Algorithms for comparative genomics of crops and other flowering plants

• Grant number: 16/01511-7
• Support Opportunities: Scholarships abroad - Research
• Start date: August 01, 2016
• End date: January 31, 2017
• Field of knowledge: Physical Sciences and Mathematics - Computer Science - Theory of Computation
• Principal Investigator: João Meidanis
• Grantee: João Meidanis
• Host Investigator: David Sankoff
• Host Institution: Instituto de Computação (IC). Universidade Estadual de Campinas (UNICAMP). Campinas , SP, Brazil
• Institution abroad: University of Ottawa (uOttawa), Canada

Abstract

Over the scale of millions of years, biological evolution entails not only mutations in individual genes, but also the rearrangement of the order of the genes on the chromosomes compared to other species descended from their common ancestor. In addition, and especially in plant genomes, the entire genome may be doubled, and most excess genes deleted in a seemingly unpredictable way. In this project, we intend to carry on our research to model all these processes mathematically and develop combinatorial algorithms and statistical analyses to understand the rearrangement of gene order within and between chromosomes. This is applied to understand the evolution of genomes, particularly of crops and other flowering plants. (AU)

Scientific publications

(References retrieved automatically from Web of Science and SciELO through information on FAPESP grants and their corresponding numbers as mentioned in the publications by the authors)

CHINDELEVITCH, LEONID; LA, SEAN; MEIDANIS, JOAO. A cubic algorithm for the generalized rank median of three genomes. Algorithms for Molecular Biology, v. 14, JUL 26 2019. (16/01511-7)

SANKOFF, DAVID; ZHENG, CHUNFANG; ZHANG, YUE; MEIDANIS, JOAO; LYONS, ERIC; TANG, HAIBAO. Models for Similarity Distributions of Syntenic Homologs and Applications to Phylogenomics. IEEE-ACM TRANSACTIONS ON COMPUTATIONAL BIOLOGY AND BIOINFORMATICS, v. 16, n. 3, p. 727-737, MAY-JUN 2019. (16/01511-7)