College of Arts & Sciences Computer Science

Carol Lushbough

Carol Lushbough
Assistant Professor
Computer Science, College of Arts & Sciences
UAS Arts & Sciences 204
Phone: 605-677-6138
Bio:
Carol Lushbough is a computer scientist with expertise in software engineering, data management, distributed systems, and cyberinfrastructure. She has been the main architect of the BioExtract Server (http://bioextract.org)
Teaching Interests:
Software Engineering Distributed Systems Systems Analysi8s
Research Interests:
Cyberinfrastructure Bioinformatic Workflows Distributed databases
Education:
  • MA, Computer Science, University of South Dakota, 1991
  • MA, Math, University of South Dakota, 1987
  • BA, Math, Westmar College, 1972
Research:
  • An Interdisciplinary Student Teaching Innovation: A Health Science and Arts and Sciences Teaching Synergy , University of South Dakota Provost Teaching Innovation Fund
Grants:
  • Cyberinfrastructure for (Comparative) Plant Genome Research through PlantGDB, NSF, (2006 - 2011)
  • IDeA Networks of Biomedical Research Excellence, NIH
  • TRPGR - Integrating the BioExtract Server with the iPlant Collaborative, NSF, (2011 - 2014)
Publications:
  • Wang, ., Ware, D., Lushbough, C., Merchant, N., Building an open Genome Wide Association Study (GWAS) platform, 2013 IEEE International Conference on Cluster Computing (CLUSTER), iss. 2013. (DOI: 10.1109/CLUSTER.2013.6702696)
  • Thavappiragasam, M., Lushbough, C., Gnimpieba, E., (2014), Automatic biosystems comparison using semantic and name similarity, ACM Press, p. 790–796. (DOI: 10.1145/2649387.2660850)
  • Larson, J., Chango, A., Conn, B., Lushbough, C., Gnimpieba, E., (2014), Biological system analysis using integrated bioinformatics tools : Levels of the central dogma in Folate Mediate One-Carbon Metabolism ( FOCM ), Proceeding of BIOCOMP’14 - The 2014 International Conference on Bioinformatics & Computational Biology, ISBN: 1-60132-265-8, H. R. A. Al., Ed. CSREA Press., p. 4–7.
  • Thavappiragasam, M., Lushbough, C., Gnimpieba, E., (2014), Heuristic parallelizable algorithm for similarity based biosystems comparison, ACM Press, p. 782–789. (DOI: 10.1145/2649387.2660849)
  • Weinandt, N., Jackson, L. M., Gnimpieba, E., Lushbough, C., (2014), Pheno2GRN, ACM Press, p. 797–804. (DOI: 10.1145/2649387.2660851)
  • Mallipeddi, S. R., Lushbough, C., Gnimpieba, E., (2014), Reference Integrator : a workflow for similarity driven multi-sources publication merging ., Proceeding of The 2014 International Conference on Information and Knowledge Engineering, IKE’14, p. 1–2.
  • Gnimpieba, E., Chango, A., Lushbough, C., (2014), RNA-seq gene and transcript expression analysis using the BioExtract server and iPlant collaborative, ACM Press, p. 661–669. (DOI: 10.1145/2649387.2660822)
  • Gnimpieba, E., Lushbough, C., (2014), WMS4HPC , a Workflow Management System bridge for High Performance Computing in life science data management, Proceeding of BIOCOMP’14 - The 2014 International Conference on Bioinformatics & Computational Biology, ISBN: 1-60132-265-8, H. R. A. Al., Ed. CSREA Press., iss. I.
  • Lushbough, C., Gnimpieba, E., Dooley, R., (2014), Life science data analysis workflow development using the bioextract server leveraging the iPlant collaborative cyberinfrastructure, Concurrency and Computation: Practice and Experience, p. n/a–n/a. (DOI: 10.1002/cpe.3237)
  • Wang, L., Ware, D., Lushbough, C., Merchant, N., Stein, L., A GWAS platform built on the iPlant cyber-infrastructure, Concurrency and Computation: Practice and Experience.
  • Lushbough, C., Life Science Data Analysis Workflow Development using the BioExtract Server leveraging the iPlant Collaborative Cyberinfrastructure, Concurrency and Computation: Practice and Experience.
  • Larson, J. J., Abalo, C., Lushbough, C., Gnimpieba Z., E., (2013), Biological System Analysis using Integrated Bioinformatics Tools: Linking metabolites, proteins, and genes in Folate Mediate One-Carbon Metabolism (FOCM).
  • Lushbough, C., (2013), BioExtract Server, a Web-based workflow enabling system, leveraging iPlant collaborative resources, 2013 IEEE International Conference on Cluster Computing (CLUSTER), iss. 2013, pp. 1-3. (DOI: 10.1109/CLUSTER.2013.6702692)
  • Gnimpieba, E., Jennewein, D., Fuhrman, L., Lushbough, C., (2013), Bioinformatics Knowledge Transmission (training, learning, and teaching): overview and flexible comparison of computer based training approaches, Proceeding of The 2013 International Conference on Information and Knowledge Engineering, IKE’13.
  • Gnimpiba Z., E., Chango, A., Lushbough, C., (2012), Folate intake and mthfr gene expression profile in Parkinson Disease risk study : in silico approach ., University of South Dakota.
  • Gnimpieba, E., Lushbough, C., Eveillard, D., Guéant, J., Chango, A., (2012), In sillico studying of gene-metabolic interaction on pathogenesis: CBS gene (21q22.3) over-expression in folate metabolism and Down Syndrome., PQCD Research Center of University of South Dakota, vol. 91, iss. 2007, p. 41.
  • Cannon, E. K., Birkett, S. M., Braun, B. L., Kodavali, S., Jennewein, D., Yilmaz, A., Antonescu, V., Antonescu, C., Harper, L. C., Gardiner, J. M., Schaeffer, M. L., Campbell, D. A., Andorf, C. M., Andorf, D., Lisch, D., Koch, K. E., McCarty, D. R., Quackenbush, J., Grotewold, E., Lushbough, C., Sen, T. Z., Lawrence, C. J., (2011), POPcorn: An Online Resource Providing Access to Distributed and Diverse Maize Project Data, Int J Plant Genomics, vol. 2011, p. 923035.
  • Lushbough, C., Jennewein, D., Brendel, V. P., (2011), The BioExtract Server: a web-based bioinformatic workflow platform, Nucleic Acids Res., vol. 39, iss. Web Server issue, p. W528–532.
  • Lushbough, C., Bouhlal, Y., Jennewein, D., Anderson, B., Reynoldson, J., Maamouri, W., Hentati, F., Amouri, R., (2011), Computational analysis of a novel SACS gene mutation with BioExtract server, J Mol Neurosci, vol. 44, iss. 1, pp. 53-8. (DOI: 10.1007)
  • Lushbough, C., Jennewein, D., Brendel, V., (2011), The BioExtract Server: a web-based bioinfromatic workflow platform, Nucl. Acids Res, vol. 39, iss. W528-W532. (DOI: 10.1093/nar/gkr286)
  • Lushbough, C., Kelley, B., (2010), : Experimental Learning and Student Attitudes, Academic Exchange Quarterly , vol. 14, iss. 1, pp. 170-174.
  • Lushbough, C., Brendel, V., (2010), An overview of the BioExtract Server: a distributed, Web-based system for genomic analysis, Springer, vol. 680, pp. 361-369.
  • Lushbough, C., Bergman, M. K., Lawrence, C. J., Jennewein, D., Brendel, V., (2010), BioExtract server–an integrated workflow-enabling system to access and analyze heterogeneous, distributed biomolecular data, IEEE/ACM Trans Comput Biol Bioinform, vol. 7, iss. 1, p. 12–24.
  • Lushbough, C., Bergman, M. K., Lawrence, C. J., Jennewein, D., Brendel, V., (2008), Implementing bioinformatic workflows within the bioextract server, Int J Comput Biol Drug Des, vol. 1, iss. 3, p. 302–312.
  • Kelley, B., Lushbough, C., Asaithambi, A., (2008), Measuring Student Self-Confidence, New Forums Press.
  • Duvick, J., Fu, A., Muppirala, U., Sabharwal, M., Wilkerson, M. D., Lawrence, C. J., Lushbough, C., Brendel, V., (2008), PlantGDB: a resource for comparative plant genomics, Nucleic Acids Res., vol. 36, iss. Database issue, p. D959–965.
  • Dong, Q., Lawrence, C. J., Schlueter, S. D., Wilkerson, M. D., Kurtz, S., Lushbough, C., Brendel, V., (2005), Comparative plant genomics resources at PlantGDB, Plant Physiol., vol. 139, iss. 2, p. 610–618.
Presentations:
  • Lushbough, C.
  • Lushbough, C. (2013, October). Creating Bioinformatic Workflows with the BioExtract Server. Presented at the Seminar Series, Charlotte, NC.
  • Lushbough, C. (2013, October). Webinar on Computational Tools and Services. Presented at the Webinar on Computational Tools and Services, Online.
  • Lushbough, C. (2013, September). ACM-BCB Tutorial on Creating Bioinformatics Workflows within the BioExtract Server. Presented at the ACM Conference on Bioinformatics, Computational Biology and Biomedical Informatics, Washington DC.
  • Lushbough, C. (2013, January). The BioExtract Server: a Web Based Bioinformatic Workflow Platform. Presented at the Plant and Animal Genome Conference XXI, San Diego, CA.
  • Lushbough, C. (2013, January). Bringing the Biologist Closer to Computational Thinking. Presented at the The National Science Foundation’s National Plant Genome Initiative Workshop, San Diego, CA.
  • Lushbough, C. (2010, April). Plenary Address: Lushbough, C., “BioExtract Server – a Web-based, Distributed System for Bioinformatic Workflow Analysis. Presented at the South Dakota Academy of Science 95th Annual Meeting, Spearfish South Dakota.