Projects

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

Gene <--> Environment

We are 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.

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).

Biology <--> Computer Science

How can interactions between disciplines be leveraged to improve understanding of the natural world and help solve society's challenges?

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

E.S. Bellis*, C.M. McLaughlin*, C.W. dePamphilis, & J.R. Lasky. The geography of parasite local adaptation to host communities (In press). Ecography preprint. *co-first authors.

J. Masanga, B. N. Mwangi, W. Kibet, M. Wamalwa, P. Sagero, R. Oduor, M. Ngugi, A. Alakonya, P. Ojola, E. Bellis, S. Runo. (2021). Physiological and ecological warnings that Dodder pose an exigent threat to farmlands in Eastern Africa. Plant Physiology

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

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

J. Stubblefield, M. Hervert, J.L. Causey, J.A. Qualls, W. Dong, L. Cai, J. Fowler, E. Bellis, K. Walker, J.H. Moore, S. Nehring & X. Huang. (2020). Transfer learning with chest X-rays for ER patient classification. Scientific Reports 10: 20900.

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. (2020). Seeds attached to refrigerated shipping containers represent a substantial risk of nonnative plant species introduction and establishment. Scientific Reports 10: 15017.

L. Lopez, K. Turner, E.S. Bellis, & J.R. Lasky. (2020). Genomics of Natural History Collections for Understanding Evolution in the Wild. Molecular Ecology Resources 20: 1153-1160.

J.S. Shaver, E.S. Bellis, C. Iwaki, J. Qualls, J. Randolph, & J. Smith. (2020). Massard Prairie Restoration and Soil Microbiome Succession. Journal of the Arkansas Academy of Science 74. cover article

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 16: 57. bioRxiv

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.

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

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

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

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.

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.K.H. Ho*, E.S. Bellis*, J. Calkins, J.R. Adrion, L.C. Latta IV, & S. Schaack. Engines of change: Transposable element mutation rates are high and vary widely among genotypes and populations of Daphnia magna. (Submitted). preprint. *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. Final Version.

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

Emilio Soriano Chavez (Undergraduate Researcher)

Emilio is a is a sophomore at A-State majoring in Computer Science and minoring in Biology and Chemistry. He is currently working on a project to develop new computational models to predict phenotype from environmental and genotype information in maize.

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. There are currently no open positions but I happy help students develop applications for independent funding opportunities such as the NSF GRFP.

Alumni

Arnesha Le'Flore, Undergraduate Researcher

Sadiq Haruna, Research Technician

Adrienne Cooper, Undergraduate Researcher

Grace Rutledge, Undergraduate Researcher

News

4.23.21

Undergraduate student researchers Daniel and Shelby are joining our AI-Campus team to work on the herbarium image project! Natalie Haydt is also joining the lab to pursue her PhD in MBS, co-advised with Dr. Neuman-Lee. We are so excited to welcome Daniel, Shelby, and Natalie!

4.21.21

An article just published in the NW Arkansas Democrat Gazette about the Tallgrass Prairie Restoration Project. The article came out just as we were all together sampling hemiparasitic plant associated soils in NW AR! Here's Dr. Bellis perfecting her soil coring technique under the tutelage of collaborators Mr. Jay Randolph & Dr. Jeff Shaver!

6.9.20

The lab is growing! Undergraduate student Emilio Soriano-Chavez joined us this summer to work on machine learning models for genomic prediction!

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.