Last updated on July 2025
Anoob Prakash
Ecological & Evolutionary Genomics · Climate Adaptation · Bioinformatics
Professional Profile
Highly skilled researcher with expertise in ecological and evolutionary genomics, plant biology, climate change, and bioinformatics. Experienced in analyzing large-scale genomic data, conducting climate change adaptation studies, and teaching advanced scientific concepts. Adept at both independent and collaborative research in academic and non-academic settings. Reach out to me for discussing ideas and for collaboration.
Skills
- Programming and scripting: R (proficient), Unix/Linux (proficient), Python (basic).
- Data tools: ArcGIS (advanced), QGIS (basic), tidyverse (proficient).
- Data analysis and bioinformatics: Management and analysis of large-scale genomic, phenotypic, and climate datasets; application of bioinformatic pipelines and climate forecasting methods; graphical data visualization.
- Design and visualization: Affinity Designer (proficient), Adobe Illustrator (proficient), Adobe After Effects (advanced).
- Presentation and documentation: Microsoft Office, Quarto (proficient), R Markdown (proficient).
- Statistical data analysis.
- Wet lab techniques.
- Field data collection methodologies.
- Built strong collaborative relationships with researchers at the University of Maryland.
- Engaged with scientists, ecologists, and practitioners at The Nature Conservancy (Maryland, West Virginia, Virginia) and the Central Appalachian Spruce Restoration Initiative (CASRI).
- Graduate Student Senator, Department of Plant Biology, University of Vermont (2018–2020).
- Captain, college basketball team – led team to inter-collegiate championship (2012).
- Assistant Hostel Secretary, College of Forestry, Kerala Agricultural University (2009).
Education
Ph.D., Plant Biology
University of Vermont, USA
Advisor: Dr. Stephen R. Keller
M.Sc., Tree Physiology and Breeding
Kerala Agricultural University, India
Advisor: Dr. A. V. Santhoshkumar
B.Sc., Forestry
Kerala Agricultural University, India
Advisor: Dr. T. K. Kunhamu
Research and Professional Experience
Postdoctoral Research Associate
Purdue University, USA
- Application of machine-learning approaches to investigate climate pre- or mal-adaptation for species with high restoration potential (SHRP).
- Identifying seed sources for regeneration planting in zones of mal-adaptation.
Graduate Research Assistant
University of Vermont, USA
Investigated genotypic and phenotypic variation and climate change adaptation in red spruce (Picea rubens).
- Quantified biomass and trait variance to identify patterns of genotypic and phenotypic responses to climate gradients using quantitative genetics and Bayesian approaches.
- Collaborated with interdisciplinary teams to collect and manage large, multi-year datasets from multiple field sources.
- Utilized molecular approaches to investigate the role of introgression underlying local adaptation.
- Identified patterns of local and climate adaptation to inform conservation strategies for fragmented red spruce populations.
- Used genome-wide association studies (GWAS) to detect loci underlying polygenic traits.
- Applied advanced bioinformatic approaches to assess the genetic architecture of locally adaptive traits.
Graduate Teaching Assistant
University of Vermont, USA
Conducted grading, lab instruction, report writing guidance, peer-review facilitation, and lab setup for wet and dry labs.
Principles of Biology I and II (2018–2021)
- Trained students in the process of scientific inquiry and genetics concepts.
- Taught wet lab protocols, microscopy, and molecular modelling approaches.
Exploring Biology (2022–2023)
- Taught bench work for protein purification, enzyme purification, SDS–PAGE, and gel analysis.
Ecology and Evolution (2022–2025)
- Trained more than 100 students in data collection protocols and data analysis in R.
- Mentored students in designing and carrying out independent research projects.
Graduate Research Intern
The Nature Conservancy, USA
Applied genomics-assisted seed source selection to identify viable seed sources for restoration of red spruce in the fragmented southern range edge, resulting in more than 58,000 seedlings planted across three U.S. states.
- Collected data from experimental plots after restoration planting to monitor and assess genomic-assisted seed sourcing strategies in Virginia, West Virginia, and Maryland.
- Communicated results in a peer-reviewed scientific journal and at national and international conferences.
Kerala Agricultural University
College of Forestry, India
- Taught undergraduate and graduate courses including biochemistry, biotechnology, tree improvement, tree physiology, world forest systems, and ecophysiology.
- Managed laboratory space and inventory; assisted students with bench work and scientific writing for coursework and research.
Courses taught
- Forest Ecophysiology, 2013, 2014, 2015
- Plant Biochemistry, 2013, 2014
- Ethnobotany, 2015
- Plant Biotechnology, 2015
- World Forestry System, 2015
- Principles of Tree Improvement, 2015
- Elementary Tree Physiology, 2014, 2015
- Medicinal and Aromatic Plants, 2015
- Weapon Training and First Aid Training, 2014, 2015
Investigated the impact of particulate pollution on growth, physiology, and anatomical properties of Tectona grandis and other moist deciduous tree species near industrial sites.
- Assessed chlorophyll content, ascorbic acid levels, relative water content, and leaf pH to evaluate air pollution tolerance across seasons.
- Analyzed dust accumulation, leaf surface area, leaf area index, and leaf area duration to quantify pollution effects on tree health and productivity.
- Compared wood anatomical properties of pollution-exposed and control populations, identifying significant differences in wood quality and structure.
- Characterized structural and functional attributes of home gardens and developed recommendations for integrated farming systems for medium and large-scale farmers.
- Assisted the Assistant Conservator of Forests in drafting a working plan for Konni Forest Division, ensuring continuity of forest management policies over a 10-year period.
- Conducted site quality mapping, growing stock assessment, and regeneration surveys as part of forest management planning.
Publications
Peer-Reviewed Publications
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Bringing genomics to the field: An integrative approach to seed sourcing for forest restoration Prakash, A., Capblancq, T., Shallows, K., Saville, D., Landau, D., Landress, C., Jacobs, T., & Keller, S. (2024). Applications in Plant Sciences, 12(3), e11600.
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Novel genomic offset metrics integrate local adaptation into habitat suitability forecasts and inform assisted migration Lachmuth, S., Capblancq, T., Prakash, A., Keller, S. R., & Fitzpatrick, M. C. (2023). Ecological Monographs.
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Genotypic variation and plasticity in climate-adaptive traits after range expansion and fragmentation of red spruce Prakash, A., DeYoung, S., Lachmuth, S., Adams, J. L., Johnsen, K., Butnor, J. R., Nelson, D. M., Fitzpatrick, M. C., & Keller, S. R. (2022). Philosophical Transactions of the Royal Society B, 377(1848), 20210008.
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Variation in climatic tolerance, but not stomatal traits, partially explains Pooideae grass species distributions Das, A., Prakash, A., Dedon, N., Doty, A., Siddiqui, M., & Preston, J. C. (2021). Annals of Botany, 128(1), 83–95.
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Fodder yield and nutritive value of mulberry (Morus indica) under varying plant density and pruning frequency in coconut garden Raj, R. M., Raj, A. K., Kunhamu, T. K., & Prakash, A. (2019). Range Management and Agroforestry, 40(2), 255–261.
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Impact of particulate pollution on photosynthesis, transpiration and plant water potential of teak (Tectona grandis) Prakash, A., Santhoshkumar, A. V., & Roby, P. C. (2017). Current Science, 113(7), 1272–1276.
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Fodder yield and nutritive value of subabul (Leucaena leucocephala) under diverse management regimes in coconut garden Raj, R. M., Raj, A. K., & Prakash, A. (2016). Indian Journal of Agroforestry, 18(2), 79–85.
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Appropriateness of moist deciduous species against particulate pollution abatement and monitoring Prakash, A., Santhoshkumar, A. V., & Roby, P. C. (2016). International Journal of Science, Environment and Technology, 5, 537–546.
Peer-Review Activities
- Journal of Heredity (2025)
- Molecular Biology and Evolution (2025)
- New Phytologist (2024)
- G3: Genes, Genomes, Genetics (2023)
- Ecological Monographs (2022)
- Frontiers in Plant Science (2022)
Conference Presentations
Conference Talks
Unraveling the genetic architecture of local adaptation in species with a history of introgression.
3rd Joint Congress on Evolutionary Biology, Montreal, Canada
Unraveling the effects of introgression on local adaptation in red spruce (Picea rubens): Genetic rescue and shaping of adaptive traits.
XXVI World Congress of IUFRO, Stockholm, Sweden
Understanding the role of introgression on local adaptation in red spruce (Picea rubens).
UVM Student Research Conference, Burlington, Vermont, USA
Exploring the drivers of selection in a range-fragmented forest tree: A case study in red spruce (Picea rubens).
Evolution 2023, Albuquerque, New Mexico, USA
Detecting signals of polygenic adaptation in the face of demographic history and population structure in red spruce (Picea rubens).
Botany 2022, Anchorage, Alaska, USA
The evolution of species’ ranges in the face of changing environments.
Forest Genetics Student and Postdoc Symposium, Virtual.
Outreach
Using genomics to assist red spruce conservation and restoration under a changing climate.
CASRI Annual Meeting, Davis, West Virginia, USA
Science Sparks: Plant Biology.
Science Olympiad outreach talk for grades 7–10, University of Vermont, USA
Demographic history of red spruce and genotypic variation in climate-adaptive traits after range expansion and fragmentation.
NSF-funded Red Spruce Climate Change Workshop, Burlington, Vermont, USA
Poster Presentations
Seeds of Hope: Sprucing up forest restoration with genomics
Invited poster at UVM CALS and Food Systems Research Center Board of Trustees event (2024)
3rd Joint Congress on Evolutionary Biology, Montreal, Canada
Investigating population differentiation in red spruce (Picea rubens) due to climate change.
Evolution, Providence, Rhode Island, USA
UVM Student Research Conference, Burlington, Vermont, USA
Anatomical changes in the wood properties of Tectona grandis due to particulate pollution.
National Biodiversity Congress, Thiruvananthapuram, Kerala, India
Vegetational composition and regeneration status of mangroves in Chetuwai backwaters, Kerala.
Indian Biodiversity Congress, Chennai, Tamil Nadu, India
Trainings and Workshops
The Festival of Genomics & Biodata, Boston, USA
Computational Biology Upskilling Workshop
Instructors: Dean Lee and Tommy Tang
Enhancing Variant Analysis and Interpretation
Instructors: Heidi Rehm and Suganthi Balasubramanian
Mastering Spatial Data Analysis: From Basics to Cutting-Edge Innovations
Instructors: Abdul Hassan Samee and Ilya Korsunsky
How to Better Computationally Analyze Your SingleCell RNA Sequencing (scRNA-seq) Data
Instructors: Gracie Gordon, Mary Piper, Meeta Mistry and Zhaleh Safikhani
Data and Open Science Summit
UVM and NASA, Vermont, USA
Next Generation Sequencing Webinar
HelixOmics Analytics, Virtual
Schrödinger Educators Week
Schrödinger, New York, USA
De novo genome assembly and annotation workshop
Botany, Alaska, USA
Echoes in Space: Introduction to RADAR Remote Sensing
EO College and ESA, Virtual
UAV Remote Sensing and Applications
Indian Institute of Remote Sensing and ISRO, Virtual
Conservation Genetics
Salim Ali Centre for Ornithology and Natural History, India
Statistics and R (PH525.1X)
HarvardX/edX
Introduction to Python for Data Science (DAT208X)
Microsoft/edX
Multiple remote sensing and GIS trainings
IIRS, ISRO, and Kerala Agricultural University
Grants and Awards
CALS Graduate Student Enhancement Fund
with 100% departmental match
Graduate College Conference Grant Program
with 100% departmental match
UVM Graduate Student Senate Mini Grants
with 100% departmental match
CALS Graduate Student Enhancement Fund
with 100% departmental match
Professional Memberships
- Botanical Society of America (BSA).
- Society for the Study of Evolution (SSE).
- American Society of Naturalists (ASN).
References
Available upon request.