CV Lattes
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Universidade Estadual de Campinas (UNICAMP). Instituto de Computação (IC) (Institutional affiliation from the last research proposal) Birthplace: Brazil
Joao Meidanis holds a bachelor's degree in Mathematics from the University of São Paulo (1980), a master's degree in Mathematics from the same school (1985), a master's degree in Computer Sciences from the University of Wisconsin-Madison (1989) and a PhD degree in Computer Sciences from the University of Wisconsin-Madison (1992). Acted as director of Scylla Informatics from 2002 to 2024. Full professor at the University of Campinas. His research focuses on analysis of algorithms, graph theory, computational biology, bioinformatics, and optimization. (Source: Lattes Curriculum)
| Articles published in Pesquisa FAPESP Magazine about the researcher: |
| Mapping sugarcanes |
| El mapa de la caña de azúcar |
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Since 1990 I have been dedicating myself to bioinformatics. Over the last five years, I have participated in projects with the Boldrini Children's Center, where all research is aimed at diagnosing, monitoring, or treating childhood cancer. This project aims to obtain resources for the continuation of this activity, collaborating with the search for more efficient and simplified methods of…
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 nod…
(Only some records are available in English at this moment)
When comparing genomes, a fundamental notion is the distance between genomes. Many proposals have been put forward in recent decades, including DCJ, SCJ, breakpoint distance, rank distance and natural distance. The median genome between three genomes A, B and C is the M genome that minimizes the sum of the distances d(A,M), d(B,M) and d(C,M). Polynomial-time algorithms for calculating …
Methods based on the notion of minimal absent words have been used to compare genomes in an alignment-free manner and to detect structural variants in genomes, both using Whole Genome Sequencing (WGS) data from long reads. Since this approach offers several advantages over alignment-based methods, it is expected that the implementation of algorithms based on the concept of minimal absent …
(Only some records are available in English at this moment)
One of the main factors responsible for the evolutionary success of mammals is the flexibility of their immune system. Antigens, foreign and harmful agents, when on the surface or inside the body, are detected by the immune system through parts of their structures, the epitopes, producing an immediate response through NK cells and a slower, but more lethal, adaptive response, through B ce…
Advances in DNA sequencing technologies have enabled easy acquisition of genomes in computational environments. Methods for reconstructing phylogenies based on rearrangement events depend on a biologically meaningful notion of distance between genomes that can be computed efficiently. Several distance models and metrics have been developed over the years to achieve these goals, among whic…
(Only some records are available in English at this moment)
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 th…
Molecular evolutionary studies systematically face a validation issue as we have no direct access to ancient molecules beyond a million years. So hypotheses about the shape of ancestral genomes which can be orders of magnitude older are difficult to test and to confirm. Methods to reconstruct ancestral genomes may be tested with simulated data, producing full scenarios they can compare wi…
The genome median problem is a very important problem in bioinformatics. We still do not know whether it is easy under the new Adjacency Algebraic Theory, or NP-Hard. We are interested in a generalization of it, the matrix median problem, that we believe is easier.We plan to study the matrix median problem, and its relation with the genome median problem. (AU)
| 1 / 1 | Ongoing grants |
| 11 / 6 | Completed research grants |
| 5 / 5 | Ongoing scholarships in Brazil |
| 29 / 9 | Completed scholarships in Brazil |
| 3 / 3 | Completed scholarships abroad |
| 49 / 24 | All research grants and scholarships |
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