Materials Research, Vol. 30, No. 7, pp. 879 – 889, April, 2015.
Emrah Atilgan, and J. Hu, A Combinatorial Genetic Algorithm for Computational Doping based Material Design. poster paper GECCO 2015


J. Lin, Z. Liu, and J. Hu, Computational identification of post-translational modification (PTM) based nuclear import regulations by characterizing nuclear localization signal-import receptor interaction, Proteins:Structure,Function, and Bioinformatics, 2014.(Accepted on 2 July 2014)
Ambrish Kumar, Jianjun Hu, HollyA LaVoie, KennethB Walsh, DonaldJ DiPette and UgraS Singh, Conformational changes and translocation of tissue-transglutaminase to the plasma membranes: role in cancer cell migration, BMC Cancer 2014.(Accepted on 4 April 2014)


Ananda Mohan Mondal, Jianjun Hu. Scored Protein-Protein Interaction to Predict Subcellular Localizations for Yeast Using Diffusion Kernel. Lecture Notes in Computer Science,Pattern Recognition and Machine Intelligence Volume 8251, 2013, pp 647-655
J. Lin and J. Hu(2013), SeqNLS: Nuclear localization signal prediction based on frequent pattern mining and linear motif scoring, PLoS ONE 8(10): e76864. doi:10.1371/journal.pone.0076864
R. Liu and J. Hu(2013), DNABind: A hybrid algorithm for structure-based prediction of DNA-binding residues by combining machine learning and template-based approaches. Proteins: Structure, Function, and Bioinformatics, DOI: 10.1002/prot.24330


A. Mondal and J. Hu(2012),Mutation analysis of disease causing proteins, IEEE Int. Conference on Bioinformatics and Biomedicine Workshop (BIBMW2012), Philadelphia, PA
J. Lin and J. Hu(2012), Frequent item set mining for nuclear localization signal analysis, Proceeding of ACM Conference on Bioinformatics, Computational Biology and Biomedicine (ACM BCB) (2012), Orlando, FL.
J. Lin, A. Mondal, R. Liu and J. Hu. Minimalist Ensemble Algorithms for Genome-wide Protein Localization Prediction. BMC Bioinformatics, 2012, 13:157.
A. Mondal and J. Hu(2012), "Protein Localization by Integrating Multiple Protein Correlation Networks", Proceeding of 2012 International Conference on Bioinformatics and Computational Biology (BIOCOMP'12: July 13-16, 2012, USA)."


R. Liu and J. Hu. Computational Prediction of Heme-Binding Residues by Exploiting Residue Interaction Network. PLoS ONE 6(10): e25560.
A. Mondal and J. Hu. Network Based subcellular prediction for multi-label proteins. The 4th Workshop on Biomolecular Network Analysis (IWBNA 2011)
R. Liu and J. Hu. HemeBIND: a novel method for heme binding residue prediction by combining structural and sequence information.BMC Bioinformatics 2011, 12:207
A. Mondal and J. Hu. Network Based Prediction of Protein Localization Using Diffusion Kernel. Int. Journal of Data Mining and Bioinformatics. (in press)
E. Atilgan and J. Hu Improving Protein Docking Using Sustainable Genetic Algorithms. International Journal of Computer Information Systems and Industrial Management (IJCISIM), Vol 3, 2011.
R. Liu and J. Hu, Prediction of discontinuous B-cell epitopes using logistic regression and structural information. Journal of Proteomics & Bioinformatics.4: 010-015. 2011.


Ananda Mondal and Jianjun Hu (2010), "NetLoc: Network Based Protein Localization Prediction Using Protein-Protein Interaction and Co-expression Networks", Proceeding of 2010 IEEE International Conference on Bioinformatics & Biomedicine (BIBM2010).
E. Atilgan and J. Hu Efficient Protein-Ligand Docking Using Sustainable Evolutionary Algorithms. Proceeding of the 10th Int. Conference on hybrid intelligence (HIS2010), Atlanta, GA. USA
H. Chen, G. Pimienta, Y. Gu, X. Sun, J. Hu, M. K. Chaerkady, M. Gucek, R. Cole, S. Sukumar, A. Pandey. Proteomic characterization of Her2/neu-overexpressing breast cancer cells. PROTEOMICS 2010 Nov;10(21):3800-10.
Gonzalez HO, Hu J, Gaworecki KM, Roling JA, Baldwin WS, Gardea-Torresdey JL, Bain LJ. Dose-responsive gene expression changes in juvenile and adult mummichogs (Fundulus heteroclitus) after arsenic exposure.Mar Environ Res. 2010
Emrah Atilgan and Jianjun Hu(2010), "Improving Protein Docking Using Efficient Sustainable Evolutionary Algorithm" Proceeding of ACM Genetic and Evolutionary Computation Conference (GECCO2010), Oregon, USA. (Poster Paper)
J. Hu and J. Xu(2010), Density based Pruning for Identificationof Differentially Expressed Genes from Microarray Data. BMC Genomics, 2010 Nov 2;11 Suppl 2:S3."
Fan Zhang and Jianjun Hu(2010), "Bioinformatics Analysis of Physicochemical Properties of Protein Sorting Signals" Proceeding of 2nd International Conference on Bioinformatics and Computational Biology (BICoB2010), Hawaii, USA.
Haiwei Luo, Ronald Benner,Richard A. Long,Jianjun Hu(2010), "Subcellular Localization of Marine Bacterial Alkaline Phosphatases " Proceeding of National Academy of Science Proc Natl Acad Sci (PNAS) 2009 Dec 15;106(50):21219-23.
Jianjun hu and Fan Zhang(2010), "BayesMotif: De novo Protein Sorting Motif Discovery from Impure Datasets" Asia Pacific Bioinformatics Conference (APBC2010). BMC Bioinformatics 2010, 11(Suppl 1):S66 (18 January 2010)


Fan Zhang and Jianjun Hu (2009), "Bayesian Classifier for Anchored Protein Sorting Discovery", Proceeding of 2009 IEEE International Conference on Bioinformatics & Biomedicine (BIBM09: Nov1-4 2009, USA).
Jianjun Hu and Jia Xu (2009), "Improved Identification of Differentially Expressed Genes Using Pareto Gene Pruning", Proceeding of 2009 International Conference on Bioinformatics and Computational Biology (BIOCOMP'09: July 13-16, 2009, USA)."
F.Zhang and J. Hu(2009), Physical Encoding based Bioinformatics analysis for Exploring protein sorting signals, Proceeding of 7th Asia Pacific Bioinformatics Conference (poster paper), Bejing, China. Jan 7, 2009
S. Li and J. Hu. (2009) , Book "Genetic Programming and Creative Design of Mechatronic Systems", China Machine Press, Beijing China. Jan 2009"
Liu CC, Hu J, Kalakrishnan M, Huang H, Zhou XJ (2009) , "Integrative Disease Classification Based on Cross-platform Microarray Data. BMC Bioinformatics,10(Suppl 1):S25 (APBC 2009)"
J. Hu, F. Zhang (2009) , "Improving Protein Localization Prediction Using Amino Acid Group Based Physichemical Encoding". Lecture Notes in Bioinformatics; Vol. 5462. First Int. conf. Bioinformatics and Computational Biology (BICoB2009)


J. Hu, E. D. Goodman, and R. C. Rosenberg (2008) , " Automated Synthesis of Mechanical Vibration Absorbers Using Genetic Programming", Journal of Artificial Intelligence for Engineering Design, Analysis and Manufacturing. 22(3), Special Issue on Genetic programming for human-competitive design
J. Hu, Z. Fan, J. Wang, X. Peng, K. Seo, J. Terpenny, and E. Goodman (2008). GPBG: A Framework for Evolutionary Synthesis of Multi-domain Engineering Systems. Eds. Kalyanmoy Deb,>

~up to 2007

Shaobo Li, Xi Chen, Jianjun Hu,Sustainable HFC Genetic Algorithms Based with Adaptive Migration Structure, International Conference on Wireless Communications, Networking and Mobile Computing (WiCom 2007), 2007..
J. Hu, Haifeng Li, Michael S Waterman, and Xianghong Jasmine Zhou (2006). Integrative missing value estimation for microarray data. BMC Bioinformatics. 7: 449.
J. Hu, Yifeng David Yang and Daisuke Kihara (2006), "EMD: an Ensemble Algorithm for discovering regulatory motifs in DNA sequences", BMC Bioinformatics, 7:342.
J. Hu, Bin Li, and Daisuke Kihara (2005), "Limitations and Potentials of Current Motif Discovery Algorithms", Nucleic Acid Research, 33: 4899-4913
Fei Pan, Kiran Kamath, Kangyu Zhang, Sudip Pulapura, Avinash Achar, Juan Nunez-Iglesias, Yu Huang, Xifeng Yan, Jiawei Han, Haiyan Hu, Min Xu, J. Hu, Xianghong Jasmine Zhou. K. Kamath et. al (2006). Integrative Array Analyzer: a software package for analysis of cross-platform and cross-species microarray data. Bioinformatics, 22: 1665-1667
J. Hu, E. Goodman, K.Seo, Z. Fan, R. Rosenberg (2005), "The Hierarchical Fair Competition (HFC) Framework for Sustainable Evolutionary Algorithms", Evolutionary Computation, 13 (2), MIT Press

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