This is Penn State

List of Publications

 
2018

El-Manzalawy Y (2018) CCA based multi-view feature selection for multi-omics data integration. IEEE Conference on Computational Intelligence in Bioinformatics and Computational Biology (CIBCB) (Accepted).

Khademi A, El-Manzalawy Y, Buxton O, Honavar V (2018) Toward Personalized Sleep-Wake Prediction from Actigraphy. IEEE International Conference on Biomedical and Health Informatics (in press). preprint

2017

El-Manzalawy Y, Buxton O, Honavar V (2017) Sleep/wake state prediction and sleep parameter estimation using unsupervised classification via clustering. IEEE International Conference on Bioinformatics and Biomedicine (BIBM 2017) (in press).

Abbas M, El-Manzalawy Y (2017) Predictive and Comparative Network Analysis of the Gut Microbiota in Type 2 Diabetes. Proceedings of the 8th ACM Conference on Bioinformatics, Computational Biology and Health Informatics: ACM. pp. 313-320.

El-Manzalawy Y, Hsieh T-Y, Shivakumar M, Kim D, Honavar V (2017) Min-Redundancy and MaxRelevance Multi-view Feature Selection for Predicting Ovarian Cancer Survival using Multi-omics Data. Presented at the 7th Annual Translational Bioinformatics Conference.

El-Manzalawy Y, Dobbs D, Honavar V (2017) In silico prediction of linear B-cell epitopes on proteins. In: Zhou Y, Faraggi E, Kloczkowski A, Yang Y, editors. Methods Mol Biol: Springer.

Walia R, El-Manzalawy Y, Dobbs D, Honavar V (2017) Sequence-based Prediction of RNA-binding Residues in Proteins. In: Zhou Y, Faraggi E, Kloczkowski A, Yang Y, editors. Methods Mol Biol: Springer.

2016

El‐Manzalawy, Y., Munoz, E. E., Lindner, S. E., & Honavar, V. (2016). PlasmoSEP: Predicting surface exposed proteins on the malaria parasite using semi‐supervised Self‐training and expert‐annotated data. Proteomics, 1-10.

El-Manzalawy, Y., Abbas, M., Malluhi, Q., & Honavar, V. (2016). FastRNABindR: Fast and Accurate Prediction of Protein-RNA Interface Residues. PLoS One, 11(7), e0158445.

2015

Abbas, M., Mohie-Eldin, M., & EL-Manzalawy, Y. (2015). Assessing the effects of data selection and representation on the development of reliable E. coli sigma 70 promoter region predictors. PLoS One, 10(3):e0119721. doi: 10.1371/journal.pone.0119721

2014

EL-Manzalawy, Y. & Honavar, V. (2014). Building Classifier Ensembles for B-Cell Epitopes Prediction. In De Rajat K. & Tomar, N. (Eds.), Immunoinformatics, Methods in Molecular Biology (pp. 285-294). Springer New York.

Walia, R. R., Xue, L. C., Wilkins, K., EL-Manzalawy, Y., Dobbs, D., & Honavar, V. (2014). RNABindRPlus: A Predictor that Combines Machine Learning and Sequence Homology-Based Methods to Improve the Reliability of Predicted RNA-Binding Residues in Proteins. PloS one, 9(5), e97725.

Xue, L. C., Jordan, R. A., EL-Manzalawy, Y., Dobbs, D., & Honavar, V. (2014). DockRank: Ranking docked conformations using partner‐specific sequence homology‐based protein interface prediction. Proteins: Structure, Function, and Bioinformatics, 82(2), 250-267.

2013

EL-Manzalawy, Y., & Honavar, V. (2013). B Cell Epitope Prediction. In Encyclopedia of Systems Biology (pp. 63-67). Springer New York.

EL-Manzalawy, Y., & Honavar, V. (2013). Major Histocompatibility Complex (MHC), Binder Prediction. In Encyclopedia of Systems Biology (pp. 1162-1166). Springer New York.

2012

EL-Manzalawy, Y., Dobbs, D., & Honavar, V. (2012). Predicting protective bacterial antigens using random forest classifiers. In Proceedings of the ACM Conference on Bioinformatics, Computational Biology and Biomedicine (pp. 426-433). ACM.

Walia, R. R., Caragea, C., Lewis, B. A., Towfic, F., Terribilini, M., EL-Manzalawy, Y., Dobbs, D., & Honavar, V. (2012). Protein-RNA interface residue prediction using machine learning: an assessment of the state of the art. BMC bioinformatics, 13(1), 89.

Jordan, R. A., EL-Manzalawy, Y., Dobbs, D., & Honavar, V. (2012). Predicting protein-protein interface residues using local surface structural similarity. BMC bioinformatics, 13(1), 41.

2011

Xue, L. C., Jordan, R. A., EL-Manzalawy, Y., Dobbs, D., & Honavar, V. (2011). Ranking docked models of protein-protein complexes using predicted partner-specific protein-protein interfaces: a preliminary study. In Proceedings of the 2nd ACM Conference on Bioinformatics, Computational Biology and Biomedicine (pp. 441-445). ACM.

Xue, L. C., Walia, R., EL-Manzalawy, Y., Dobbs, D., & Honavar, V. (2011). Improving protein-RNA interface prediction by combining sequence homology based method with a naive Bayes classifier: preliminary results. In Proceedings of the 2nd ACM Conference on Bioinformatics, Computational Biology and Biomedicine (pp. 556-558). ACM.

EL-Manzalawy, Y., Dobbs, D., & Honavar, V. (2011). Predicting MHC-II binding affinity using multiple instance regression. Computational Biology and Bioinformatics, IEEE/ACM Transactions on, 8(4), 1067-1079.

2010

EL-Manzalawy, Y., & Honavar, V. (2010). Recent advances in B-cell epitope prediction methods. Immunome research, 6(Suppl 2), S2.

EL-Manzalawy, Y., & Honavar, V. (2010). A framework for developing epitope prediction tools. In Proceedings of the First ACM International Conference on Bioinformatics and Computational Biology (pp. 660-662). ACM.

2009

EL-Manzalawy, Y., & Honavar, V. (2009). MICCLLR: Multiple-Instance Learning Using Class Conditional Log Likelihood Ratio. In Discovery Science (pp. 80-91). Springer Berlin/Heidelberg.

2008

EL-Manzalawy, Y., Dobbs, D., & Honavar, V. (2008). Predicting Protective Linear B-Cell Epitopes Using Evolutionary Information. In Proceedings of the 2008 IEEE International Conference on Bioinformatics and Biomedicine (pp. 289-292). IEEE Computer Society.

EL-Manzalawy, Y., Dobbs, D., & Honavar, V. (2008). On evaluating MHC-II binding peptide prediction methods. PloS one, 3(9), e3268-e3268.

EL‐Manzalawy, Y., Dobbs, D., & Honavar, V. (2008). Predicting linear B‐cell epitopes using string kernels. Journal of molecular recognition, 21(4), 243-255.

EL‐Manzalawy, Y., Dobbs, D., & Honavar, V. (2008). Predicting flexible length linear B-cell epitopes. In Computational Systems Bioinformatics (Vol. 7, p. 121).

2005

EL-Manzalawy, Y., & Honavar, V. (2005). WLSVM: Integrating libsvm into WEKA environment. Software available at http://www.cs.iastate.edu/yasser/wlsvm.