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Items: 18

1.

Partner-specific prediction of RNA-binding residues in proteins: A critical assessment.

Jung Y, El-Manzalawy Y, Dobbs D, Honavar VG.

Proteins. 2019 Mar;87(3):198-211. doi: 10.1002/prot.25639. Epub 2018 Dec 30.

2.

Min-redundancy and max-relevance multi-view feature selection for predicting ovarian cancer survival using multi-omics data.

El-Manzalawy Y, Hsieh TY, Shivakumar M, Kim D, Honavar V.

BMC Med Genomics. 2018 Sep 14;11(Suppl 3):71. doi: 10.1186/s12920-018-0388-0.

3.

In Silico Prediction of Linear B-Cell Epitopes on Proteins.

El-Manzalawy Y, Dobbs D, Honavar VG.

Methods Mol Biol. 2017;1484:255-264. doi: 10.1007/978-1-4939-6406-2_17.

PMID:
27787831
4.

Sequence-Based Prediction of RNA-Binding Residues in Proteins.

Walia RR, El-Manzalawy Y, Honavar VG, Dobbs D.

Methods Mol Biol. 2017;1484:205-235. doi: 10.1007/978-1-4939-6406-2_15.

5.

PlasmoSEP: Predicting surface-exposed proteins on the malaria parasite using semisupervised self-training and expert-annotated data.

El-Manzalawy Y, Munoz EE, Lindner SE, Honavar V.

Proteomics. 2016 Dec;16(23):2967-2976. doi: 10.1002/pmic.201600249. Epub 2016 Nov 21.

6.

FastRNABindR: Fast and Accurate Prediction of Protein-RNA Interface Residues.

El-Manzalawy Y, Abbas M, Malluhi Q, Honavar V.

PLoS One. 2016 Jul 6;11(7):e0158445. doi: 10.1371/journal.pone.0158445. eCollection 2016.

7.

Assessing the effects of data selection and representation on the development of reliable E. coli sigma 70 promoter region predictors.

Abbas MM, Mohie-Eldin MM, El-Manzalawy Y.

PLoS One. 2015 Mar 24;10(3):e0119721. doi: 10.1371/journal.pone.0119721. eCollection 2015.

8.

Building classifier ensembles for B-cell epitope prediction.

EL-Manzalawy Y, Honavar V.

Methods Mol Biol. 2014;1184:285-94. doi: 10.1007/978-1-4939-1115-8_15.

9.

RNABindRPlus: a predictor that combines machine learning and sequence homology-based methods to improve the reliability of predicted RNA-binding residues in proteins.

Walia RR, Xue LC, Wilkins K, El-Manzalawy Y, Dobbs D, Honavar V.

PLoS One. 2014 May 20;9(5):e97725. doi: 10.1371/journal.pone.0097725. eCollection 2014.

10.

DockRank: ranking docked conformations using partner-specific sequence homology-based protein interface prediction.

Xue LC, Jordan RA, El-Manzalawy Y, Dobbs D, Honavar V.

Proteins. 2014 Feb;82(2):250-67. doi: 10.1002/prot.24370. Epub 2013 Oct 17.

11.

Protein-RNA interface residue prediction using machine learning: an assessment of the state of the art.

Walia RR, Caragea C, Lewis BA, Towfic F, Terribilini M, El-Manzalawy Y, Dobbs D, Honavar V.

BMC Bioinformatics. 2012 May 10;13:89. doi: 10.1186/1471-2105-13-89.

12.

Predicting protein-protein interface residues using local surface structural similarity.

Jordan RA, El-Manzalawy Y, Dobbs D, Honavar V.

BMC Bioinformatics. 2012 Mar 18;13:41. doi: 10.1186/1471-2105-13-41.

13.
14.

Recent advances in B-cell epitope prediction methods.

El-Manzalawy Y, Honavar V.

Immunome Res. 2010 Nov 3;6 Suppl 2:S2. doi: 10.1186/1745-7580-6-S2-S2.

15.

Predicting MHC-II binding affinity using multiple instance regression.

EL-Manzalawy Y, Dobbs D, Honavar V.

IEEE/ACM Trans Comput Biol Bioinform. 2011 Jul-Aug;8(4):1067-79. doi: 10.1109/TCBB.2010.94.

16.

On evaluating MHC-II binding peptide prediction methods.

El-Manzalawy Y, Dobbs D, Honavar V.

PLoS One. 2008 Sep 24;3(9):e3268. doi: 10.1371/journal.pone.0003268.

17.

Predicting linear B-cell epitopes using string kernels.

El-Manzalawy Y, Dobbs D, Honavar V.

J Mol Recognit. 2008 Jul-Aug;21(4):243-55. doi: 10.1002/jmr.893.

18.

Predicting flexible length linear B-cell epitopes.

El-Manzalawy Y, Dobbs D, Honavar V.

Comput Syst Bioinformatics Conf. 2008;7:121-32.

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