Current Projects

Genomics of Coevolution

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 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 and understand how parasites adapt across broad spatial scales and diverse environmental gradients (Funding: USAID PEER; PI: Steven Runo, Kenyatta University; US-supported partner: Emily Bellis).

G x E contributions to Phenotype

We are interested in understanding how genotype-by-environment interaction (when response to environmental variation depends on an organism's genotype) influences variation in phenotype. Currently we are trying to figure out how to best integrate information reflecting G x E in machine learning frameworks to predict fitness across different environments, leveraging the extensive genomic and phenotypic data resources available for crop systems. This research is supported by an Arkansas NSF EPSCoR DART seed grant.

Adaptation to Novel Environments

Invasive species are fascinating model systems for studying how organisms can persist and rapidly adapt to new environmental conditions. We are contributing to a variety of projects that seek to predict how non-native invasive plants will perform in novel environments and understanding the factors shaping their success (Funding: USFS-Southern Research Station).

Publications

Peer-reviewed

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. (Accepted). PLoS Genetics. preprint. *co-first authors.

J. Masanga, R. Odour, A. Alakonya, P. Ojola, E.S. Bellis*, and S.M. Runo*. (Accepted). Comparative phylogeographic analysis of Cuscuta campestris and C. reflexa in Kenya: Implications for management of highly invasive vines. Plants, People, Planet. *co-corresponding

E.S. Bellis*, C.M. McLaughlin*, C.W. dePamphilis, & J.R. Lasky. The geography of parasite local adaptation to host communities (2021). Ecography 44: 1205-1217. *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 Physiology4: 1457-1467.

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

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.

Our group welcomes individuals from diverse backgrounds and strives to support all team members in an vibrant, respectful, and supportive atmosphere. The organization of our group is inspired by the 'nested multi-mentoring model' described by Montgomery & Page (2018). In this type of mentoring model, multiple mentors work collaboratively to support mentees, who also support each other and benefit from multiple mentors and resources.

Members of the Bellis 'subnetwork' are encouraged to attend a weekly lab group meeting with several other faculty members in the Bioinformatics working group, as well as to engage with other students and faculty members across the country as part of the AI-Campus program.

Currently we comprise Dr. Bellis, Natalie Haydt (MBS Ph.D. student), and three stellar undergraduate students: E. Soriano-Chavez (CS major), S. McCormick (Math/Stat major), and D. Delgadillo (CS major).

Current opportunities:

Undergraduate students from any major are always welcome to contact Dr. Bellis and to inquire about availability of paid research opportunities. Prior coding experience is not necessary, however, you should have a deep interest in learning R and/or Python and applying computational techniques to interesting problems in biology, agriculture, or computer science!

I mentor Ph.D. students through the Molecular Biosciences program, and Master's students through the Computer Science program. All graduate positions are currently filled, but I am happy to help students develop applications for independent funding opportunities such as the NSF GRFP.

WE ARE CURRENTLY HIRING AN UNDERGRADUATE STUDENT WORKER TO HELP WITH WEB APPLICATION AND DESIGN (TO START IN JANUARY 2021). The student will work closely with Dr. Bellis and another current student to develop an interactive web application for deployment of our 'AgAdapt' algorithm.

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.