Projects

Here is just a brief overview of some of the new and ongoing projects we are working on at A-State:

Reference-free approaches for population genomics

Following on previous work, the lab is continuing a special focus on coevolutionary genomics of the parasitic witchweed Striga hermonthica and its cereal hosts, which include sorghum, rice, millet, and maize. S. hermonthica is a devastating constraint to food security across much of Africa, and we are leveraging ecological and evolutionary genomic perspectives to help inform sorghum breeding and weed management in smallholder farming systems. The lab is exploring development of new bioinformatic approaches to help characterize population variation 'beyond SNPs' in large and complex plant genomes. Funding: USAID PEER (PI: Steven Runo, USG-supported partner: Emily Bellis)

Machine learning for genomic prediction and gene-environment association mapping

We are also working on approaches for improved understanding and prediction of plant-environment interactions, through integration of machine learning and evolutionary genomic modeling frameworks.

Temporal dynamics of soil microbiome communities

As part of the Arkansas Tallgrass Prairie Collaborative, we are contributing to a study focused on understanding changes in soil microbe communities and impacts on competition dynamics. Funding: Arkansas INBRE.

Publications

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

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. (In revision). Seeds attached to refrigerated shipping containers represent a substantial risk of nonnative plant species introduction and establishment.

J.S. Shaver, E.S. Bellis, C. Iwaki, J. Qualls, J. Randolph, & J. Smith. (In revision). Massard Prairie Restoration and Soil Microbiome Succession.

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

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

Grace Rutledge (Undergraduate Researcher)

Grace is in her freshman year at A-State majoring in Pre-Professional Biological Sciences. She is working on a project using bioinformatics to study strigolactone receptor presence-absence variation in parasitic witchweed.

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.

You?

We're always recruiting enthusiastic undergraduate students. Please contact Emily for more information on projects of potential mutual interest.

Ph.D. Students are advised through the Molecular Biosciences program and Master's Students are advised through MBS or Computer Science. Funding for prospective Master's/Ph.D. students is currently limited, but I am a big advocate of co-advising and also 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.

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.