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.

Aayudh Das, Ph.D.

Scientist at Garuda therapeutics, specialized in Genomics and Computational Biology

Boston, Massachusetts, United States of America

Research Expertise

Transcriptomics

Genomics

Proteomics

Computational Biology

Metabolomics

Ecology, Evolution, Behavior and Systematics

Ecology

Plant Science

Immunology and Allergy

Molecular Biology

Infectious Diseases

Microbiology (medical)

Genetics

Biochemistry

Biotechnology

About

Publications

Metabolomic Profiling of Soybeans (Glycine max L.) Reveals the Importance of Sugar and Nitrogen Metabolism under Drought and Heat Stress

Plants / May 25, 2017

Das, A., Rushton, P., & Rohila, J. (2017). Metabolomic Profiling of Soybeans (Glycine max L.) Reveals the Importance of Sugar and Nitrogen Metabolism under Drought and Heat Stress. Plants, 6(4), 21. https://doi.org/10.3390/plants6020021

Leaf Proteome Analysis Reveals Prospective Drought and Heat Stress Response Mechanisms in Soybean

BioMed Research International / Jan 01, 2016

Das, A., Eldakak, M., Paudel, B., Kim, D.-W., Hemmati, H., Basu, C., & Rohila, J. S. (2016). Leaf Proteome Analysis Reveals Prospective Drought and Heat Stress Response Mechanisms in Soybean. BioMed Research International, 2016, 1–23. https://doi.org/10.1155/2016/6021047

Unraveling Key Metabolomic Alterations in Wheat Embryos Derived from Freshly Harvested and Water-Imbibed Seeds of Two Wheat Cultivars with Contrasting Dormancy Status

Frontiers in Plant Science / Jul 12, 2017

Das, A., Kim, D.-W., Khadka, P., Rakwal, R., & Rohila, J. S. (2017). Unraveling Key Metabolomic Alterations in Wheat Embryos Derived from Freshly Harvested and Water-Imbibed Seeds of Two Wheat Cultivars with Contrasting Dormancy Status. Frontiers in Plant Science, 8. https://doi.org/10.3389/fpls.2017.01203

A Quantitative Proteomics View on the Function of Qfhb1, a Major QTL for Fusarium Head Blight Resistance in Wheat

Pathogens / Jun 22, 2018

Eldakak, M., Das, A., Zhuang, Y., Rohila, J., Glover, K., & Yen, Y. (2018). A Quantitative Proteomics View on the Function of Qfhb1, a Major QTL for Fusarium Head Blight Resistance in Wheat. Pathogens, 7(3), 58. https://doi.org/10.3390/pathogens7030058

Potentials of Proteomics in Crop Breeding

Advances in Plant Breeding Strategies: Breeding, Biotechnology and Molecular Tools / Jan 01, 2015

Das, A., Paudel, B., & Rohila, J. S. (2015). Potentials of Proteomics in Crop Breeding. In Advances in Plant Breeding Strategies: Breeding, Biotechnology and Molecular Tools (pp. 513–537). Springer International Publishing. https://doi.org/10.1007/978-3-319-22521-0_18

Proteomic Responses of Switchgrass and Prairie Cordgrass to Senescence

Frontiers in Plant Science / Mar 14, 2016

Paudel, B., Das, A., Tran, M., Boe, A., Palmer, N. A., Sarath, G., Gonzalez-Hernandez, J. L., Rushton, P. J., & Rohila, J. S. (2016). Proteomic Responses of Switchgrass and Prairie Cordgrass to Senescence. Frontiers in Plant Science, 7. https://doi.org/10.3389/fpls.2016.00293

Variation in climatic tolerance, but not stomatal traits, partially explains Pooideae grass species distributions

Annals of Botany / Mar 27, 2021

Das, A., Prakash, A., Dedon, N., Doty, A., Siddiqui, M., & Preston, J. C. (2021). Variation in climatic tolerance, but not stomatal traits, partially explains Pooideae grass species distributions. Annals of Botany, 128(1), 83–95. https://doi.org/10.1093/aob/mcab046

Evolution of cold acclimation in temperate grasses (Pooideae)

Oct 27, 2017

Schubert, M., Grønvold, L., Sandve, S. R., Hvidsten, T. R., & Fjellheim, S. (2017). Evolution of cold acclimation in temperate grasses (Pooideae). https://doi.org/10.1101/210021

Investigation of the Cardiotonic Steroids, Marinobufagenin and Resibufogenin, in the Acute Respiratory Distress Syndrome

The FASEB Journal / Apr 01, 2016

Abbas, M. M. K., Chen, Q., Das, A., Oliver, J., Jiang, W., Moorthy, B., Patel, B., Morin, K., & Puschett, J. (2016). Investigation of the Cardiotonic Steroids, Marinobufagenin and Resibufogenin, in the Acute Respiratory Distress Syndrome. The FASEB Journal, 30(S1). Portico. https://doi.org/10.1096/fasebj.30.1_supplement.982.4

Testing the chilling‐ before drought‐tolerance hypothesis in Pooideae grasses

Molecular Ecology / Dec 07, 2022

Das, A., Dedon, N., Enders, D. J., Fjellheim, S., & Preston, J. C. (2022). Testing the chilling‐ before drought‐tolerance hypothesis in Pooideae grasses. Molecular Ecology, 32(4), 772–785. Portico. https://doi.org/10.1111/mec.16794

Education

University of Vermont

PhD, Plant Biology / April, 2022

Burlington, Vermont, United States of America

Texas A&M University

Master's in Biochemistry, Biochemistry & Biophysics / May, 2016

College Station, Texas, United States of America

University of Calcutta

Master's, Biotechnology

Kolkata

Presidency University

Bachelor's, Botany

Kolkata

Experience

Garuda therapeutics

Scientist / July, 2023 — Present

The Pennsylvania State University - University Park Campus

Postdoctoral Researcher / June, 2022 — July, 2023

University of Vermont

Research Assistant / May, 2016 — May, 2022

Texas A&M University

Graduate research assistant / July, 2014 — May, 2016

South Dakota State University

Graduate research assistant / January, 2014 — July, 2014

Links & Social Media

Research Web Site

Google scholar

Researchgate

Twitter

Penn State

ORCID

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