Carol Lushbough

Carol Lushbough

Assistant Professor, Research

BIOMEDICAL ENGINEERING PROGRAM

BIOMEDICAL ENGINEERING PROGRAM

Phone: (605) 677-6138

Email: Carol.Lushbough@usd.edu

Bio:

Carol Lushbough is a computer scientist with expertise in software engineering, cloud computing, and bioinformatics workflows. She has been the main architect of the BioExtract Server (http://bioextract.org)


Teaching Interests:

Software Engineering Distributed Systems Systems Analysis


Research Interests:

Cyberinfrastructure Bioinformatic Workflows Distributed Systems


Education:

  • MA, Computer Science, University of South Dakota, 1991
  • MA, Math, University of South Dakota, 1987
  • BA, Math, Westmar College, 1972

Licensures and Certifications:

  • Java Certification, Sun Microsystem

Research:

  • An Interdisciplinary Student Teaching Innovation: A Health Science and Arts and Sciences Teaching Synergy , University of South Dakota Provost Teaching Innovation Fund

Grants:

  • EAGER: GETBIO-PGR Gateway for Education, Training, Broader Impacts and Outreach in Plant Genome Research, NSF. (2016 - 2017)
  • TRPGR - Integrating the BioExtract Server with the iPlant Collaborative, NSF. Grant Role: Principal. (2011 - 2014)
  • Cyberinfrastructure for (Comparative) Plant Genome Research through PlantGDB, NSF. Grant Role: Co-Principal. (2006 - 2011)
  • IDeA Networks of Biomedical Research Excellence, NIH. Grant Role: Other.

Publications:

Citations listed below are presented in a standardized, modified format for display purposes only. They do not necessarily reflect the preferred style and conventions of the faculty member or discipline.

  • Gnimpieba, Etienne, VanDiermen, M S., Gustafson, S M., Conn, B, and Lushbough, Carol. Bio-TDS: bioscience query tool discovery system., D1117-D1122. Vol. 45, Iss. D1. Nucleic acids research, 2017. (DOI: 10.1093/nar/gkw940)
  • Lushbough, Carol, Gnimpieba, Etienne, and Dooley, Rion. Life science data analysis workflow development using the bioextract server leveraging the iPlant collaborative cyberinfrastructure, 408-419. Vol. 27. Concurrency Computation, 2015. (DOI: 10.1002/cpe.3237)
  • Gnimpieba, Etienne, Thavappiragasam, Mathialakan, Chango, Abalo, Conn, Bill, and Lushbough, Carol. SBMLDock: Docker driven systems biology tool development and usage. In Lecture Notes in Computer Science (including subseries Lecture Notes in Artificial Intelligence and Lecture Notes in Bioinformatics), 282-285. Vol. 9308.. (DOI: 10.1007/978-3-319-23401-4_24)
  • Thavappiragasam, Mathialakan, Lushbough, Carol, and Gnimpieba, Etienne. Automatic biosystems comparison using semantic and name similarity. In Proceedings of the 5th ACM Conference on Bioinformatics, Computational Biology, and Health Informatics - BCB '14, 790-796. New York, New York, USA: ACM Press, 2014. (DOI: 10.1145/2649387.2660850)
  • Larson, Jordy, Chango, Abalo, Conn, Bill, Lushbough, Carol, and Gnimpieba, Etienne. Biological system analysis using integrated bioinformatics tools : Levels of the central dogma in Folate Mediate One-Carbon Metabolism ( FOCM ), 4-7. Proceeding of BIOCOMP'14 - The 2014 International Conference on Bioinformatics & Computational Biology, ISBN: 1-60132-265-8, H. R. A. Al., Ed. CSREA Press., 2014.
  • Thavappiragasam, Mathialakan, Lushbough, Carol, and Gnimpieba, Etienne. Heuristic parallelizable algorithm for similarity based biosystems comparison. In Proceedings of the 5th ACM Conference on Bioinformatics, Computational Biology, and Health Informatics - BCB '14, 782-789. New York, New York, USA: ACM Press, 2014. (DOI: 10.1145/2649387.2660849)
  • Weinandt, Nick, Jackson, Laura M., Gnimpieba, Etienne, and Lushbough, Carol. Pheno2GRN. In Proceedings of the 5th ACM Conference on Bioinformatics, Computational Biology, and Health Informatics - BCB '14, 797-804. New York, New York, USA: ACM Press, 2014. (DOI: 10.1145/2649387.2660851)
  • Mallipeddi, Suman R., Lushbough, Carol, and Gnimpieba, Etienne. Reference Integrator : a workflow for similarity driven multi-sources publication merging ., 1-2. Proceeding of The 2014 International Conference on Information and Knowledge Engineering, IKE'14, 2014.
  • Gnimpieba, Etienne, Chango, Abalo, and Lushbough, Carol. RNA-seq gene and transcript expression analysis using the BioExtract server and iPlant collaborative. In Proceedings of the 5th ACM Conference on Bioinformatics, Computational Biology, and Health Informatics - BCB '14, 661-669. New York, New York, USA: ACM Press, 2014. (DOI: 10.1145/2649387.2660822)
  • Gnimpieba, Etienne, and Lushbough, Carol. WMS4HPC , a Workflow Management System bridge for High Performance Computing in life science data management. Iss. I. Proceeding of BIOCOMP'14 - The 2014 International Conference on Bioinformatics & Computational Biology, ISBN: 1-60132-265-8, H. R. A. Al., Ed. CSREA Press., 2014.
  • Lushbough, Carol. BioExtract Server, a Web-based workflow enabling system, leveraging iPlant collaborative resources, 1-3. Iss. 2013. 2013 IEEE International Conference on Cluster Computing (CLUSTER), 2013. (DOI: 10.1109/CLUSTER.2013.6702692)
  • Gnimpieba, Etienne, Jennewein, Douglas, Fuhrman, Luke, and Lushbough, Carol. Bioinformatics Knowledge Transmission (training, learning, and teaching): overview and flexible comparison of computer based training approaches. Edited by Al., Hamid R. Arabnia. Las Vegas: Proceeding of The 2013 International Conference on Information and Knowledge Engineering, IKE'13, 2013.
  • Larson, Jordyn J., Abalo, Chango, Lushbough, Carol, and Gnimpieba Z., Etienne. Biological System Analysis using Integrated Bioinformatics Tools: Linking metabolites, proteins, and genes in Folate Mediate One-Carbon Metabolism (FOCM). In SD-BRIN 2013 UGF convocation..
  • Gnimpiba Z., Etienne, Chango, Abalo, and Lushbough, Carol. Folate intake and mthfr gene expression profile in Parkinson Disease risk study : in silico approach .. In CHI NGS'12. University of South Dakota, 2012.
  • Gnimpieba, Etienne, Lushbough, Carol, Eveillard, Damien, Gueant, Jean-louis, and Chango, Abalo. In sillico studying of gene-metabolic interaction on pathogenesis: CBS gene (21q22.3) over-expression in folate metabolism and Down Syndrome.. In Proceeding of the 2nd annual Symp. on Ubiquintin, Protein Quality Control, and Mol. Path, PQCD'12, edited by Wang, Xuenjun, 41. Vol. 91, Iss. 2007. Deadwood Gulch Resort: PQCD Research Center of University of South Dakota, 2012.
  • Lushbough, Carol, Jennewein, Douglas, and Brendel, V. P.. The BioExtract Server: a web-based bioinformatic workflow platform, W528-532. Vol. 39, Iss. Web Server issue. Nucleic Acids Res., 2011.
  • Lushbough, Carol, Jennewein, Douglas, and Brendel, Volker. The BioExtract Server: a web-based bioinfromatic workflow platform. Vol. 39, Iss. W528-W532. Nucl. Acids Res, 2011. (DOI: 10.1093/nar/gkr286)
  • Lushbough, Carol, Bouhlal, Yosr, Jennewein, Douglas, Anderson, Brent, Reynoldson, Joe, Maamouri, Wiem, Hentati, Fayçal, and Amouri, Rim. Computational analysis of a novel SACS gene mutation with BioExtract server, 53-8. Vol. 44, Iss. 1. J Mol Neurosci, 2011. (DOI: 10.1007)
  • Cannon, E. K., Birkett, S. M., Braun, B. L., Kodavali, S., Jennewein, Douglas, 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, Carol, Sen, T. Z., and Lawrence, C. J.. POPcorn: An Online Resource Providing Access to Distributed and Diverse Maize Project Data, 923035. Vol. 2011. Int J Plant Genomics, 2011.
  • Lushbough, Carol, and Kelley, Bruce. : Experimental Learning and Student Attitudes, 170-174. Vol. 14, Iss. 1. Academic Exchange Quarterly , 2010.
  • Lushbough, Carol, and Brendel, Volker. An overview of the BioExtract Server: a distributed, Web-based system for genomic analysis. In . Adv Exp Med Biol, 361-369. Vol. 680. Springer, 2010.
  • Lushbough, Carol, Bergman, M. K., Lawrence, C. J., Jennewein, Douglas, and Brendel, V.. BioExtract server-an integrated workflow-enabling system to access and analyze heterogeneous, distributed biomolecular data, 12-24. Vol. 7, Iss. 1. IEEE/ACM Trans Comput Biol Bioinform, 2010.
  • Lushbough, Carol, Bergman, M. K., Lawrence, C. J., Jennewein, Douglas, and Brendel, V.. Implementing bioinformatic workflows within the bioextract server, 302-312. Vol. 1, Iss. 3. Int J Comput Biol Drug Des, 2008.
  • Kelley, Bruce, Lushbough, Carol, and Asaithambi, Asai. Measuring Student Self-Confidence. In It Works for Me in Scholarship. Stillwater, OK: New Forums Press, 2008.
  • Duvick, J., Fu, A., Muppirala, U., Sabharwal, M., Wilkerson, M. D., Lawrence, C. J., Lushbough, Carol, and Brendel, V.. PlantGDB: a resource for comparative plant genomics, D959-965. Vol. 36, Iss. Database issue. Nucleic Acids Res., 2008.
  • Dong, Q., Lawrence, C. J., Schlueter, S. D., Wilkerson, M. D., Kurtz, S., Lushbough, Carol, and Brendel, V.. Comparative plant genomics resources at PlantGDB, 610-618. Vol. 139, Iss. 2. Plant Physiol., 2005.
  • Wang, Liya, Ware, Doreen, Lushbough, Carol, and Merchant, Nivar. Building an open Genome Wide Association Study (GWAS) platform. Iss. 2013. 2013 IEEE International Conference on Cluster Computing (CLUSTER). (DOI: 10.1109/CLUSTER.2013.6702696)
  • Wang, Liya, Ware, Doreen, Lushbough, Carol, Merchant, Nivar, and Stein, Lincoln. A GWAS platform built on the iPlant cyber-infrastructure. Concurrency and Computation: Practice and Experience.
  • Lushbough, Carol. Life Science Data Analysis Workflow Development using the BioExtract Server leveraging the iPlant Collaborative Cyberinfrastructure. Concurrency and Computation: Practice and Experience.

Presentations:

  • Gnimpieba, Etienne, Lushbough, Carol. G et Organized, Get Connected, Get Noticed and Get Funded : Introducing (GETBIO - PGR) The Gateway for Education, Training, Broader Impacts and Outreach in Plant Genome Research. Presented at the ASPB: Plant Biology 2017, Honolulu. (June 24, 2017)
  • Gnimpieba, Etienne, Lushbough, Carol. Getbio-PGR: The Gateway for Education, Training, Broader Impacts and Outreach in Plant Genome Research. Presented at the PAG: Plant Animal Genome 2017, San Diego. (January 17, 2017)
  • Gnimpieba, Etienne, Lushbough, Carol. GET ORGANIZED, GET CONNECTED, GET NOTICED and GET FUNDED: Introducing (GETBIO) The Gateway for Education, Training, Broader Impacts and Outreach in Plant Genome Research. Presented at the PAG: Plant Animal Conference 2017, San Diego. (January 14, 2017)
  • Gnimpieba, Etienne, Lushbough, Carol. Bio-Question Driven Bioimage Informatics Workflow Design Using Bio-TDS. Presented at the PAG: Plant Animal Genome 2017, San Diego. (January 14, 2017)
  • Gnimpieba, Etienne, Lushbough, Carol. Bio-TDS: a BioScience Query Tools Discovery System. Presented at the Plant Animal Genome 2017, San Diego. (January 14, 2017)
  • Gnimpieba, Etienne, Lushbough, Carol. Bio-TDS: a BioScience Query Tools Discovery System. Presented at the Plant Animal Genome 2017, San Diego. (January 14, 2017)
  • Lushbough, Carol. Webinar on Computational Tools and Services. Presented at the Webinar on Computational Tools and Services, Online. (October 11, 2013)
  • Lushbough, Carol. 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. (September 24, 2013)
  • Lushbough, Carol. The BioExtract Server: a Web Based Bioinformatic Workflow Platform. Presented at the Plant and Animal Genome Conference XXI, San Diego, CA. (January 15, 2013)
  • Lushbough, Carol. Bringing the Biologist Closer to Computational Thinking. Presented at the The National Science Foundation's National Plant Genome Initiative Workshop, San Diego, CA. (January 12, 2013)