April 2010 – March 2015: Doctor of Philosophy (PhD), Mention in Basic and Applied Sciences, Universidad Nacional de Quilmes, Buenos Aires, Argentina
Title: Molecular evolution and conformational diversity in proteins
Supervisors: Gustavo Parisi and Cristina Marino-Buslje.
2003 – 2009: Licentiate degree in Biotechnology, Orientation to Genetics and Molecular Biology, Universidad Nacional de Quilmes, Buenos Aires, Argentina.
2003 – 2006: Bachelor of Technology, Laboratory Technician, Universidad Nacional de Quilmes, Buenos Aires, Argentina.
September 2022: Associate professor (Maître de conférences), Université Paris-Saclay, I2BC, Gif-sur-Yvette, France.
15 April 2022 – August 31, 2022: Postdoctoral Fellow, UMR 7205 CNRS, ISYEB, Muséum national d'Histoire naturelle, Paris, France. I worked on modeling the evolution of protein structures under the supervision of Olivier Gascuel.
March 2018 – September 30, 2020: Postdoctoral Fellow, UMR 7238 CNRS "Biologie Computationnelle et Quantitative", Sorbonne Université, Paris, France. Research focused on the evolution of alternative splicing and the development of tools for identifying homologous exons, conducted under the supervision of Elodie Laine and Hugues Richard.
January 2018 – March 2018: Postdoctoral Fellow, UMR 7205 ISYEB, "AIRE", Sorbonne Université, Paris, France. Conducted studies on the evolution of domain architectures through network analysis, under the supervision of Eric Bapteste.
September 2017 – January 2018: Postdoctoral Fellow (short-term research stay), Sorbonne Université, Paris, France. Focused on the evolution of domain architectures through network analysis, under the supervision of Cristina Marino-Buslje and Eric Bapteste.
April 2015 – January 2018: Postdoctoral Fellow, CONICET, Leloir Institute Foundation, Buenos Aires, Argentina. I developed tools integrating coevolution and structural data, supervised by Cristina Marino-Buslje.
July 2013 – September 2013: PhD student (short-term research stay), Università degli Studi di Padova, Padova, Italy. I studied protein disorder as another aspect of conformational diversity, supervised by Silvio Tosatto and Gustavo Parisi.
April 2010 – March 2015: PhD student, CONICET, Universidad Nacional de Quilmes, Buenos Aires, Argentina. Researched the relationship between protein conformational diversity and molecular evolution, supervised by Gustavo Parisi and Cristina Marino-Buslje.
September 2022: Associate professor (Maître de conférences), Université Paris-Saclay, Gif-sur-Yvette, France.
March 2020: Temporary teacher (Enseignant vacataire), "Advanced Programming", Station Biologique de Roscoff UFR937, Sorbonne Université, Paris, France.
February 2019 – March 2019: Temporary teacher (Enseignant vacataire), "Introduction to Bioinformatics", Sorbonne Université, Paris, France.
April 2017 – May 2017: Adjunct Professor, MSc Bioinformatics and Systems Biology course: "Categorical Data Analysis", Universidad Nacional de Quilmes, Buenos Aires, Argentina.
August 2010 – May 2017: Assistant Professor, Department of Physics, Universidad Nacional de Quilmes, Buenos Aires, Argentina.
June 2016 – August 2016: Adjunct Professor, MSc Bioinformatics and Systems Biology course: "Categorical Data Analysis", Universidad Nacional del Noroeste de la Provincia de Buenos Aires, Buenos Aires, Argentina.
August 2014 – December 2014: Adjunct Professor, Agrobiotechnology Engineering course: "Bioinformatics", Universidad Nacional de General San Martín, Buenos Aires, Argentina.
March 2009 – December 2009: Student Assistant, Department of Physics, Universidad Nacional de Quilmes, Buenos Aires, Argentina.
March 2007 – December 2007: Student Assistant, Department of Mathematics, Universidad Nacional de Quilmes, Buenos Aires, Argentina.
Zea, D. J. (2022). Interactive Visualization and Plotting with Julia: Create impressive data visualizations through Julia packages such as Plots, Makie, Gadfly, and more. Packt Publishing Ltd. link
Banchero, M., Bustamante, J. P., Lanzarotti, E., Revuelta, M. V., Teppa, E., Zea, D. J., & Stocchi, N. (2022). Vida.exe: Desafíos y aventuras de la bioinformática. Fondo de Cultura Económica Argentina. link
Bret, H., Gao, J., Zea, D. J., Andreani, J., & Guerois, R. (2024). From interaction networks to interfaces, scanning intrinsically disordered regions using AlphaFold2. Nature Communications, 15(1), 597. link
Szatkownik, A., Zea, D. J., Richard, H., & Laine, E. (2023). Building alternative splicing and evolution-aware sequence-structure maps for protein repeats. Journal of Structural Biology, Volume 215, Issue 3. link
Zea, D. J., Mac Donagh, J., Benitez, G., Donadio, C. G., Marchetti, J., Palopoli, N., Fornasari, M. S., & Parisi, G. (2022). Evolutionary rates in human amyloid proteins reveal their intrinsic metastability. bioRxiv, 2022–09. link
Zea, D. J., Richard, H., & Laine, E. (2022). ASES: visualizing evolutionary conservation of alternative splicing in proteins. Bioinformatics, 38(9), 2615–2616. link
Saldaño, T., Escobedo, N., Marchetti, J., Zea, D. J., Mac Donagh, J., Velez Rueda, A. J., Gonik, E., Garcia, A. M., Salas, M., Peters, T. & Demitroff, N. (2022). Impact of protein conformational diversity on AlphaFold2 predictions. Bioinformatics link
Zea, D. J., Laskina, S., Baudin, A., Richard, H., & Laine, E. (2021). Assessing conservation of alternative splicing with evolutionary splicing graphs. Genome Research, gr-274696. link
Palopoli, N., Marchetti, J., Monzon, A. M., Zea, D. J., Tosatto, S. C. E., Fornasari, M. S. & Parisi, G. (2020). Intrinsically Disordered Protein Ensembles Shape Evolutionary Rates Revealing Conformational Patterns. Journal of Molecular Biology link
Teppa, E., Zea, D. J., Oteri, F. & Carbone, A. (2020). COVTree: Coevolution in OVerlapped sequences by Tree analysis server. Nucleic Acids Research, gkaa330 link
Teppa, E., Nadalin, F., Combet, C., Zea, D. J., David, L. & Carbone, A. (2020). Coevolution analysis of amino-acids reveals diversified drug resistance solutions in viral sequences: the case study of Hepatitis B Virus. Virus Evolution, 6(1), veaa006 link
Ait-hamlat, A., Zea, D. J., Labeeuw, A., Polit, L., Richard, H. & Laine, E. (2020). Transcripts' evolutionary history and structural dynamics give mechanistic insights into the functional diversity of the JNK family. Journal of Molecular Biology link
Ochoa, S., Martínez‐Pérez, E., Zea, D. J., Molina‐Vila, M. A., & Marino‐Buslje, C. (2019). Comutation and exclusion analysis in human tumors: A tool for cancer biology studies and for rational selection of multitargeted therapeutic approaches. Human mutation, 40(4), 413-425. link
Zea, D. J., Monzon, A. M., Parisi, G., & Marino-Buslje, C. (2018). How is structural divergence related to evolutionary information?. Molecular phylogenetics and evolution, 127, 859-866. link
Marino-Buslje, C., Monzon, A. M., Zea, D. J., Fornasari, M. S., & Parisi, G. (2017). On the dynamical incompleteness of the Protein Data Bank. Briefings in Bioinformatics link
Teppa, E., Zea, D. J., & Marino‐Buslje, C. (2017). Protein–protein interactions leave evolutionary footprints: High molecular coevolution at the core of interfaces. Protein Science, 26(12), 2438-2444. link
Monzon, A. M., Zea, D. J., Marino-Buslje, C., & Parisi, G. (2017). Homology modeling in a dynamical world. Protein Science, 26(11), 2195-2206. link
Monzon, A. M., Zea, D. J., Fornasari, M. S., Saldaño, T., Fernandez-Alberti, S., Tosatto, S. C., & Parisi, G. (2017). Conformational diversity analysis reveals three functional mechanisms in proteins. PLOS Computational Biology, 13, no. 2: e1005398. link
Zea, D. J., Anfossi, D., Nielsen, M., & Marino-Buslje, C. (2016). MIToS. jl: mutual information tools for protein sequence analysis in the Julia language. Bioinformatics, btw646. link
Zea, D. J., Monzon, A. M., Gonzalez, C., Fornasari, M. S., Tosatto, S. C., & Parisi, G. (2016). Disorder transitions and conformational diversity cooperatively modulate biological function in proteins. Protein Science, 25(6), 1138-1146. link
Iserte, J., Simonetti, F. L., Zea, D. J., Teppa, E., & Marino-Buslje, C. (2015). I-COMS: interprotein-COrrelated mutations server. Nucleic acids research, 43(W1), W320-W325. link
Parisi, G., Zea, D. J., Monzon, A. M., & Marino-Buslje, C. (2015). Conformational diversity and the emergence of sequence signatures during evolution. Current opinion in structural biology, 32, 58-65. link
Zea, D. J., Monzon, A. M., Fornasari, M. S., Marino-Buslje, C., & Parisi, G. (2013). Protein conformational diversity correlates with evolutionary rate. Molecular biology and evolution, 30(7), 1500-1503. link
Parra, R. G., Defelipe, L. A., Guzovsky, A. B., Monzon, A. M., Cravero, F., Mancini, E., ... & Gonzalez, N. N. (2016). Highlights of the 1st Argentine Symposium of Young Bioinformatics Researchers (1SAJIB) organized by the ISCB RSG-Argentina. PeerJ Preprints, 4, e2494v1. link
Zea, D. J., Teppa, E., & Marino-Buslje, C. (2023). Easy Not Easy: Comparative Modeling with High-Sequence Identity Templates. In Homology Modeling: Methods and Protocols (pp. 83–100). Springer US New York, NY. link
Teppa, E., Zea, D. J., & Buslje, C. M. (2012). Identification of Coevolving Amino Acids using Mutual Information. iConcept Press. link
Monzon, A. M., Fornasari, M. S., Zea, D. J., & Parisi, G. (2019). Exploring Protein Conformational Diversity. In Computational Methods in Protein Evolution (pp. 353-365). Humana Press, New York, NY. link