Tools

BisoGenet

Bioinformatic tool for searching, visualizing and analizing molecular interactions information around a set of genes/proteins.

 

Isotopica

Calculation and visualization of the isotopic distribution from molecular formulas or the sequence of peptides, proteins, DNA, RNA and carbohydrates.

 

Structures superposition

Web server for the structural alignment of protein pairs and the analysis of conformational changes.

Websites of Interest

 

 

 

 

 

 

Publications
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Fernandez-de-Cossio J. Computation of the Isotopic Distribution in Two Dimensions. Anal Chem. [Epub ahead of print] 2010 Jul 8. [abstract][full text]

 

Martin A, Ochagavia ME, Rabasa LC, Miranda J, Fernandez-de-Cossio J, Bringas R. Bisogenet: A new tool for gene network building, visualization and analysis. BMC Bioinformatics , 10:91 , 2010. [abstract][full text]

 

Fernandez-de-Cossio J. Efficient Packing Fourier-Transform Approach for Ultrahigh Resolution Isotopic Distribution Calculations. Anal Chem. [Epub ahead of print] 2010 [abstract] [full text]

 

Trujillo LE, Menéndez C, Ochagavía ME, Hernández I, Borrás O, Rodríguez R, Coll Y, Arrieta JG, Banguela A, Ramírez R, Hernández L. Engineering drought and salt tolerance in plants using SodERF3, a novel sugarcane ethylene responsive factor. Biotecnología Aplicada 26(2):168-171, 2009.[abstract] [full text]

 

Cutiño-Jiménez AM, Martins-Pinheiro M, Lima WC, Martín-Tornet A, Morales OG, Menck CFM. Evolutionary placement of xanthomonadales based on conserved protein signature sequences. Molecular Phylogenetics and Evolution, 2009.[abstract] [full text]

 

Sánchez A, Betancourt L, González LJ, Ramos Y, Gil J, Solano Y, Morera V, García Y, Álvarez F, Moya G, Fernández-de-Cossio J, Padrón G, Besada V. Desarrollo de nuevos métodos para el estudio del péptido N-terminal de proteínas y sus aplicaciones en la industria biotecnológica. Biotecnología Aplicada 25(4):384-387, 2008.[abstract] [full text]

 

Junco J.A., Basulto R., Fuentes F., Bover E., Reyes O., Pimentel E., Calzada L., Castro M.D.,Arteaga N., López Y., Hernández H., Bringas R., Garay H., Peschke P., Bertot J., Guillén G. Gonadotropin Releasing Hormone-Based Vaccine, an Effective Candidate for Prostate Cancer and Other Hormone-sensitive Neoplasms. In: Adv Exp Med Biol 617:581-7, 2008. [abstract] [full text]

 

Junco JA, Basulto R, Fuentes F, Bover E, Castro MD, Reyes O, Pimentel E, Calzada L, López Y, Bringas R, Arteaga N, Hernández H, Garay H, Aguero L, Guillén G. Inducción de ablación androgénica e inhibición de tumores hormonosensibles de próstata mediante la inmunización con el péptido sintético GnRHm1-TT adyuvado con VSSP. Biotecnología Aplicada 25(2):171-173, 2008. [abstract] [full text]

 

Miranda J, Bringas R. Análisis de Datos de Microarreglos de ADN. Part I: Antecedentes de la tecnología y diseño experimental. Biotecnología Aplicada 25. 2008 [abstract] [full text]

 

Miranda J, Bringas R. Análisis de Datos de Microarreglos de ADN. Parte II: Cuantificación y Análisis de la Expresión Génica. Biotecnología Aplicada 25. 2008 [abstract] [full text]

 

Ramos Y, Gutierrez E, Machado Y, Sánchez A, Castellanos-Serra L, González LJ, Fernández-de-Cossio J, Pérez-Riverol Y, Betancourt L, Gil J, Padrón G, Besada V. Proteomics based on peptide fractionation by SDS-free PAGE. J Proteome Res 7:2427-34, 2008.[abstract] [full text]

 

Trujillo LE, Sotolongo M, Menéndez C, Ochagavía ME, Coll Y, Hernández I, Borrás O, Thomma BPHJ, Vera P, Hernández L Different stress signals determine the expression pattern of sugarcane SodERF3, a novel sugarcane Ethylene Responsive Factor (ERF) enhances salt and drought tolerance when over-expressed in tobacco plants, Plant and Cell Physiology , 2008. [abstract] [full text]

 

Lee HJ, Manke T, Bringas R, Vingron M. Prioritization of gene regulatory interactions from large-scale modules in yeast, BMC Bioinformatics , 9: 32, 2008. [abstract] [full text]

 

Junco JA, Peschke P, Zuna I, Ehemannd V, Fuentes F, Bover E, Pimentel E, Basulto R, Reyes O, Calzada L, Castro MD, Arteaga N, López Y, Garay H, Hernández H, Bringas R, Guillén GE. Immunotherapy of prostate cancer in a murine model using a novel GnRH based vaccine candidate, Vaccine, 25: 8460-68, 2007. [abstract] [full text]

 

Ferrer A, Nazábal M, Companioni O, Fernandez de Cossio ME, Camacho H, Cintado A, Benítez J, Casalvilla R, Sautié M, Villareal A, Díaz T, Marrero A, Fernández-de-Cossío J, Hodelin A, Leal L, Ballester L, Novoa LI, Middleton D, Dueñas M. HLA class I polymorphism in the Cuban population, Human Immunology , 68 (11): 918-27, 2007. [abstract] [full text]

 

Bringas R. Book Review: Microcompetition with foreign DNA and origin of chronic disease, by Hanan Polansky, Biotecnologia Aplicada , 23 (1): 52, 2006. [abstract] [full text]

 

Sánchez A, González LJ, Betancourt L, Gil J, Besada V, Fernandez-de-Cossio J, Rodriguez-Ulloa A, Marrero K, Alvarez F, Fando F, Padrón G. Selective isolation of multiple positively-charged peptides for 2DE-free quantitative proteomics, Proteomics, 6 (16): 4444-55, 2006. [abstract] [full text]

 

Sánchez A., González LJ, Ramos Y, Betancourt L, Gil J, Besada V, Fernandez-de-Cossio J, Alvarez F, Padrón G. Selective isolation of lysine-free tryptic peptides delimited by arginine residues: A new tool for proteome analysis, J Proteome Res, 5: 1204-1213, 2006. [abstract] [full text]

 

Betancourt L, Gil J, Besada V, Gonzalez LJ, Fernandez-de-Cossio J, Garcia L, Pajon R,Sanchez A, Alvarez F, Padron G. SCAPE: a new tool for the Selective CApture of PEptides in protein identification, J Proteome Res, 4(2): 491-496, 2005. [abstract] [full text]


Fernandez-de-Cossio J, Gonzalez LJ, Satomi Y, Betancourt L, Ramos Y, Huerta V, Besada V, Padron G, Minamino N, Takao T Automated interpretation of mass spectra of complex mixtures by matching of isotope peak distributions, Rapid Commun Mass Spectrom, 18(20): 2465-72, 2004. [abstract] [full text]

 

Fernández-de-Cossío J., Gonzalez L.J., Satomi Y., Betancourt L., Ramos Y., Huerta V., Amaro A., Besada V., Padron G., Minamino N.,Takao T. Isotopica: a tool for the calculation and viewing of complex isotopic envelopes, Nucl. Acids. Res., 32: w674-w678, 2004. [abstract] [full text]

 

Ochagavía M.E. and Wodak, S. Progressive Combinatorial Algorithm for Multiple Structural Alignments: Application to Distantly Related Proteins, Proteins: Structure, Function, and Genetics, 55: 436-454, 2004. [abstract] [full text]

 

Manke T.,Bringas R., Vingron M. Correlating Protein-DNA and Protein-Protein Interaction Networks, Journal of Molecular Biology, 333: 75-85, 2003. [abstract] [full text]

 

Ochagavía M.E., Richelle J. and Wodak S.J. Advanced pairwise structure alignment of proteins and analysis of conformational changes, Bioinformatics, 18: 637-640, 2002. [abstract] [full text]

 

García C. A., Pérez G., Peña C., Ortega M., Quintana M. , Miranda J. Estrategia para el establecimiento de las especificaciones de calidad en el Centro de Ingeniería Genética y Biotecnología de La Habana, Cuba, Biotecnologia Aplicada , 18: 211-221, 2001. [abstract] [full text]

 

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