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2019

Identifying Structural Changes in Correlation Networks Models of Cancer Gene Expression by Stage

Li, Q., Ghersi, D., Thapa, I., Zhang, L., Ali, H. & Cooper, K., Nov 2019, Proceedings - 2019 IEEE International Conference on Bioinformatics and Biomedicine, BIBM 2019. Yoo, I., Bi, J. & Hu, X. T. (eds.). Institute of Electrical and Electronics Engineers Inc., p. 2075-2082 8 p. 8983069. (Proceedings - 2019 IEEE International Conference on Bioinformatics and Biomedicine, BIBM 2019).

Research output: Chapter in Book/Report/Conference proceedingConference contribution

Network Analysis of Antibiotic Resistance Identifies Compelling Mutations across Pathways

Ameri, K. & Cooper, K., Nov 2019, Proceedings - 2019 IEEE International Conference on Bioinformatics and Biomedicine, BIBM 2019. Yoo, I., Bi, J. & Hu, X. T. (eds.). Institute of Electrical and Electronics Engineers Inc., p. 188-192 5 p. 8983099. (Proceedings - 2019 IEEE International Conference on Bioinformatics and Biomedicine, BIBM 2019).

Research output: Chapter in Book/Report/Conference proceedingConference contribution

2017

A compartmental network model for the spread of whooping cough

Ameri, H. & Cooper, K., Dec 15 2017, Proceedings - 2017 IEEE International Conference on Bioinformatics and Biomedicine, BIBM 2017. Yoo, I., Zheng, J. H., Gong, Y., Hu, X. T., Shyu, C-R., Bromberg, Y., Gao, J. & Korkin, D. (eds.). Institute of Electrical and Electronics Engineers Inc., p. 2224-2225 2 p. (Proceedings - 2017 IEEE International Conference on Bioinformatics and Biomedicine, BIBM 2017; vol. 2017-January).

Research output: Chapter in Book/Report/Conference proceedingConference contribution

Analysis of structural measurements in correlation networks built from gene expression data across different tissue types in Mus musculus

Li, Q. & Cooper, K., Dec 15 2017, Proceedings - 2017 IEEE International Conference on Bioinformatics and Biomedicine, BIBM 2017. Yoo, I., Zheng, J. H., Gong, Y., Hu, X. T., Shyu, C-R., Bromberg, Y., Gao, J. & Korkin, D. (eds.). Institute of Electrical and Electronics Engineers Inc., p. 1716-1722 7 p. (Proceedings - 2017 IEEE International Conference on Bioinformatics and Biomedicine, BIBM 2017; vol. 2017-January).

Research output: Chapter in Book/Report/Conference proceedingConference contribution

1 Scopus citations

Analyzing T cell receptor alpha/beta usage in binding to the pMHC

Ehrlich, R. & Ghersi, D., Dec 15 2017, Proceedings - 2017 IEEE International Conference on Bioinformatics and Biomedicine, BIBM 2017. Yoo, I., Zheng, J. H., Gong, Y., Hu, X. T., Shyu, C-R., Bromberg, Y., Gao, J. & Korkin, D. (eds.). Institute of Electrical and Electronics Engineers Inc., p. 83-87 5 p. (Proceedings - 2017 IEEE International Conference on Bioinformatics and Biomedicine, BIBM 2017; vol. 2017-January).

Research output: Chapter in Book/Report/Conference proceedingConference contribution

A network-based approach to mine temporal genes exhibiting significant expression variation in Caenorhabditis elegans

Cooper, K., Hassan, W. & Ali, H., Dec 15 2017, Proceedings - 2017 IEEE International Conference on Bioinformatics and Biomedicine, BIBM 2017. Yoo, I., Zheng, J. H., Gong, Y., Hu, X. T., Shyu, C-R., Bromberg, Y., Gao, J. & Korkin, D. (eds.). Institute of Electrical and Electronics Engineers Inc., p. 2151-2156 6 p. (Proceedings - 2017 IEEE International Conference on Bioinformatics and Biomedicine, BIBM 2017; vol. 2017-January).

Research output: Chapter in Book/Report/Conference proceedingConference contribution

A systems biology approach for modeling microbiomes using split graphs

Kim, S., Thapa, I., Lu, G., Zhu, L. & Ali, H. H., Dec 15 2017, Proceedings - 2017 IEEE International Conference on Bioinformatics and Biomedicine, BIBM 2017. Yoo, I., Zheng, J. H., Gong, Y., Hu, X. T., Shyu, C-R., Bromberg, Y., Gao, J. & Korkin, D. (eds.). Institute of Electrical and Electronics Engineers Inc., p. 2062-2068 7 p. (Proceedings - 2017 IEEE International Conference on Bioinformatics and Biomedicine, BIBM 2017; vol. 2017-January).

Research output: Chapter in Book/Report/Conference proceedingConference contribution

2 Scopus citations

Bioinformatics for middle school aged children: Activities for exposure to an interdisciplinary field

Cooper, K., McGraw, A. & Khazanchi, D., Apr 24 2017, ISEC 2017 - Proceedings of the 7th IEEE Integrated STEM Education Conference. Institute of Electrical and Electronics Engineers Inc., p. 1-9 9 p. 7910217. (ISEC 2017 - Proceedings of the 7th IEEE Integrated STEM Education Conference).

Research output: Chapter in Book/Report/Conference proceedingConference contribution

1 Scopus citations

Correlation networks: Biologically driven relationships from gene expression data

Huff, G. W. & Cooper, K., Dec 15 2017, Proceedings - 2017 IEEE International Conference on Bioinformatics and Biomedicine, BIBM 2017. Yoo, I., Zheng, J. H., Gong, Y., Hu, X. T., Shyu, C-R., Bromberg, Y., Gao, J. & Korkin, D. (eds.). Institute of Electrical and Electronics Engineers Inc., p. 1712-1715 4 p. (Proceedings - 2017 IEEE International Conference on Bioinformatics and Biomedicine, BIBM 2017; vol. 2017-January).

Research output: Chapter in Book/Report/Conference proceedingConference contribution

In-silico analysis of the 'memory anti-Naïve' effect in anti-viral cross-reactive responses

Castiglione, F., Ghersi, D. & Celada, F., Dec 15 2017, Proceedings - 2017 IEEE International Conference on Bioinformatics and Biomedicine, BIBM 2017. Yoo, I., Zheng, J. H., Gong, Y., Hu, X. T., Shyu, C-R., Bromberg, Y., Gao, J. & Korkin, D. (eds.). Institute of Electrical and Electronics Engineers Inc., p. 1433-1437 5 p. (Proceedings - 2017 IEEE International Conference on Bioinformatics and Biomedicine, BIBM 2017; vol. 2017-January).

Research output: Chapter in Book/Report/Conference proceedingConference contribution

2016

Recovering bound forms of Protein structures using the Elastic Network Model and Molecular Interaction Fields

Ghersi, D. & Sanchez, R., Oct 2 2016, ACM-BCB 2016 - 7th ACM Conference on Bioinformatics, Computational Biology, and Health Informatics. Association for Computing Machinery, Inc, p. 50-57 8 p. (ACM-BCB 2016 - 7th ACM Conference on Bioinformatics, Computational Biology, and Health Informatics).

Research output: Chapter in Book/Report/Conference proceedingConference contribution

2015

A novel approach to identify shared fragments in drugs and natural products

Balasubramanya, A., Thapa, I., Bastola, D. & Ghersi, D., Dec 16 2015, Proceedings - 2015 IEEE International Conference on Bioinformatics and Biomedicine, BIBM 2015. Schapranow, L. M., Zhou, J., Hu, X. T., Ma, B., Rajasekaran, S., Miyano, S., Yoo, I., Pierce, B., Shehu, A., Gombar, V. K., Chen, B., Pai, V. & Huan, J. (eds.). Institute of Electrical and Electronics Engineers Inc., p. 575-580 6 p. 7359746. (Proceedings - 2015 IEEE International Conference on Bioinformatics and Biomedicine, BIBM 2015).

Research output: Chapter in Book/Report/Conference proceedingConference contribution

Evaluating the robustness of correlation network analysis in the aging mouse hypothalamus

Cooper, K. M., Bonasera, S. & Ali, H., Jan 1 2015, Biomedical Engineering Systems and Technologies - 8th International Joint Conference, BIOSTEC 2015, Revised Selected Papers. Elias, D., Fred, A. & Gamboa, H. (eds.). Springer Verlag, p. 224-238 15 p. (Communications in Computer and Information Science; vol. 574).

Research output: Chapter in Book/Report/Conference proceedingConference contribution

Identification of biologically significant elements using correlation networks in high performance computing environments

Cooper, K. D., Pawaskar, S. & Ali, H. H., Jan 1 2015, Bioinformatics and Biomedical Engineering - 3rd International Conference, IWBBIO 2015, Proceedings. Ortuño, F. & Rojas, I. (eds.). Springer Verlag, p. 607-619 13 p. (Lecture Notes in Computer Science (including subseries Lecture Notes in Artificial Intelligence and Lecture Notes in Bioinformatics); vol. 9044).

Research output: Chapter in Book/Report/Conference proceedingConference contribution

1 Scopus citations

Identifying aging genes in the aging mouse hypothalamus using gateway node analysis of correlation networks

Cooper, K. M., Bonasera, S. & Ali, H., Jan 1 2015, BIOINFORMATICS 2015 - 6th International Conference on Bioinformatics Models, Methods and Algorithms, Proceedings; Part of 8th International Joint Conference on Biomedical Engineering Systems and Technologies, BIOSTEC 2015. Sinoquet, C., Pastor, O., Gamboa, H., Fred, A. & Elias, D. (eds.). SciTePress, p. 36-43 8 p. (BIOINFORMATICS 2015 - 6th International Conference on Bioinformatics Models, Methods and Algorithms, Proceedings; Part of 8th International Joint Conference on Biomedical Engineering Systems and Technologies, BIOSTEC 2015).

Research output: Chapter in Book/Report/Conference proceedingConference contribution

1 Scopus citations

On the comparison of state-and transition-based analysis of biological relevance in gene co-expression networks

Cooper, K., Vemuri, P. & Ali, H., Dec 16 2015, Proceedings - 2015 IEEE International Conference on Bioinformatics and Biomedicine, BIBM 2015. Schapranow, L. M., Zhou, J., Hu, X. T., Ma, B., Rajasekaran, S., Miyano, S., Yoo, I., Pierce, B., Shehu, A., Gombar, V. K., Chen, B., Pai, V. & Huan, J. (eds.). Institute of Electrical and Electronics Engineers Inc., p. 1197-1203 7 p. 7359852. (Proceedings - 2015 IEEE International Conference on Bioinformatics and Biomedicine, BIBM 2015).

Research output: Chapter in Book/Report/Conference proceedingConference contribution

2014

On the robustness of the biological correlation network model

Dempsey, K. M. & Ali, H. H., Jan 1 2014, BIOINFORMATICS 2014 - 5th Int. Conf. on Bioinformatics Models, Methods and Algorithms, Proceedings; Part of 7th Int. Joint Conference on Biomedical Engineering Systems and Technologies, BIOSTEC 2014. SciTePress, p. 186-195 10 p. (BIOINFORMATICS 2014 - 5th Int. Conf. on Bioinformatics Models, Methods and Algorithms, Proceedings; Part of 7th Int. Joint Conference on Biomedical Engineering Systems and Technologies, BIOSTEC 2014).

Research output: Chapter in Book/Report/Conference proceedingConference contribution

3 Scopus citations

Recognizing patient safety importance through instrument validation on physicians' assessment of an EHR

Noteboom, C., Dempsey, K. & Fruhling, A., Jan 1 2014, Proceedings of the 47th Annual Hawaii International Conference on System Sciences, HICSS 2014. IEEE Computer Society, p. 2828-2837 10 p. 6758954. (Proceedings of the Annual Hawaii International Conference on System Sciences).

Research output: Chapter in Book/Report/Conference proceedingConference contribution

2 Scopus citations
2013

Analysis of incrementally generated clusters in biological networks using graph-theoretic filters and ontology enrichment

West, S., Dempsey, K., Bhowmick, S. & Ali, H., 2013, Proceedings - IEEE 13th International Conference on Data Mining Workshops, ICDMW 2013. IEEE Computer Society, p. 584-591 8 p. 6753973

Research output: Chapter in Book/Report/Conference proceedingConference contribution

A structure-preserving hybrid-chordal filter for sampling in correlation networks

Dempsey, K., Chen, T. Y., Srinivasan, S., Bhowmick, S. & Ali, H., Nov 26 2013, Proceedings of the 2013 International Conference on High Performance Computing and Simulation, HPCS 2013. p. 243-250 8 p. 6641422. (Proceedings of the 2013 International Conference on High Performance Computing and Simulation, HPCS 2013).

Research output: Chapter in Book/Report/Conference proceedingConference contribution

1 Scopus citations

Identifying pathway proteins in networks using convergence

Dempsey, K. & Ali, H., Nov 28 2013, 2013 ACM Conference on Bioinformatics, Computational Biology and Biomedical Informatics, ACM-BCB 2013. p. 853-860 8 p. (2013 ACM Conference on Bioinformatics, Computational Biology and Biomedical Informatics, ACM-BCB 2013).

Research output: Chapter in Book/Report/Conference proceedingConference contribution

On identifying and analyzing significant nodes in protein-protein interaction networks

Khazanchi, R., Dempsey, K., Thapa, I. & Ali, H., 2013, Proceedings - IEEE 13th International Conference on Data Mining Workshops, ICDMW 2013. IEEE Computer Society, p. 343-348 6 p. 6753940

Research output: Chapter in Book/Report/Conference proceedingConference contribution

2 Scopus citations

On mining biological signals using correlation networks

Dempsey, K., Thapa, I., Cortes, C., Eriksen, Z., Bastola, D. K. & Ali, H., 2013, Proceedings - IEEE 13th International Conference on Data Mining Workshops, ICDMW 2013. IEEE Computer Society, p. 327-334 8 p. 6753938

Research output: Chapter in Book/Report/Conference proceedingConference contribution

3 Scopus citations
2012

A novel multithreaded algorithm for extracting maximal chordal subgraphs

Halappanavar, M., Feo, J., Dempsey, K., Ali, H. & Bhowmick, S., Dec 20 2012, Proceedings - 41st International Conference on Parallel Processing, ICPP 2012. p. 58-67 10 p. 6337567. (Proceedings of the International Conference on Parallel Processing).

Research output: Chapter in Book/Report/Conference proceedingConference contribution

4 Scopus citations

Function-preserving filters for sampling in biological networks

Dempsey, K., Bhowmick, S. & Ali, H., 2012, Procedia Computer Science. Elsevier, Vol. 9. p. 587-595 9 p.

Research output: Chapter in Book/Report/Conference proceedingConference contribution

7 Scopus citations

On the design of advanced filters for biological networks using graph theoretic properties

Dempsey, K., Chen, T. Y., Bhowmick, S. & Ali, H., Dec 1 2012, Proceedings - 2012 IEEE International Conference on Bioinformatics and Biomedicine, BIBM 2012. p. 556-560 5 p. 6392617. (Proceedings - 2012 IEEE International Conference on Bioinformatics and Biomedicine, BIBM 2012).

Research output: Chapter in Book/Report/Conference proceedingConference contribution

1 Scopus citations

The development of parallel adaptive sampling algorithms for analyzing biological networks

Dempsey, K., Duraisamy, K., Bhowmick, S. & Ali, H., Oct 18 2012, Proceedings of the 2012 IEEE 26th International Parallel and Distributed Processing Symposium Workshops, IPDPSW 2012. p. 725-734 10 p. 6270712. (Proceedings of the 2012 IEEE 26th International Parallel and Distributed Processing Symposium Workshops, IPDPSW 2012).

Research output: Chapter in Book/Report/Conference proceedingConference contribution

7 Scopus citations
2011

A noise reducing sampling approach for uncovering critical properties in large scale biological networks

Duraisamy, K., Dempsey, K., Ali, H. & Bhowmick, S., Sep 26 2011, Proceedings of the 2011 International Conference on High Performance Computing and Simulation, HPCS 2011. p. 721-728 8 p. 5999898. (Proceedings of the 2011 International Conference on High Performance Computing and Simulation, HPCS 2011).

Research output: Chapter in Book/Report/Conference proceedingConference contribution

11 Scopus citations

A novel correlation networks approach for the identification of gene targets

Dempsey, K., Bonasera, S., Bastola, D. & Ali, H., Mar 28 2011, Proceedings of the 44th Annual Hawaii International Conference on System Sciences, HICSS-44 2010. 5718537. (Proceedings of the Annual Hawaii International Conference on System Sciences).

Research output: Chapter in Book/Report/Conference proceedingConference contribution

10 Scopus citations

A parallel graph sampling algorithm for analyzing gene correlation networks

Dempsey, K., Duraisamy, K., Ali, H. & Bhowmick, S., 2011, Procedia Computer Science. Vol. 4. p. 136-145 10 p.

Research output: Chapter in Book/Report/Conference proceedingConference contribution

15 Scopus citations

Evaluation of essential genes in correlation networks using measures of centrality

Dempsey, K. & Ali, H., Dec 1 2011, 2011 IEEE International Conference on Bioinformatics and Biomedicine Workshops, BIBMW 2011. p. 509-515 7 p. 6112421. (2011 IEEE International Conference on Bioinformatics and Biomedicine Workshops, BIBMW 2011).

Research output: Chapter in Book/Report/Conference proceedingConference contribution

7 Scopus citations

Identifying modular function via edge annotation in gene correlation networks using Gene Ontology search

Dempsey, K., Thapa, I., Bastola, D. & Ali, H., Dec 1 2011, 2011 IEEE International Conference on Bioinformatics and Biomedicine Workshops, BIBMW 2011. p. 255-261 7 p. 6112384. (2011 IEEE International Conference on Bioinformatics and Biomedicine Workshops, BIBMW 2011).

Research output: Chapter in Book/Report/Conference proceedingConference contribution

4 Scopus citations
2010

An intelligent data-centric approach toward identification of conserved motifs in protein sequences

Dempsey, K., Currall, B., Hallworth, R. & Ali, H., Oct 25 2010, 2010 ACM International Conference on Bioinformatics and Computational Biology, ACM-BCB 2010. p. 398-401 4 p. (2010 ACM International Conference on Bioinformatics and Computational Biology, ACM-BCB 2010).

Research output: Chapter in Book/Report/Conference proceedingConference contribution

4 Scopus citations

Applying neural networks to classify influenza virus antigenic types and hosts

Attaluri, P. K., Chen, Z. & Lu, G., Aug 20 2010, 2010 IEEE Symposium on Computational Intelligence in Bioinformatics and Computational Biology, CIBCB 2010. p. 279-284 6 p. 5510726. (2010 IEEE Symposium on Computational Intelligence in Bioinformatics and Computational Biology, CIBCB 2010).

Research output: Chapter in Book/Report/Conference proceedingConference contribution

9 Scopus citations

Sequence comparison using multi-order Markov chains

Fang, X., Lu, G. & Zhang, S., Sep 6 2010, 2010 4th International Conference on Bioinformatics and Biomedical Engineering, iCBBE 2010. 5515258. (2010 4th International Conference on Bioinformatics and Biomedical Engineering, iCBBE 2010).

Research output: Chapter in Book/Report/Conference proceedingConference contribution

2009

Integrating decision tree and hidden markov model (hmm) for subtype prediction of human influenza a virus

Attaluri, P. K., Chen, Z., Weerakoon, A. M. & Lu, G., Aug 17 2009, Cutting-Edge Research Topics on Multiple Criteria Decision Making: 20th International Conference, MCDM 2009, Chengdu/Jiuzhaigou, Proceedings. p. 52-58 7 p. (Communications in Computer and Information Science; vol. 35).

Research output: Chapter in Book/Report/Conference proceedingConference contribution

5 Scopus citations
2008

A parallel architecture for regulatory motif algorithm assessment

Quest, D., Dempsey, K., Shafiullah, M., Bastola, D. & Ali, H., Sep 10 2008, IPDPS Miami 2008 - Proceedings of the 22nd IEEE International Parallel and Distributed Processing Symposium, Program and CD-ROM. 4536178. (IPDPS Miami 2008 - Proceedings of the 22nd IEEE International Parallel and Distributed Processing Symposium, Program and CD-ROM).

Research output: Chapter in Book/Report/Conference proceedingConference contribution

2 Scopus citations
2007

AffyMiner - A tool for significant gene mining in affymetrix GeneChip microarray data

Lu, G., Nguyen, T., Xia, Y., Wang, Z. & Fromm, M., Dec 1 2007, Proceedings of the 40th Annual Hawaii International Conference on System Sciences 2007, HICSS'07. 4076628. (Proceedings of the Annual Hawaii International Conference on System Sciences).

Research output: Chapter in Book/Report/Conference proceedingConference contribution

Influenza A virus informatics: Genotype-centered database and genotype annotation

Lu, G., Buyyani, K., Goty, N., Donis, R. & Chen, Z., Dec 1 2007, Proceedings - 2nd International Multi-Symposiums on Computer and Computational Sciences, IMSCCS'07. p. 76-83 8 p. 4392583. (Proceedings - 2nd International Multi-Symposiums on Computer and Computational Sciences, IMSCCS'07).

Research output: Chapter in Book/Report/Conference proceedingConference contribution

3 Scopus citations

Modeling miRNA data

Lopez, S., Lu, G. & Chen, Z., Jan 1 2007, Proceedings of the 2007 ACM Symposium on Applied Computing. Association for Computing Machinery, p. 158-162 5 p. (Proceedings of the ACM Symposium on Applied Computing).

Research output: Chapter in Book/Report/Conference proceedingConference contribution

2006

GenomeBlast: A Web tool for small genome comparison

Lu, G., Jiang, L., Kotalik, R. M., Rowley, T. W., Zhang, L., Chen, X. & Moriyama, E. N., Dec 22 2006, First International Multi- Symposiums on Computer and Computational Sciences, IMSCCS'06. p. 136-141 6 p. 1636030. (First International Multi- Symposiums on Computer and Computational Sciences, IMSCCS'06; vol. 1).

Research output: Chapter in Book/Report/Conference proceedingConference contribution

2003

A new approach for gene annotation using unambiguous sequence joining

Tchourbanov, A., Quest, D., Ali, H., Pauley, M. & Norgren, R., Jan 1 2003, Proceedings of the 2003 IEEE Bioinformatics Conference, CSB 2003. Institute of Electrical and Electronics Engineers Inc., p. 353-362 10 p. 1227336. (Proceedings of the 2003 IEEE Bioinformatics Conference, CSB 2003).

Research output: Chapter in Book/Report/Conference proceedingConference contribution

5 Scopus citations