Nalvo F. Almeida Jr

Publications

2025

  • F.A.Mesquita, W.M.C.daSilva, T.Raiol, M.M.Brigido, N.F.Almeida, B.Fuga, D.A.Cavalcante, M.T.deSouza. Genome Mining Reveals Pathways for Terpene Production in Aerobic Endospore-Forming Bacteria Isolated from Brazilian Soils. Microorganisms 2025, 13(11), 2528.

  • M.P.M. Silva, N.F. Almeida, M.G. Speziali, L.M. Spinosa, R.D. Vieira. O CONFAP e a promoção da Ciência Aberta no Brasil. In SILVA, Fabiano Couto Corrêa da; STUEBER, Ketlen; SEGUNDO, Washington (org.). Ciência Aberta no Brasil: conquistas e desafios. Porto Alegre: Letra1; São Paulo: SciELO, 83-100. Brasil. ISBN: 978-65-87422-37-4 (2025).

  • U.C.M. Silva, D.R.C. da Silva, S.Cuadros-Orellana, L.M. Moreira, L.R. Leite, J.D. Medeiros, E.B. Felestrino, W.L. Caneschi, N.F. Almeida, R.S. Silva, C.A. Oliveira-Paiva, V.L. dos Santos. Genomic and phenotypic insights into Serratia interaction with plants from an ecological perspective. Braz J Microbiol (2025).

  • R.A.B. Assis, R.M. Ferreira, A.C.P. deOliveira, F.M.S. Carvalho, J.A. Ferro, R.F. deSouza, E.G. Orellano, N.F. Almeida, C.C.M. Garcia, A.M. Dandekar, S.C. Chakraborty, A.M. Varani, L.M. Moreira. Exploring Multitasking Proteins in Xanthomonas Secretomes: Insights into Mechanisms of Plant-Pathogen Interactions. Heliyon, Volume 0, Issue 0, e42979(2025).

2024

  • D.F. Ribeiro, J.P. de Matos, L.C.M. Rocha, A.K. da Silva, C.H. de Paula, I.F. Cordeiro, C.G.C. Lemes, A.B. Sanchez, C.C.M. Garcia, J.C. Setubal, R.F. de Souza, A.M. Varani, N.F. Almeida, L.M. Moreira. From cactus to crop: genomic insights of a beneficial and non-pathogenic Curtobacterium flaccumfaciens strain and the evolution of its pathosystem. Molecular Genetics and Genomics 299, 105(2024).

  • K.G. Luz, F.R.O. Bezerra, M.A. Sicolo, A.A.R.S. Silva, A.A. Egito, P.A.P. Suniga, J.C.K. Moriya, M.G. Santos, C.Mantovani, J.S. Silva, N.F. Almeida, A.M.S. Guimarães, A.M.R. Dávila, R. Jardim, L.R. Santos, F.R. Araújo. Clinical and Molecular Characterization of Human Burkholderia mallei Infection, Brazil. Emerg Infect Dis. 2024 Nov.(2024).

  • A.R. de Oliveira, B. de Toledo Rós, R. Jardim, N. Kotowski, A. de Barros, R.H.G. Pereira, N.F. Almeida and A.M.R. Dávila. A comparative genomics study of the microbiome and freshwater resistome in Southern Pantanal. Front. Genet. 15:1352801 (2024).

2023

2022

  • C.E.P. Cerri, F. Barros, D.C. Grande, F.E.S. Costa, M.A. Pereira, N.F. Almeida. Você já salvou o planeta hoje? Como a Bioeconomia pode transformar o Brasil em player central na agenda positiva da transição climática. In: Instituto Fórum do Futuro. (Org.). As soluções sustentáveis que vêm dos trópicos: desenvolver sem desmatar por um novo pacto global do alimento. 01a ed. v. 01, p. 273-286. (2022).

2021

  • R.A.B. Assis, A.M. Varani, C.H.D. Sagawa, J.S.L.Patané, J.C.Setubal, G.Uceda-Campos, A.M. da-Silva, P.A. Zaini, N.F. Almeida, L.M. Moreira, A.M. Dandekar. A comparative genomic analysys of Xanthomonas arboricola pv. juglandis strains reveal hallmarks of mobile genetic elements in the adaptation and accelerated evolution of virulence. Genomics 113(4):2513-2525 (2021).

2020

  • E.B. Felestrino, A.B. Sanchez, W.L. Caneschi, C.G. Lemes, R.A.B. Assis, I.F. Cordeiro, N.P. Fonseca, M.M. Villa, I.T. Vieira, L.H.Y. Kamino, F.F. doCarmo, A.M. daSilva, A.M. Thomas, J.S. Patané, F.C. Ferreira, L.G. deFreitas, A.M. Varani, J.A. Ferro, R.S. Silva, N.F. Almeida, C.C.M. Garcia, J.C. Setubal, L.M. Moreira. Complete genome sequence and analysis of Alcaligenes faecalis strain Mc250, a new potential plant bioinoculant. PLOS ONE 15(11): e0241546 (2020).

  • C.M. de-Souza-Silva, F.A. Hurtado, A.H. Tavares, G.P. de Oliveira, T. Raiol, C. Nishibe, D.P. Agustinho, N.F. Almeida, M.E.M.T. Walter, A.M. Nicola, A.L. Bocca, P. Albuquerque, I. Silva-Pereira. Transcriptional remodeling patterns in murine dendritic cells infected with Paracoccidioides brasiliensis: more is not necessarily better. Journal of Fungi, 6(4), 311 (2020).

  • E.M. de Armas, M. Holanda, D. de Oliveira, N.F. Almeida, S. Lifschitz. A Classification of de Bruijn Graph Approaches for De Novo Fragment Assembly. Lecture Notes in Computer Science, vol 12558. Springer, Cham. (2020).

  • Deiviston S. Aguena, H. Mongelli, N.F. Almeida. A Survey on Solutions for Planted Motif Search Challenging Instances. Revista de Sistemas de Informação da FSMA n 26(2020) pp. 10-30 (2020).

2019

  • W.L. Caneschi, A.B. Sanchez, É.B. Felestrino, C.G. Lemes, I.F. Cordeiro, N.P. Fonseca, M.M. Villa, I.T. Vieira, L.A.G. Moraes, R.A.B. Assis, F.F. doCarmo, L.H. Kamino, R.S. Silva , J.A. Ferro, M.I.T. Ferro, R.M. Ferreira, V.L. Santos, U.C.M. Silva, N.F. Almeida, A.M.Varani, C.C.M. Garcia, J.C. Setubal, L.M. Moreira. Serratia liquefaciens FG3 isolated from a metallophyte plant sheds light on the evolution and mechanisms of adaptive traits in extreme environments. Scientific Reports 9,18006 (2019).

  • M. Bigi, C.L. Vazquez, A.B.C. Castelão, E.A. García, A.A. Cataldi, M. Jackson, M. McNeil, M. Soria, M.J. Zumárraga, M. Cabruja, G. Gag o, F.C. Blanco, C. Nishibe, N.F. Almeida, F.R de Araújo, F. Bigi. Analysing nonsynonymous mutations between two Mycobacterium bovis strains with contrasting pathogenic profiles. Veterinary Microbiology 2019, 108482 (2019).

  • N.P Fonseca, J.S.L. Patané, A.M. Varani, É.B. Felestrino, W.L. Caneschi, A.B. Sanchez, I.F. Cordeiro, C.G.C. Lemes, R.A.B. Assis, C.C.M. Garcia, J. Belasque Jr., A.P. Facincani, R.M. Ferreira, F.J. Jaciani, N.F. Almeida, J.A. Ferro, L.M. Moreira, J.C. Setubal. Analyses of Seven New Genomes of Xanthomonas citri pv. aurantifolii Strains, Causative Agents of Citrus Canker B and C, Show a Reduced Repertoire of Pathogenicity-Related Genes. Frontiers in Microbiology 10, 2631 (2019).

  • N.P. Fonseca, E.B. Felestrino, W.L. Caneschi, A.B. Sanchez, I.F. Cordeiro, C.G.C. Lemes, R.A.B. Assis, F.M.S. Carvalho, J.A. Ferro, A.M. Varani, J. Belasque, J.C. Setubal, G.P. Telles, D.S. Aguena, N.F. Almeida, L.M. Moreira. Detection and identification of Xanthomonas pathotypes associated with citrus diseases using comparative genomics and multiplex PCR. PeerJ 7:e7676 (2019).

  • J.S.L. Patané, J.Martins Jr, L.T. Rangel, J. Belasque, L.A. Digiampietri, A.P. Facincani, R.M. Ferreira, F.J. Jaciani, Y. Zhang, A.M. Varani, N.F. Almeida, N. Wang, J.A. Ferro, L.M. Moreira, João C. Setubal. Origin and diversification of Xanthomonas citri subsp. citri pathotypes revealed by inclusive phylogenomic, dating, and biogeographic analyses. BMC Genomics Volume 20, Article number 700 (2019).

2018

  • R. Güths, G.P. Telles, M.E.M.T. Walter, N.F. Almeida. A heuristic for the Live Parsimony Problem. CCIS 881, pp 248-67, N.Peixoto et al. (Eds.) Springer Nature (2018)

  • Rafael L. Fernandes, Rogério Güths, Guilherme P. Telles, Nalvo F. Almeida, Maria Emília M.T. Walter. A genetic algorithm for character state live phylogeny. Lecture Notes in Bioinformatics Volume 11228. 11th Brazilian Symposium on Bioinformaticvs, BSB 2018, Niterói, Brazil, Alves, Ronnie (Ed.). Proceedings ISBN: 978-3-030-01722-4, p. 114-123.

  • U.C. Silva, D.R.C .Silva, L.R. Leite, L.D. Medeiros, E.B. Felestrino, W.L. Felestrino, W.L. Caneschi, L.M. Moreira, N.F. Almeida, R. Silva, C.A. Oliveira-Paiva, V.L. dos_Santos. Genômica comparativa de Serratia marcescens endofíticas isoladas de Zea mays com linhagens de Serratia de diferentes estilos de vida. Embrapa Milho e Sorgo-Resumo em anais de congresso (ALICE).

  • Guilherme P. Telles, Graziela S. Araújo, Maria E. M. T. Walter, Marcelo M. Brigido, Nalvo F. Almeida. Live neighbor-joining. BMC Bioinformatics 19:172.

  • G. Licciardello, A. Caruso, P. Bella, R. Gheleri, C.P. Strano, A. Anzalone, E.A. Trantas, P.F. Sarris, N.F. Almeida and V. Catara. The LuxR regulators PcoR and RfiA co-regulate antimicrobial peptide and alginate production in Pseudomonas corrugata Frontiers in Microbiology 9:521.

  • J.C. Setubal, N.F. Almeida & Alice R. Wattam. Comparative Genomics for Prokaryotes. In J.C. Setubal et al. (eds.), Comparative Genomics: Methods and Protocols, Methods in Molecular Biology, vol 1704. ISBN 978-1-4939-7463-4. Springer Science+Business Media LLC 2018.

2017

  • Renata de A.B. Assis, Lorraine C. Polloni, José S. L. Patané, Shalabh Thakur, Érica B. Felestrino, Julio Diaz-Caballero, Luciano A. Digiampietri, Luiz R. Goulart, Nalvo F. Almeida, Rafael Nascimento, Abhaya M. Dandekar, Paulo A. Zaini, João C. Setubal, David S. Guttman, Leandro Márcio Moreira. Identifcation and analysis of seven efector protein families with diferent adaptive and evolutionary histories in plantassociated members of the Xanthomonadaceae. Scientific Reports 7:16133

  • L.A.G .de Moraes, E.B. Felestrino, R.A.B. Assis, D. Matos, J.C. Lima, L.A. Lima, N.F. Almeida, J.C. Setubal, C. C.M. Garcia, L.M. Moreira. TabPath: interactive Tables for Metabolic Pathway analysis. Bioinformatics, btx714

  • U.C. Silva, D.R. Silva, L.R. Leite, E.B. Felestrino, L.M. Moreira, N.F. Almeida, C.A. Oliveira, V.L. Santos. Predições guiadas por genômica do potencial de promoção de crescimento vegetal de isolados de Serratia marcescens endofíticos de milho (Zea mays). Resumo no IV Simpósio de Microbiologia da UFMG

  • R.A. Assis, L.C. Polloni, J.S. Patané, S. Thakur, E.B. Felestrino, J.D. Caballero, L.A. Digiampietri, L.R. Goulart, N.F. Almeida, R. Nascimento, A.M. Dandekar, P.A. Zaini, J.C. Setubal, D.S. Guttman, L.M Moreira. Comparative analysis of 69 Xanthomonadaceae genomes reveals seven effector protein families with diverse adaptive and evolutionary histories. Resumo no IV Simpósio de Microbiologia da UFMG

  • N.P. Fonseca, E.B. Felestrino, W.L. Caneschi, J. Belasque-Jr., N.F. Almeida, L.M. Moreira. Genômica Comparativa de Xanthomonas como Ferramenta para o Desenvolvimento de Diagnóstico Molecular a partir de Genes Espécie-Específicos. Resumo no IV Simpósio de Microbiologia da UFMG

  • E.B. Felestrino, R.A. Assis, C.G. Lemes, I.F. Cordeiro, N.P. Fonseca, M.M. Villa, I.T. Vieira, L.H. Kamino, F.F. Carmo, C. Carrião, J.C. Setubal, N.F. Almeida, L.M. Moreira. Análise genômica de Alcaligenes faecalis MC250: uma rizobactéria adaptada a campos rupestres ferruginosos Resumo no IV Simpósio de Microbiologia da UFMG

  • W.L. Caneschi, E.B. Felestrino, R.A. Assis, C.G. Lemes, I.F. Cordeiro, N.P. Fonseca, M.M. Villa, I.T. Vieira, L.H. Kamino, F.F. Carmo, A.Sanchez, C.C. Garcia, N.F. Almeida, J.A. Ferro, M.I. Ferro, A.M. Varani, R. Marini, V.L. dos Santos, U. Cássia, J.C. Setubal, L.M. Moreira. O primeiro genoma completo de Serratia liquefaciens, associada a planta de campos ferruginosos, revelou distintos mecanismos adaptativos para sobrevivência em ambiente inóspito. Resumo no IV Simpósio de Microbiologia da UFMG

  • W.L. Caneschi, E.B. Felestrino, R.A. Assis, C.G. Lemes, I.F. Cordeiro, N.P. Fonseca, M.M. Villa, I.T. Vieira, L.H. Kamino, F.F. Carmo, A.Sanchez, C.C. Garcia, N.F. Almeida, J.A. Ferro, M.I. Ferro, A.M. Varani, R. Marini, V.L. dos Santos, U. Cássia, J.C. Setubal, L.M. Moreira. Prospecção de bactérias cultiváveis de campos ferruginosos: novas possibilidades biotecnológicas a partir de um estudo piloto. Resumo no IV Simpósio de Microbiologia da UFMG

  • L. Sanabria, L. Lagrave, C. Nishibe, A. Ribas, M.J. Zumárraga, N.F. Almeida, F.R. Araújo. Draft genome of two Mycobacterium bovis strains isolated from beef cattle in Paraguay. Genome Announcement 5 28

  • L.R. Salgado, R. Lima, B.F. dos Santos, K.T. Shirakawa, M.A. Vilela, N.F. Almeida, R.M. Pereira, A.L. Nepomuceno, L. Chiari. De novo RNA sequencing and analysis of the transcriptome of signalgrass (Urochloa decumbens) roots exposed to aluminum. Plant Grown Regul (2017) 83:157–170

  • J.S.L. Patané, J. Martins-Jr, A.B. Castelão, C. Nishibe, L. Montera, F. Bigi, M.J. Zumárraga, A.A. Cataldi, A.Fonseca-Jr, E. Roxo, A.L.A.R. Osório, K.S. Jorge, T.C. Thacker, N.F. Almeida, F.R. Araújo, J.C. Setubal. Patterns and Processes of Mycobacterium bovis Evolution Revealed by Phylogenomic Analyses. Genome Biol Evol 9(3):521-535.

  • I.M. Siqueira, R.J.A. Castro, L.C.M. Leonhardt, M.S. Jerônimo, A.C. Soares, T. Raiol, C. Nishibe, N.F. Almeida, A.H. Tavares, C. Hoffmann, A.L. Bocca. Modulation of the immune response by Fonsecaea pedrosoi morphotypes in the course of experimental chromoblastomycosis and their role on inflammatory response chronicity. PLOS Neglected Tropical Diseases 11(3):e0005461.

  • R. Güths, G.P. Telles, M.E.M.T. Walter, N.F. Almeida. A Branch and Bound for the Large Live Parsimony Problem. Proc of the 10th International Joint Conference on Biomedical Engineering Systems and Technologies (BIOSTEC 2017)ISBN 978-989-758-214-1, pages 184-189.

  • G.S. Araújo, G.P. Telles, M.E.M.T. Walter, N.F. Almeida. Distance-Based Live Phylogeny. Proc of the 10th International Joint Conference on Biomedical Engineering Systems and Technologies (BIOSTEC 2017)ISBN 978-989-758-214-1, pages 196-201.

2016

  • R. Lima, C. Nishibe, T. Raiol and N.F. Almeida. DEPICTViz - Differential Expression and Protein InteraCTions Visualization Tool. ISCB-Latin America 2016, Buenos Aires, Argentina

  • D.S. Aguena, R. A. B. Assis, A. M. Varani, L. M. Moreira and N.F. Almeida. COVERT - COnserVEd Regulon Tool. ISCB-Latin America 2016, Buenos Aires, Argentina

  • G. Licciardello, A. Caruso, P. Bella, R. Lima, C.P. Strano, E.A. Trantas, P.F. Sarris, N.F. Almeida and V. Catara. RNA-Seq-based transcriptome analysis of Pseudomonas corrugata Luxr regulators PCOR and RFIA. XXII Congress of the Italian Society for Plant Pathology, 2016, Rome, Italy

  • G. Licciardello, A. Caruso, R. Lima,C.P. Strano, E. Trantas, P.F. Sarris, P. Bella, R. Lo-Piero, N.F. Almeida and V. Catara. Transciptome-based analysis of two luxr regulators involved in Pseudomonas corrugata interaction with host and non-host plants. 60th Annual Congress of The Italian Society of Agricultural Genetics, 2016, Catania, Italy.

  • F.R. Araújo & N.F. Almeida. Mycobacterium. In Dongyou Liu (Ed.) Laboratory Models for Foodborne Infections (Chapter 12). ISBN 9781498721677. CRC Press 2016.

  • F.R. Araújo, N.F. Almeida, M.J. Zumárraga. Diagnostic tools to detect pathogens causing tuberculosis in cattle and prevent their transmission through dairy products to humans. FAO International Symposium on The Role of Agricultural Biotechnologies in Sustainable Food Systems and Nutrition. February 2016. FAO Headquarters, Rome, Italy (extended abstract).

2015

  • R. Lima, C. Nishibe, T. Raiol, N.F. Almeida. Differential expression and functional associations of Hox genes. X-Meeting 2015+Brazilian Symposium on Bioinformatics São Paulo, 2015 (abstract).

  • E.A. Trantas, G. Licciardello, N.F. Almeida, K. Witek, C.P. Strano, Z. Duxbury, F. Ververidis, D.E. Goumas, J.D. Jones, D.S. Guttman, V. Catara, P.F. Sarris. Comparative genomic analysis of multiple strains of two unusual plant pathogens: Pseudomonas corrugata and Pseudomonas mediterranea. Frontiers in Microbiology 6:811.

  • A.B.C. Castelão, C. Nishibe, A.A. Fonseca-Jr, J. Martins-Jr, A.L.A. Osório, J.S.L. Patané, E. Roxo, T. Thacker, M.J. Zumárraga, N.F. Almeida, J.C. Setubal, F.R. Araújo. Comparative genomics of M. bovis strains of Brazil, Argentina and USA. 28° Congresso Brasileiro de Microbiologia, Florianópolis, Brazil, 2015.

  • J.C. Setubal and N.F. Almeida. The Azotobacter vinelandii genome: an update. In Frans J. de Bruijn (Ed.) Biological Nitrogen Fixation. Wiley-Blackwell.

  • J.C. Setubal and N.F. Almeida. TCBB Special Section on the Brazilian Symposium on Bioinformatics 2013. Guest editorial for a special section of ACM/IEEE Transactions on Computational Biology and Bioinformatics, 2015.

  • A.R. Schwartz, N. Potnis, S. Timilsina, M. Wilson, J. Patane, J. Martins, G.V. Minsavage, D. Dahlbeck, A. Akhunova, N.F. Almeida, G.E. Vallad, J.D. Barak, F.F. White, S.A. Miller, D. Ritchie, E. Goss, R.S. Bart, J.C. Setubal, J.B. Jones and B.J. Staskawicz. Phylogenomics of Xanthomonas field strains infecting pepper and tomato reveals diversity in effector repertoires and identifies determinants of host specificity. Frontiers in Microbiology 6:535.

2014

  • B. Cezar, C. Nishibe, N.F. Almeida, L. Montera. Mapping short reads may be harder in anomalous regions. Proc. of The third International Society for Computational Biology Latin America (ISCB-Latin America 2014), Belo Horizonte, Brazil, 2014 (abstract).

  • R. Güths, G.P. Telles, M.E.M.T.Walter, N.F. Almeida. The weight small live parsimony problem. Proc. of The third International Society for Computational Biology Latin America (ISCB-Latin America 2014), Belo Horizonte, Brazil, 2014 (abstract).

  • G.S.Araújo, G.P. Telles, M.E.M.T.Walter, N.F. Almeida Distance-based live phylogeny. Proc. of The third International Society for Computational Biology Latin America (ISCB-Latin America 2014), Belo Horizonte, Brazil, 2014 (abstract).

  • R.A. Cardoso, F.R. Araújo, N.F. Almeida Finding specific primers from syntenic blocks and characteristic strings. Proc. of The third International Society for Computational Biology Latin America (ISCB-Latin America 2014), Belo Horizonte, Brazil, 2014 (abstract).

  • T. Raiol, M.T. De-Souza, J.V. Oliveira, H.S. Silva, J.C. Orem, D.A. Cavalcante, N.F. Almeida, G.P. Telles, J.C. Setubal, M.M. Brigido, F.A.G. Torres, P.S. Stadler, M.E.M.T. Walter, L.M.P. Moraes. Draft Genome Sequence of FT9, a Novel Bacillus cereus Strain Isolated from a Brazilian Thermal Spring. Genome Announc. 2(5):e01027-14.

  • A.B.C. Castelão, C. Nishibe, M.J. Zumárraga, A.A. Cataldi, F.C. Blanco, A.A. Fonseca-Jr, M.A. Hodon, P.M. Soares-Filho, M.A. Issa, N.F. Almeida, F.R. Araújo. Comparison of virulence genes of two Mycobacterium bovis strains by next-generation whole genome sequencing. Proc. of VII Meeting of the SLAMTB, Canela, RS, Brazil, Sep 2014. Revista de Epidemiologia e Controle de Infecção 4(2) 2014, Edição Especial, ISSN 2238-3360, pp 86-87 (abstract).

  • A.B.C. Castelão, C. Nishibe, A. Moura, A.P. de Alencar, M.A. Issa, M.A. Hodon, P.M.P.C. Mota, E.B. Sales, A.A. Fonseca-Junior, N.F. Almeida, F.R. Araújo. Draft genome of AN5 strain of Mycobacterium bovis, used for production of Purified Protein Derivative. Genome Announc. 2(2):e00277-14.

  • C.P.Araújo, A.L.A.R.Osório, K.S.G.Jorge, C.A.N.Ramos, A.F.S.Filho, C.E.S.Vidal, E.Roxo, C.Nishibe, N.F.Almeida, A.A.F.Júnior, M.R.Silva, J.D.B.Neto, V.D.Cerqueira, M.J.Zumárraga and F.R.Araújo. Detection of Mycobacterium bovis in bovine and bubaline tissues using nested-PCR for TbD1. PLOS ONE 9(3):e91023.

  • Jucele F.A. Vasconcellos, Christiane Nishibe, Nalvo F. Almeida and Edson N. Cáceres. Efficient Parallel Implementations of Multiple Sequence Alignment using BSP/CGM Model. Proc. of PPoPP’14 ACM SIGPLAN Symposium on Principles and Practice of Parallel Programming Orlando, FL, USA — February 15-19, 2014, pp 103-110.

  • N.A. Wulff, S. Zhang, J.C Setubal, N.F. Almeida, E.C. Martins, R. Harakava, D. Kumar, L.T. Rangel, X. Foissac, J. Bove, and D.W. Gabriel. The complete genome sequence of Candidatus Liberibacter americanus, associated with citrus Huanglongbing. Molecular Plant-Microbe Interactions 27(2):163-176.

2013

  • C. Nishibe, A.B.C. Castelão, R.D. Costa, B.J. Pinto, L. Varuzza, A.A. Cataldi, A. Bernardelli, F. Bigi, F.C. Blanco, M.J. Zumárraga, N.F. Almeida, and F.R. Araújo. Draft Genome Sequence of M.bovis 04-303, a Highly Virulent Strain from Argentina. Genome Announc. 1(6):e00931-13.

  • N.A. Wulff, S. Zhang, E.C. Martins, J.C. Setubal, D. Kumar, X. Foissac, N.F. Almeida, R. Harakava, J. Bové, D.W. Gabriel. The complete genome sequence of Candidatus Liberibacter americanus, a bacterium associated with Citrus Huanglongbing in Brazil. Journal of Citrus Pathology, 1(1)

  • J.C. Setubal, N.F. Almeida, Editors. Advances in Bioinformatics and Computational Biology. Lecture Notes in Computer Science. Volume 8213. 8th Brazilian Symposium on Bioinformatics, BSB 2013, Recife, Brazil, November 3-7, 2013, Proceedings ISBN: 978-3-319-02623-7 (Print) 978-3-319-02624-4 (Online).

  • P.F. Sarris, E.A. Trantas, D.A. Baltrus, C.T. Bull, W.P. Wechter, S. Yan, F. Ververidis, N.F. Almeida, C.D. Jones, J.L. Dangl, N.J. Panopoulos, B.A. Vinatzer, D.E. Goumas. Comparative Genomics of Multiple Strains of Pseudomonas cannabina pv. alisalensis, a Potential Model Pathogen of Both Monocots and Dicots. PLoS ONE 8(3):e59366.

  • G.P. Telles, N.F. Almeida, R. Minghim, M.E.M.T. Walter. Live Phylogeny. Journal of Computational Biology 20(1):30-37.

  • G.P. Telles, N.F. Almeida, P. Alvarez and M.E.M.T. Walter. A method to find groups of orthogous genes across multiple genomes. Revista de Sistemas de Informação da FSMA 12:02-07 (ISSN 1983-5604).

2012

  • S. Slater, J.C. Setubal, B. Goodner, K. Houmiel, J. Sun, R. Kaul, B.S. Goldman, S.K. Farrand, N.F. Almeida, T. Burr, E. Nester, D.M. Rhoads, R. Kadoi, T. Ostheimer, N. Pride, A. Sabo, E. Henry, E. Telepak, L. Cromes, A. Harkleroad, L. Oliphant, P. Pratt-Szegila, R. Welch, D. Wood. Reconciliation of Sequence Data and Updated Annotation of the Genome of Agrobacterium tumefaciens C58, and Distribution of a Linear Chromosome in the Genus Agrobacterium. Appl. Environ. Microbiol. AEM.03192-12.

  • A.R. Wattam, T.J. Inzana, K.P. Williams, S.P. Mane, M. Shukla, N.F. Almeida, A.W. Dickerman, S. Mason, I. Moriyón, D. O’Callaghan, A.M. Whatmore, B.W. Sobral, R.V. Tiller, A.R. Hoffmaster, M.A. Frace, C. de-Castro, A. Molinaro, S.M. Boyle, B.K. De, J.C. Setubal. Comparative Genomics of Early-Diverging Brucella Strains Reveals a Novel Lipopolysaccharide Biosynthesis Pathway. mBio 3(5):e00246-12.

  • A. Mazzaglia, D.J. Studholme, M.C. Taratufolo, R. Cai, N.F. Almeida, T. Goodman, D.S. Guttman, B.A. Vinatzer, G.M. Balestra. Pseudomonas syringae pv. actinidiae (PSA) isolates from recent bacterial canker of kiwifruit outbreaks belong to the same genetic lineage. PLoS ONE 7(5):e36518.

  • M. Polastro and N.F. Almeida. The Usage of OCR to Support Computer Forensics Exams. 6th European Academy of Forensic Science Conf. Abstract Book Towards Forensic Science 2.0 6th EAFS, The Hague, The Netherlands, August 20-24, 2012

  • J.V.A. Oliveira, T. Raiol, N.C. Farias, N.F. Almeida, G.P. Telles, J.C. Setubal, M.L. Araujo, F.P. Lima, C. Benoit-Pilven, M.M. Brigido, M.T. Souza, L.M.P. Moraes and M.E.T. Walter. Genome sequence of a Brazilian Bacillus cereus isolate. BSB2012 Digital Proceedings (ISSN:2316-1248), 7th Brazilian Symposium on Bioinformatics, BSB 2012, Campo Grande, Brazil, August 15-17, 2012.

  • F.R. Araujo, A.B.C. Castelao, A.A. Fonseca-Jr., M.A. Hodon, M.A. Issa, A.K. Ramalho, G.M.T. Mendes, C.A.N. Ramos, E.B.Sales, P.M. Soares-Filho, N.C. Farias, C. Nishibe and N.F. Almeida. Typing of a Brazilian Mycobacterium isolate by whole-genome sequencing. BSB2012 Digital Proceedings (ISSN:2316-1248), 7th Brazilian Symposium on Bioinformatics, BSB 2012, Campo Grande, Brazil, August 15-17, 2012.

  • H.Muniz, N.C.Farias, T.Raiol, A.L.Cunha-Laura, G.P.Telles and N.F.Almeida A comparison of two approaches for species identication BSB2012 Digital Proceedings (ISSN:2316-1248), 7th Brazilian Symposium on Bioinformatics, BSB 2012, Campo Grande, Brazil, August 15-17, 2012.

2011

  • F.I. Staquicini, M. Cardó-Vila, M.G. Kolonin, M. Trepel, J.K. Edwards, D.N. Nunes, A. Sergeeva, E. Efstathiou, J. Sun, N.F. Almeida, Shi-Ming Tu, G.H. Botz, M.J. Wallace, D.J. O’Connell, S. Krajewski, J.E. Gershenwald, J.J. Molldrem, A.L. Flamm, E. Koivunen, R.D. Pentz, E. Dias-Neto, J.C. Setubal, D.J. Cahill, P. Troncoso, Kim-Ahn Do, C.J. Logothetis, R.L. Sidman, R. Pasqualini, W. Arap. Vascular ligand-receptor mapping by direct combinatorial selection in cancer patients. PNAS 108(46):18637–18642.

  • R. Cai, J. Lewis, S. Yan, H. Liu, C. Clarke, F. Campanile, N.F. Almeida, D.J. Studholme, M. Lindeberg, D. Schneider, M. Zaccardelli, J.C. Setubal, N.P. Morales-Lizcano, A. Bernal, G. Coaker, C. Baker, C.L. Bender, S. Leman, B.A. Vinatzer. The plant pathogen Pseudomonas syringae pv. tomato is genetically monomorphic and under strong selection to evade tomato immunity. PLoS Pathogens 7(8):e1002130.

  • N. Potnis, K. Krasileva, V. Chow, N.F. Almeida, P. Patil, R. Ryan, M. Sharlach, F. Behlau, J.M. Dow, F. White, J. Preston, B. Vinatzer, R. Koebnik, J.C. Setubal, D.J. Norman, B. Staskawicz and J.B. Jones Comparative genomics reveals diversity among xanthomonads infecting tomato and pepper. BMC Genomics 12(146).

  • M.C. Polastro and N.F. Almeida. OCR errors and their effects on computer forensics. ICoFCS – The Sixth International Conference on Forensic Computer Science, pp. 115-121. ICoFCS 2011. Associação Brasileira De Especialistas Em Alta Tecnologia (ABEAT), Brasília, Brazil, 2011.

  • G.P. Telles, N.F. Almeida, M.M. Brigido, P.A. Alvarez and M.E. Walter. kGC: Finding Groups of Homologous Genes across Multiple Genomes. BSB 2011, LNBI 6832, pp. 79-82, 2011, Osmar Norberto de Souza, Guilherme Pimentel Telles and Mathew J. Palakal (Eds.), Springer-Verlag Berlin Heidelberg 2011.

  • N.F. Almeida, H. Asseiss and J.C. Setubal. Using assembly and phylogeny to classify metagenomic sequences. BSB2011 Digital Proc. (ISSN 2178-5120)

2010

  • Daniel S.G.Jr., F.R. Araújo, N.F. Almeida, S.S. Adi, L.M. Cheung, S.P. Fragoso, C.A.N. Ramos, R.H.M. de Oliveira, C.S. Santos, G. Bacanelli, C.O. Soares, G.M.S. Rosinha, A.H.Fonseca. Analysis of membrane protein genes in a Brazilian isolate of Anaplasma marginale. Mem Inst Oswaldo Cruz 105(7):843-849.

  • L.M. Moreira, N.F. Almeida, N. Potnis, L.A. Digiampietri, S.S. Adi, J.C. Bortolossi, A.C. da Silva, A.M. da Silva, F.E. de Moraes, J.C. de Oliveira, R.F. de Souza, A.P. Fancincani, A.L. Ferraz, M.I. Ferro, L.R. Furlan, D.F. Gimenez, J.B. Jones, E.W. Kitajima, M.L. Laia, R.P. Leite-Jr, M.Y. Nishiyama, J. Rodrigues-Neto, L.A. Nociti, D.J. Norman, E.H. Ostroski, H.A. Pereira Jr, B.J. Staskawicz, R.I. Tezza, J.A. Ferro, B.A. Vinatzer and J.C. Setubal. Novel insights into the genomic basis of citrus canker based on the genome sequences of two strains of Xanthomonas fuscans subsp. aurantifolii. BMC Genomics 11(238):e1471-2164.

  • N.F. Almeida, S. Yan, R. Cai, C.R. Clarke, C.E. Morris, N.W. Schaad, E.L. Schuenzel, G.H. Lacy, X. Sun, J.B. Jones, J.A. Castillo, C.T. Bull, S. Leman, D.S. Guttman, J.C. Setubal, B.A. Vinatzer. PAMDB, a Multilocus sequence typing and analysis database and website for plant-associated microbes. Phytopathology 100(3):208-215.

2009

  • J.C. Setubal, P. dos-Santos, B.S. Goldman, H. Ertesvag, G. Espin, L.M. Rubio, S. Valla, N.F. Almeida, D.Balasubramanian, L. Cromes, L. Curatti, Z. Du, E.Godsy, B. Goodner, K. Hellner-Burris, J.A. Hernandez, K. Houmiel, J. Imperial, C. Kennedy, T.J. Larson, P. Latreille, L. Ligon, J. Lu, M.Mark, N. Miller, S. Norton, I.P. O'Carroll, I. Paulsen, E.C. Raulfs, R. Roemer, J. Rosser, D. Segura, S. Slater, S. Stricklin, D. Studholme, J. Sun, C.J. Viana, E. Wallin, B. Wang, C. Wheeler. The genome sequence of Azotobacter vinelandii, an obligate aerobe specialized to support diverse anaerobic metabolic processes. Journal of Bacteriology 191(14):4534-4545.

  • A.R.Wattam, K. Williams, E. Snyder, N.F. Almeida, M. Shukla, A. Dickerman, O. Crasta, R. Kenyon, J. Lu, J. Shallom, H.Yoo, T. Ficht, R. Tsolis, C. Munk, R. Tapia, C. Han, J. Detter, D. Bruce, T. Brettin, B. Sobral, S. Boyle, J.C. Setubal. Analysis of ten Brucella genomes reveals evidence for horizontal gene transfer despite a preferred intracellular lifestyle. Journal of Bacteriology 191(11):3569-3579.

  • S. Slater, B. Goldman, B. Goodner, J.C. Setubal, S. Farrand, E. Nester, T. Burr, L. Banta, A. Dickerman, I. Paulsen, L. Otten, G. Suen, R. Welch, N.F. Almeida, F. Arnold, O. Burton, Z. Du, A. Ewing, E.Godsy, S. Heisel, K. Houmiel, J. Jhaveri, J. Lu, N. Miller, S. Norton, Q. Chen, W. Phoolcharoen, V. Ohlin, D. Ondrusek, N. Pride, S. Stricklin, J. Sun, C. Wheeler, L. Wilson, H. Zhu, D. Wood. Genome sequences of three Agrobacterium biovars help elucidate the evolution of multichromosome genomes in bacteria. Journal of Bacteriology 191(8):2501-2511.

  • N.F. Almeida, S. Yan, M. Lindeberg, D.J. Studholme, D.J. Schneider, B. Condon, H. Liu, C.J. Viana, A. Warren, C. Evans, E. Kemen, D. MacLean, A. Angot, G.B. Martin, J.D. Jones, A. Collmer, J.C. Setubal and B.A. Vinatzer. A draft genome sequence of Pseudomonas syringae pv. tomato T1 reveals a Type III Effector repertoire significantly divergent from that of P. syringae pv. tomato DC3000. Molecular Plant-Microbe Interactions 22(1):52-62.

  • C. Clarke, D.J. Studholme, N.F. Almeida, J.D. Jones, J.C. Setubal, D.S. Guttman, B.A. Vinatzer. Characterization of a subgroup of Pseudomonas syringae strains that lack a typical type three secretion system and effector gene orthologues. XIV International Congress on Plant-Microbe Interactions, July 19-23 2009, Quebec City, Canada (abstract).

2008

  • S. Yan, N.F. Almeida, M. Lindeberg, H. Liu, A. Warren, D.J. Schneider, M. Moore, A. Collmer, J.C. Setubal, B.A. Vinatzer. Using a plant-bacterial pathogen interaction model to study host range and virulence evolution of infectious bacteria. Deans’ Forum on Infectious Diseases, September 28-29 2008, Blacksburg, VA (abstract).

  • P.C. Xavier, M.R. Chang, M.O. Nunes, D.B. Palhares, R. Andreotti e Silva, G.F. Bonfim, N.F. Almeida. Candidemia neonatal em hospital público do Mato Grosso do Sul. Rev. Soc. Bras. Medicina Tropical 41(5).

  • S. Yan, N.F. Almeida, M. Lindeberg, H. Liu, A. Warren, D.J. Schneider, M. Moore, A. Collmer, J.C. Setubal, B.A. Vinatzer. Dissecting Arabidopsis host and nonhost interactions with Pseudomonas syringae, taking advantage of comparative evolutionary genomics. 19th International Conference on Arabidopsis Research, July 23-27 2008, Montreal, Canada.

  • S.Yan, N.F. Almeida, M. Lindeberg, D.J. Schneider, H. Liu, A. Collmer, J.C. Setubal, B.A. Vinatzer. A comparative genomics investigation into host specificity in the plant pathogen Pseudomonas syringae. American Society of Microbiology 108th General Meeting. 1-5 June 2008, Boston, MA, USA (abstract)

  • R.D. Tezza, M.L. Laia, A.P. Facincani, N.F. Almeida, J.A. Ferro, M.I.T. Ferro. Predição computacional de promotores em Xanthomonas axonopodis pv. citri. III Encontro Nacional de Pós-Graduação em Microbiologia. 23-24 setembro 2008, FCAV, Jaboticabal, SP. (abstract).

2007

  • N.F. Almeida, A.C. Lima, S.S. Adi, C.J.M. Viana, M.Y. Nakazaki, A.A. Tamura, L.Y. Hiratsuka and L.P. Brazil. EGGview: Visualization of EGG comparative data using GBrowse. BSB2007 Poster Proceedings (ISBN:978-85-7669-123-5), [2nd Brazilian Symposium on Bioinformatics, BSB 2007[(http://bsb2007.inf.puc-rio.br/), Angra dos Reis, Brazil, August 29-31, 2007.

  • D. Anjos, G. Zerlotini, G. Pinto, M.E.M. Walter, M.M. Brigido, G.P. Telles, C.J.M. Viana and N.F. Almeida. A method for inferring biological functions using homologous genes among three genomes BSB’07, LNBI 4643, pp. 70-81, M.-F.Sagot and M.E.M.T.Walter (Eds.), Springer-Verlag Berlin Heidelberg 2007.

  • N.F. Almeida, A.C. Lima, S.S. Adi, C.J.M. Viana, M.Y. Nakazaki, A.A. Tamura, L.Y. Hiratsuka, L.P. Brazil. Mapping contigs onto reference genomes BSB’07, LNBI 4643, pp. 153-157, M.-F. Sagot and M.E.M.T. Walter (Eds.), Springer-Verlag Berlin Heidelberg 2007.

2005

  • R.V. Andrade, S.P. da-Silva, F.A.G. Torres, M.J. Poças-Fonseca, I. Silva-Pereira, A.Q. Maranhão, E.G. Campos, L.M.P. Moraes, R.S.A. Jesuino, M. Pereira, C.M.A. Soares, M.E.M.T. Walter, M.J.A. Carvalho, N.F. Almeida, M.M. Brigido and M.S.S. Felipe. Overview and perspectives on the trasncriptome of Paracoccidioides brasiliensis. Rev Iberoam Micol 22:203-212.

  • M.M. Brigido, M.M.T. Walter, A.G. Oliveira, M.K. Inoue, D.S. Anjos, E.F.O. Sandes, J.J. Gondim, M.J.A. Carvalho, N.F. Almeida and M.S.S. Felipe. Bioinformatics of the Paracoccidioides brasiliensis EST Project Genet. Mol. Res. 4(2):203-215.

  • M.S.S. Felipe, R.V. Andrade, F.B.M. Arraes, A.M. Nicola, A.Q. Maranhão, F.A.G. Torres, I. Silva-Pereira, M.J. Poças-Fonseca, E.G. Campos, L.M.P. Moraes, P.A. Andrade, A.H.F.P. Tavares, S.S. Silva, C.M. Kyaw, D.P. Souza, M. Pereira, R.S.A. Jesuino, E.V. Andrade, J.A. Parente, G.S. Oliveira, M.S. Barbosa, N.F. Martins, A.L. Fachin, R.S. Cardoso, G.A.S. Passos, N.F. Almeida, M.E.M.T. Walter, C.M.A. Soares, M.J.A. Carvalho and M.M. Brigido. Transcriptional profiles of the human pathogenic fungus Paracoccidioides brasiliensis in mycelium and yeast cells. J. Biol. Chem. 280(26):24706-24714.

  • F.R. Araújo, V.S.P. Melo, C.A.N. Ramos, C.R.Madruga, C.O.Soares, R.H. Kessler, N.F. Almeida Jr., G.S. Araujo, L.C. Alves, R.A.A. Torres-Jr., S.P. Fragoso, P.R.C. Arauco, G. Bacanelli, M.B. Oliveira and L.R. Santos. Development of enzyme-linked immunosorbent assays based on recombinant MSP1a and MSP2 of Anaplasma marginale. Mem Inst Oswaldo Cruz 100(7):765-769.

  • G.P. Telles, M.M. Brigido, N.F. Almeida, C.J.M. Viana, D.A.S. Anjos and M.E.M.T. Walter. A method for comparing three genomes BSB’05, LNBI 3594, pp. 160-169, J.C.Setubal and S.Verjovski-Almeida (Eds.), Springer-Verlag Berlin Heidelberg.

  • G.P. Telles, N.F. Almeida, F.H.V. Martinez. Algoritmos e heurísticas para comparações exata e aproximada de sequêencias. XXIV Jornadas de Atualização em Informática. A. Loureiro, M.Barcelos. (Org.), 2005, p. 1545-1587.

  • P.P. Pires, N.F. Almeida, E.J. Hanashiro, W.M. Dias, P.F.I. Goiozo. Interface de hardware e software para conexão de balança, identificador eletrônico e teclado do peão com PC Anais do ZOOTE-2005, Campo Grande MS, Brasil, Maio de 2005 (abstract).

2004

  • L.M. Moreira, R.F. de Souza, N.F. Almeida, J.C. Setubal, J.C.F. Oliveira, L.R. Furlan, J.A. Ferro and A.C.R da Silva. Comparative genomics analyses of citrus-associated bacteria. Annu. Rev. Phytopathology 42:163-184.

  • C.B. Monteiro-Vitorello, L.E.A. Camargo, M.A.V. Sluys, J.P. Kitajima, D. Truffi, A.M. do Amaral, R. Harakava, J.C.F. de Oliveira, D. Wood, M.C. de Oliveira, C. Miyaki, M.A. Takita, A.C.R. da Silva, L.R. Furlan, D.M. Carraro, G. Camarotte, N.F.Almeida, H. Carrer, L.L. Coutinho, H.A. El-Dorry, M.I.T. Ferro, P.R. Gagliardi, E. Giglioti, M.H.S. Goldman, G.H. Goldman, E.T. Kimura, E.S. Ferro, E.E. Kuramae, E.G.M. Lemos, M.V.F. Lemos, S.M.Z. Mauro, M.A.Machado, C.L.Marino, C.F. Menck, L.R. Nunes, R.C. Oliveira, G.G. Pereira, W. Siqueira, A.A. de Souza, S.M. Tsai, A.S. Zanca, A.J.G. Simpson, S.M. Brumbley and J.C. Setubal. The genome sequence of the gram-positivesugarcane pathogen Leifsonia xyli subsp. xyli. Molelular Plant-Microbe Interactions 17(8):827-836.

  • N.F. Almeida, J.C. Setubal, M.H. Carvalho, C.J.M. Viana. A method to determine homologous protein families based on graph cliques and profiles. Anais do 3rd Brazilian Workshop on Bioinformatics, Brasília DF, Brasil, Outubro de 2004 (abstract)

2003

  • N.F. Almeida, C.E.R. Alves, E.N. Cáceres and S.W. Song. Comparison of Genomes using High-Performance Parallel Computing. Proc. of 15th Symposium on Computer Architecture and High Performance Computing SBAC-PAD 2003 IEEE Computer Society, pp. 142-148

  • M.S.S. Felipe, R.V. Andrade, S.S. Petrofeza, A.Q. Maranhao, F.A.G. Torres, P. Albuquerque, F.B.M. Arraes, M. Arruda, M.O. Azevedo, A.J. Baptista, L.A.M. Bataus, C.L. Borges, E.G.Campos, M.R. Cruz, B.S. Daher, A. Dantas, M.A.S.V. Ferreira, G.V.Ghil, R.S.A. Jesuino, C.M. Kyaw, L. Leitao, C.R. Martins, L.M.P. Moraes, E.O.Neves, A.M. Nicola, E.S. Alves, J.A. Parente, M. Pereira, M.J. Poças-Fonseca, R. Resende, B.M. Ribeiro, R.R. Saldanha, S.C. Santos, I. Silva-Pereira, M.A.S. Silva, E. Silveira, I.C. Simoes, R.B.A. Soares, D.P. Souza, M.T. de-Souza, E.V. Andrade, M.A.S. Xavier, H.P. Veiga, E.J. Venancio, M.J.A. Carvalho, A.G. Oliveira, M.K. Inoue, N.F. Almeida, M.E.M.T. Walter, C.M.A. Soares and M.M. Brigido. Transcriptome characterization of the dimorphic and pathogenic fungus Paracoccidioides brasiliensis by EST analysis. Yeast 20(3):263-271.

  • M.A. Van Sluys, M.C.de Oliveira, C.B.Monteiro-Vitorello, C.Y. Miyaki, L.R .Furlan, L.E.A.Camargo, A.C.R. da Silva, D. H. Moon, M.A. Takita, E.G.M. Lemos, M.A. Machado, M.I.T. Ferro, F.R. da-Silva, M.H.S. Goldman, G.H. Goldman, M.V.F. Lemos, H. El-Dorry, S.M. Tsai, H. Carrer, D.M. Carraro, R.C.de Oliveira, L.R. Nunes, W.J. Siqueira, L.L. Coutinho, E.T. Kimura, E.S. Ferro, R. Harakava, E.E. Kuramae, C.L. Marino, E. Giglioti, I.L. Abreu, L.M.C. Alves, A.M. do Amaral, G.S. Baia, S.R. Blanco, M.S. Brito, F.S. Cannavan, A.V.Celestino, A.F. da Cunha, R.C. Fenille, J.A. Ferro, E.F. Formighieri, L.T. Kishi, S.G. Leoni, A.R. Oliveira, V.E. Rosa Jr., F.T. Sassaki, J.A.D. Sena, A.A. de Souza,D. Truffi, F. Tsukumo, G.M. Yanai, L.G. Zaros, E.L. Civerolo, A.J.G. Simpson, N.F. Almeida, J.C. Setubal and J.P. Kitajima. Comparative analyses of the complete genome sequences of Pierce’s Disease and Citrus Variegated Chlorosis strains of Xylella fastidiosa. J. Bacteriology 185(3):1018-1026.

  • N.F. Almeida, L. Montera. Determinação de regiões ortólogas múltiplas. Anais do 2nd Brazilian Workshop on Bioinformatics, Macaé, RJ, Brasil, Dezembro de 2003 (poster)

  • C.R.Madruga, F.R.Araujo, N.F. Almeida Jr. et al. Análise de 18S rRNA em isolados brasileiros de Trypanosoma vivax Anais do XI Congresso latinoamericano de Buiatria Salvador, BA, Setembro de 2003 (poster)

  • C.R.Madruga, F.R.Araujo, N.F.Almeida et al. Diagnóstico de infecções por isolados brasileiros de Trypanosoma vivax e Trypanosoma evansi por PCR-RFLP Anais do XI Congresso latinoamericano de Buiatria, Salvador, BA, Setembro de 2003 (poster)

  • N.F. Almeida e J.C. Setubal. Ferramentas para comparação genômica. Anais do XXIII Congresso da Sociedade Brasileira de Computação, Campinas, SP, Agosto de 2003, pp 13-20). Trabalho premiado (terceiro lugar) no XVI Concurso de Teses e Dissertações, CTD’2003.

2002

  • A.C.R. da Silva, J.A. Ferro, F.C. Reinach, C.S. Farah, L.R. Furlan, R.B. Quaggio, C.B. Monteiro-Vitorello, M.A. Van Sluys, N.F. Almeida, L.M.C. Alves, A.M. do-Amaral, M.C. Bertolini, L.E.A. Camargo, G. Camarotte, F. Cannavan, J. Cardozo, F. Chambergo, L.P. Ciapina, R.M.B. Cicarelli, L.L. Coutinho, J.R. Cursino-Santos, H. El-Dorry, J.B. Faria, A.J.S.Ferreira, R.C.C. Ferreira, M.I.T. Ferro, E.F. Formighieri, M.C. Franco, C.C. Greggio, A. Gruber, A.M. Katsuyama, L.T. Kishi, R.P. Leite, E.G.M. Lemos, M.V.F. Lemos, E.C. Locali, M.A. Machado, A.M.B.N. Madeira, N.M. Martinez-Rossi, E.C. Martins, J. Meidanis, C.F.M. Menck, C.Y. Miyaki, D.H. Moon, L.M. Moreira, M.T.M. Novo, V.K. Okura, M.C. Oliveira, V.R. Oliveira, H.A. Pereira, A. Rossi, J.A.D. Sena, C. Silva, R.F. de-Souza, L.A.F. Spinola, M.A. Takita, R.E. Tamura, E.C. Teixeira, R.I.D. Tezza, M. Trindade dos Santos, D. Truffi, S.M. Tsai, F.F. White, J.C. Setubal, J.P. Kitajima. Comparison of the genomes of two Xanthomonas pathogens with differing host specifities. Nature 417(6887):459-463.

  • G.S. Araújo and N.F. Almeida. Phylogeny from whole genome comparison. Proc. of the 1st Brazilian Workshop on Bioinformatics, pp 9-15, Gramado RS, Brazil, October 18, 2002.

  • N.F. Almeida. Tools for genome comparison, Doctoral Thesis (in Portuguese). IC-UNICAMP, Campinas, SP, May, 2002.

2001

  • D.W. Wood, J.C. Setubal, R. Kaul, D.E. Monks, J.P. Kitajima, V.K. Okura, Y. Zhou, L. Chen, G.E. Wood, N.F. Almeida., L. Woo, Y. Chen, I.T. Paulsen, J.A. Eisen, P.D. Karp, D. Bovee Sr., P. Chapman, J. Clendenning, G. Deatherage, W. Gillet, C. Grant, T. Kutyavin, R. Levy, Meng-Jin Li, E. McClelland, A. Palmieri, C. Raymond, G. Rouse, C. Saenphimmachak, Z. Wu, P. Romero, D. Gordon, S. Zhang, H. Yoo, Y. Tao, P. Biddle, M. Jung, W. Krespan, M. Perry, B. Gordon-Kamm, L. Liao, S. Kim, C. Hendrick, Z. Zhao, M. Dolan, F. Chumley, S.V. Tingey, J. Tomb, M.P.Gordon, M.V. Olson, E.W. Nester. The Genome of the Natural Genetic Engineer Agrobacterium tumefaciens C58. Science 294(5550):2317-2323.

  • J.C. Setubal and N.F. Almeida. Detection of related genes in procaryotes using syntenic regions. DIMACS Workshop on Whole Genome Comparison, Rutgers University, Piscataway, NJ, March, 2001.

  • D.Wood, J.C. Setubal, N. F. Almeida et al. Sequencing and analysis of the Agrobacterium tumefaciens genome. 10th Int’l congress on Molecular plant-microbe interactions. Madison, WI, 2001 (abstract)

1999

1998

1993

  • N.F. Almeida and V.C. Barbosa. Um algoritmo de String-Matching para o modelo CREW-PRAM. Anais da XIX Conferencia Latinoamericana de Informática, Buenos Aires, 1993. 22 JAIO PANEL’93, pp 437-446.

  • N.F. Almeida and V.C. Barbosa. A String-Matching Algorithm for the CREW PRAM. Information Processing Letters 47(5):257-259.

1992

  • N.F. Almeida Parallel Algorithms for String-matching. Master Thesis (in Portuguese) COPPE-UFRJ, Rio de Janeiro, September, 1992.

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