Kathryn M Cooper, PhD

Assistant Professor

  • 209 Citations
  • 7 h-Index
20082019
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Research Output 2008 2019

  • 209 Citations
  • 7 h-Index
  • 27 Conference contribution
  • 8 Article
  • 3 Editorial
  • 2 Chapter
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Conference contribution
2017

A compartmental network model for the spread of whooping cough

Ameri, H. & Cooper, K. M., 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

Whooping Cough
Bordetella pertussis
Epidemiology
Health care
Health Personnel

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

Li, Q. & Cooper, K. M., 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

Gene expression
Tissue
Gene Expression
Genes
Cluster Analysis

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

Cooper, K. M., Hassan, W. & 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. 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

Caenorhabditis elegans
Genes
Gene Regulatory Networks
Biological systems
Biomedical Research
1 Citation (Scopus)

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

Cooper, K. M., 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

Bioinformatics
Engineering technology
engineering
science
Students

Correlation networks: Biologically driven relationships from gene expression data

Huff, G. W. & Cooper, K. M., 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

Gene expression
Transcription factors
Transcription Factors
Gene Expression
Genes
2015

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

Cooper, K. M., Bonasera, S. J. & Ali, H. 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

Electric network analysis
Aging of materials
Genes
Benchmarking
Assays
1 Citation (Scopus)

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

Cooper, K. M., 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

Gateway
High Performance
Genes
Aging of materials
Computing
1 Citation (Scopus)

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

Cooper, K. M., Bonasera, S. J. & Ali, H. 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

Hypothalamus
Genes
Aging of materials
Gene Regulatory Networks
Research

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

Cooper, K. M., Vemuri, P. & Ali, H. 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

Genes
Gene Expression
Cluster Analysis
Research
Gene expression
2014
3 Citations (Scopus)

On the robustness of the biological correlation network model

Cooper, 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

Network Model
Robustness
Bioinformatics
Model
Causation
2 Citations (Scopus)

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

Noteboom, C., Cooper, K. M. & Fruhling, A. L., 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

Information technology
Health
Factor analysis
Medicine
2013

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

West, S., Cooper, K. M., Bhowmick, S. & Ali, H. 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

Bioinformatics
Medical problems
Gene expression
Yeast
Data mining
1 Citation (Scopus)

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

Cooper, K. M., Chen, T. Y., Srinivasan, S., Bhowmick, S. & Ali, H. 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

Electric network analysis
Throughput
Filter
Sampling
Biological Networks

Identifying pathway proteins in networks using convergence

Cooper, K. M. & Ali, H. 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

Aptitude
Proteins
Biological Phenomena
Guilt
Systems Biology
2 Citations (Scopus)

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

Khazanchi, R., Cooper, K. M., Thapa, I. & Ali, H. 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

Proteins
Transcription factors
Circuit theory
Yeast
Data mining
3 Citations (Scopus)

On mining biological signals using correlation networks

Cooper, K. M., Thapa, I., Cortes, C., Eriksen, Z., Bastola, D. R. & Ali, H. 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

Transcription factors
Binding sites
Gene expression
Genes
Throughput
2012
4 Citations (Scopus)

A novel multithreaded algorithm for extracting maximal chordal subgraphs

Halappanavar, M., Feo, J., Cooper, K. M., Ali, H. 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

Subgraph
Chordal Graphs
Graph in graph theory
Maximum Clique
Proof of correctness
7 Citations (Scopus)

Function-preserving filters for sampling in biological networks

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

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

Sampling
Complex networks
Data structures
Assays
Genes
1 Citation (Scopus)

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

Cooper, K. M., Chen, T. Y., Bhowmick, S. & Ali, H. 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

Noise
Genes
Gene Regulatory Networks
Essential Genes
Biological systems
7 Citations (Scopus)

The development of parallel adaptive sampling algorithms for analyzing biological networks

Cooper, K. M., Duraisamy, K., Bhowmick, S. & Ali, H. 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

Sampling
Bioinformatics
Computational methods
Data mining
Genes
2011
11 Citations (Scopus)

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

Duraisamy, K., Cooper, K. M., Ali, H. 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

Biological Networks
Genes
Sampling
Gene
Chordal Graphs
10 Citations (Scopus)

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

Microarrays
Genes
Ontology
Availability
15 Citations (Scopus)

A parallel graph sampling algorithm for analyzing gene correlation networks

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

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

Genes
Sampling
Complex networks
6 Citations (Scopus)

Evaluation of essential genes in correlation networks using measures of centrality

Cooper, K. M. & Ali, H. 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

Essential Genes
Gene expression
Genes
Gene Expression
Proteins
4 Citations (Scopus)

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

Cooper, K. M., Thapa, I., Bastola, D. R. & Ali, H. 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

Gene Ontology
Gene Regulatory Networks
Ontology
Genes
Protein Interaction Maps
2010
4 Citations (Scopus)

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

Cooper, K. M., Currall, B., Hallworth, R. & Ali, H. 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

Amino Acid Motifs
Bioinformatics
Software
Proteins
Biological Science Disciplines
2008
2 Citations (Scopus)

A parallel architecture for regulatory motif algorithm assessment

Quest, D., Cooper, K. M., Shafiullah, M., Bastola, D. R. & Ali, H. 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

Parallel architectures
Automation
Cluster computing
Bioinformatics
Tuning