Work with thought leaders and academic experts from South Dakota State University

Researchers on NotedSource with connections to South Dakota State University include Aayudh Das, Ph.D., Marilen Nampijja, Val Kovalsky, Ryan Lefers, Dr. Anne Huss, Ph.D., and Kayla Almekhlafi.

Aayudh Das, Ph.D.

Boston, Massachusetts, United States of America
Scientist at Garuda therapeutics, specialized in Genomics and Computational Biology
Experience

Garuda therapeutics

Scientist / July, 2023Present

The Pennsylvania State University - University Park Campus

Postdoctoral Researcher / June, 2022July, 2023

University of Vermont

Research Assistant / May, 2016May, 2022

Texas A&M University

Graduate research assistant / July, 2014May, 2016

South Dakota State University

Graduate research assistant / January, 2014July, 2014

Research Expertise
Transcriptomics
Genomics
Proteomics
Computational Biology
Metabolomics
And 10 more
About
I am a dedicated Scientist-I at Garuda Therapeutics, where I specialize in computational biology and genomics within the R&D department. My work primarily revolves around developing and optimizing pipelines for variant calling using Strelka2 and GATK4 with Whole Genome Sequencing (WGS) to identify oncogenes in human induced pluripotent stem cells (iPSCs). This involves extensive work in the qualification and validation of these pipelines for regulatory filings, as well as leveraging databases such as ClinVar, COSMIC, and DepMap to craft targeted oncogenes panels for deep sequencing. I also apply Next-Generation Sequencing (NGS) for downstream sequencing to validate CRISPR knockouts, including the identification and validation of CRISPR off-targets using techniques like rhAMPseq and Induce-seq. Additionally, my expertise extends to single-cell sequencing analysis and understanding structural variants with Optical Genome Mapping (Bionano). Prior to joining Garuda Therapeutics, I completed a postdoctoral fellowship in computational biology at Pennsylvania State University, where I honed my skills in identifying climate-adaptive variants and conducted Genome-Wide Association Studies (GWAS) to uncover resistance genes against parasites and other stressors. My academic journey began at the University of Vermont, where I explored abiotic stress resistance genes using transcriptomics and developed a robust understanding of RNA-seq data analysis, from assembly to gene annotation. My work is driven by a passion for leveraging computational and genomics tools to address pressing challenges in biology and healthcare, combining my rigorous academic training with a practical, solution-oriented approach to research and development.

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Marilen Nampijja

Washington State University
Education

PhD / December, 2024 (anticipated)

Pullman, Washington, United States of America

South Dakota State University

Master's, Plant Pathology / August, 2019

Brookings, South Dakota, United States of America
Experience

Washington State University

Graduate Research Assistant / JanuaryPresent

• Prepared research articles for publication • Designed experiments and analyzed data. • Diagnosed plant diseases including those caused by viruses, nematodes, fungi, and bacteria. • Characterized fungal and bacterial pathogens using biochemical and molecular methods. • Analyzed gene fragments and whole genomes of Pseudomonas syringae pv. aptata using Geneious, R, and Python software and platforms such as Integrated Microbial Genomes and Microbes of the Joint Genomic Institute (US Department of Energy), and High-Performance Computing Cluster to handle large data sets. • Monitored colonization of Pseudomonas syringae pv. aptata tagged with a green fluorescent protein by employing confocal microscopy and analyzed images in FIJI. • Ensured proper procurement of microbial specimens and stored them under the right environmental conditions using required permits. • Wrote progress reports to stakeholders. • Presented research progress to stakeholders.

North Dakota State University

Research Technician / August, 2019December, 2019

• Worked with soilborne pathogens Aphanomyces euteiches and Fusarium species affecting field pea crops. • Evaluated the impacts of seed treatments on commercial rhizobial inoculants and the relative nodulation of chickpea using different rhizobial isolates native to western North Dakota.

South Dakota State University

Graduate Research and Teaching Assistant / August, 2017August, 2019

• Taught undergraduate students laboratory techniques in General Biology (153) and Microbiology (231) through active learning. • Set up greenhouse and field experiments. • Applied pesticides to crops in the greenhouse and in the field. • Prepared medium for bacterial isolates. • Characterized bacteria from wheat seeds using biochemical and molecular methods. • Prepared research articles for publication. • Presented research findings during the American Phytopathological Society, field days, and during meetings organized by the Plant Science Department. • Set up experimental field plots. • Identified small grain diseases and rated their incidence and severity. • Set up irrigation systems, and established alleys to set plot boundaries. Isolated fungal and bacterial pathogens, and prepared fungal, bacterial, and viral inoculum for field applications.

Self-employed

Passion Fruit Grower / August, 2016July, 2017

• Ran my own passion fruit orchard. Procured passion fruit varieties, sowed seeds, cared for seedlings, applied fertilizer, and managed diseases and weeds.

Hall Hunter Partnership, United Kingdom

Horticultural Technician / April, 2016July, 2016

• Monitored and controlled pests, diseases, and disorders through identification, procuring relevant pesticides, and applying pesticides. • Managed seed sowing operations and other standard soft fruit production practices. • Monitored and recorded environmental conditions for protected crops, mainly raspberries and strawberries. Managed fruit crops to deliver to customers in good condition. • Ensured hygiene and biosecurity measures were implemented in the workplace.

Research Expertise
Plant pathology
microbiology
About
* PhD in Plant Pathology with 6+ years’ experience in research resulting in 7 publications including 2 in Plant Disease and 4 technical abstracts in Phytopathology of the American Phytopathological Society.   * Experienced in designing and executing assays including isolation, quantification and characterization of bacteria and fungi from diverse environments using molecular and standard biochemical tests leading to the development and fulfillment of new and existing projects with the ability to assess the current state of existing technology related to microbiology and plant pathology, as evidenced by 1 Book Chapter, and a news article in the American Phytopathological Society News.  * Strong communication skills with an ability to manage assigned projects relevant to the characterization and quantification of bacteria and fungi, as evidenced by 4 presentations at National Meetings of the American Phytopathological Society and 10 to stakeholders and collaborators.

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