Getting to Know Our Fellows

 Hunter Merrill, one of our 2016 Fellows is an UFII Pre-Doctoral Fellow and a graduate student in the Agricultural and Biological Engineering Department. His research is in statistical methodology for big, dependent data, typically with applications to agriculture, ecology, epidemiology, and the environment, with a focus on Bayesian methods, spatio-temporal statistics and semiparametric modeling. 

“The purpose of my research is to develop computationally efficient statistical methods for big, messy, correlated data, particularly with applications to spatio-temporal predictions in agricultural, ecological, environmental, and epidemiological settings. For example, I have analyzed cholera in Haiti and hand, foot, and mouth disease in China to help inform the distribution of medicines; I have made forecasts for water use in Tampa to help utilities manage resources; and I have identified significant environmental drivers of soil nitrogen in Florida and used them to quantify the risk of high levels of soil nitrogen throughout the state.” 

Hunter received his B.S. in Mathematics (2012) from Mississippi State University. He knew that he wanted to use data science to study and solve major problems such as food security and climate change. Hunter received his Master in Statistics (2014) from the University of Florida and has continued toward a Ph.D. in Agricultural and Biological Engineering with a concentration in statistics. “I came to UF for their highly ranked programs in agricultural and life sciences as well as their strong data science programs,” Hunter says. “Not only are the programs strong, in addition there are many opportunities for applying the skills and knowledge learned in courses to real problems through UF’s close contact with industry.”

When Hunter is not busy with school and work, he enjoys being outdoors, hiking and biking and other outdoor sports. His main hobby is birding. According to Hunter, Florida is an excellent (if not the best) state in the U.S. for birding.

After  Hunter is awarded his Ph.D., his goal is to continue to conduct research with an eye towards solving real-world problems, whether in academia, government, or industry employment. Within five years, he will be conducting high-impact research and development and, within 10 years, he will be supervising and managing a team of researchers.

Prompted to define how UFII has benefitted him, Hunter replies, “UFII regularly brings in speakers which has exposed me to cutting-edge informatics research. There are often opportunities for meeting peers and exchanging ideas which has greatly improved my research. An added bonus is UFII has provided excellent space for work and collaboration.”

Hunter’s publications and CV can be found on his website: https://sites.google.com/site/hreidmerrill/.

 

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2016 Fellow and Ph.D. Student of Materials Science and Engineering Joshua Paul‘s research focuses in using computational tools to rapidly discover and characterize novel 2D materials with exceptional stability. In the early  years of the 21st Century, a new class of materials began to be investigated: 2D materials. These materials are only a few atoms thick and have shown to have very exciting properties when compared to many of their 3D counterparts. These included higher conductivity, magnetism, and rare electronic behavior. Such properties make these materials useful for many applications, but especially electronic devices. Between their powerful properties and small size, 2D materials are exciting for making smaller, faster electronics. However, synthesizing these materials is difficult right now. Without knowing what the structure and composition of the 2D material is prior to synthesis, it is very unlikely to actually grow a 2D material.

My research works to discover the structure and composition of 2D materials that display useful behaviors, and thus would be exciting to synthesize. Using calculations from the quantum mechanical simulation software VASP (Vienna Ab initio Simulation Package) and high throughput frameworks, I work to rapidly discover and characterize novel 2D materials. The primary way in which I do this is through a process called chemical substitution. An additional method is to search though 3D materials databases to find 2D materials. The most famous 2D material, graphene, comes from a material called graphite.  We in the Hennig group searched through the Materials Project database to find such structures, and discovered over 650 2D materials.”

Before coming to UF, Joshua received his B.S. in Materials Science and Engineering from the University of Arizona. During that time, he volunteered in several research labs, reviewing the literature of the ZnCl2-NaCl-KCl pseudo-ternary system, and using a scanning electron microscopy to measure the crack growth in silicon wafers under various atmospheric conditions. That being said, I wasn’t very fond of lab work. While I found the idea of research compelling, physical experimentation was not as fulfilling as I had hoped. Near the end of my undergrad work, however, I began to work on a computational project. I realized how much more engrossed I was with this work, and decided to pursue computational materials science for my PhD work. The field of 2D materials wasn’t one that I explicitly wanted to get into when looking at schools for my graduate degree. However, after discussing the topic with Prof. Richard Hennig, I knew it was a topic I could whole heartedly invest myself in. The potential of 2D materials in future technologies and the use of computational tools to explore that potential made the project a perfect fit for me.”

Whenever Joshua needs a break from his research, he heads outdoors and finds camping, hiking, and rock climbing to be the most rejuvenating. He is a fan of table top board games and video games. One of  his favorite pastimes is in visiting the many springs surrounding Gainesville.

After graduating, Joshua plans on working at a national laboratory. “Though I may not still be working on 2D materials, I expect to still be involved in the development of high throughput algorithms,” Joshua says. “Materials discovery is applicable to many fields, with algorithms and methods constantly being developed that can improve the discovery process. I’m unsure what direction I will be pulled after working at a national lab over time, but I look forward to finding out.”

Joshua gives credit to the UF Informatics Institute for significantly improving his development as a researcher. “The funding graciously provided by the institute has allowed me more flexibility in what I research and, as a result, broadened my understanding of the world of 2D materials. The institute has also opened up my awareness of other computational topics. New computational techniques are always of interest to me due to the nature of my research. The seminars hosted by the UF Informatics Institute have given me opportunities to learn not only how other fields use informatics tools, but also how to approach my research problems in novel ways.”

The list of 2D materials found by Joshua Paul and others in Prof. Richard Hennig’s research group can be found in their 2D material database at https://materialsweb.org/. You can follow Joshua’s publications about 2D materials and other topics at http://hennig.mse.ufl.edu/publications/.

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Raganhildur Bjarnadottir, known around UFII as Raga, is one of our 2017 Fellows and  is an UFII Post-Doctoral Fellow in the College of Nursing. Raga’s research broadly focuses on leveraging nurse-generated data to improve quality of care for underserved and vulnerable populations. Her current research addressed the clinical issue of patient falls in the hospital.

“Hospital falls are a continuing national concern, resulting in up to 100,000 severe injuries and 10,000 deaths annually. The associated direct medical cost of hospital falls is around $34 billion, and is projected to reach $55 billion in the year 2020. Significant efforts have been made to reduce hospital falls through practice and policy changes, but no sustained reduction has been achieved. This may be in part because existing assessment tools and prediction models to detect patients at risk for falling have limited predictive value and lack specificity. To address this issue, my research focuses on examining nurses’ progress notes to identify text features that can predict a patient falling during their hospitalization. My hope is that these text features can be combined with structured data to develop improved prediction models to detect patients at higher risk of falling.”

Raga received her B.S. in Nursing (2008) from the University of Iceland, in her hometown of Reykjavik. At this time, her research focused on the translated and validation of a psychometric tool to assess toddler temperament. After graduation she worked as an RN in a pediatric hospital and later as a school nurse and public health nurse. Through this work Raga became interested in leveraging consumer technology to support health promotion for the vulnerable youth population. She earned a Master of Public Health (2013) at the Columbia University Mailman School of Public Health. “My thesis examined online health information-seeking behaviors in a low income Hispanic community. While continuing my focus on leveraging technology to improve health and care for vulnerable populations, my research led me to shift my focus from consumer to provider-based technology.”  She received a PhD in Nursing (2016) at Columbia University School of Nursing, completing her dissertation defense in July 2016. Her dissertation focused on examining nurse documentation of sexual orientation and gender identity in home health care, using both qualitative methods and text mining. 

“In my current research I continue my work with text mining in nurses’ notes, but with a focus on a different vulnerable population: hospitalized patients and the elderly. Nurses are at the frontline of care, have constant contact with patients and conduct rigorous documentation through each episode of care. Despite this, nurse-generated data and particularly unstructured data are understudied. Therefore I think it is of great importance to examine nurses’ progress notes and other potentially rich nurse-generated data sourced to identify meaningful information that can help us improve quality of care and patient outcomes.”

Raga came to the University of Florida as a postdoc due to the rich program of research that the College of Nursing has in the field of nursing informatics. The Informatics Institute, and particularly the fellowship program offered, were also significant factors in my decision. 

“In the future, I aim to continue to identify and extract meaningful information from nurses’ progress notes using text mining. My goal is to move one step further to feed this information back to nurses and administrators through clinical decision support to support nurses in improving care quality and patient outcomes. In five years, I see myself as a tenure track assistant professor at a research-intensive university, with a strong program of research in text mining and decisions support,”

 

 

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Jugpreet Singh, one of our 2017 Fellows is an UFII Post-Doctoral Fellow in the Department of Horticultural Science. His research focus is to integrate different physiological, genetic, genomics and crop modeling approaches for identifying and selecting superior crop characteristics to train climate-resilient crops. Jugpreet is using common bean (kidney and other bean classes) for conducting his research work.

How a plant grows and performs is mainly dependent upon the genes it carries, the surrounding environment and an interaction between them. The genes bear an upper hand as they control the expression of plants features (phenotypes) that are required for its success under varying climate conditions. Thus, genetic information can help predict the performance of a crop in a given environment. Towards this goal, I am perusing different genomics and quantitative genetic approaches to identify the genes that control various growth and developmental phenotypes in common bean. The techniques involve extensive data recording under different environmental conditions and simultaneous genome sequencing from genetically diverse plants, followed by linking the genotype to phenotype through known statistical models. Currently, I am sequencing and analyzing a large panel of genotypes that were evaluated under diverse climates ranging from North Dakota, Puerto Rico to Colombia. These results will be used to create a gene-based crop model that can predict the productivity of a crop plant using the genetic and environmental data.” 

Jugpreet is originally from Punjab, a northwestern state close to Himalayan Mountains in India. Punjab produces a major proportion of wheat and rice and is known as the bread basket of India. “Being from a farming family and motivated by my father, I choose agriculture research as a career and received my  B.S. (Hons.) in Agriculture and M.S in Vegetable Breeding from Punjab Agriculture University in Ludhiana. I collected several indigenous landraces and wild cucurbit plants and characterized them for various morphological and economic traits. To gain more experience, I came to UF and earned my PhD in Bean Physiology and Genetics from the Horticultural Sciences Department and worked in the PhD Lab to study the genetic architecture of root growth traits during the domestication process.”

When Jugpreet is away from his work at the University of Florida, he enjoys running, swimming, hiking and just being outdoors. Since coming to UF, he has traveled extensively throughout the U.S.

After he earned his Ph.D. from UF, Jugpreet spent two winters in Ames, Iowa, as a computational biologist, studying in a crop genome informatics lab. His research was on cold genes. He came back to UF in 2016 and is continuing his study in bean genetics in the PhD Lab. Ultimately, Jugpreet has set his parameters of continuing research in crops with a product-oriented goal, either in academic or industrial settings.

“The fellowship funding from the UF Informatics Institute is extremely helpful for continuing my work. UFII has provided a great avenue to interact and gain knowledge about other research areas in informatics and data science. I appreciate UFII’s efforts to offer space, organize workshops, and provide an interdisciplinary environment to engage in collaborative activities.”

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Joe Sagues, a 2016 Fellow, has developed a new 3-step process in which high yields of monomeric aromatics and free sugars are obtained from agricultural residues using an inert atmosphere, earth abundant catalyst, and reasonable reaction time. Aspen Plus, the world leading dynamic process modeling software, is being used to conduct a techno-economic analysis of the new process. To establish the most cost-effective process possible for the production of the targeted products, process synthesis techniques will be used to combine various operations of proven biomass conversion technologies with those from the new process. For more information on his research as a Fellow, read his most recent publication, in which he employed similar techno-economic analysis techniques. http://www.sciencedirect.com/science/article/pii/S0960852416300694

Oncotherapy has evolved from surgery, radiotherapy, chemotherapy, endocrine therapy to targeted therapy and is entering the era of personalized medicine, owing to the large amount of patient tumor sequencing data available. 2016 Fellow and Ph.D. Candidate in Molecular Genetics and Microbiology Varsha Sundaresan‘s thesis will have three interrelated parts. First, Varsha will identify patterns of non-synonymous mutations using high throughput exome/ whole genome sequencing data of cancers from patients. Following that, she will expand her analysis to study how genetic mutations in regulatory regions affect tumorigenesis and cancer cell sensitivity to therapeutic agents, by taking advantage of a comparative genomics approach. Finally, in collaboration with computational scientists and statisticians, they will try to integrate genetic mutation, epigenetic regulation and gene expression information to generate predictive model that can assess the sensitivity of cancer cells to anticancer drugs/irradiation. To learn more about Varsha and her research, visit http://oge.med.ufl.edu/Students/Current/Sundaresan,Varsha.html