Projects

Most of our research projects focus somehow on understanding interactions, such as:

Gene <--> Environment

We working on developing machine learning approaches for improved understanding and prediction of gene-environment interactions, leveraging the extensive genomic and phenotypic resources available for crop systems. This project is not funded yet, but we hope it will be soon!

Host <--> Symbiont

Much of our past and ongoing work seeks to understand dynamics of interactions between hosts and their parasite or mutualist partners. We have worked in a broad range of systems, from marine invertebrates (corals & sea anemones) and their symbiotic microbes to parasitic plants (Striga hermonthica) and their cereal hosts (including sorghum, rice, millet, and maize).

Current projects are leveraging ecological & evolutionary genomic perspectives to inform parasitic weed management in East Africa (Funding: USAID PEER; PI: Steven Runo, Kenyatta University; US-supported partner: Emily Bellis). As part of the Arkansas Tallgrass Prairie Collaborative, we are contributing to a study focused on understanding changes in soil microbe communities during prairie restoration and impacts on competition dynamics. (Funding: Arkansas INBRE Collaborative Research Grant & Core Facility Vouchers).

Human <--> Computer

How best can new technologies be leveraged to improve understanding of the natural world and help solve society's challenges? We are exploring this problem in the context of developing computer vision models of UAS-derived remote sensing imagery of rice fields in Arkansas (Funding: U of Arkansas Division of Agriculture).

As part of the Center for No-Boundary Thinking we contribute to training in AI and machine learning research that prioritizes a human-centered approach and values interactions among disciplines in defining and solving research problems.

Publications

Peer-reviewed

12. R.D. Lucardi, E.S. Bellis, C.E. Cunard, J.K. Gravesande, S.C. Hughes, L.E. Whitehurst, S.J. Worthy, K.S. Burgess, T.D. Marsico. (Accepted). Seeds attached to refrigerated shipping containers represent a substantial risk of nonnative plant species introduction and establishment. Scientific Reports.

11. L. Lopez, K. Turner, E.S. Bellis, & J.R. Lasky. (Accepted). Genomics of Natural History Collections for Understanding Evolution in the Wild. Molecular Ecology Resources.

10. J.S. Shaver, E.S. Bellis, C. Iwaki, J. Qualls, J. Randolph, & J. Smith. (Accepted). Massard Prairie Restoration and Soil Microbiome Succession. Journal of the Arkansas Academy of Science.

9. M. Staton, C. Addo-Quaye, [and 29 others including E.S. Bellis]. (2020). A reference genome assembly and adaptive trait analysis of Castanea mollissima 'Vanuxem', a source of resistance to chestnut blight in restoration breeding. Tree Genetics & Genomes. bioRxiv

8. R.M. Gutaker, S.C. Groen, E.S. Bellis, J.Y. Choi, I.S. Pires, R.K. Bocinsky, E. Slayton, O. Wilkins, C.C. Castillo, S. Negrão, M.M. Oliveira, D.Q. Fuller, J.A. d’Alpoim Guedes, J.R. Lasky, and M.D. Purugganan. (2020). Genomic history and ecology of the geographic spread of rice. Nature Plants 6: 492-502. code

7. E.S. Bellis, E.A. Kelly, C.M. Lorts, H. Gao, V.L. DeLeo, G. Rouhan, A. Budden, G.B. Bhaskara, Z. Hu, R. Muscarella, M.P. Timko, B. Nebie, S.M. Runo, N.D. Chilcoat, T.E. Juenger, G.P. Morris, C.W. dePamphilis, and J.R. Lasky. (2020). Genomics of sorghum local adaptation to a parasitic plant. PNAS 117: 4243-4251. press

6. L. Lopez, E.S. Bellis, E. Wafula, S. Hearne, L. Honaas, P. Ralph, N. Unachukwu, C.W. dePamphilis, and J.R. Lasky. (2019). Transcriptomics of host-specific interactions in natural populations of the parasitic plant Striga hermonthica. Weed Science 67: 397-411.

5. E.S. Bellis, R.B. Edlund, H.K. Berrios, H.A. Lessios, and D.R. Denver (2018). Molecular signatures of host specificity linked to habitat specialization in Exaiptasia sea anemones. Ecology and Evolution 8: 5413-5426. data/code

4. E.S. Bellis and D.R. Denver (2017). Natural variation in responses to acute heat and cold stress in a sea anemone model system for coral bleaching. The Biological Bulletin 23: 168-181. data/code. cover article

3. E.S. Bellis, D.K. Howe, and D.R. Denver (2016). Genome-wide polymorphism and signatures of selection in the symbiotic sea anemone Aiptasia. BMC Genomics 17: 160. data

2. W.S. Philips, A.L Coleman-Hulbert, E.S. Weiss, D.K. Howe, S. Ping, R.I. Wernick, S. Estes, and D.R. Denver (2015). Selfish mitochondrial DNA proliferates and diversifies in small, but not large, experimental populations of Caenorhabditis briggsae. Genome Biology and Evolution 7: 2023-2037.

1. A. Emblem, S. Okkenhaug, E.S. Weiss, D.R. Denver, B.O. Karlsen, T. Moum, S.D. Johansen (2014). Sea anemones possess dynamic mitogenome structures. Molecular Phylogenetics and Evolution 75: 184-193.

Preprints/Submitted

E.S. Bellis*, C.M. McLaughlin*, C.W. dePamphilis, & J.R. Lasky. Macroecology of host specialization to a parasitic plant (Submitted). preprint. *co-first authors.

E.K.H. Ho*, E.S. Bellis*; J. Calkins; J.R. Adrion; L.C. Latta IV; S. Schaack. Variation in transposable element activity over spatial and temporal scale (Submitted). *co-first authors.

W. Zhou, E. Bellis, J. Stubblefield, J. L. Causey, Jake A. Qualls, Karl Walker, Xiuzhen Huang (2019). Minor QTLs mining through the combination of GWAS and machine learning feature selection. biorxiv.

Emily Bellis, Ph.D. (PI)

Emily is from Arkansas and earned a B.S. in Genetics & Biochemistry at Texas A&M University (College Station, TX) in 2010 and a Ph.D. in Integrative Biology in 2017 from Oregon State University (Corvallis, OR), working with Dee Denver. After a short postdoc on population genomics of transposable elements with Sarah Schaack at Reed College (Portland, OR), she worked with Jesse Lasky and Claude dePamphilis at Penn State (State College, PA) as an NSF Postdoctoral Research Fellow in Biology through the National Plant Genome Initiative. She joined A-State in late 2019 and is currently an Assistant Professor of Bioinformatics. In her spare time, she enjoys hiking, knitting, and attempting unsuccessfully to tire out her energetic Border Collie/Aussie, Pascal.
Emily's CV

Sadiq Haruna (Research Technician)

Sadiq recently earned a B.S. in Computer Science from University of Arkansas Pine Bluff and is currently developing machine learning models to help detect early signatures of stress in rice using UAS-derived imagery, as part of a large collaboration with multiple A-State faculty.

Emilio Soriano Chavez (Undergraduate Researcher)

Emilio is a visiting student from the Arkansas State University Queretaro Campus in Mexico, where he is currently a sophomore majoring in Biotechnology and Chemistry. He is currently working on a project to develop new computational models to predict phenotype from environmental and genotype information in maize.

Adrienne Cooper (Undergraduate Researcher)

Adrienne is an undergraduate Biology major on the pre-med track. Her research is contributing to the Arkansas Tallgrass Prairie Project, using machine learning based models to characterize the abiotic niche of parasitic plants in the genus Castilleja.

Arnesha Le'Flore (Undergraduate Researcher)

Arnesha is an undergraduate Biology major, also contributing to the Arkansas Tallgrass Prairie Project. Her project is using bioinformatic techniques to characterize interactions among soil microbes and dynamics of antibiotic resistance in the environment.

You?

Undergraduate students are always welcome to inquire about the availability of open positions in the lab. Please contact Emily for more information on projects of potential mutual interest. Please include your resume/CV, unofficial transcript, and a brief statement describing why you are interested in a research position in the lab.

Ph.D. Students are advised through the Molecular Biosciences program and Master's Students are advised through Computer Science. Current funding could support a Graduate Assistantship for one Master's student for two years. I am also a big advocate of co-advising and happy help students develop applications for independent funding opportunities such as the NSF GRFP. Please contact Emily to discuss particular research projects you might pursue in the lab to help you progress along your desired career path.

Alumni

Grace Rutledge, Undergraduate Researcher

News

6.9.20

The lab is growing! (and Emily is bad at posting updates..) Undergraduate student Emilio Soriano-Chavez joined us this summer to work on machine learning models for genomic prediction, and Prapti Pandey will be joining to pursue her M.S. in the Fall!

10.25.19 Emily is off to the annual Arkansas INBRE conference, in Fayetteville, AR!

Contact

You can find me in room 202 of the Arkansas Biosciences Institute on the A-State main campus in Jonesboro, or reach me by email at ebellis[at]astate[dot]edu.