Getiria Onsongo

Getiria Onsongo, *Samantha Fritsche, *Thy Nguyen, *Ayoub Belemlih, Jeffery Thompson, and Kevin AT Silverstein. "ITALLIC: A tool for identifying and correcting errors in location- based plant breeding data". Computers and Electronics in Agriculture, 197:106947, 2022. technique for data cleaning in plant breeding data. A major challenge in predictive agriculture is inability to collectively analyze different types of data because of errors in the data. This work presents a tool for cleaning location-based plant breeding data. Acceptance Rate: 18% 2. Elizabeth Leininger, Kelly Shaw, Niema Moshiri, Kelly Neiles, Getiria Onsongo, and Anna Ritz. "Ten Simple Rules for Attending Your First Conference". (2021) PLoS Comput Biol 17(7).

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This article shares tips for trainees attending a conference for the first time. It highlights my commitment to advising and mentorship. I wrote the original draft for two of the rules: Rule 7 and Rule 8. The paper has an accompanying web portal which I put together that is being hosted at Macalester:https://sites.google.com/macalester.edu/simplerules/home 3. Getiria Onsongo, Ham Ching Lam, Matthew Bower & Bharat Thyagarajan. "Hadoop-CNV- RF: A scalable Copy Number Variation Detection Tool for Next-Generation Sequencing Data". Proceedings of the 11th ACM International Conference on Bioinformatic, Computational Biology and Health Informatics, (2020) Sep 21 (pp. 1-8). rapidly scales to analyze large amounts of data. Prior to this work, existing clinical copy number variant detection software were less than ideal because of long runtimes on large data. This software is currently being used in a Molecular Diagnostics Lab at the University of Minnesota. Acceptance Rate: 27% 4. Paige Hartman, Kenneth Beckman, Kevin Silverstein, Sophia Yohe, Matthew Schomaker, Christine Henzler, Getiria Onsongo, Ham Ching Lam, Sarah Munro, Jerry Daniel, et al.

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Next generation sequencing for clinical diagnostics: Five-year experience of an academic laboratory. Molecular genetics and metabolism reports, 19:100464, 2019.

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"Leveraging public cloud services for clia-certied personalized medicine pipelines". In Proceedings of the Practice and Experience in Advanced Research Computing on Rise of the Machines (learning), pages 1-4. Association for Computing Machinery, 2019.

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Andrew Gustafson, Jesse Erdmann, Michael Milligan, Getiria Onsongo, Philip Pardey, Tom Prather, Kevin Silverstein, James Wilgenbusch, and Ying Zhang. "A platform for computationally advanced collaborative agroinformatics data discovery and analysis". In Proceedings of the Practice and Experience in Advanced Research Computing 2017 on Sustainability, Success and Impact, pages 1-4. Association for Computing Machinery, 2017.

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PARK AVE SOUTH, NEW YORK, NY 10010-1710 USA, 2017.

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Curriculum Vitae | Getiria Onsongo 6. Getiria Onsongo, Linda B. Baughn, Matthew Bower, Christine Henzler, Matthew Schomaker, Kevin A.T. Silverstein, Bharat Thyagarajan. "CNV-RF is a random-forest based copy number variation detection method using next generation sequencing". The Journal of Molecular Diagnostics 18.6 (2016): 872-881. detect small deletions and duplications in the genome. I led the development of the method and contributed the key idea behind the method. I implemented the method in a software package (CNV-RF) and did the testing.

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Curriculum Vitae | Getiria Onsongo 12. Pratik Japtap, Getiria Onsongo, Candace Guerrero, James Johnson, Thomas McGowan, Matthew Andrews, and Timothy Griffin. "Proteogenomics in galaxy: Identifying novel 'constellations' of proteoforms using transcriptomic and proteomic data". F1000Research, 5, 2016.

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Sophia Yohe, Adam Hauge, Kari Bunjer, Teresa Kemmer, Matthew Bower, Matthew Schomaker, Getiria Onsongo, Jon Wilson, Jon Wilson, Jesse Erdmann, Yi Zhou, Archana Deshpande, Michael D. Spears, Kenneth Beckman, Kevin A.T. Silverstein Bharat Thyagarajan. "Clinical validation of targeted next generation sequencing for inherited disorders". Arch Pathol Lab Med. 2015 Feb;139(2):204-10.

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Gloria M Sheynkman, James E Johnson, Pratik D Jagtap, Michael R Shortreed, Getiria Onsongo, Brian L Frey, Timothy J Griffin, and Lloyd M Smith. "Using galaxy-p to leverage rna-seq for the discovery of novel protein variations". BMC genomics, 15(1):703, 2014.

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Pratik D Jagtap, James E Johnson, Getiria Onsongo, Fredrik W Sadler, Kevin Murray, Yuanbo Wang, Gloria M Shenykman, Sricharan Bandhakavi, Lloyd M Smith, and Timothy J Griffin. "Flexible and accessible workflows for improved proteogenomic analysis using the galaxy framework". Journal of Proteome Research, 13(12):5898, 2014.

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Getiria Onsongo, Jesse Erdmann, Michael D. Spears, John Chilton, Kenneth Beckman, Adam Hauge, Sophia Yohe, Matthew Schomaker, Matthew Bower, Kevin A. T. Silverstein, Bharat Thyagarajan. "Implementation of Cloud based Next Generation Sequencing data analysis in a clinical laboratory". BMC Res Notes. 2014, May; 23;7(1): 314

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This article describes how to build a cloud-based clinical pipeline on a shared resource such as the High-Performance Computing cluster at the University of Minnesota. I built the proof- of-concept pipeline and did initial testing. It covers technical aspects not covered in my 2014 paper in BMC Res Notes.

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J Johnson, B Gottschalk, G Onsongo, S Bandhakavi, EP deJong, JA Kooren, TW Markowsk, L Higgins, JD Rudney, TJ Griffin, et al. "The galaxy framework as a unifying bioinformatics solution for 'omics' core facilities". Journal of Biomolecular Techniques: JBT, 25(Suppl): S5, 2014.

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Michael Spears, Getiria Onsongo, Kevin Silverstein, Kenneth Beckman, Matthew Schomaker, Sophia Yohe, Matthew Bower, Kerry Hansen, Lisa Baumann Kreuziger, Mark Reding, et al. "A next-generation sequencing approach to investigating inherited thrombophilias". In AMERICAN JOURNAL OF CLINICAL PATHOLOGY, volume 140, pages 423-424. AMER SOC CLINICAL PATHOLOGY 2100 W HARRISON ST, CHICAGO, IL 60612 USA, 2013.

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Jess Peterson, Kenneth Beckman, Matthew Bower, Kari Bunjer, Adam Hauge, Teresa Kemmer, Randolph Peterson, Getiria Onsongo, Matthew Schomaker, Kevin Silverstein, et al. "Technical and clinical validation of a next-generation sequencing diagnostic assay for fanconi anemia". In AMERICAN JOURNAL OF CLINICAL PATHOLOGY, volume 138, pages 461. AMER SOC CLINICAL PATHOLOGY 2100 W HARRISON ST, CHICAGO, IL 60612 USA, 2012.

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Ying Zhang, Jesse Erdmann, John Chilton, Getiria Onsongo, Matthew Bower, Kenny Beckman, Bharat Thyagarajan, Kevin Silverstein, and Anne-Francoise Lamblin. "Clia- certified next generation sequencing analysis in the cloud". In BMC Proceedings, volume 6, pages 1. BioMed Central, 2012.

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B Thyagarajan, M Bower, G Onsongo, K Silverstein, S Yohe, A Hauge, M Schomaker, K Bunjer, T Kemmer, J Erdmann, et al. "Next-generation sequencing diagnostic assays for genetic diagnosis of inherited disorders". In JOURNAL OF MOLECULAR DIAGNOSTICS, volume 14, pages 638. ELSEVIER SCIENCE INC 360 PARK AVE SOUTH, NEW YORK, NY 10010-1710 USA, 2012.

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Getiria Onsongo, Matthew D Stone, Susan K Van Riper, John Chilton, Baolin Wu, Leeann Higgins, Troy C Lund, John V Carlis, and Timothy J Griffin. "Ltq-iquant: A freely available software pipeline for automated and accurate protein quantification of isobaric tagged peptide data from ltq instruments". Proteomics, 10(19):3533-3538, 2010.

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Getiria Onsongo, Hongwei Xie, Timothy J Griffin, and John V Carlis. "Relational operators for prioritizing candidate biomarkers in high-throughput differential expression data". In Proceedings of the First ACM International Conference on Bioinformatics and Computational Biology, pages 25-34, 2010.

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Curriculum Vitae | Getiria Onsongo 22. Sricharan Bandhakavi, Young-Mi Kim, Seung-Hyun Ro, Hongwei Xie, Getiria Onsongo, Chang-Bong Jun, Do-Hyung Kim, and Timothy J Griffin. "Quantitative nuclear proteomics identifies mtor regulation of dna damage response". Molecular & Cellular Proteomics: MCP, 9(2):403, 2010.

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"Quantitative proteomics reveals myosin and actin as promising saliva biomarkers for distinguishing pre-malignant and malignant oral lesions". PloS one, 5(6): e11148, 2010.

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Matthew D Stone, Rick M Odland, Thomas McGowan, Getiria Onsongo, Chaunning Tang, Nelson L Rhodus, Pratik Jagtap, Sricharan Bandhakavi, and Timothy J Griffin. "Novel in situ collection of tumor interstitial from a head and neck squamous carcinoma reveals a unique proteome with diagnostic potential". Clinical proteomics, 6(3):75-82, 2010.

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Sara Mullen and Getiria Onsongo. "Decentralized agent-based underfrequency load shedding". Integrated Computer-Aided Engineering, 17(4):321-329, 2010.

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Sricharan Bandhakavi, Matthew D Stone, Getiria Onsongo, Susan K Van Riper, and Timothy J Griffin. "A dynamic range compression and three-dimensional peptide fractionation analysis platform expands proteome coverage and the diagnostic potential of whole saliva". Journal of proteome research, 8(12): 5590-5600, 2009.

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Getiria Onsongo, Hongwei Xie, Timothy J Griffin, and John Carlis. "Generating go slim using relational database management systems to support proteomics analysis". In 2008 21st IEEE International Symposium on Computer-Based Medical Systems, pages 215-217. IEEE, 2008.

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Hongwei Xie, Getiria Onsongo, Jonathan Popko, Ebbing P de Jong, Jing Cao, John V Carlis, Robert J Gri n, Nelson L Rhodus, and Timothy J Griffin. "Proteomics analysis of cells in whole saliva from oral cancer patients via value added three-dimensional peptide fractionation and tandem mass spectrometry". Molecular & cellular proteomics: MCP, 7(3):486-498, 2008.

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Elizabeth Shoop, Paulo Casaes, Getiria Onsongo, Lisa Lesnett, Erla Osk Petursdottir, Edward Kofi Yeboah Donkor, Dennis Tkach, and Michael Cosimini. "Data exploration tools for the gene ontology database". Bioinformatics (Oxford, England), 20(18):3442-3454, 2004.

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Ebbing P de Jong, Hongwei Xie, Getiria Onsongo, Matthew D Stone, Xiao-Bing Chen, Joel A Kooren, Eric W Refsland, Robert J Griffin, Frank G Ondrey, Baolin Wu, et al.

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This article describes the implementation of a genetic testing essay and our experience of using this essay in the clinic for 5 years. Two types of genomic changes are analyzed: mutations (changes at a single genomic position) and small deletions and duplications (CNV). I developed and implemented the method being used for CNV detection implemented in Hadoop-CNV-RF.

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This article presents the GEMSTM platform. The method I developed for identifying and correcting errors in plant breeding data presented in the software ITALLIC has been integrated into this platform.

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This article describes the first implementation of a genetic testing essay using Next- Generation Sequencing data at the Molecular Diagnostics Lab at the University of Minnesota. This paper highlights the challenge and significance of validating software for clinical use. I was the analyst on the project responsible for running the pipelines and analyzing results.

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This article describes the implementation of a cloud-based analysis pipeline for genetic testing using Next-Generation Sequencing data. I built the proof-of-concept pipeline and did initial testing.

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Evan F Bollig, Christine Henzler, Ham C Lam, Sarah A Munro, Rebecca LaRue, Getiria Onsongo, Sophia Yohe, Andrew C Nelson, Matthew Bower, Matthew Schomaker, et al.

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A Rangan, C Henzler, R Larue, G Onsongo, M Bower, A Nelson, B Thyagarajan, and S Yohe. "Defining minimum coverage in next generation sequencing (ngs)". In JOURNAL OF MOLECULAR DIAGNOSTICS, volume 19, pages 1049-1049. ELSEVIER SCIENCE INC 360

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Matthew C Chambers, Pratik D Jagtap, James E Johnson, Thomas McGowan, Praveen Kumar, Getiria Onsongo, Candace R Guerrero, Harald Barsnes, Marc Vaudel, Lennart Martens, et al. "An accessible proteogenomics informatics resource for cancer researchers".

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