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Your search keyword '"Paschoal, Alexandre R."' showing total 35 results
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35 results on '"Paschoal, Alexandre R."'

1. Make No Mistake! Why Do Tools Make Incorrect Long Non-coding RNA Classification?

Author

Chiquitto, Alisson G., Silva, Lucas Otávio L., Oliveira, Liliane Santana, Domingues, Douglas S., Paschoal, Alexandre R., Goos, Gerhard, Founding Editor, Hartmanis, Juris, Founding Editor, Bertino, Elisa, Editorial Board Member, Gao, Wen, Editorial Board Member, Steffen, Bernhard, Editorial Board Member, Yung, Moti, Editorial Board Member, Reis, Marcelo S., editor, and de Melo-Minardi, Raquel C., editor

Published
2023
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4. 44 Current Challenges in miRNomics

Author

Akgül, Bünyamin, primary, Stadler, Peter F., additional, Hawkins, Liam J., additional, Hadj-Moussa, Hanane, additional, Storey, Kenneth B., additional, Ergin, Kemal, additional, Çetinkaya, Rahmi, additional, Paschoal, Alexandre R., additional, Nachtigall, Pedro G., additional, Tutar, Yusuf, additional, Yousef, Malik, additional, and Allmer, Jens, additional

Published
2021
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5. Classification of Transposable Elements by Convolutional Neural Networks

Author

da Cruz, Murilo H. P., Saito, Priscila T. M., Paschoal, Alexandre R., Bugatti, Pedro H., 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, Rutkowski, Leszek, editor, Scherer, Rafał, editor, Korytkowski, Marcin, editor, Pedrycz, Witold, editor, Tadeusiewicz, Ryszard, editor, and Zurada, Jacek M., editor

Published
2019
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8. Genomic decoding of Theobroma grandiflorum (cupuassu) at chromosomal scale: evolutionary insights for horticultural innovation

Author

Alves, Rafael Moysés, primary, de Abreu, Vinicius A C, additional, Oliveira, Rafaely Pantoja, additional, Almeida, João Victor dos Anjos, additional, de Oliveira, Mauro de Medeiros, additional, Silva, Saura R, additional, Paschoal, Alexandre R, additional, de Almeida, Sintia S, additional, de Souza, Pedro A F, additional, Ferro, Jesus A, additional, Miranda, Vitor F O, additional, Figueira, Antonio, additional, Domingues, Douglas S, additional, and Varani, Alessandro M, additional

Published
2024
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9. Genomic decoding ofTheobroma grandiflorum(cupuassu) at chromosomal scale: Evolutionary insights for horticultural innovation

Author

Alves, Rafael Moyses, primary, de Abreu, Vinicius A.C, additional, Oliveira, Rafaely P., additional, dos Anjos, Joao Victor, additional, Oliveira, Mauro de Medeiros, additional, Silva, Saura R., additional, Paschoal, Alexandre R., additional, Almeida, Sintia S., additional, de Souza, Pedro A.F., additional, Ferro, Jesus Aparecido, additional, Miranda, Vitor F.O., additional, Figueira, Antonio, additional, Domingues, Douglas S., additional, and Varani, Alessandro M., additional

Published
2023
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13. An integrated analysis of mRNA and sRNA transcriptional profiles in Coffea arabica L. roots: insights on nitrogen starvation responses

Author

dos Santos, Tiago Benedito, Soares, João D. M., Lima, Joni E., Silva, Juliana C., Ivamoto, Suzana T., Baba, Viviane Y., Souza, Silvia G. H., Lorenzetti, Alan P. R., Paschoal, Alexandre R., Meda, Anderson R., Nishiyama Júnior, Milton Y., de Oliveira, Úrsula C., Mokochinski, João B., Guyot, Romain, Junqueira-de-Azevedo, Inácio L. M., Figueira, Antônio V. O., Mazzafera, Paulo, Júnior, Osvaldo R., Vieira, Luiz G. E., Pereira, Luiz F. P., and Domingues, Douglas S.

Published
2019
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14. The nuclear and mitochondrial genomes of Frieseomelitta varia – a highly eusocial stingless bee (Meliponini) with a permanently sterile worker caste

Author

de Paula Freitas, Flávia C., Lourenço, Anete P., Nunes, Francis M. F., Paschoal, Alexandre R., Abreu, Fabiano C. P., Barbin, Fábio O., Bataglia, Luana, Cardoso-Júnior, Carlos A. M., Cervoni, Mário S., Silva, Saura R., Dalarmi, Fernanda, Del Lama, Marco A., Depintor, Thiago S., Ferreira, Kátia M., Gória, Paula S., Jaskot, Michael C., Lago, Denyse C., Luna-Lucena, Danielle, Moda, Livia M., Nascimento, Leonardo, Pedrino, Matheus, Oliveira, Franciene Rabiço, Sanches, Fernanda C., Santos, Douglas E., Santos, Carolina G., Vieira, Joseana, Barchuk, Angel R., Hartfelder, Klaus, Simões, Zilá L. P., Bitondi, Márcia M. G., and Pinheiro, Daniel G.

Published
2020
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19. Raman evidence for pressure-induced formation of diamondene

Author

Martins, Luiz Gustavo Pimenta, Matos, Matheus J. S., Paschoal, Alexandre R., Freire, Paulo T. C., Andrade, Nadia F., Aguiar, Acrísio L., Kong, Jing, Neves, Bernardo R. A., de Oliveira, Alan B., Mazzoni, Mário S.C., Filho, Antonio G. Souza, and Cançado, Luiz Gustavo

Published
2017
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20. Na-TiNT Nanocrystals: Synthesis, Characterization, and Antibacterial Properties

Author

Agressott, Enzo V. H., primary, Oliveira, Mauro M., additional, Freitas, Thiago S., additional, Pereira, Raimundo L. S., additional, Silva, Ana R. P., additional, Cruz, Rafael P., additional, Santos, Antonia T. L., additional, Teixeira, Alexandre M. R., additional, Oliveira, Tainara G., additional, da Silva, João H., additional, Paschoal, Alexandre R., additional, Viana, Bartolomeu C., additional, Freire, Paulo de Tarso C., additional, Siyadatpanah, Abolghasem, additional, Wilairatana, Polrat, additional, and Coutinho, Henrique D. M., additional

Published
2022
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21. Thermodynamics of Linear Carbon Chains

Author

Costa, Nathalia L., primary, Sharma, Keshav, additional, Kim, Yoong Ahm, additional, Choi, Go Bong, additional, Endo, Morinobu, additional, Barbosa Neto, Newton M., additional, Paschoal, Alexandre R., additional, and Araujo, Paulo T., additional

Published
2021
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23. Additional file 1 of The nuclear and mitochondrial genomes of Frieseomelitta varia – a highly eusocial stingless bee (Meliponini) with a permanently sterile worker caste

Author

Freitas, Flávia C. De Paula, Lourenço, Anete P., Nunes, Francis M. F., Paschoal, Alexandre R., Abreu, Fabiano C. P., Barbin, Fábio O., Bataglia, Luana, Cardoso-Júnior, Carlos A. M., Cervoni, Mário S., Silva, Saura R., Dalarmi, Fernanda, Lama, Marco A. Del, Depintor, Thiago S., Ferreira, Kátia M., Gória, Paula S., Jaskot, Michael C., Lago, Denyse C., Luna-Lucena, Danielle, Moda, Livia M., Nascimento, Leonardo, Pedrino, Matheus, Oliveira, Franciene Rabiço, Sanches, Fernanda C., Santos, Douglas E., Santos, Carolina G., Vieira, Joseana, Barchuk, Angel R., Hartfelder, Klaus, Simões, Zilá L. P., Bitondi, Márcia M. G., and Pinheiro, Daniel G.

Abstract

Additional file 1 : Figure S1: Multiple alignment (A) and Maximum Parsimony phylogenetic tree (B) of miR-34.

Published
2020
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24. Additional file 8 of The nuclear and mitochondrial genomes of Frieseomelitta varia – a highly eusocial stingless bee (Meliponini) with a permanently sterile worker caste

Author

Freitas, Flávia C. De Paula, Lourenço, Anete P., Nunes, Francis M. F., Paschoal, Alexandre R., Abreu, Fabiano C. P., Barbin, Fábio O., Bataglia, Luana, Cardoso-Júnior, Carlos A. M., Cervoni, Mário S., Silva, Saura R., Dalarmi, Fernanda, Lama, Marco A. Del, Depintor, Thiago S., Ferreira, Kátia M., Gória, Paula S., Jaskot, Michael C., Lago, Denyse C., Luna-Lucena, Danielle, Moda, Livia M., Nascimento, Leonardo, Pedrino, Matheus, Oliveira, Franciene Rabiço, Sanches, Fernanda C., Santos, Douglas E., Santos, Carolina G., Vieira, Joseana, Barchuk, Angel R., Hartfelder, Klaus, Simões, Zilá L. P., Bitondi, Márcia M. G., and Pinheiro, Daniel G.

Abstract

Additional file 8 : Figure S8 Unrooted phylogenetic trees for core set of genes of the JAK/STAT and RNAi pathways. Amino acid sequences were aligned using MAFFT and the tree was generated in an ML approach (1000 replicates). In red are the orthologs of Frieseomelitta varia. Gene names are abbreviated. Species names are in three letters acronyms, Acer: Apis cerana, Ador: Apis dorsata, Aflo: Apis florea, Amel: Apis mellifera, Bter: Bombus terrestris, Bimp: Bombus impatiens, Dnov: Dufourea novaeangliae, Edil: Euglossa dilemma, Emex: Eufriesea mexicana, Fvar: Frieseomelitta varia, Hlab: Habropoda laboriosa, Lalb: Lasioglossum albipes, Mrot: Megachile rotundata, Mqua: Melipona quadrifasciata.

Published
2020
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25. Additional file 9 of The nuclear and mitochondrial genomes of Frieseomelitta varia – a highly eusocial stingless bee (Meliponini) with a permanently sterile worker caste

Author

Freitas, Flávia C. De Paula, Lourenço, Anete P., Nunes, Francis M. F., Paschoal, Alexandre R., Abreu, Fabiano C. P., Barbin, Fábio O., Bataglia, Luana, Cardoso-Júnior, Carlos A. M., Cervoni, Mário S., Silva, Saura R., Dalarmi, Fernanda, Lama, Marco A. Del, Depintor, Thiago S., Ferreira, Kátia M., Gória, Paula S., Jaskot, Michael C., Lago, Denyse C., Luna-Lucena, Danielle, Moda, Livia M., Nascimento, Leonardo, Pedrino, Matheus, Oliveira, Franciene Rabiço, Sanches, Fernanda C., Santos, Douglas E., Santos, Carolina G., Vieira, Joseana, Barchuk, Angel R., Hartfelder, Klaus, Simões, Zilá L. P., Bitondi, Márcia M. G., and Pinheiro, Daniel G.

Abstract

Additional file 9 : Table S1 Genome databases used in blastp searches for protein-coding genes included in the gene set for manual curation of their MAKER 2 gene model predictions.

Published
2020
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26. Additional file 7 of The nuclear and mitochondrial genomes of Frieseomelitta varia – a highly eusocial stingless bee (Meliponini) with a permanently sterile worker caste

Author

Freitas, Flávia C. De Paula, Lourenço, Anete P., Nunes, Francis M. F., Paschoal, Alexandre R., Abreu, Fabiano C. P., Barbin, Fábio O., Bataglia, Luana, Cardoso-Júnior, Carlos A. M., Cervoni, Mário S., Silva, Saura R., Dalarmi, Fernanda, Lama, Marco A. Del, Depintor, Thiago S., Ferreira, Kátia M., Gória, Paula S., Jaskot, Michael C., Lago, Denyse C., Luna-Lucena, Danielle, Moda, Livia M., Nascimento, Leonardo, Pedrino, Matheus, Oliveira, Franciene Rabiço, Sanches, Fernanda C., Santos, Douglas E., Santos, Carolina G., Vieira, Joseana, Barchuk, Angel R., Hartfelder, Klaus, Simões, Zilá L. P., Bitondi, Márcia M. G., and Pinheiro, Daniel G.

Abstract

Additional file 7 : Figure S7 Unrooted phylogenetic trees for core set of genes of the Toll (A) and IMD/JNK pathways. Amino acid sequences were aligned using MAFFT and the tree was generated in an ML approach (1000 replicates). In red are the orthologs of Frieseomelitta varia. Gene names are abbreviated. Species names are in three letters acronyms, Acer: Apis cerana, Ador: Apis dorsata, Aflo: Apis florea, Amel: Apis mellifera, Bter: Bombus terrestris, Bimp: Bombus impatiens, Dnov: Dufourea novaeangliae, Edil: Euglossa dilemma, Emex: Eufriesea mexicana, Fvar: Frieseomelitta varia, Hlab: Habropoda laboriosa, Lalb: Lasioglossum albipes, Mrot: Megachile rotundata, Mqua: Melipona quadrifasciata.

Published
2020
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29. Raman evidence for pressure-induced formation of diamondene

Author

Massachusetts Institute of Technology. Department of Electrical Engineering and Computer Science, Kong, Jing, Martins, Luiz Gustavo Pimenta, Matos, Matheus J. S., Paschoal, Alexandre R., Freire, Paulo T. C., Andrade, Nadia F., Aguiar, Acrísio L., Neves, Bernardo R. A., de Oliveira, Alan B., Mazzoni, Mário S.C., Filho, Antonio G. Souza, Cançado, Luiz Gustavo, Massachusetts Institute of Technology. Department of Electrical Engineering and Computer Science, Kong, Jing, Martins, Luiz Gustavo Pimenta, Matos, Matheus J. S., Paschoal, Alexandre R., Freire, Paulo T. C., Andrade, Nadia F., Aguiar, Acrísio L., Neves, Bernardo R. A., de Oliveira, Alan B., Mazzoni, Mário S.C., Filho, Antonio G. Souza, and Cançado, Luiz Gustavo

Abstract

Despite the advanced stage of diamond thin-film technology, with applications ranging from superconductivity to biosensing, the realization of a stable and atomically thick two-dimensional diamond material, named here as diamondene, is still forthcoming. Adding to the outstanding properties of its bulk and thin-film counterparts, diamondene is predicted to be a ferromagnetic semiconductor with spin polarized bands. Here, we provide spectroscopic evidence for the formation of diamondene by performing Raman spectroscopy of double-layer graphene under high pressure. The results are explained in terms of a breakdown in the Kohn anomaly associated with the finite size of the remaining graphene sites surrounded by the diamondene matrix. Ab initio calculations and molecular dynamics simulations are employed to clarify the mechanism of diamondene formation, which requires two or more layers of graphene subjected to high pressures in the presence of specific chemical groups such as hydroxyl groups or hydrogens.

Published
2018

30. An integrated analysis of mRNA and sRNA transcriptional profiles in Coffea arabica L. roots: insights on nitrogen starvation responses

Author

dos Santos, Tiago Benedito, primary, Soares, João D. M., additional, Lima, Joni E., additional, Silva, Juliana C., additional, Ivamoto, Suzana T., additional, Baba, Viviane Y., additional, Souza, Silvia G. H., additional, Lorenzetti, Alan P. R., additional, Paschoal, Alexandre R., additional, Meda, Anderson R., additional, Nishiyama Júnior, Milton Y., additional, de Oliveira, Úrsula C., additional, Mokochinski, João B., additional, Guyot, Romain, additional, Junqueira-de-Azevedo, Inácio L. M., additional, Figueira, Antônio V. O., additional, Mazzafera, Paulo, additional, Júnior, Osvaldo R., additional, Vieira, Luiz G. E., additional, Pereira, Luiz F. P., additional, and Domingues, Douglas S., additional

Published
2018
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31. Mining Novel Candidate Imprinted Genes Using Genome-Wide Methylation Screening and Literature Review

Author

Bonaldi, Adriano, primary, Kashiwabara, André, additional, Araújo, Érica S.de, additional, Pereira, Lygia V., additional, Paschoal, Alexandre R., additional, Andozia, Mayra B., additional, Villela, Darine, additional, Rivas, Maria P., additional, Suemoto, Claudia K., additional, Pasqualucci, Carlos A., additional, Grinberg, Lea T., additional, Brentani, Helena, additional, Maria-Engler, Silvya S., additional, Carraro, Dirce M., additional, Vianna-Morgante, Angela M., additional, Rosenberg, Carla, additional, Vasques, Luciana R., additional, and Krepischi, Ana, additional

Published
2017
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34. Raman evidence for pressure-induced formation of diamondene.

Author

Pimenta Martins, Luiz Gustavo, Matos, Matheus J. S., Paschoal, Alexandre R., Freire, Paulo T. C., Andrade, Nadia F., Aguiar, Acrísio L., Jing Kong, Neves, Bernardo R. A., de Oliveira, Alan B., Mazzoni, Mário S. C., Filho, Antonio G. Souza, and Gustavo Cançado, Luiz

Abstract

Despite the advanced stage of diamond thin-film technology, with applications ranging from superconductivity to biosensing, the realization of a stable and atomically thick two-dimensional diamond material, named here as diamondene, is still forthcoming. Adding to the outstanding properties of its bulk and thin-film counterparts, diamondene is predicted to be a ferromagnetic semiconductor with spin polarized bands. Here, we provide spectroscopic evidence for the formation of diamondene by performing Raman spectroscopy of double-layer graphene under high pressure. The results are explained in terms of a breakdown in the Kohn anomaly associated with the finite size of the remaining graphene sites surrounded by the diamondene matrix. Ab initio calculations and molecular dynamics simulations are employed to clarify the mechanism of diamondene formation, which requires two or more layers of graphene subjected to high pressures in the presence of specific chemical groups such as hydroxyl groups or hydrogens. [ABSTRACT FROM AUTHOR]

Published
2017
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35. 44 Current Challenges in miRNomics.

Author

Akgül B, Stadler PF, Hawkins LJ, Hadj-Moussa H, Storey KB, Ergin K, Çetinkaya R, Paschoal AR, Nachtigall PG, Tutar Y, Yousef M, and Allmer J

Subjects
Gene Expression Regulation, Genomics, RNA, Messenger, MicroRNAs genetics
Abstract

Mature microRNAs (miRNAs) are short RNA sequences about 18-24 nucleotide long, which provide the recognition key within RISC for the posttranscriptional regulation of target RNAs. Considering the canonical pathway, mature miRNAs are produced via a multistep process. Their transcription (pri-miRNAs) and first processing step via the microprocessor complex (pre-miRNAs) occur in the nucleus. Then they are exported into the cytosol, processed again by Dicer (dsRNA) and finally a single strand (mature miRNA) is incorporated into RISC (miRISC). The sequence of the incorporated miRNA provides the function of RNA target recognition via hybridization. Following binding of the target, the mRNA is either degraded or translation is inhibited, which ultimately leads to less protein production. Conversely, it has been shown that binding within the 5' UTR of the mRNA can lead to an increase in protein product. Regulation of homeostasis is very important for a cell; therefore, all steps in the miRNA-based regulation pathway, from transcription to the incorporation of the mature miRNA into RISC, are under tight control. While much research effort has been exerted in this area, the knowledgebase is not sufficient for accurately modelling miRNA regulation computationally. The computational prediction of miRNAs is, however, necessary because it is not feasible to investigate all possible pairs of a miRNA and its target, let alone miRNAs and their targets. We here point out open challenges important for computational modelling or for our general understanding of miRNA-based regulation and show how their investigation is beneficial. It is our hope that this collection of challenges will lead to their resolution in the near future., (© 2022. Springer Science+Business Media, LLC, part of Springer Nature.)

Published
2022
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