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2020

iScore: An MPI supported software for ranking protein–protein docking models based on a random walk graph kernel and support vector machines

Renaud, N., Jung, Y., Honavar, V., Geng, C., Bonvin, A. M. J. J. & Xue, L. C., Jan 1 2020, In : SoftwareX. 11, 100462.

Research output: Contribution to journalArticle

Open Access

IScore: A novel graph kernel-based function for scoring protein-protein docking models

Geng, C., Jung, Y., Renaud, N., Honavar, V., Bonvin, A. M. J. J., Xue, L. C. & Valencia, A., Jan 1 2020, In : Bioinformatics. 36, 1, p. 112-121 10 p.

Research output: Contribution to journalArticle

Open Access
5 Scopus citations

The Virtual Data Collaboratory: A Regional Cyberinfrastructure for Collaborative Data-Driven Research

Parashar, M., Simonet, A., Rodero, I., Ghahramani, F., Agnew, G., Jantz, R. & Honavar, V., May 1 2020, In : Computing in Science and Engineering. 22, 3, p. 79-92 14 p., 8686134.

Research output: Contribution to journalArticle

1 Scopus citations
2019

Biomarker discovery in inflammatory bowel diseases using network-based feature selection

Abbas, M., Matta, J., Le, T., Bensmail, H., Obafemi-Ajayi, T., Honavar, V. & EL-Manzalawy, Y., Jan 1 2019, In : PloS one. 14, 11, e0225382.

Research output: Contribution to journalArticle

Open Access

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

Jung, Y., EL-Manzalawy, Y., Dobbs, D. & Honavar, V. G., Mar 1 2019, In : Proteins: Structure, Function and Bioinformatics. 87, 3, p. 198-211 14 p.

Research output: Contribution to journalArticle

Personalized sleep parameters estimation from actigraphy: A machine learning approach

Khademi, A., El-Manzalawy, Y., Master, L., Buxton, O. M. & Honavar, V. G., Jan 1 2019, In : Nature and Science of Sleep. 11, p. 387-399 13 p.

Research output: Contribution to journalArticle

Open Access
1 Scopus citations
2018

A user similarity-based Top-N recommendation approach for mobile in-application advertising

Hu, J., Liang, J., Kuang, Y. & Honavar, V., Nov 30 2018, In : Expert Systems With Applications. 111, p. 51-60 10 p.

Research output: Contribution to journalArticle

6 Scopus citations
7 Scopus citations
2017

Template-based protein-protein docking exploiting pairwise interfacial residue restraints

Xue, L. C., Rodrigues, J. P. G. L. M., Dobbs, D., Honavar, V. & Bonvin, A. M. J. J., May 1 2017, In : Briefings in bioinformatics. 18, 3, p. 458-466 9 p.

Research output: Contribution to journalArticle

10 Scopus citations
2016

FastRNABindR: Fast and accurate prediction of protein-RNA interface residues

El-Manzalawy, Y., Abbas, M., Malluhi, Q. & Honavar, V., Jul 1 2016, In : PloS one. 11, 7, e0158445.

Research output: Contribution to journalArticle

7 Scopus citations

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

El-Manzalawy, Y., Munoz, E. E., Lindner, S. E. & Honavar, V., Dec 1 2016, In : Proteomics. 16, 23, p. 2967-2976 10 p.

Research output: Contribution to journalArticle

7 Scopus citations

Temporal causality analysis of sentiment change in a cancer survivor network

Bui, N., Yen, J. & Honavar, V., Jun 2016, In : IEEE Transactions on Computational Social Systems. 3, 2, p. 75-87 13 p., 7539545.

Research output: Contribution to journalArticle

7 Scopus citations
2014

A conceptual framework for secrecy-preserving reasoning in knowledge bases

Tao, J., Slutzki, G. & Honavar, V., Dec 29 2014, In : ACM Transactions on Computational Logic. 16, 1, 3.

Research output: Contribution to journalArticle

7 Scopus citations

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

Xue, L. C., Jordan, R. A., Yasser, E. M., Dobbs, D. & Honavar, V., Feb 1 2014, In : Proteins: Structure, Function and Bioinformatics. 82, 2, p. 250-267 18 p.

Research output: Contribution to journalArticle

17 Scopus citations

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

Walia, R. R., Xue, L. C., Wilkins, K., El-Manzalawy, Y., Dobbs, D. & Honavar, V., May 20 2014, In : PloS one. 9, 5, e97725.

Research output: Contribution to journalArticle

50 Scopus citations

The promise and potential of big data: A case for discovery informatics

Honavar, V. G., Jul 2014, In : Review of Policy Research. 31, 4, p. 326-330 5 p.

Research output: Contribution to journalArticle

12 Scopus citations
2013

Mobile health technology evaluation: The mHealth evidence workshop

Kumar, S., Nilsen, W. J., Abernethy, A., Atienza, A., Patrick, K., Pavel, M., Riley, W. T., Shar, A., Spring, B., Spruijt-Metz, D., Hedeker, D., Honavar, V., Kravitz, R., Craig Lefebvre, R., Mohr, D. C., Murphy, S. A., Quinn, C., Shusterman, V. & Swendeman, D., Aug 2013, In : American Journal of Preventive Medicine. 45, 2, p. 228-236 9 p.

Research output: Contribution to journalArticle

407 Scopus citations

Predicting the Binding Patterns of Hub Proteins: A Study Using Yeast Protein Interaction Networks

Andorf, C. M., Honavar, V. & Sen, T. Z., Feb 19 2013, In : PloS one. 8, 2, e56833.

Research output: Contribution to journalArticle

8 Scopus citations
2012

B-cell ligand processing pathways detected by large-scale comparative analysis

Towfic, F., Gupta, S., Honavar, V. & Subramaniam, S., Jun 1 2012, In : Genomics, Proteomics and Bioinformatics. 10, 3, p. 142-152 11 p.

Research output: Contribution to journalArticle

Predicting protein-protein interface residues using local surface structural similarity

Jordan, R. A., El-Manzalawy, Y., Dobbs, D. & Honavar, V., Mar 18 2012, In : BMC bioinformatics. 13, 1, 41.

Research output: Contribution to journalArticle

53 Scopus citations

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

Walia, R. R., Caragea, C., Lewis, B. A., Towfic, F., Terribilini, M., El-Manzalawy, Y., Dobbs, D. & Honavar, V., May 10 2012, In : BMC bioinformatics. 13, 1, 89.

Research output: Contribution to journalArticle

52 Scopus citations

PSPACE tableau algorithms for acyclic modalized ALC

Tao, J., Slutzki, G. & Honavar, V., Dec 1 2012, In : Journal of Automated Reasoning. 49, 4, p. 551-582 32 p.

Research output: Contribution to journalArticle

4 Scopus citations
2011

HomPPI: A class of sequence homology based protein-protein interface prediction methods

Xue, L. C., Dobbs, D. & Honavar, V., Jun 17 2011, In : BMC bioinformatics. 12, 244.

Research output: Contribution to journalArticle

52 Scopus citations

Predicting MHC-II binding affinity using multiple instance regression

El-Manzalawy, Y., Dobbs, D. & Honavar, V., Jun 1 2011, In : IEEE/ACM Transactions on Computational Biology and Bioinformatics. 8, 4, p. 1067-1079 13 p., 5582079.

Research output: Contribution to journalArticle

15 Scopus citations

Predicting RNA-Protein Interactions Using Only Sequence Information

Muppirala, U. K., Honavar, V. G. & Dobbs, D., Dec 22 2011, In : BMC bioinformatics. 12, 1, 489.

Research output: Contribution to journalArticle

169 Scopus citations

PRIDB: A protein-RNA interface database

Lewis, B. A., Walia, R. R., Terribilini, M., Ferguson, J., Zheng, C., Honavar, V. & Dobbs, D., Jan 1 2011, In : Nucleic acids research. 39, SUPPL. 1, p. D277-D282

Research output: Contribution to journalArticle

80 Scopus citations

Representing and reasoning with qualitative preferences for compositional systems

Santhanam, G. R., Basu, S. & Honavar, V., Sep 1 2011, In : Journal of Artificial Intelligence Research. 42, p. 211-274 64 p.

Research output: Contribution to journalArticle

13 Scopus citations
2010

Characterization of the retinal proteome during rod photoreceptor genesis

Barnhill, A. E., Hecker, L. A., Kohutyuk, O., Buss, J. E., Honavar, V. G. & Greenlee, H. W., Mar 30 2010, In : BMC Research Notes. 3, 25.

Research output: Contribution to journalArticle

7 Scopus citations

Detection of gene orthology from gene co-expression and protein interaction networks

Towfic, F., VanderPIas, S., OIiver, C. A., Couture, OI., TuggIe, C. K., West GreenIee, M. H. & Honavar, V., Apr 29 2010, In : BMC bioinformatics. 11, SUPPL. 3, S7.

Research output: Contribution to journalArticle

13 Scopus citations

Methods for transcriptomic analyses of the porcine host immune response: Application to Salmonella infection using microarrays

Tuggle, C. K., Bearson, S. M. D., Uthe, J. J., Huang, T. H., Couture, O. P., Wang, Y. F., Kuhar, D., Lunney, J. K. & Honavar, V., Dec 15 2010, In : Veterinary Immunology and Immunopathology. 138, 4, p. 280-291 12 p.

Research output: Contribution to journalArticle

10 Scopus citations

Semi-supervised prediction of protein subcellular localization using abstraction augmented Markov models

Caragea, C., Caragea, D., Silvescu, A. & Honavar, V., Oct 26 2010, In : BMC bioinformatics. 11, SUPPL. 8, S6.

Research output: Contribution to journalArticle

12 Scopus citations

Struct-NB: Predicting protein-RNA binding sites using structural features

Towfic, F., Caragea, C., Gemperline, D. C., Dobbs, D. & Honavar, V., Jan 2010, In : International Journal of Data Mining and Bioinformatics. 4, 1, p. 21-43 23 p.

Research output: Contribution to journalArticle

33 Scopus citations
2009

ANEXdb: An integrated animal ANnotation and microarray EXpression database

Couture, O., Callenberg, K., Koul, N., Pandit, S., Younes, R., Hu, Z. L., Dekkers, J., Reecy, J., Honavar, V. & Tuggle, C., Nov 23 2009, In : Mammalian Genome. 20, 11-12, p. 768-777 10 p.

Research output: Contribution to journalArticle

23 Scopus citations

Efficient markov network structure discovery using independence tests

Bromberg, F., Margaritis, D. & Honavar, V., Aug 13 2009, In : Journal of Artificial Intelligence Research. 35, p. 449-485 37 p.

Research output: Contribution to journalArticle

28 Scopus citations

Mixture of experts models to exploit global sequence similarity on biomolecular sequence labeling

Caragea, C., Sinapov, J., Dobbs, D. & Honavar, V., Apr 29 2009, In : BMC bioinformatics. 10, SUPPL. 4, S4.

Research output: Contribution to journalArticle

4 Scopus citations
2008

Animal trait ontology: The importance and usefulness of a unified trait vocabulary for animal species

Hughes, L. M., Bao, J., Hu, Z. L., Honavar, V. & Reecy, J. M., Jun 1 2008, In : Journal of animal science. 86, 6, p. 1485-1491 7 p.

Research output: Contribution to journalArticle

35 Scopus citations

Characterization of protein-protein interfaces

Yan, C., Wu, F., Jernigan, R. L., Dobbs, D. & Honavar, V., Jan 1 2008, In : Protein Journal. 27, 1, p. 59-70 12 p.

Research output: Contribution to journalArticle

69 Scopus citations

MoSCoE: An approach for composing web services through iterative reformulation of functional specifications

Pathak, J., Basu, S., Lutz, R. & Honavar, V., Feb 1 2008, In : International Journal on Artificial Intelligence Tools. 17, 1, p. 109-138 30 p.

Research output: Contribution to journalArticle

16 Scopus citations

On evaluating MHC-II binding peptide prediction methods

EL-Manzalawy, Y., Dobbs, D. & Honavar, V., Sep 24 2008, In : PloS one. 3, 9, e3268.

Research output: Contribution to journalArticle

38 Scopus citations

Predicting flexible length linear B-cell epitopes.

El-Manzalawy, Y., Dobbs, D. & Honavar, V., 2008, In : Computational systems bioinformatics / Life Sciences Society. Computational Systems Bioinformatics Conference. 7, p. 121-132 12 p.

Research output: Contribution to journalArticle

109 Scopus citations

Predicting linear B-cell epitopes using string kernels

El-Manzalawy, Y., Dobbs, D. & Honavar, V., Jul 1 2008, In : Journal of Molecular Recognition. 21, 4, p. 243-255 13 p.

Research output: Contribution to journalArticle

349 Scopus citations

Proteomic differentiation between murine retinal and brain-derived progenitor cells

Dunn-Thomas, T. E., Dobbs, D. L., Sakaguchi, D. S., Young, M. J., Honovar, V. G. & Greenlee, M. H. W., Feb 1 2008, In : Stem Cells and Development. 17, 1, p. 119-131 13 p.

Research output: Contribution to journalArticle

4 Scopus citations

Use of machine learning algorithms to classify binary protein sequences as highly-designable or poorly-designable

Peto, M., Kloczkowski, A., Honavar, V. & Jernigan, R. L., Nov 18 2008, In : BMC bioinformatics. 9, 487.

Research output: Contribution to journalArticle

3 Scopus citations
2007

Exploring inconsistencies in genome-wide protein function annotations: A machine learning approach

Andorf, C., Dobbs, D. & Honavar, V., Aug 3 2007, In : BMC bioinformatics. 8, 284.

Research output: Contribution to journalArticle

21 Scopus citations

Glycosylation site prediction using ensembles of Support Vector Machine classifiers

Caragea, C., Sinapov, J., Silvescu, A., Dobbs, D. & Honavar, V., Nov 9 2007, In : BMC bioinformatics. 8, 438.

Research output: Contribution to journalArticle

123 Scopus citations

Reports on the 2006 AAAI Fall Symposia

Bongard, J., Brock, D., Collins, S. G., Duraiswami, R., Finin, T., Harrison, I., Honavar, V., Hornby, G. S., Jonsson, A., Kassoff, M., Kortenkamp, D., Kumar, S., Murray, K., Rudnicky, A. I. & Trajkovski, G., Mar 1 2007, In : AI Magazine. 28, 1, p. 88-92 5 p.

Research output: Contribution to journalArticle

1 Scopus citations

RNABindR: A server for analyzing and predicting RNA-binding sites in proteins

Terribilini, M., Sander, J. D., Lee, J. H., Zaback, P., Jernigan, R. L., Honavar, V. & Dobbs, D., Jul 1 2007, In : Nucleic acids research. 35, SUPPL.2, p. W578-W584

Research output: Contribution to journalArticle

143 Scopus citations
2006

Learning accurate and concise naïve Bayes classifiers from attribute value taxonomies and data

Zhang, J., Kang, D. K., Silvescu, A. & Honavar, V., Feb 1 2006, In : Knowledge and Information Systems. 9, 2, p. 157-179 23 p.

Research output: Contribution to journalArticle

39 Scopus citations

Predicting DNA-binding sites of proteins from amino acid sequence

Yan, C., Terribilini, M., Wu, F., Jernigan, R. L., Dobbs, D. & Honavar, V., May 19 2006, In : BMC bioinformatics. 7, 262.

Research output: Contribution to journalArticle

116 Scopus citations

Prediction of RNA binding sites in proteins from amino acid sequence

Terribilini, M., Lee, J. H., Yan, C., Jernigan, R. L., Honavar, V. & Dobbs, D., Aug 3 2006, In : RNA. 12, 8, p. 1450-1462 13 p.

Research output: Contribution to journalArticle

138 Scopus citations