Andrea Zuccolo

Research Scientists

Research Scientist



Research Interests

My career in scientific research mostly took place at the interface between genomics and bioinformatics with an emphasis on plant comparative genomics.
My main scientific interest is the study of repetitive sequences in plants. In particular I focus on the role played by Transposable Elements (TEs) in shaping plant genome structures and contributing to their evolution and remodeling. I mostly analyzed TEs in a comparative context, especially in the case of the genus Oryza 

Selected Publications

  • A platinum standard pan-genome resource that represents the population structure of Asian rice,Y. Zhou, D. Chebotarov, D. Kudrna, ... A. Zuccolo, K. McNally, J. Zhang, R. A. Wing, Scientific Data (2019)
  • LTR Retrotransposons Show Low Levels of Unequal Recombination and High Rates of Intraelement Gene Conversion in Large Plant Genomes, R.M. Cossu, C. Casola, S. Giacomello, A. Vidalis, D.G. Scofield, A. Zuccolo, Genome Biololgy and Evolution (2017)
  • Identification and characterization of abundant repetitive sequences in Eragrostis tef cv. Enatite genome, Y.G Gebre, E. Bertolini, M.E: Pè, A. Zuccolo, BMC Plant Biol. (2016)
  • The Ty1-copia LTR retroelement family PARTC is highly conserved in conifers over 200 MY of evolution, A. Zuccolo, D.G. Scofield, E. De Paoli, M. Morgante,  Gene (2015)
  • The Norway spruce genome sequence and conifer genome evolution, B. Nystedt, N. R. Street, A. Wetterbom, A. Zuccolo, Y.C. Lin, D.G. Scofield et al., Nature. (2013)
  • A physical map for the Amborella trichopoda genome sheds light on the evolution of angiosperm genome structure, A. Zuccolo A, J.E. Bowers, J.C. Estill, Z. Xiong, M. Luo, A. Sebastian et al., Genome Biology (2011)
  • Human gut microbiota in obesity and after gastric bypass, H. Zhang, J.K DiBaise, A. Zuccolo, D. Kudrna, M. Braidotti, Y. Yu, P. Parameswaran, M.D. Crowell, R. Wing, B.E. Rittmann, R. Krajmalnik-Brown, Proceedings of the National Academy of Sciences of the USA (2009)
  • Transposable element distribution, abundance and role in genome size variation in the genus Oryza, A. Zuccolo, Sebastian A., Talag J., Yu Y., Kim H., Collura K., Kudrna D., R. Wing, BMC Evolutionary Biology (2007)
  • Evolutionary dynamics of an ancient retrotransposon family provides insights into evolution of genome size in the genus Oryza, S. Jetty, A. Zuccolo, Y. Yu, X. Song, B. Piegu, F. Chevalier, J. Walling, J. Ma, J. Talag, D. Brar, P. SanMiguel, N. Jiang, S. Jackson, O. Panaud, R. Wing, The plant Journal (2007) 
  • Gene duplication and exon shuffling by helitron-like transposons generate intraspecies diversity in maize, M. Morgante, S. Brunner, G. Pea, K. Fengler, A. Zuccolo, A. Rafalski, Nature Genetics (2005) 


  • Ph.D., Plant Biotechnology, Università degli Studi di Udine, Udine, Italy, 2003
  • M.Sc. Molecular Biology, Università degli Studi di Trieste, Trieste, Italy, 1998 

Professional Profile

  • Since May 2019: Research Scientist at KAUST, Saudi Arabia
  • Since June 2015: Tenured Assistant Professor at Scuola Superiore Sant'Anna, Pisa, Italy. On Leave of Absence since May 2019
  • December 2011-June 2015: Assistant Professor at Scuola Superiore Sant'Anna, Pisa, Italy
  • June 2011-December 2011: Senior Scientist at the Applied Genomics Institute, Udine,Italy
  • July 2006-May 2011: Coordinator of the Bioinformatics Team at the Arizona Genomic Institute (The University of Arizona, Tucson, AZ, USA)
  • November 2004- July 2006: Research Associate at the Arizona Genomics Institute (The University of Arizona, Tucson, AZ, USA)
  • June 2003-October 2004: Research Associate in the Plant Molecular Breeding Laboratory (Department of Crop Science and Agricultural Engineering, University of Udine, Italy) 

KAUST Affiliations

Prof. Rod Wing's Group

CDA - Center for Desert Agriculture

BESE - Biological and Environmental Science and Engineering Division

Research Interests Keywords

Plant comparative genomics, Bioinformatics, Transposable elements, Evolution, Genome sequencing, Genome assembly, Genome annotation