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. April 2010, Volume 11, Number 238

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. March 2010, Volume 100, Number 3, 208-215

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.OCarroll, 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. July 2009, Volume 191, Number 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. June 2009, Volume 191, Number 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. April 2009, Volume 191, Number 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. Jan 2009, Volume 22, Number 1: 52-62.

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, 2007, 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 and L.P.Brazil
Mapping Contigs onto Reference Genomes
BSB'07, LNBI 4643, pp. 153-157, 2007, M.-F.Sagot and M.E.M.T.Walter (Eds.), Springer-Verlag Berlin Heidelberg 2007.

R.V.Andrade, S.P.da Silva, F.A.G.Torres, M.J.Pocas-Fonseca, I.Silva-Pereira, A.Q.Maranhao, 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.Brígido and M.S.S.Felipe
Overview and perspectives on the trasncriptome of Paracoccidioides brasiliensis
Rev Iberoam Micol 2005; 22: 203-212.

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, 2005, J.C.Setubal and S.Verjovski-Almeida (Eds.), Springer-Verlag Berlin Heidelberg 2005.

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 (2005).

M.S.S.Felipe, R.V.Andrade, F.B.M.Arraes, A.M.Nicola, A.Q.Maranhao, F.A.G.Torres, I.Silva-Pereira, M.J.Pocas-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., Vol. 280, No. 26, Issue of July 1, pp. 24706-24714, 2005.

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, 163-184, Vol. 42, 2004.

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, 827-836, Vol. 17, No. 8, 2004.

N.F.Almeida, C.E.R.Alves, E.N.Csceres and S.W.Song,
Comparison of Genomes using High-Performance Parallel Computing
Proceedings of 15th Symposium on Computer Architecture and High Performance Computing
SBAC-PAD 2003- Brazilian Computer Society (SBC), Sao Paulo, SP, Brazil, November 10-12, 2003 IEEE Computer Society, pp. 142-148, 2003.

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, Vol. 20, No. 3, 263-271, 2003.

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, Vol. 185, No. 3, 1018-1026, 2003.

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, May 23 2002.

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, Dec 14 2001.

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

N. F. Almeida Jr & V. C. Barbosa
A String-Matching Algorithm for the CREW PRAM,
Information Processing Letters, 47(5), October 1993, pp 257-259.