Studies on genome comparison

• Grant number: 18/00031-7
• Support Opportunities: Regular Research Grants
• Start date: December 01, 2018
• End date: November 30, 2021
• Field of knowledge: Physical Sciences and Mathematics - Computer Science - Theory of Computation
• Principal Investigator: João Meidanis
• Grantee: João Meidanis
• Host Institution: Instituto de Computação (IC). Universidade Estadual de Campinas (UNICAMP). Campinas , SP, Brazil
• Associated scholarship(s): 20/00975-5 - Applications of the Matrix-Based Theory for Genome Rearrangements, BP.TT

Abstract

This project aims at advancing the matrix theory of genome rearrangements,introduced by Meidanis, Zanetti, and Biller, by applying it to practicalcases of genome comparison in microbes, fungi, plants, and mammals,in colalboration with bioscientists. The main problems tackled here arebuilding phylogenetic trees for the species, and inferring the ancestralgenomes occupying the internal nodes of these phylogenies.At the same time, it is our goalto refine the methods from the mathematical and computational point ofview, improving the algorithms and complementing the implementationwith supporting software that streamlines their use in practice. (AU)

Scientific publications

(7)

(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)

MEIDANIS, JOAO; CHINDELEVITCH, LEONID. Fast median computation for symmetric, orthogonal matrices under the rank distance. Linear Algebra and its Applications, v. 614, n. SI, p. 394-414, APR 1 2021. (18/00031-7)

MENDOZA, JULIO; PEDRINI, HELIO; FARINELLA, GM; RADEVA, P; BRAZ, J. Self-supervised Depth Estimation based on Feature Sharing and Consistency Constraints. VISAPP: PROCEEDINGS OF THE 15TH INTERNATIONAL JOINT CONFERENCE ON COMPUTER VISION, IMAGING AND COMPUTER GRAPHICS THEORY AND APPLICATIONS, VOL 4: VISAPP, v. N/A, p. 8-pg., 2020-01-01. (17/12646-3, 18/00031-7)

BILLER, PRISCILA; PEREIRA ZANETTI, JOAO PAULO; MEIDANIS, JOAO; SETUBAL, JC; SILVA, WM. Center Genome with Respect to the Rank Distance. ADVANCES IN BIOINFORMATICS AND COMPUTATIONAL BIOLOGY, BSB 2020, v. 12558, p. 9-pg., 2020-01-01. (12/13865-7, 12/14104-0, 18/00031-7)

MEIDANIS, JOAO; CHINDELEVITCH, LEONID. Fast median computation for symmetric, orthogonal matrices under the rank distance. Linear Algebra and its Applications, v. 614, p. 21-pg., 2021-02-02. (18/00031-7)

GIUSTI, GUILHERME NAVARRO NILO; JOTTA, PATRICIA YOSHIOKA; LOPES, CAROLINE DE OLIVEIRA; GANAZZA, MONICA APARECIDA; AZEVEDO, AMILCAR CARDOSO; BRANDALISE, SILVIA REGINA; MEIDANIS, JOAO; YUNES, JOSE ANDRES. Test trial of spike-in immunoglobulin heavy-chain (IGH) controls for next generation sequencing quantification of minimal residual disease in acute lymphoblastic leukaemia. British Journal of Haematology, v. 189, n. 4, MAR 2020. (18/00031-7, 17/03942-8)

PEREIRA ZANETTI, JOAO PAULO; OLIVEIRA, LUCAS PERES; CHINDELEVITCH, LEONID; MEIDANIS, JOAO. Generalizations of the genomic rank distance to indels. Bioinformatics, v. 39, n. 3, p. 10-pg., 2023-03-01. (17/02748-3, 20/00740-8, 18/00031-7)

MENDOZA, JULIO; PEDRINI, HELIO; PENG, Y; HU, SM; GABBOUJ, M; ZHOU, K; ELAD, M; XU, K. Adaptive Self-supervised Depth Estimation in Monocular Videos. IMAGE AND GRAPHICS (ICIG 2021), PT III, v. 12890, p. 13-pg., 2021-01-01. (18/00031-7, 17/12646-3)