My name is Avinash Karn, I go by Avi, I am a plant quantitative geneticist and computational biologist, and digital agriculture and robotics enthusiast; and an amateur astronomer, painter, online blogger, photographer and vivid cook. :)
I obtained my secondary and higher secondary education in my hometown Birgunj, Nepal. Next, I came to the United States to earn my Bachelor of Science degree in Agricultural Sciences, specializing in plant genetics at Truman State University, and finally, earned my PhD at the University of Missouri Columbia specializing in plant breeding, genetics and genomics.
I specialize in plant breeding, statistical genetics and computational biology. Currently, I am a post-doctoral computational biologist at Cornell University in Geneva, New York. I intend to use my education and training in pursuing a career in a research organization that is involved to improve human nutrition, health and environment for both developed and developing communities.
Why I became a scientist? I believe that some traits you are just born with. I know personally, I have had one burning inside of me since I was very young. It was the trait that at times strayed me to trouble when I was a small boy, the very same trait that led me to take apart the television set to see how it worked, to make my own telescope to explore space firsthand, and later on took me on an adventure across the world to America where I could successfully fulfill my thirst for knowledge. Curiosity to know, to learn how, and to make things better has been a driving force in my life. It often led me to the lush backyard garden in the Nepalese house I called home for so many years. As a small child I remember standing crouched over my mother’s plants in the day’s early hours with a toothbrush protruding from one side of my mouth, more concerned about looking at the plants than I ever was about brushing my teeth. Over the years I could not shake my want to learn of those plants. Despite my mother and father’s wishes, as well as the Nepalese culture urging of young intelligent men to enter the medical field, I kept my interest in plants alive; I started taking classes in general agriculture in elementary school, continuing them in high school. I went on to leave Nepal for the United States at the age of 19 where I earned my Bachelor’s degree in Agricultural Science from Truman State University in Kirksville, Missouri. It is my Nepalese roots that give birth to my devotion to study Agriculture Science. I was brought up in a sub-urban city of Nepal, the location of most of the country’s agro-based industrial activities. In every monsoon season, my house would become surrounded with green paddy fields. I enjoyed watching farmers plowing their fields with oxen, sowing rice plants with their bare hands in the muddy soil, and harvesting in the fall. But I also witnessed natural disasters in those same fields; floods and droughts came and went, negatively affecting the socio-economic conditions of poor farmers in the region. Eighty percent of the Nepal’s total population is directly involved in agriculture, so these harsh times left me wanting to help the farmers; I knew the most powerful tool was an agriculture education. I have always been inspired by great people in our history, believing that there are great lessons to be learned from their achievements as well as their hardships. My life has been greatly influenced by the livelihoods of Isaac Newton, Nicola Tesla and Thomas Elva Edison. Edison once stated, “There is always a better way. Find it.” This quote has motivated and inspired me to assist the agricultural world in finding “better” farming techniques by improving crop varieties. Like Edison, I believe that strides toward improvement can always be made and goals can never be set too high.
Professional and Research ExperienceI am very passionate about plants and cutting-edge technology.I have in-depth knowledge and rigorous hands on experience in the field of plant breeding, quantitative genetics, high-throughput phenotyping and computational biology for over 10 years now, which I earned during my research work with plant breeders/geneticists in undergraduate, graduate school and my postdoctoral career here in the United States. Briefly, I hold a PhD in plant, insect and microbial sciences from the University of Missouri-Columbia and a Bachelor of Science in Agricultural Science from Truman State University in Kirksville, Missouri. And currently, I am a postdoctoral computational biologist at Cornell University in VitisGen2, a multi-institutional project funded by the US Department of Agriculture-Agricultural Research Service (USDA-ARS). I was first introduced in the field of plant breeding and genetics in my freshmen year in college, and was involved in plowing field with a tractor, planting seeds with hand, pollinating and collecting agronomic data from field trials, harvesting and statistically analyzing data. While still pursuing my undergraduate career, I worked with diverse panel of maize germplasms, and developed gene specific markers to aid in the development of high amylose maize lines. Carrying my passion in plant genetics and big data analysis to my graduate school, I was involved in the development of two novel populations: near isogenic (NIL) and synthetic lines derived from domesticated corn and its wild relative, teosinte to elucidate the teosinte genetic diversity for agronomic and domestication traits in maize. While still in graduate school, I developed statistical models to non-destructively estimate seed composition traits (total starch, protein, oil and individual fatty acids) traits in intact maize kernels and soybean seeds using near infrared reflectance spectroscopy (NIRS) and nuclear magnetic resonance (NMR) instruments. The key findings from my PhD dissertation research were that the teosinte bears novel alleles for various plant and kernel architecture traits, which can be utilized for the improvement modern maize germplasm, and in addition can provide unique source of variations to breeders and geneticist in further QTL and molecular studies, which will accelerate in the development of future elite maize germplasm. Currently, as a computation biologist in VitisGen2 project at Cornell, I am involved in the analyzing large-scale genotyping data from various platforms such as Simple Sequence Repeats (SSR), Genotyping-by-Sequencing (GBS), Amplicon Sequencing (AmpSeq), Whole genome sequencing (WGS) for variant and haplotype calling, genome alignment, assembly and genomic selection and prediction. I have also co-lead in the development of a rhAmpSeq (RNase H2 enzyme-dependent amplicon sequencing) haplotype strategy targeting the collinear core genome to improve marker transferability across a diverse genus. Similarly, I work with nation-wide grape breeders to apply AmpSeq/rhAmpSeq marker data for accelerated marker-assisted breeding. In addition, I build genetic maps (in Lep-Map3) of inter- and intraspecific Vitis populations; performed quality control (QC) analysis, interval mapping (in R/QTL) and genome-wide association (GLM, MLM, FarmCPU); and big data visualization in R software using packages such as ggPlot and CIRCOS (written in PERL). In addition, I have been also involved in managing grapevine breeding database www.VitisBase.org in collaboration with Boyce Thompson Institute and Breeding Insight project (USDA); as well as led setting up trials and high-throughput phenotype data collection on Field Book® android application. So far I have supervised three undergraduate research summer scholars from different parts of the country as well as assisted graduate students (both national and international) in genetic and statistical analyses. In my spare time, I do write tutorials on my blog https://AviKarn.com , and as of right now I have written about ten tutorials. And to this date, I have had 3,394 visitors from 63 countries since June 21, 2018.
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