Etienne Gnimpieba

Etienne Gnimpieba

Research Assistant Professor

BIOMEDICAL ENGINEERING PROGRAM

BIOMED ENGINEERING

Phone: (605) 274-9578

Email: Etienne.Gnimpieba@usd.edu

Bio:

Dr. Etienne Z. Gnimpieba is a Research Assistant Professor of bioinformatics in the University of South Dakota (USD) Biomedical Engineering program. As faculty, Dr. Gnimpieba is involved in multiple research activities, including computational systems biology, and advanced cyberinfrastructure development for data analysis for bioscience and biomedicine knowledge discovery. He has published articles in Nucleic Acid Research, Molecular Cancer Research (AACR), Molecular Biosystems journal (RSC Publishing), Brain Sciences, Faseb journal, and several conference proceedings related to computer science usage in Bioscience and Biomedicine. Before Dr. Gnimpieba joined USD faculty, he received a Ph.D. in biotechnology and bioinformatics, an MS in computational engineering in Informatics and Mathematics for Integrative Biology, and an MS in computer science specialized on systems modeling, artificial intelligence, and human-machine interface.


Teaching Interests:

Bioinformatics, systems biology, data mining, natural language processing, machine learning


Research Interests:

My lab focus on Systems and Data integration for Bioscience and Biomedicine knowledge discovery. We develop intuitive data acquisition and management systems for relevant knowledge extraction. I use Systems Biology and Data Mining approaches to aid in providing a better understanding of biosystem-phenotype interaction (e.g. gene-disease, social behavior-drug, cell environment-protein expression...). The long-term goal is to develop new decision support knowledgebase for predictive and precision bioscience and biomedicine. We use integrative approaches (algorithm, process, tools) for life science multi-scale systems integration and analysis using a combination of big data mining, machine learning, and Systems Biology approaches. This includes 1) a novel reusable multi-scale data manipulation model (collect, store, manage, mining) for knowledge discovery; based on adaptative intuitive user interface, adaptive machine learning and artificial intelligence; 2) new algorithms for data transformation and integration to handle the heterogeneity among the integrated data sources and Systems Biology data (images, text, relational data, etc.). 3) a flexible implementation easy to use tools on a HPC and big data infrastructure using R Bioconductor, Matlab, Java J2EE; 4) Computational Biology use cases development. The lab's industry experience includes the development of data analysis workflows for clinical and biotechnology applications. This translational research allow us to collaborate with industry partners such as ABBOTT Pharma to develop a Systems Biology framework to study a drug mechanism using big data from High Throughput sequencing technologies. Data science Advisor at INANOVATE Inc., a biotechnology company specializing in therapy and diagnosis systems development. Working with INANOVATE, we developed new predictive systems for cancer and related disease diagnoses, using data science tools. The lab activities also include bioinformatics training and outreach, I'm currently the Bioinformatics Educational Director of the SDBRIN (South Dakota Biomedical Research Infrastructure Network). The lab has mentored over 30 students in small research projects (high school, undergraduate, graduate, postdoc), and trained over 200 students through hands-on workshops such as our annual Bioinformatics Undergraduate Workshop Series. The lab's educational goal is to bridge the gap between math, computer science and biomedicine related STEM disciplines. ?


Education:

  • Ph D, Biotechnology, University of technology of Compiegne, 2011
  • MS, Informatics and Mathematics for integrative Biology, University of Evry Val d'Esonne, 2007
  • MS, Computer Science, University of Yaounde I, 2005
  • BS, Mathematic and Computer Science, University of Dschang, 2002

Research:

  • Bioinformatics Tools Library annotation process design, BioSNTR, (2015 - 2015)
  • Bioinformatics Tools Library Database curation, SD-ESPCoR, (2015 - 2015)
  • Bioimage data analysis for cell growth modeling, SD-ESPCoR
  • BioSNTR Traveling fellowship award, BioSNTR
  • NSF Traveling fellowship award, NSF

Grants:

  • I-Corps: Development of Analytic Tool Discovery System for Interdisciplinary Data Analysis, NSF. Grant Role: Principal. (2018 - 2019)
  • SERC minigrant, SERC. Grant Role: Supporting. (2018 - 2018)
  • Hyperoxic Modulation of Thioredoxin Signaling (R01), NIH. (2017 - 2022)
  • Oxytocin and Attachment Preference in Young Adults, Center for Brain and Behavior Research. Grant Role: Principal. (2017 - 2018)
  • EAGER: GETBIO-PGR Gateway for Education, Training, Broader Impacts and Outreach in Plant Genome Research, NSF. (2016 - 2017)
  • Predictive model and single cell transcriptomic profiling in Atypical Teratoid Rhabdoid Tumors (ATRT), BioSNTR. Grant Role: Principal. (2016 - 2017)
  • High-Performance Computing Cluster to Enable the Next Generation of Computationally Assisted Research, South Dakota Board of Regents. Grant Role: Supporting. (2015 - 2016)
  • Web services driven Systems Biology: Online SBML Editor for Workflow Management Systems (WMS), SDBRIN. (2013 - 2020)

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.

  • Messerli, S M., Hoffman, M M., Gnimpieba, Etienne, and Bhardwaj, R D.. Therapeutic Targeting of PTK7 is Cytotoxic in Atypical Teratoid Rhabdoid Tumors., 973-983. Vol. 15, Iss. 8. Molecular cancer research : MCR, 2017. (DOI: 10.1158/1541-7786.MCR-16-0432)
  • 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)
  • Messerli, Shanta M., Hoffman, Mariah M., Gnimpieba, Etienne, Kohlhof, Hella, and Bhardwaj, Ratan D.. 4SC-202 as a Potential Treatment for the Pediatric Brain Tumor Medulloblastoma. Vol. 7, Iss. 11. BRAIN SCIENCES, 2017. (DOI: 10.3390/brainsci7110147)
  • Gray-Lobe, Geoffrey, Suriani, Alexandra, and Gnimpieba, Etienne. DISCOVERING GENETIC PATHWAYS INVOLVED IN SOYBEAN ROOT NODULE DEVELOPMENT VIA BIOINFORMATIC ANALYSIS. In Proceedings of the South Dakota Academy of Science, 189-189. Vol. 96. PROCEEDINGS OF THE SOUTH DAKOTA ACADEMY OF SCIENCE, VOL 96, 2017.
  • Hoffman, Mariah M., Minette, Carrie J., Messerli, Shanta M., Bhardwaj, Ratan D., and Gnimpieba, Etienne. NanoStringBioNet: Integrated R Framework for Bioscience Knowledge Discovery from NanoString nCounter Data. In IEEE International Conference on Bioinformatics and Biomedicine-BIBM, 2157-2162. 2017 IEEE INTERNATIONAL CONFERENCE ON BIOINFORMATICS AND BIOMEDICINE (BIBM), 2017.
  • 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)
  • Gnimpieba, Etienne, Bousserouel, Souad, and Chango, Abalo. Mathematical Modeling of a Metabolic Network to Study the Impact of Food Contaminants on Genomic Methylation and DNA Instability, 1-7. Vol. 02, Iss. 10. Journal of Biosciences and Medicines, 2014. (DOI: 10.4236/jbm.2014.210001)
  • 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.
  • Kone, Kisselmina Y., Druon, Cyril, Gnimpieba, Etienne, Delmotte, Michel, Duquenoy, Albert, and Laguerre, Jean-Claude. Power density control in microwave assisted air drying to improve quality of food, 750-757. Vol. 119, Iss. 4. Journal of Food Engineering, 2013. (DOI: 10.1016/j.jfoodeng.2013.06.044)
  • 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.
  • Lushbough, Caro M., Gnimpieba, Etienne, and Dooley, Rion. BioExtract Server, a Web-based workflow enabling system, leveraging iPlant collaborative resources. In 2013 IEEE International Conference on Cluster Computing (CLUSTER), 1-3. IEEE, 2013. (DOI: 10.1109/CLUSTER.2013.6702692)
  • Chango, Abalo, Gnimpieba, Etienne, and Eveillard, Damien. Mathematical modeling of one-carbon metabolism in trisomy 21, lb420. Vol. 26. The FASEB Journal, 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.
  • Gnimpieba, Etienne, Eveillard, Damien, Gueant, Jean-Louis, and Chango, Abalo. Using logic programming for modeling the one-carbon metabolism network to study the impact of folate deficiency on methylation processes., 2508-21. Vol. 7, Iss. 8. Molecular bioSystems, 2011. (DOI: 10.1039/c1mb05102d)
  • Gnimpieba, Etienne, Eveillard, D, Gueant, J L., and Chango, A. Using logic programming for modeling the one-carbon metabolism network to study the impact of folate deficiency on methylation processes., 2508-21. Vol. 7, Iss. 8. Molecular bioSystems, 2011. (DOI: 10.1039/c1mb05102d)
  • Chango, Abalo, Bousserouel, Souad, Gnimpieba, Etienne, Nour, Afif A M Abdel, Abdennebi-Najar, Latifa, Etienne Z. Gnimpieba, Afif Abdel Nour, Latifa Abdennebi-Najar, Abalo, and Chango. Arsenic Exposure and Folate Deficiency and Methyl Group Metabolism in Human Fibroblast Cell Lines, S42. Vol. 2, Iss. S1. Journal of Developmental Origins of Health and Disease, 2011. (DOI: 10.1017/S2040174411000481)
  • Chango, Abalo, and Gnimpieba, Etienne. Mathematical modelling of the one-carbon metabolism network by using logic programming, 987.6. Vol. 25. The FASEB Journal, 2011.

Awards and Honors:

  • NSF I-Corps Team Award, NSF, 2018
  • PostDoc Research Excelence Award, Computer Science Department, 2014
  • 1st Prize for Innovation and Entrepreneurship, Doctoriales Champagne Ardenne et Picardie 2009 (CAP09), 2009

Presentations:

  • Freeman, Harry, Gnimpieba, Etienne, AnisAbdellatif, Musheera, Haper, Irene. The WHMT A web-based diagramic measure of attachment networks. Presented at the Society for Research on Adolescence, Minneapolis. (April 01, 2018)
  • 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)
  • Freeman, Harry, Gnimpieba, Etienne, . Convergent and Discriminant Validity of Two Measures of Attachment Preference in Young Adulthood. Presented at the Society of Research in Child Development, Austin, TX. (April 6, 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)