| Roberto Togawa
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Background
Ph.D. at the University of Bedforshire, former University of Luton, under the supervision of Dr. Jonathan Mullins, developing a Suite of Bioinformatics Tools for the Analysis and Prediction of Membrane Protein Structure - 2006 - UK;
Birkbeck College's Advanced Certificate in the Principles of Protein Structure using the Internet. This course is accredited by the University of London - 2005 - UK;
B.Sc. in computer science at Brasilia University (UnB) 1984 - Brazil;
Working at Embrapa Genetic Resources and Biotechnology from 1993 to 1994 as a system manager in the bioinformatics laboratory under supervision of Dr. Goran Neshich;
Bioinformatics training at Barry Honig's Lab at Department of Biochemistry and Molecular Biophysics located at Columbia University - New York - USA - 3 months - summer '97;
Development of STING and a suite of programs to analyze protein sequence structures developed in perl, javascript and HTML.
Activities
Working at Embrapa - Genetic resources and Biotechnology - Bioinformatics laboratory - Brasilia - Brazil since 1995 (permanent contract January 1995);
Activities at the Bioinformatics laboratory - Embrapa Genetic resources and Biotechnology:
Working in the team that developed SisGen - SisGen is a genomic annotation system developed at the Bioinformatics Laboratory of Embrapa Genetic Resource and Biotechnology. The system integrates tools for analysis and visualization of nucleotide sequences and chromatograms produced by automatic sequencing equipments (Megabace, ABI 3700, ABI 3100). Base call is done using PHRED and after quality analysis and cleaning the accepted sequences are stored in a relational database for further investigation. Analysis, such as clustering, similarity search (BLAST), differential expression, search for molecular markers, are created in batch mode and are easily browsed or searched;
Web administrator;
Web designer;
System administrator - LINUX servers and PC/windows machines;
Perl programmer;
Participating at the Membrane Protein Structural Bioinformatics group at Swansea (Swansea University - UK);
Participating at the Musa Genomics - Brazil group;
Participating at the Genoma bovino group;
Participating at the Projeto Orygens group (Genomic inovations for gene discovery and breeding of grasses);
Participating at the Nutrigenomics Project (Functional Foods);
Participating at the MusaGeneBR Project
Participating at the Rede Genomica Animal Project
Participating at the Genetica molecular e melhoramento de arroz Project
Participating in the team that developed STING under supervision of Dr. Goran Neshich - STING is a new Java-based WWW tool for the simultaneous display of information about macro molecular structure and sequence. Includes graphical amino acid Contacts, Ramachandran plot, Surfaces, Sequence neighbors and other features. Parsing of data from relevant Data Bases (HSSP and SwissProt) is one of the key features of this integrated environment for structure/function analysis of the proteins, DNA and their complexes.
Work presented at scientific meetings
Costa M.M , Martins N.F. , Togawa R.C. , Pappas G.J. Functional Annotation tool as SisGen. X-meeting 2009 - Angra dos Reis - Rio de Janeiro - Brazil.
Togawa, R.C.; Miranda, V.; Neshich, L.M.C.; Couri, S. and Monte D.C. Using web 2.0 to manage the Portal of the Functional Food (nutrigenomics) Project of Embrapa. XXXVII Annual Meeting of the Brazilian Society of Biochemistry and Molecular Biology (SBBq) - Aguas de Lindoia - SP - Brazil - 2008.
Barbosa, A. E. A. D.; Souza, D. S. L.; Lima, L. M.; Fragoso, R. R.; Guimarães, L. M.; Viana, A. A. B.; Oliveira Neto, O. B.; Paes, N.; Carneiro, R.; Togawa, R. C.; Martins, N. F.; Grossi De Sá, M. F. Análise de genótipos de algodão contrastantes quanto a resistência ao nematóide Meloidogyne incognita. Congresso Brasileiro de Genética, 53., 2007, Águas de Lindóia. Resumos... Águas de Lindóia: Sociedade Brasileira de Genética, 2007. p. 282.
Togawa, R.C.; Antoniw, J.F.; Mullins, J.G.L. Prediction of Transmembrane Region Adjacencies in Membrane Proteins. 14th Annual International Conference on Intelligent Systems for Molecular Biology - ISMB - Fortaleza - CE - Brazil - 2006.
Togawa, R.C.; Brigido, M.M.; Santos, C.M.R.; Júnior, M.T. The use of the PHPH tool to assembly the gene sequences that are candidate to the biotic and abiotic stress in Musa acumitana. XXXV Annual Meeting of the Brazilian Society of Biochemistry and Molecular Biology (SBBq) - Aguas de Lindoia - SP - Brazil - 2006.
Ramos, A.R.; Togawa, R.C.; Martins, N.F.; Gander, E.S.; Marcellino, L.H. Caracterização do gene codificante para osmotina (Osm 1) em cacau ( Theobroma cacao L.). Congresso Brasileiro de Genética. Aguas de Lindoia - SP - Brasil - 2005.
Catelan, R.; Togawa, R.C.; Costa, M.M.C.; Martins, N.F.; Pessoa Filho, M.A.C.P.; Ferreira, M.E. Desenvolvimento de marcadores âncora baseados em reação de polimerase em cadeia para estudos de sintenia em gramíneas. Congresso Brasileiro de Genética. Aguas de Lindoia - SP - Brasil - 2005.
da Silva, F.R.; Santos, C.M.R.; Martins, N.F.; Togawa, R.C.; Ciampi, A.Y.; Vilarinhos, A.; Pifanelli, P.; Souza Júnior, M.T. Musa acuminata genome fragments reveal some banana secrets. XXXIII Annual Meeting of the Brazilian Society of Biochemistry and Molecular Biology (SBBq)- Caxambu - MG - Brazil - 2004.
Costa M.M., Togawa R.C., Miranda R. and Pappas G. Distributed BLAST using grid service technology. Second Brazilian Workshop on Bioinformatics - WOB 2003. Macaé Rio de Janeiro, Brazil December 3-5, 2003.
Martins N.F., Santos C.R., de Almeida P.C.M., Coelho M.C.F., Togawa R.C., da Silva F.R. and Souza Junior M.T. Transcriptoma em Musa Acuminata analise preliminar. V simposio Brasileiro sobre Bananicultura - I Workshop do genoma Musa. p. 259-261. 10-14 November 2003 - Paracatu - MG - Brazil.
Silva, F. F. da; Ciamp, A. Y.; Martins, N. F.; Togawa, R. C.; Souza Junior, M. T. Fragmentos do genoma de musa acuminata análise preliminar. V simposio Brasileiro sobre Bananicultura - I Workshop do genoma Musa. p.262-265. 10-14 November 2003 - Paracatu - MG - Brazil.
Goran Neshich, Togawa R.C., Walter Rocchia, Adauto L. Mancini, Paula R. Kuser, Michel E. B. Yamagishi, Alexandre Alvaro, Christian Baudet and Roberto H. Higa "STING MILLENNIUM SUITE v.3 and JAVA PROTEIN DOSSIER: a novel concept in data visualization and analysis of the protein structure/function relationship" has been accepted for presentation at ISMB2003, Brisbane, 29th June - 3rd July, 2003.
Martins N.F., Rossi A., Ruiz M.C., Togawa R.C., Costa M.M. BtDAT Structural database for delta-endotoxins. XXXII Reunião Anual da SBBq May 2003 - Caxambu - MG - Brazil
Togawa R.C. and Brigido M.M. PHPH: Web based tool for simple electropherogram quality analysis. 1st International conference on Bioinformatics and Computational Biology IcoBiCoBi May 14th 16th 2003 Ribeirão Preto - Brazil.
Goran Neshich, Togawa R.C., Wellington Vilella Torres, Tharsis Fonseca e Campos, Leonardo Lima Ferreira, Adilton Guedes Oliveira, Ronald Tetsuo Miura, Marcus Kiyoshi Inoue, Luiz Gustavo Horita, Georgios Pappas Jr.,Barry Honig: "STING Millennium: Web based suite of programs for comprehensive and simultaneous analysis of structure and sequence", ISMB 2001, Denmark, abstract#87.
Sarakinou K.S., Antoniw J.F. , Togawa R.C., Mullins J.G.L. TMAlpha: A software tool for analysis of transmembrane region alpha helices. Biochem. Soc. Trans. 29, (3), A74, 36. 2001
Da Silva M.C.M., Neshich G., Ghrispeels M., Togawa R.C. & Grossi de Sa, M.F: Molecular Basis of the Interactions Between Insect Alpha-Amylases and Inhibitors. XXVIII Reuniao Anual da Sociedade Brasileira de Bioquimica e Biologia Molecular - SBBq - Caxambu,MB - May 22-25, 1999. e Biologia Molecular - SBBq - Caxambu, MB - May 22-25, 1999.
Da Silva M.C.M., Neshich G., Togawa R.C., M.Crispeels & Grossi de Sa M.F. Molecular Modeling of Plant alpha-amylase inhibitors and insect alpha-amylases complexes. III Encontro Latino Americano De Biotecnologia Vegetal, La Havana, Cuba, June 1-5, 1998.
Cavalcante T.B., Aidar A.R., Togawa R.C. & Neshich G.: Field data collection, relational data-base data formating, printing of the data on the self-adhesive labels and data distribution through World Wide Web. XLVII Congresso Nacional de Botanica, Nova Friburgo/RJ, 21-26 de Julho de 1996.
Publications
Mullins J.G., Parker J.E., Cools H.J., Togawa R.C., Lucas J.A., Fraaije B.A., Kelly DE, Kelly S.L. Molecular modelling of the emergence of azole resistance in Mycosphaerella graminicola. PLoS One. 2011;6(6):e20973. Epub 2011 Jun 27.
Arango R.E. ; Togawa R.C. ; Carpentier S.C. ; Roux N. ; Hekkert B.L. ; Kema G.H.J. ; Souza M.T. Genome-wide BAC-end sequencing of Musa acuminata DH Pahang reveals further insights into the genome organization of banana. Tree Genetics & Genomes (Print), v. 7, p. 933-940, 2011.
Ribeiro C., Togawa R.C., Neshich I.A., Mazoni I., Mancini A.L., Minardi R.C., da Silveira C.H., Jardine J.G., Santoro M.M., Neshich G. Analysis of binding properties and specificity through identification of the interface forming residues (IFR) for serine proteases in silico docked to different inhibitors. BMC Struct Biol. 2010 Oct 20;10:36.
Martel C.M., Warrilow A.G., Jackson C.J., Mullins J.G., Togawa R.C., Parker J.E., Morris M.S., Donnison I.S., Kelly D.E. and Kelly S.L. Expression, purification and use of the soluble domain of Lactobacillus paracasei beta-fructosidase to optimise production of bioethanol from grass fructans. Bioresour Technol. 2010 Jun;101(12):4395-402. Epub 2010 Feb 12.
Arrial, Roberto T ; Togawa, R.C. ; Brigido, Marcelo M . Screening non-coding RNAs in transcriptomes from neglected species using PORTRAIT: case study of the pathogenic fungus Paracoccidioides brasiliensis. BMC Bioinformatics, 10:239, 2009.
Silva, Tulio C. , Berger, Pedro A., Arrial, Roberto T., Togawa R.C., Brigido, Marcelo M. and Walger, Maria Emilia M. T. SOM-PORTRAIT: Identifying Non-coding RNAs Using Self-Organizing Maps.Lecture Notes in Computer Science, v. 5676, p. 73-85, 2009.
Santos, Candice M.R. ; Martins, N.F. ; Araujo, M.M.M. ; Silva, F.R. ; Togawa, R.C. ; Souza Jr, M. T. Screening of the DATAMusa Database for orthologs of Genes Known to be related to Biotic and Abiotic Stresses to identify and characterize candidate genes. Acta Horticulturae, v. 828, p. 341-352, 2009.
Miller, R.N.; Bertioli, D.J.; Baurens, F.C.; Santos, C.M.; Alves, P.C.; Martins, N.F.; Togawa, R.C.; Souza, M.T.Jr. and Pappas G.J.Jr. (2008) Analysis of non-TIR NBS-LRR resistance gene analogs in Musa acuminata Colla: isolation, RFLP marker development, and physical mapping. BMC Plant Biol. 8:15.
Pappas GJ Jr. ; Miranda, R.P. ; Martins N.F. ; Togawa R.C. ; Costa, M.M.C. SisGen: A CORBA Based Data Management Program for DNA Sequencing Projects. Lecture Notes in Computer Science, v. 5109, p. 116-123, 2008.
Arrial, R.T., Togawa, R.C., Brigido M.M. (2007) Outlining a strategy for screening non-coding RNAs on a transcriptome through support vector machines. Springer-Verlag Berlin Heidlberg, M.-F. Sargot and M.E.M.T. Walter (eds.): BSB 2007, LNBI 4643, pp. 149-152.
Neshich, G., Borro, L.C., Higa, R.H., Kuser, P.R., Yamagishi, M.E., Franco, E.H., Krauchenco, J.N., Fileto, R., Ribeiro, A.A., Bezerra, G.B., Velludo, T.M., Jimenez, T.S., Furukawa, N., Teshima, H., Kitajima, K., Bava, A., Sarai, A., Togawa, R.C., Mancini, A.L. (2005) The Diamond STING server. Nucleic Acids Res. 33(Web Server issue):W29-35.
Santos, C.M., Martins, N.F., Horberg, H.M., de Almeida, E.R., Coelho, M.C., Togawa, R.C., da Silva, F.R., Caetano, A.R., Miller, R.N., Souza, M.T. Jr. (2005). Analysis of expressed sequence tags from Musa acuminata ssp. burmannicoides, var. Calcutta 4 (AA) leaves submitted to temperature stresses. Theor Appl Genet. 110(8):1517-22. Epub 2005 Apr 20.
Neshich, G., Rocchia, W., Mancini, A.L., Yamagishi, M.E., Kuser, P.R., Fileto, R., Baudet, C., Pinto, I.P., Montagner, A.J., Palandrani, J.F., Krauchenco, J.N., Torres, R.C., Souza, S., Togawa, R.C., Higa, R.H. (2004). JavaProtein Dossier: a novel web-based data visualization tool for comprehensive analysis of protein structure. Nucleic Acids Res. ;32(Web Server issue):W595-601.
Higa, R.H., Togawa, R.C. Montagner, A.J., Palandrani, J.C., Okimoto, I.K., Kuser, P.R., Yamagishi, M.E., Mancini, A.L., Neshich, G. (2004) STING Millennium Suite: integrated software for extensive analyses of 3d structures of proteins and their complexes. BMC Bioinformatics. 5(1):107.
Higa, R.H., Montagner, A.J., Togawa, R.C., Kuser, P.R., Yamagishi, M.E., Mancini, A.L., Pappas, G. Jr., Miura, R.T., Horita, L.G., Neshich, G. (2004) ConSSeq: a web-based application for analysis of amino acid conservation based on HSSP database and within context of structure. Bioinformatics. 20(12):1983-5. Epub 2004 Mar 25.
Higa, R.H., Oliveira, A.G., Horita, L.G., Miura, R.T., Inoue, M.K., Kuser, P.R., Mancini, A.L., Yamagishi, M.E., Togawa, R.C., Neshich, G. (2004) Defining 3D residue environment in protein structures using SCORPION and FORMIGA. Bioinformatics. 20(12):1989-91. Epub 2004 Mar 25.
Mancini A.L., Higa R.H., Oliveira A., Dominiquini F., Kuser P.R., Yamagishi M.E., Togawa R.C., Neshich G. (2004). STING contacts: a web-based application for identification and analysis of amino acid contacts within protein structure and across protein interfaces. Bioinformatics.
Neshich, G., Togawa, R.C., Mancini, A.L., Kuser, P.R., Yamagishi, M.E., Pappas, G. Jr., Torres, W.V., Campos, T.F., Ferreira, L.L., Luna, F.M., Oliveira, A.G., Miura, R.T., Inoue, M.K., Horita, L.G., De Souza, D.F., Dominiquini, F., Alvaro, A., Lima, C.S., Ogawa,F,O., Gomes, G.B., Palandrani, J.F., Dos Santos, G.F., De Freitas, E.M., Mattiuz, A.R., Costa, I.C., De Almeida, C.L., Souza, S., Baudet, C., Higa, R.H. (2003). STING Millennium: a web-based suite of programs for comprehensive and simultaneous analysis of protein structure and sequence Nucleic Acids Research 31(13):3386-3392.
Togawa R.C., Antoniw J.F. and, Mullins J.G.L. (2001) TMCompare : transmembrane region sequence and structure. Bioinformatics.17:1238-1239. [PDF]
Da Silva M.C.M., Grossi de Sá M.F., Chrispeels M.J., Togawa R.C. and G. Neshich (2000) Analysis of Structural and Physico-chemical Parameters Involved in the Specificity of Binding between Alpha-Amylases and their Inhibitors. Protein Engineering, 3:167-177.
Neshich G., Togawa R.C., Villela W. and Honig B. (1998) Sequence To and withIN Graphics PDB Viewer (STING-PDB viewer) - PDB Quarterly NewsLetter, July 1998, page 6 - electronic edition.
Neshich G., Togawa R.C., Prilusky J. , Suussman J. and Honig B. (1998). Searching for the Right PDB File with the 3DB Browser and Displaying Structure and Sequence Data with STING - PDB Quarterly NewsLetter, July 1998, page 7 - electronic edition.
Cavalcante T.B. ,Rezende A. ,Togawa R.C. , Rodrigues P., Magalhaes L. and Neshich G. (1998). A new field tested data gathering, recording, transfer and dissemination via the World Wide Web. - Taxon , 47:381-386.
Links of interest
Electropherogram quality analysis Main Website @Brasilia University / mirror @Embrapa / mirror @Brasilia Catholic University
PDB - Protein Data Bank
Swiss-Prot - Protein Sequences
Modelling @ ILS (Institute of Life Science - University of Swansea)
Bioinformatics Laboratory at Universidade Catolica de Brasilia - Brasil
CHIME Plugin
The VRML Repository
Dr.Bob's Delphi Clinic
NCBI Entrez PubMed
DNA Database Growth
The 5K page
