Search

Your search keyword '"Meidanis, João"' showing total 173 results
Start Over Author "Meidanis, João"
173 results on '"Meidanis, João"'

1. The genome and population genomics of allopolyploid Coffea arabica reveal the diversification history of modern coffee cultivars

Author

Salojärvi, Jarkko, Rambani, Aditi, Yu, Zhe, Guyot, Romain, Strickler, Susan, Lepelley, Maud, Wang, Cui, Rajaraman, Sitaram, Rastas, Pasi, Zheng, Chunfang, Muñoz, Daniella Santos, Meidanis, João, Paschoal, Alexandre Rossi, Bawin, Yves, Krabbenhoft, Trevor J., Wang, Zhen Qin, Fleck, Steven J., Aussel, Rudy, Bellanger, Laurence, Charpagne, Aline, Fournier, Coralie, Kassam, Mohamed, Lefebvre, Gregory, Métairon, Sylviane, Moine, Déborah, Rigoreau, Michel, Stolte, Jens, Hamon, Perla, Couturon, Emmanuel, Tranchant-Dubreuil, Christine, Mukherjee, Minakshi, Lan, Tianying, Engelhardt, Jan, Stadler, Peter, Correia De Lemos, Samara Mireza, Suzuki, Suzana Ivamoto, Sumirat, Ucu, Wai, Ching Man, Dauchot, Nicolas, Orozco-Arias, Simon, Garavito, Andrea, Kiwuka, Catherine, Musoli, Pascal, Nalukenge, Anne, Guichoux, Erwan, Reinout, Havinga, Smit, Martin, Carretero-Paulet, Lorenzo, Filho, Oliveiro Guerreiro, Braghini, Masako Toma, Padilha, Lilian, Sera, Gustavo Hiroshi, Ruttink, Tom, Henry, Robert, Marraccini, Pierre, Van de Peer, Yves, Andrade, Alan, Domingues, Douglas, Giuliano, Giovanni, Mueller, Lukas, Pereira, Luiz Filipe, Plaisance, Stephane, Poncet, Valerie, Rombauts, Stephane, Sankoff, David, Albert, Victor A., Crouzillat, Dominique, de Kochko, Alexandre, and Descombes, Patrick

Published
2024
Full Text
View/download PDF

3. Tumor-Promoted Changes in Pediatric Brain Histology Can Be Distinguished from Normal Parenchyma by Desorption Electrospray Ionization Mass Spectrometry Imaging.

Author

Seidinger, Ana L., Silva, Felipe L. T., Euzébio, Mayara F., Krieger, Anna C., Meidanis, João, Gutierrez, Junier M., Bezerra, Thais M. S., Queiroz, Luciano, Silva, Alex A. Rosini., Hoffmann, Iva L., Daiggi, Camila M. M., Tedeschi, Helder, Eberlin, Marcos N., Eberlin, Livia S., Yunes, José A., Porcari, Andreia M., and Cardinalli, Izilda A.

Subjects
DESORPTION ionization mass spectrometry, ELECTROSPRAY ionization mass spectrometry, DESORPTION electrospray ionization, SURGICAL equipment, CENTRAL nervous system, BRAIN tumors
Abstract

Background: Central nervous system (CNS) tumors are the second most frequent type of neoplasm in childhood and adolescence, after leukemia. Despite the incorporation of molecular classification and improvement of protocols combining chemotherapy, surgery, and radiotherapy, CNS tumors are still the most lethal neoplasm in this age group. Mass spectrometry imaging (MSI) is a powerful tool to map the distribution of molecular species in tissue sections. Among MSI techniques, desorption electrospray ionization (DESI-MSI) has been demonstrated to enable reliable agreement with the pathological evaluation of different adult cancer types, along with an acceptable time scale for intraoperative use. Methods: In the present work, we aimed to investigate the chemical profile obtained by DESI-MSI as an intraoperative surgical management tool by profiling 162 pediatric brain biopsies and reporting the results according to the histopathology and molecular profile of the tumors. Results: The 2D chemical images obtained by DESI-MSI allowed us to distinguish tumor-transformed tissue from non-tumor tissue with an accuracy of 96.8% in the training set and 94.3% in the validation set after statistical modeling of our data using Lasso. In addition, high-grade and low-grade tumors also displayed a distinct chemical profile when analyzed by DESI-MSI. We also provided evidence that the chemical profile of brain tumors obtained by DESI-MSI correlates with methylation-based molecular classes and specific immunophenotypes found in brain biopsies. Conclusions: The results presented herein support the incorporation of DESI-MSI analysis as an intraoperative assistive tool in prospective clinical trials for pediatric brain tumors management in the near future. [ABSTRACT FROM AUTHOR]

Published
2024
Full Text
View/download PDF

4. Center Genome with Respect to the Rank Distance

Author

Biller, Priscila, Zanetti, João Paulo Pereira, Meidanis, João, Goos, Gerhard, Founding Editor, Hartmanis, Juris, Founding Editor, Bertino, Elisa, Editorial Board Member, Gao, Wen, Editorial Board Member, Steffen, Bernhard, Editorial Board Member, Woeginger, Gerhard, Editorial Board Member, Yung, Moti, Editorial Board Member, Setubal, João C., editor, and Silva, Waldeyr Mendes, editor

Published
2020
Full Text
View/download PDF

6. Generalizations of the Genomic Rank Distance to Indels

Author

Zanetti, João Paulo Pereira, Chindelevitch, Leonid, Meidanis, João, Hutchison, David, Editorial Board Member, Kanade, Takeo, Editorial Board Member, Kittler, Josef, Editorial Board Member, Kleinberg, Jon M., Editorial Board Member, Mattern, Friedemann, Editorial Board Member, Mitchell, John C., Editorial Board Member, Naor, Moni, Editorial Board Member, Pandu Rangan, C., Editorial Board Member, Steffen, Bernhard, Editorial Board Member, Terzopoulos, Demetri, Editorial Board Member, Tygar, Doug, Editorial Board Member, Goos, Gerhard, Founding Editor, Hartmanis, Juris, Founding Editor, Holmes, Ian, editor, Martín-Vide, Carlos, editor, and Vega-Rodríguez, Miguel A., editor

Published
2019
Full Text
View/download PDF

7. Counting Sorting Scenarios and Intermediate Genomes for the Rank Distance

Author

Zanetti, João Paulo Pereira, Chindelevitch, Leonid, Meidanis, João, Hutchison, David, Editorial Board Member, Kanade, Takeo, Editorial Board Member, Kittler, Josef, Editorial Board Member, Kleinberg, Jon M., Editorial Board Member, Mattern, Friedemann, Editorial Board Member, Mitchell, John C., Editorial Board Member, Naor, Moni, Editorial Board Member, Pandu Rangan, C., Editorial Board Member, Steffen, Bernhard, Editorial Board Member, Terzopoulos, Demetri, Editorial Board Member, Tygar, Doug, Editorial Board Member, Goos, Gerhard, Founding Editor, Hartmanis, Juris, Founding Editor, Holmes, Ian, editor, Martín-Vide, Carlos, editor, and Vega-Rodríguez, Miguel A., editor

Published
2019
Full Text
View/download PDF

8. On the Rank-Distance Median of 3 Permutations

Author

Chindelevitch, Leonid, Meidanis, João, Hutchison, David, Series editor, Kanade, Takeo, Series editor, Kittler, Josef, Series editor, Kleinberg, Jon M., Series editor, Mattern, Friedemann, Series editor, Mitchell, John C., Series editor, Naor, Moni, Series editor, Pandu Rangan, C., Series editor, Steffen, Bernhard, Series editor, Terzopoulos, Demetri, Series editor, Tygar, Doug, Series editor, Weikum, Gerhard, Series editor, Meidanis, Joao, editor, and Nakhleh, Luay, editor

Published
2017
Full Text
View/download PDF

9. On the Matrix Median Problem

Author

Zanetti, João Paulo Pereira, Biller, Priscila, and Meidanis, João

Subjects
Quantitative Biology - Quantitative Methods, Computer Science - Computational Engineering, Finance, and Science, Computer Science - Discrete Mathematics
Abstract

The Genome Median Problem is an important problem in phylogenetic reconstruction under rearrangement models. It can be stated as follows: given three genomes, find a fourth that minimizes the sum of the pairwise rearrangement distances between it and the three input genomes. Recently, Feijao and Meidanis extended the algebraic theory for genome rearrangement to allow for linear chromosomes, thus yielding a new rearrangement model (the algebraic model), very close to the celebrated DCJ model. In this paper, we study the genome median problem under the algebraic model, whose complexity is currently open, proposing a more general form of the problem, the matrix median problem. It is known that, for any metric distance, at least one of the corners is a 4/3-approximation of the median. Our results allow us to compute up to three additional matrix median candidates, all of them with approximation ratios at least as good as the best corner, when the input matrices come from genomes. From the application point of view, it is usually more interesting to locate medians farther from the corners. We also show a fourth median candidate that gives better results in cases we tried. However, we do not have proven bounds for this fourth candidate yet., Comment: Peer-reviewed and presented as part of the 13th Workshop on Algorithms in Bioinformatics (WABI2013)

Published
2013

10. A Cubic Algorithm for the Generalized Rank Median of Three Genomes

Author

Chindelevitch, Leonid, Meidanis, Joao, Hutchison, David, Series Editor, Kanade, Takeo, Series Editor, Kittler, Josef, Series Editor, Kleinberg, Jon M., Series Editor, Mattern, Friedemann, Series Editor, Mitchell, John C., Series Editor, Naor, Moni, Series Editor, Pandu Rangan, C., Series Editor, Steffen, Bernhard, Series Editor, Terzopoulos, Demetri, Series Editor, Tygar, Doug, Series Editor, Weikum, Gerhard, Series Editor, Blanchette, Mathieu, editor, and Ouangraoua, Aïda, editor

Published
2018
Full Text
View/download PDF

12. The genome and population genomics of allopolyploidCoffea arabicareveal the diversification history of modern coffee cultivars

Author

Salojärvi, Jarkko, primary, Rambani, Aditi, additional, Yu, Zhe, additional, Guyot, Romain, additional, Strickler, Susan, additional, Lepelley, Maud, additional, Wang, Cui, additional, Rajaraman, Sitaram, additional, Rastas, Pasi, additional, Zheng, Chunfang, additional, Muñoz, Daniella Santos, additional, Meidanis, João, additional, Paschoal, Alexandre Rossi, additional, Bawin, Yves, additional, Krabbenhoft, Trevor, additional, Wang, Zhen Qin, additional, Fleck, Steven, additional, Aussel, Rudy, additional, Bellanger, Laurence, additional, Charpagne, Aline, additional, Fournier, Coralie, additional, Kassam, Mohamed, additional, Lefebvre, Gregory, additional, Métairon, Sylviane, additional, Moine, Déborah, additional, Rigoreau, Michel, additional, Stolte, Jens, additional, Hamon, Perla, additional, Couturon, Emmanuel, additional, Tranchant-Dubreuil, Christine, additional, Mukherjee, Minakshi, additional, Lan, Tianying, additional, Engelhardt, Jan, additional, Stadler, Peter, additional, De Lemos, Samara Mireza Correia, additional, Suzuki, Suzana Ivamoto, additional, Sumirat, Ucu, additional, Man, Wai Ching, additional, Dauchot, Nicolas, additional, Orozco-Arias, Simon, additional, Garavito, Andrea, additional, Kiwuka, Catherine, additional, Musoli, Pascal, additional, Nalukenge, Anne, additional, Guichoux, Erwan, additional, Reinout, Havinga, additional, Smit, Martin, additional, Carretero-Paulet, Lorenzo, additional, Filho, Oliveiro Guerreiro, additional, Braghini, Masako Toma, additional, Padilha, Lilian, additional, Sera, Gustavo Hiroshi, additional, Ruttink, Tom, additional, Henry, Robert, additional, Marraccini, Pierre, additional, Van de Peer, Yves, additional, Andrade, Alan, additional, Domingues, Douglas, additional, Giuliano, Giovanni, additional, Mueller, Lukas, additional, Pereira, Luiz Filipe, additional, Plaisance, Stephane, additional, Poncet, Valerie, additional, Rombauts, Stephane, additional, Sankoff, David, additional, Albert, Victor A., additional, Crouzillat, Dominique, additional, de Kochko, Alexandre, additional, and Descombes, Patrick, additional

Published
2023
Full Text
View/download PDF

14. A Visualization-Based Approach for Project Portfolio Selection

Author

da Silva, Celmar Guimarães, Meidanis, João, Moura, Arnaldo Vieira, Souza, Maria Angélica, Viadanna, Paulo, Jr., Costa Lima, Gabriel A., de Barros, Rafael S. V., Kacprzyk, Janusz, Series editor, Rocha, Álvaro, editor, Correia, Ana Maria, editor, Adeli, Hojjat, editor, Reis, Luis Paulo, editor, and Mendonça Teixeira, Marcelo, editor

Published
2016
Full Text
View/download PDF

15. The genome and population genomics of allopolyploid Coffea arabicareveal the diversification history of modern coffee cultivars

Author

Salojärvi, Jarkko, Rambani, Aditi, Yu, Zhe, Guyot, Romain, Strickler, Susan, Lepelley, Maud, Wang, Cui, Rajaraman, Sitaram, Rastas, Pasi, Zheng, Chunfang, Muñoz, Daniella Santos, Meidanis, João, Paschoal, Alexandre Rossi, Bawin, Yves, Krabbenhoft, Trevor J., Wang, Zhen Qin, Fleck, Steven J., Aussel, Rudy, Bellanger, Laurence, Charpagne, Aline, Fournier, Coralie, Kassam, Mohamed, Lefebvre, Gregory, Métairon, Sylviane, Moine, Déborah, Rigoreau, Michel, Stolte, Jens, Hamon, Perla, Couturon, Emmanuel, Tranchant-Dubreuil, Christine, Mukherjee, Minakshi, Lan, Tianying, Engelhardt, Jan, Stadler, Peter, Correia De Lemos, Samara Mireza, Suzuki, Suzana Ivamoto, Sumirat, Ucu, Wai, Ching Man, Dauchot, Nicolas, Orozco-Arias, Simon, Garavito, Andrea, Kiwuka, Catherine, Musoli, Pascal, Nalukenge, Anne, Guichoux, Erwan, Reinout, Havinga, Smit, Martin, Carretero-Paulet, Lorenzo, Filho, Oliveiro Guerreiro, Braghini, Masako Toma, Padilha, Lilian, Sera, Gustavo Hiroshi, Ruttink, Tom, Henry, Robert, Marraccini, Pierre, Van de Peer, Yves, Andrade, Alan, Domingues, Douglas, Giuliano, Giovanni, Mueller, Lukas, Pereira, Luiz Filipe, Plaisance, Stephane, Poncet, Valerie, Rombauts, Stephane, Sankoff, David, Albert, Victor A., Crouzillat, Dominique, de Kochko, Alexandre, and Descombes, Patrick

Abstract

Coffea arabica, an allotetraploid hybrid of Coffea eugenioidesand Coffea canephora, is the source of approximately 60% of coffee products worldwide, and its cultivated accessions have undergone several population bottlenecks. We present chromosome-level assemblies of a di-haploid C. arabicaaccession and modern representatives of its diploid progenitors, C. eugenioidesand C. canephora. The three species exhibit largely conserved genome structures between diploid parents and descendant subgenomes, with no obvious global subgenome dominance. We find evidence for a founding polyploidy event 350,000–610,000 years ago, followed by several pre-domestication bottlenecks, resulting in narrow genetic variation. A split between wild accessions and cultivar progenitors occurred ~30.5 thousand years ago, followed by a period of migration between the two populations. Analysis of modern varieties, including lines historically introgressed with C. canephora, highlights their breeding histories and loci that may contribute to pathogen resistance, laying the groundwork for future genomics-based breeding of C. arabica.

Published
2024
Full Text
View/download PDF

21. Extending the Algebraic Formalism for Genome Rearrangements to Include Linear Chromosomes

Author

Feijao, Pedro, Meidanis, Joao, Hutchison, David, editor, Kanade, Takeo, editor, Kittler, Josef, editor, Kleinberg, Jon M., editor, Mattern, Friedemann, editor, Mitchell, John C., editor, Naor, Moni, editor, Nierstrasz, Oscar, editor, Pandu Rangan, C., editor, Steffen, Bernhard, editor, Sudan, Madhu, editor, Terzopoulos, Demetri, editor, Tygar, Doug, editor, Vardi, Moshe Y., editor, Weikum, Gerhard, editor, Istrail, Sorin, editor, Pevzner, Pavel, editor, Waterman, Michael S., editor, de Souto, Marcilio C., editor, and Kann, Maricel G., editor

Published
2012
Full Text
View/download PDF

22. SCJ: A Variant of Breakpoint Distance for Which Sorting, Genome Median and Genome Halving Problems Are Easy

Author

Feijão, Pedro, Meidanis, João, Hutchison, David, Series editor, Kanade, Takeo, Series editor, Kittler, Josef, Series editor, Kleinberg, Jon M., Series editor, Mattern, Friedemann, Series editor, Mitchell, John C., Series editor, Naor, Moni, Series editor, Nierstrasz, Oscar, Series editor, Pandu Rangan, C., Series editor, Steffen, Bernhard, Series editor, Sudan, Madhu, Series editor, Terzopoulos, Demetri, Series editor, Tygar, Doug, Series editor, Vardi, Moshe Y., Series editor, Weikum, Gerhard, Series editor, Istrail, Sorin, editor, Pevzner, Pavel, editor, Waterman, Michael S., editor, Salzberg, Steven L., editor, and Warnow, Tandy, editor

Published
2009
Full Text
View/download PDF

25. Current Challenges in Bioinformatics

Author

Meidanis, João, Goos, Gerhard, editor, Hartmanis, Juris, editor, van Leeuwen, Jan, editor, Nascimento, Mario A., editor, de Moura, Edleno S., editor, and Oliveira, Arlindo L., editor

Published
2003
Full Text
View/download PDF

27. Sorting by Prefix Transpositions

Author

Dias, Zanoni, Meidanis, João, Goos, Gerhard, editor, Hartmanis, Juris, editor, van Leeuwen, Jan, editor, Laender, Alberto H. F., editor, and Oliveira, Arlindo L., editor

Published
2002
Full Text
View/download PDF

30. On the clique operator

Author

Gutierrez, Marisa, Meidanis, JoÃo, Goos, Gerhard, editor, Hartmanis, Juris, editor, van Leeuwen, Jan, editor, Lucchesi, Cláudio L., editor, and Moura, Arnaldo V., editor

Published
1998
Full Text
View/download PDF

32. On edge-colouring indifference graphs

Author

de Figueiredo, Celina M. H., Meidanis, João, de Mello, Célia Picinin, Goos, Gerhard, editor, Hartmanis, Juris, editor, van Leeuwen, Jan, editor, Baeza-Yates, Ricardo, editor, Goles, Eric, editor, and Poblete, Patricio V., editor

Published
1995
Full Text
View/download PDF

34. Generalizations of the genomic rank distance to indels.

Author

Zanetti, João Paulo Pereira, Oliveira, Lucas Peres, Chindelevitch, Leonid, and Meidanis, João

Subjects
PROKARYOTIC genomes, GENERALIZATION, GENE regulatory networks, CHROMOSOMES, GENOMES, ESCHERICHIA coli, GENETIC distance, GENE clusters
Abstract

Motivation The rank distance model represents genome rearrangements in multi-chromosomal genomes as matrix operations, which allows the reconstruction of parsimonious histories of evolution by rearrangements. We seek to generalize this model by allowing for genomes with different gene content, to accommodate a broader range of biological contexts. We approach this generalization by using a matrix representation of genomes. This leads to simple distance formulas and sorting algorithms for genomes with different gene contents, but without duplications. Results We generalize the rank distance to genomes with different gene content in two different ways. The first approach adds insertions, deletions and the substitution of a single extremity to the basic operations. We show how to efficiently compute this distance. To avoid genomes with incomplete markers, our alternative distance, the rank-indel distance, only uses insertions and deletions of entire chromosomes. We construct phylogenetic trees with our distances and the DCJ-Indel distance for simulated data and real prokaryotic genomes, and compare them against reference trees. For simulated data, our distances outperform the DCJ-Indel distance using the Quartet metric as baseline. This suggests that rank distances are more robust for comparing distantly related species. For real prokaryotic genomes, all rearrangement-based distances yield phylogenetic trees that are topologically distant from the reference (65% similarity with Quartet metric), but are able to cluster related species within their respective clades and distinguish the Shigella strains as the farthest relative of the Escherichia coli strains, a feature not seen in the reference tree. Availability and implementation Code and instructions are available at https://github.com/meidanis-lab/rank-indel. Supplementary information Supplementary data are available at Bioinformatics online. [ABSTRACT FROM AUTHOR]

Published
2023
Full Text
View/download PDF

37. Tree loop graphs

Author

Alcón, Liliana, Cerioli, Márcia R., de Figueiredo, Celina M.H., Gutierrez, Marisa, and Meidanis, João

Published
2007
Full Text
View/download PDF

38. Genome Sequence and Assembly of Bos indicus

Author

Canavez, Flavio C., Luche, Douglas D., Stothard, Paul, Leite, Katia R. M., Sousa-Canavez, Juliana M., Plastow, Graham, Meidanis, João, Souza, Maria Angélica, Feijao, Pedro, Moore, Steve S., and Camara-Lopes, Luiz H.

Published
2012
Full Text
View/download PDF

39. Test trial of spike‐in immunoglobulin heavy‐chain ( IGH ) controls for next generation sequencing quantification of minimal residual disease in acute lymphoblastic leukaemia

Author

Giusti, Guilherme Navarro Nilo, primary, Jotta, Patrícia Yoshioka, additional, Lopes, Caroline de Oliveira, additional, Ganazza, Monica Aparecida, additional, Azevedo, Amilcar Cardoso, additional, Brandalise, Sílvia Regina, additional, Meidanis, João, additional, and Yunes, José Andrés, additional

Published
2020
Full Text
View/download PDF

50. An improved visualization-based approach for project portfolio selection

Author

da Silva, Celmar G., primary, Meidanis, João, additional, Moura, Arnaldo V., additional, Souza, Maria Angélica, additional, Viadanna, Paulo, additional, de Oliveira, Marcello R., additional, de Oliveira, Maurício R., additional, Jardim, Lidianne H., additional, Costa Lima, Gabriel A., additional, and de Barros, Rafael S.V., additional

Published
2017
Full Text
View/download PDF

Catalog

Books, media, physical & digital resources
See catalog results