
Lab Tabs
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Katie Baker (Research Assistant)
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Lucas Czech (Postdoctoral Fellow)
Lucas is a computer scientist and bioinformatician who is interested in analyzing and visualizing biological data. His goal is to develop and apply novel methods that help biologistis and ecologists to make sense of life and nature. Hence, he focusses on algorithm and software development, with a particular interest in machine learning and high performance computing. During his studies, he also gained experience in areas such as speech recognition, cryptography, and physics. During his PhD, he worked on novel methods to analyze metagenomic data in a phylogenetic context. In the Moi lab, his first postdoc position, he wants to develop and implement new ways to integrate biological data with other sources of information such as satellite images. His goal is to help understanding the patterns and interactions that govern ecology and evolution, from mutations in DNA to transformations of landscapes, in the global context of climate change.
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Maliheh Esfahanian (Research Associate)
Maliheh Esfahanian is a molecular geneticist interested in evolutionary biology and plant genetic adaptations to their environments in the face of climate change. Dr. Esfahanian received her PhD in Molecular and Cellular Biology at Illinois State University in the laboratory of Dr. John Sedbrook, where she used CRISPR/Cas9 genome editing techniques to rapidly domesticate the emerging oilseed crop, pennycress (Thlaspi arvense). Mali earned her B.S. in Plant Breeding and her M.S. in Plant Biotechnology in Iran and continued her research as a Visiting Scholar at the University of Wisconsin-Madison. During her PhD, she worked as an intern for the start-up company, CoverCress Inc., and contributed to interdisciplinary research as a member of the USDA-funded Integrate Pennycress Research Enabling Farm and Energy Resilience (IPREFER) project and the DOE-funded Integrated Pennycress Resilience Project (IPReP). Outside of the lab, Mali enjoys cooking/baking, gardening/growing house plants, and nature.
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Shannon Hateley (Postdoctoral Fellow)
Shannon Hateley is a computational biologist interested in using genomics methods to understand organismal response to climate change. Prior to coming to Carnegie, she was a senior staff scientist at AncestryDNA. Dr. Hateley obtained her Ph.D. in Molecular and Cell Biology from University of California, Berkeley, with a designated emphasis in Computational and Genomics Biology. During her studies, she worked both at lab bench and computationally on gene expression, building tools for RNA transcript characterization, and detecting disease-associated genetic variants. Dr. Hateley also holds a B.A. from St. John’s College where she studied the Great Books. She spends her free time on dance, tinkering, and climate organizing.
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Keegan Pham (Research Assistant)
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Megan Ruffley (Postdoctoral Fellow)
I am interested in using machine learning algorithms to understand selection across plant genomes in response to stress. I received my PhD in Bioinformatics and Computational Biology at the University of Idaho where I focused on performing simulation-based model inference using machine learning algorithms in areas ranging from demographic inference and phylogenetics to community-wide assembly mechanisms. This research was concentrated on disjunct plants of the Pacific Northwest temperate rainforest, but also focused on community-wide plant ecosystems, such as island plant communities. I am currently interested in continuing to apply machine learning algorithms to novel problems in evolutionary biology that can aid in solving our world’s most challenging problems. In the Moi and Rhee labs, I continue to investigate these algorithms as I study the relationship between genetic adaptation and response to stress in economically and agriculturally important crop plants. Investigating such adaptations to stress aid in our struggle to understand the future impacts of climate change.
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Sebastian Toro Arana (Graduate Student)
Sebastian is interested in using computational tools and engineering principles to study the underlying mechanisms of plant stress resistance, immunity and plant-microbe-environment interactions. His goal is to use new technologies to help tackle the challenges of climate change and food security. As an undergraduate and research technician at MIT, he worked on exploring brain decision making systems using computational analysis tools and genetic engineering but recently he has decided to work on more pressing global problems. On a more personal note, he loves enjoying nature and music.
2013-2018, Biological Engineering and Computer Science, MIT
2018-2020, Research Technician, McGovern Institute for Brain Research
2020-on, Graduate Student in Biology, Stanford University
ORCID Profile: 0000-0001-5711-0700
2020
Seasonal timing adaptation across the geographic range of Arabidopsis thaliana. Exposito-Alonso M. (2020). PNAS, 117 (18) 9665-9667
Evolutionary genomics improves prediction of species responses to climate change. Waldvogel AM, Feldmeyer B, Rolshausen G, Exposito-Alonso M, Rellstab C, Kofler R, Mock T, Schmid K, Schmitt I, Bataillon T, Savolainen O, Bergland A, Flatt T, Guillaume F, Pfenninger M. (2020) Evolution Letters, https://doi.org/10.1002/evl3.154
2019
The Earth BioGenome project: Opportunities and Challenges for Plant Genomics and Conservation Exposito-Alonso, M., Drost, HG., Burbano, H.A., Weigel, D. (2019) The Plant Journal, https://doi.org/10.1111/tpj.14631
Natural selection on the Arabidopsis thaliana genome in present and future climates. Exposito-Alonso, M., 500 Genomes Field Experiment Team, Burbano, H. A., Bossdorf, O., Nielsen, R., Weigel, D. (2019) Nature, https://doi.org/10.1038/s41586-019-1520-9
Highlights: Surridge C. Genomic futurology. Nat Plants. 2019;5: 1027. doi:10.1038/s41477-019-0532-7
A rainfall-manipulation experiment with 517 Arabidopsis thaliana accessions. Exposito-Alonso, M., Rodríguez, R.G., Barragán, C., Capovilla, G., Chae, E., Devos, J., Dogan, E.S., Friedemann, C., Gross, C.**, Lang, P., Lundberg, D., Middendorf, V.**, Kageyama, J., Karasov, T., Kersten, S., Petersen, S., Rabbani, L., Regalado, J., Reinelt, L.**, Rowan, B., Seymour, D.K., Symeonidi, E., Schwab, R., Tran, D.T.N., Venkataramani, K., Van de Weyer, A.-L., Vasseur, F., Wang, G., Wedegärtner, R.**, Weiss, F., Wu, R., Xi, W., Zaidem, M., Zhu, W., García-Arenal, F., Burbano, H.A., Bossdorf, O., Weigel, D., (2019) bioRxiv (final version), https://doi.org/10.1101/186767.
2018
Spatio-temporal variation in fitness responses to contrasting environments in Arabidopsis thaliana. Exposito-Alonso, M., Brennan, A., Alonso-Blanco, C., Picó, F.X., (2018) Evolution, 71:550. https://doi.org/10.1111/evo.13508.
Adaptive diversification of growth allometry in the plant Arabidopsis thaliana. Vasseur, F., Exposito-Alonso, M., Ayala-Garay, O., Wang, G., Enquist, B.J., Violle, C., Ville, D., Weigel, D., (2018) PNAS, https://doi.org/10.1073/pnas.1709141115
The rate and effect of new mutations in a colonizing plant lineage. Exposito-Alonso, M.*, Becker, C*., Schuenemann, V.J., Reitter, E., Setzer, C., Slovak, R., Brachi, B., Hagmann, J., Grimm, D.G., Jiahui, C., Busch, W., Bergelson, J., Ness, R.W., Krause, J., Burbano, H.A., Weigel, D., (2018) PLOS Genetics, 14, e1007155. https://doi.org/10.1371/journal.pgen.1007155
Cover highlight > http://blogs.plos.org/biologue/files/2018/02/Feb_2018.pdf
Max Planck Highlight: Evolutionwatch for plants > https://www.mpg.de/11956930/evolutionwatch-plants
Genomic basis and evolutionary potential for extreme drought adaptation in Arabidopsis thaliana. Exposito-Alonso, M., Vasseur, F., Ding, W., Wang, G., Burbano, H.A., Weigel, D., (2018). Nature Ecology & Evolution 2, 352–358. https://doi.org/10.1038/s41559-017-0423-0
Max Planck Highlight: Life on the edge > https://www.mpg.de/11861946/arabidopsis-climate-change
Behind the paper > https://natureecoevocommunity.nature.com/users/77335-moises-exposito-alo...
2017
On the post-glacial spread of human commensal Arabidopsis thaliana. Lee, C.-R., Svardal, H., Farlow, A., Exposito-Alonso, M., Ding, W., Novikova, P., Alonso-Blanco, C., Weigel, D., Nordborg, M., (2017). Nature Communications. 8, 14458. https://doi.org/10.1038/ncomms14458.
2016
Epigenomic diversity in a global collection of Arabidopsis thaliana accessions. Kawakatsu, T., Huang, S. C., Jupe, F., Sasaki, E., Schmitz, R. J., Urich, M. A., Castanon, R., Nery, J. R., Barragan, C., He, Y., Chen, H., Dubin, M., Lee, C. R., Wang, C., Bemm, F., Becker, C., O'Neil, R., O'Malley, R. C., Quarless, D. X., 1001 Genomes Consortium, Schork, N. J., Weigel, D., Nordborg, M., Ecker, J. R. (2016). Cell 166, 492-505, doi.org/10.1016/j.cell.2016.06.044.
Effector-triggered immune response in Arabidopsis thaliana is a quantitative trait. Iakovidis, M., Teixeira, P.J.P.L., Exposito-Alonso, M., Cowper, M.G., Law, T.F., Liu, Q., Vu, M.C., Dang, T.M., Corwin, J.A., Weigel, D., Dangl, J.L., Grant, S.R., (2016). Genetics 204, 337–353. https://doi.org/10.1534/genetics.116.190678.
1,135 Genomes reveal the global pattern of polymorphism in Arabidopsis thaliana. 1001 Genomes Consortium, (2016). Cell 166, 481–491. https://doi.org/10.1016/j.cell.2016.05.063.
My Website
Check opportunities here: https://moisesexpositoalonso.org/team