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Universidade Estadual de Campinas (UNICAMP). Instituto de Computação (IC) (Institutional affiliation for 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). 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 |
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…
In this report we present the activities performed by our group in the Sugarcane EST Project (SUCEST), during the period from July 2000 to June 2001. A summary of the main facts and activities follows: 1) change in team composition; 2) migration of data and services to new machine; 3) project ended its data submission phase; 4) comparison to other genomes; 5) categorization of our ESTs; 6…
(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…
The main objective of the project is to significantly increase, in an appropriate direction, the candidate's knowledge in machine learning, especially with regard to Deep Learning techniques. In order to do so, the candidate must carry out theoretical studies and a substantial practical activity, which consists in understanding the problem of identification of humpback whales by their tai…
Genome comparison can be made in several ways. In many applications, reducing the differences between two genomes to a single real number expressing their distance is important. In recent years, a measure called DCJ distance, which combines biological appeal with computational efficiency, has been heavily used. Another measure called algebraic distance, related to the rank distance in mat…
(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 research grants |
| 10 / 5 | Completed research grants |
| 2 / 2 | Ongoing scholarships in Brazil |
| 27 / 7 | Completed scholarships in Brazil |
| 3 / 3 | Completed scholarships abroad |
| 43 / 18 | All research grants and scholarships |
| Associated processes | |
(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)
| Publications | 9 |
| Citations | 61 |
| Cit./Article | 6.8 |
| Data from Web of Science | |
PEREIRA ZANETTI, JOAO PAULO; BILLER, PRISCILA; MEIDANIS, JOAO. Median Approximations for Genomes Modeled as Matrices. Bulletin of Mathematical Biology, v. 78, n. 4, p. 786-814, APR 2016. Web of Science Citations: 3. (12/13865-7, 12/14104-0)
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. Web of Science Citations: 4. (16/01511-7)
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. Web of Science Citations: 0. (16/01511-7)
RAJARAMAN, ASHOK; PEREIRA ZANETTI, JOAO PAULO; MANUCH, JAN; CHAUVE, CEDRIC. Algorithms and Complexity Results for Genome Mapping Problems. IEEE-ACM TRANSACTIONS ON COMPUTATIONAL BIOLOGY AND BIOINFORMATICS, v. 14, n. 2, p. 418-430, MAR-APR 2017. Web of Science Citations: 2. (13/07868-6)
BILLER, PRISCILA; GUEGUEN, LAURENT; KNIBBE, CAROLE; TANNIER, ERIC. Breaking Good: Accounting for Fragility of Genomic Regions in Rearrangement Distance Estimation. GENOME BIOLOGY AND EVOLUTION, v. 8, n. 5, p. 1427-1439, MAY 2016. Web of Science Citations: 9. (13/25084-2)
BILLER, PRISCILA; GUEGUEN, LAURENT; TANNIER, ERIC. Moments of genome evolution by Double Cut-and-Join. BMC Bioinformatics, v. 16, n. 14, OCT 2 2015. Web of Science Citations: 8. (13/25084-2)
FEIJAO, PEDRO; MEIDANIS, JOAO. SCJ: A Breakpoint-Like Distance that Simplifies Several Rearrangement Problems. IEEE-ACM TRANSACTIONS ON COMPUTATIONAL BIOLOGY AND BIOINFORMATICS, v. 8, n. 5, p. 1318-1329, SEP-OCT 2011. Web of Science Citations: 35. (09/09307-6)
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. Web of Science Citations: 0. (18/00031-7, 17/03942-8)
(References retrieved automatically from State of São Paulo Research Institutions)
TELLES, Guilherme Pimentel. Propriedade dos uns consecutivos e arvores PQR. Dissertação (Mestrado) - Instituto de Computação. Universidade Estadual de Campinas (UNICAMP). (96/08571-0)
BRAGA, Marilia Dias Vieira. Grafos de sequencias de DNA. Dissertação (Mestrado) - Instituto de Computação. Universidade Estadual de Campinas (UNICAMP). (97/11629-2)
FORTUNA, Vinicius Jose. Distancias de transposição entre genomas. Dissertação (Mestrado) - Instituto de Computação. Universidade Estadual de Campinas (UNICAMP). (03/04578-5)
TELLES, Guilherme Pimentel. Um algoritmo quase-linear para arvores PQR e um esquema para clustering de sequencias expressas de cana-de-açucar. Tese (Doutorado) - Instituto de Matematica, Estatistica e Computação Cientifica. Universidade Estadual de Campinas (UNICAMP). (97/12126-4)
COGO, Patricia Pilisson. Comparação de genomas completos de especies da familia Vibrionacea empregando rearranjo de genomas. Dissertação (Mestrado) - Instituto de Computação. Universidade Estadual de Campinas (UNICAMP). (05/53279-6)
BILLER, Priscila Do Nascimento. Statistical analysis of evolution by genome rearrangements = Análise estatística da evolução por rearranjo de genomas. Tese (Doutorado) - Universidade Estadual de Campinas, Instituto de Computação. (12/14104-0)
ZANETTI, João Paulo Pereira. Methods for phylogenetic reconstruction = Métodos de reconstrução filogenética. Tese (Doutorado) - Universidade Estadual de Campinas, Instituto de Computação. (12/13865-7)
DIAS, Zanoni. Rearranjo de genomas : uma coletanea de artigos. Tese (Doutorado) - Instituto de Computação. Universidade Estadual de Campinas (UNICAMP). (98/04432-0)
PINTO, Marcelo Cezar. Um algoritmo para comparação sintatica de genomas baseado na complexidade condicional de Kolmogorov. Dissertação (Mestrado) - Instituto de Computação. Universidade Estadual de Campinas (UNICAMP). (00/04776-3)
MIRA, Cleber Valgas Gomes. Analise algebrica de problemas de rearranjo em genomas : algoritmos e complexidade. Tese (Doutorado) - Instituto de Computação. Universidade Estadual de Campinas (UNICAMP). (03/00731-3)
BILLER, Priscila Do Nascimento. Statistical analysis of evolution by genome rearrangements = Análise estatística da evolução por rearranjo de genomas. Tese (Doutorado) - Universidade Estadual de Campinas, Instituto de Computação. (12/14104-0)
ZANETTI, João Paulo Pereira. Methods for phylogenetic reconstruction = Métodos de reconstrução filogenética. Tese (Doutorado) - Universidade Estadual de Campinas, Instituto de Computação. (12/13865-7)