Shashank Prakash Katiyar

Ph.D. in computational biology, a perfect blend of computer science in biological sciences, manifested the power of computational methods to solve biological problems that were unimaginable otherwise. I learned to use computer languages (Perl or python did a fantastic job) and statistics for biological data analysis, solving equations with an unthinkable amount of complexity, and automation of labor's work that eventually led me to the path of the never-ending urge to learn more and do more with it. 
    Postdoctoral, I joined an NGS start-up company in South Korea, Eone Diagnomics Genome Center (EDGC) as a research scientist. Being a start-up company, the work environment was open and dynamic. I was tasked with a variety of jobs such as the development of tools to ease and speed up the analysis-related jobs, refinement of existing pipelines, and development of pipelines for new projects.

    At EDGC, after having initial experience with WGS, WES pipeline, data, and analysis, I was tasked with the deployment of SNV based cancer screening and monitoring service framework. In response, I developed a pipeline to identify, annotate and classify the cancer-specific SNV markers. Followed by the primer designing for the selected cancer-specific markers and set up of the monitoring pipeline. This service is still in development as more data is gathered.

    After a successful deployment of the above, the next task at EDGC was to develop a pipeline, tools, algorithms, and methods for methylation-based cancer-specific NGS  panel. I developed a pipeline for data processing, methods for the identification of differentially methylated markers, implementation of machine learning algorithms for sample classification, data visualization, and assistive tools. This service is in the process of approval for Korea MFDS (KFDA).

    I recently moved to Los Angeles, California, and obtained a work permit (EAD card on J2 visa type), after working as a Global Scientific Consultant and Senior Research Scientist in Eone Diagnomics Genome Center (EDGC), South Korea. 

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Here, I would like to emphasize some of the major highlights of my work experiences so far.

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• I was involved in the development of custom targeted panels for the liquid biopsy monitoring service, in which I designed and developed a patient-specific SNV marker selection algorithm, primer identification algorithm for the target markers, and pipeline to analyze patient-specific custom targeted panel data.

• A more recent and major EDGC project was to develop cancer detection panels of various cancer types using machine learning algorithms on the NGS-based epigenetic data. I was tasked with the design and development of the NGS-based epigenetic data analysis, statistical modeling to identify the cancer-specific markers, and implementation of machine learning algorithms to identify cancer patient samples.

• An important requirement for an R&D team of a company is to have independent in-house tools. I have experience in developing NGS analysis-related in-house tools such as sequence data preprocessing, PCR duplicate removal and error correction, in-house variant caller, variant annotator, and SNV classifier, etc.

• I also have extensive experience in writing research articles, gained during routine project-related white paper production as well as a part of my Ph.D. training.