Kathryn M Cooper, PhD

  • 234 Citations
  • 7 h-Index
20082020

Research output per year

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Research Output

  • 234 Citations
  • 7 h-Index
  • 29 Conference contribution
  • 9 Article
  • 3 Editorial
  • 2 Chapter
2020
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

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

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

2016
2 Scopus citations
2015

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., 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

Identifying aging-related genes in mouse hippocampus using gateway nodes

Dempsey, K. M. & Ali, H. H., May 27 2014, In : BMC systems biology. 8, 1, 62.

Research output: Contribution to journalArticle

10 Scopus citations

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 new approach for sequence analysis: Illustrating an expanded bioinformatics view through exploring properties of the prestin protein

Dempsey, K., Hallworth, R., Currall, B. & Ali, H., Mar 31 2013, Bioinformatics: Concepts, Methodologies, Tools, and Applications. IGI Global, Vol. 3. p. 1536-1556 21 p.

Research output: Chapter in Book/Report/Conference proceedingChapter

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., 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

4 Scopus citations

On the discovery of cellular subsystems in gene correlation networks using measures of centrality

Dempsey, K. M. & Ali, H. H., Jan 1 2013, In : Current Bioinformatics. 8, 3, p. 305-314 10 p.

Research output: Contribution to journalArticle

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

CD4+ regulatory and effector/memory T cell subsets profile motor dysfunction in Parkinson's disease

Saunders, J. A. H., Estes, K. A., Kosloski, L. M., Allen, H. E., Dempsey, K. M., Torres-Russotto, D. R., Meza, J. L., Santamaria, P. M., Bertoni, J. M., Murman, D. L., Ali, H. H., Standaert, D. G., Mosley, R. L. & Gendelman, H. E., Dec 1 2012, In : Journal of Neuroimmune Pharmacology. 7, 4, p. 927-938 12 p.

Research output: Contribution to journalArticle

112 Scopus citations
6 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 new approach for sequence analysis: Illustrating an expanded bioinformatics view through exploring properties of the prestin protein

Dempsey, K., Currall, B., Hallworth, R. & Ali, H., Dec 1 2011, Handbook of Research on Computational and Systems Biology: Interdisciplinary Applications. IGI Global, p. 202-223 22 p.

Research output: Chapter in Book/Report/Conference proceedingChapter

2 Scopus citations

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

12 Scopus citations

A novel correlation networks approach for the identification of gene targets

Dempsey, K., Bonasera, S., Bastola, D. & Ali, H., 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

16 Scopus citations

Evaluation of essential genes in correlation networks using measures of centrality

Dempsey, K. & Ali, H., 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., 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
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

MTAP: The motif tool assessment platform

Quest, D., Dempsey, K., Shafiullah, M., Bastola, D. & Ali, H., Aug 12 2008, In : BMC bioinformatics. 9, SUPPL. 9, S6.

Research output: Contribution to journalArticle

7 Scopus citations