Sandro Souza

Professor de Souza graduated in Biological Sciences from The Federal University of Paraná in 1989. He obtained his Ph.D in Biochemistry from the University of São Paulo in 1993. He was a Pew Latin American Fellow in Harvard from 1995 to 1998. After returning to Brazil, he has become one of the pioneers of the Genomics and Bioinformatics initiatives in the country. Presently, he is Professor of Bioinformatics at the Brain Institute of the Federal University of Rio Grande do Norte. Elected in 2009 by the World Economic Forum a Young Global Leader. He was Tinker Visiting Professor at the University of Chicago in 2011.

BioME is a bioinformatics initiative created in 2016 in the UFRN, Natal - Brazil. However, the history of BioME is directly linked to UFRN's efforts to recruit important leaders with expertise in the field of Bioinformatics and training of personnel; in the establishment of the Digital Metropolis Institute (IMD) and its innovative model, and the creation of the Postgraduate Program in Bioinformatics.

In 2011, the establishment of the Brain Institute and the IMD, motivated the recruitment of group leaders working at the interface of computer and life sciences. Since then, IMD has been acting on the frontier of basic research and innovation, promoting a culture of entrepreneurship, as well as research and technological innovation. In 2012, Prof. Sandro José de Souza, one of the pioneers of the area in Brazil and with a history of success in training human resources in Bioinformatics, was recruited by the Brain Institute. More recently, four other bioinformaticians were recruited by UFRN. This group of newcomers joined other professors already established at UFRN, who are exponents in their fields.

The approval of the "Cancer Systemic Biology" project (BSC) under CAPES’ Computational Biology call (051/2013) also contributed to define bioinformatics as a priority within UFRN. The main objective of the BSC network is to promote computational biology and system biology in Brazil, and is coordinated by Prof. Sandro J. de Souza, and is formed by twenty professors/researchers in teams at UFRN, UFMG, USP and the Antonio Prudente Foundation, as well as foreign researchers at the University of California San Diego, University of Heidelberg and University of Oslo.

In early 2014, discussions between Prof. Sandro José de Souza and Prof. José Ivonildo do Rêgo (director of IMD and former rector of UFRN) led to the establishment of an emphasis on Bioinformatics in the Bachelor's degree in Information Technology (BTI). By mid-2015, after internal discussions in UFRN involving professors from several departments including Prof. José Ivonildo do Rêgo, Prof. Edna Maria da Silva (at the time, pro-rector of post-graduation) and Prof. Ângela Cruz (dean of UFRN), the Postgraduate Program in Bioinformatics at UFRN was established. As part of the Digital Metropolis Institute, the program has the following research lines: Genomics; Systems Biology; and Development of product and processes. Its master and doctorate courses began their activities in 2016 with a CAPES score of 5 (of maximum 7).

Finally, in 2016 the Bioinformatics Multidisciplinary Environment (BioME) was created with the mission to promote bioinformatics at the regional and national scenario, acting in four different levels.

(1) At the teaching level, BioME professors/researchers work at the undergraduate and postgraduate levels with the objective to build human resources highly skilled in bioinformatics, for both the academic field and the productive/industrial sectors.

(2) At the research level, multidisciplinary groups involved with BioME produce cutting- edge bioinformatics science applied to several areas such as: cancer biology, systems modeling, systems biology, genomics, proteomics, molecular evolution, structural bioinformatics, etc.

(3) At the services sector, a multi-user technical center provides bioinformatics and data analysis services to both academic and biotechnology companies.

(4) At the corporate program, seeking to foster productive interaction with the biotechnology industry and extending to the society the knowledge produced in the university.


Publications


  • Silva VL, Santos AMR, Blanco W, Souza SJ. Gain of transcription factor binding sites is associated to changes in the expression signature of human brain and testis and is correlated to genes with higher expression breadth. Sci. China Life Sci. 2019;62:526.
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  • Putnam, C. D. et al. A genetic network that suppresses genome rearrangements in Saccharomyces cerevisiae and contains defects in cancers. Nat. Commun. 7:11256 doi: 10.1038/ncomms11256 (2016).
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  • Stransky, Beatriz ; de Souza, Sandro J. . Modeling tumor evolutionary dynamics. Frontiers in Physiology, v. 3, p. 480, 2013.
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  • SCHRIDER, DANIEL R. ; NAVARRO, FABIO C. P. ; Galante, Pedro A. F. ; Parmigiani, Raphael B. ; CAMARGO, ANAMARIA A. ; HAHN, MATTHEW W. ; de Souza, Sandro J. . Gene Copy-Number Polymorphism Caused by Retrotransposition in Humans. PLOS Genetics (Online), v. 9, p. e1003242, 2013.
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  • de Souza, J. E. ; Galante, P A ; VALIERIS, R. ; da Cunha, J. P. C. ; Ohno-Machado, L. ; Old, L. J. ; de Souza, Sandro J. . SurfaceomeDB: a cancer-orientated database for genes encoding cell curface proteins. Cancer Immunity, v. 12, p. 15, 2012.
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  • KROLL, JOSÉ EDUARDO ; Galante, Pedro A.F. ; OHARA, DANIEL T. ; NAVARRO, FABIO C.P. ; OHNO-MACHADO, LUCILA ; de Souza, Sandro J. . SPLOOCE: A new portal for the analysis of human splicing variants. RNA Biology, v. 9, p. 1339-1343, 2012.
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  • de Souza, Sandro J. . Domain shuffling and the increasing complexity of biological networks. BioEssays (Cambridge), v. 34, p. 655-657, 2012.
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  • FRANÇA, GUSTAVO S. ; CANCHERINI, DOUGLAS V. ; Souza, Sandro J. . Evolutionary history of exon shuffling. Genetica (Dordrecht. Online), v. 140, p. 249-257, 2012.
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  • ZHAO, Q. ; CABALLERO, O. L. D. ; GALANTE, Pedro Alexandre Favoretto ; PARMIGIANI, Raphael Bessa ; EDSHALL, L. ; KUAN, S. ; LEVY S. ; YE, Z. ; Ana Tereza Ribeiro de Vasconcelos ; REN BING ; de Souza, Sandro J ; CAMARGO, Anamaria Aranha ; SIMPSON, Andrew J G ; STRAUSBERG, Robert L . Systematic detection of putative tumor suppressor genes throuh the combined use of exome and transcriptome sequencing. GenomeBiology.com (London. Print), v. 11, p. R114, 2011.
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  • Daniel O Vidal ; SOUZA, Jorge Estefano Santana de ; PIRES, Lilian C ; MASOTTI, C. ; SALIM, A. C. M. ; COSTA, Maria C R ;GALANTE, Pedro Alexandre F ; de Souza SJ ; CAMARGO, Anamaria Aranha . Analysis of allelic differential expression in the human genome using allele-specific serial analysis of gene expression tags. Genome (Ottawa. Print), v. 54, p. 120-127, 2011.
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  • Galante, P. A. F. PARMIGIANI, R. B. ZHAO, Q. CABALLERO, O. L. de Souza, J. E. Navarro, F. C. P. Gerber, A. L. Nicolas, M. F. SALIM, A. C. M. Silva, A. P. M. Edsall, L. Devalle, S. Almeida, L. G. YE, Z. KUAN, S. Pinheiro, D. G. Tojal, I. Pedigoni, R. G. de Sousa, R. G. M. A. Oliveira, T. Y. K. de Paula, M. G. Ohno-Machado, L. KIRKNESS, E. F. LEVY, S. da Silva, W. A. , et al. ; Distinct patterns of somatic alterations in a lymphoblastoid and a tumor genome derived from the same individual. Nucleic Acids Research, v. 39, p. 6056-6068, 2011.
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  • CERUTTI, J. M. ; Oler, G. ; Delcelo, R. ; Gerardt, R. ; Michaluart, P. ; de Souza, S. J. ; Galante, P. A. F. ; Huang, P. ; Riggins, G. J. . PVALB, a New Hurthle Adenoma Diagnostic Marker Identified through Gene Expression. The Journal of Clinical Endocrinology and Metabolism, v. 96, p. E151-E160, 2011.
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  • de Souza, J. E. S. ; RAMALHO, R. F. ; Galante, P. A. F. ; MEYER, D. ; de Souza, S. J. . Alternative splicing and genetic diversity: silencers are more frequently modified by SNVs associated with alternative exon/intron borders. Nucleic Acids Research, v. 39, p. 4942-4948, 2011.
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  • Maschietto, M ; Trapé, A P ; Piccoli, F S ; Ricca, T I ; Dias, A A M ; Coudry, R A ; Galante, P A ; Torres, C ; Fahhan, L ; Lourenço, S ; Grundy, P E ; de Camargo, B ; de Souza, S ; Neves, E J ; Soares, F A ; Brentani, H ; Carraro, D M . Temporal blastemal cell gene expression analysis in the kidney reveals new Wnt and related signaling pathway genes to be essential for Wilms' tumor onset. CELL DEATH DIS, v. 2, p. e224, 2011.
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  • Zhao, Qi ; Kirkness, Ewen F ; CABALLERO, Otavia L ; Galante, Pedro A ; Parmigiani, Raphael B ; Edsall, Lee ; Kuan, Samantha ; Ye, Zhen ; Levy, Samuel ; Vasconcelos, Ana Tereza R ; Ren, Bing ; de Souza, Sandro J ; CAMARGO, Anamaria A ; Simpson, Andrew JG ; STRAUSBERG, Robert L . Systematic detection of putative tumor suppressor genes through the combined use of exome and transcriptome sequencing. GenomeBiology.com (London. Print), v. 11, p. R114, 2010.
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  • Cancherini, Douglas V ; França, Gustavo S ; de Souza, Sandro J . The role of exon shuffling in shaping protein-protein interaction networks. BMC Genomics, v. 11, p. S11, 2010.
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  • FERREIRA, Elisa Napolitano e ; Rangel, M.C. ; Galante, P. A. F. ; MOLINA, G. C. ; de Souza, J. E. ; de Souza, S. J. ; CARRARO, Dirce M . Alternative splicing enriched cDNA libraries to identify breast cancer associated transcripts. BMC Genomics, v. 11, p. S4, 2010.
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  • BETTONI, Fabiana ; Filho, Fernando Camargo ; Grosso, Daniela M. ; Galante, Pedro A.F. ; Parmigiani, Raphael B. ; Geraldo, Murilo V. ; Henrique-Silva, Flávio ; Oba-Shinjo, Sueli M. ; Marie, Suely K.N. ; Soares, Fernando A. ; BRENTANI, Helena Paula ; SIMPSON, A. J. G. ; de Souza SJ ; Camargo, A. A. . Identification of FAM46D as a novel cancer/testis antigen using EST data and serological analysis?. Genomics (San Diego), v. 94, p. 153-160, 2009.
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  • Galante, Pedro A. F. ; Sandhu, Devraj ; de Sousa Abreu, Raquel ; Gradassi, Michael ; Slager, Natanja ; Vogel, Christine ; Jose de Souza, Sandro ; Penalva, Luiz O.F. . A comprehensive in silico expression analysis of RNA binding proteins in normal and tumor tissue; identification of potential players in tumor formation. RNA Biology, v. 6, p. 426-433, 2009.
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  • PINHEIRO, Daniel G ; Galante, Pedro AF ; de Souza, Sandro J ; ZAGO, Marco A ; Silva, Wilson A . A score system for quality evaluation of RNA sequence tags: an improvement for gene expression profiling. BMC Bioinformatics, v. 10, p. 170, 2009.
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  • de Souza SJ . Exploiting EST in human health. Methods in Molecular Biology (Clifton), v. 533, p. 311-324, 2009.
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  • ZHAO, Q. ; CABALLERO, O. L. ; LEVY, S. ; STEVENSON, Brian J ; ISELI, C. ; de Souza SJ ; GALANTE, Pedro A F ; BUSAM, D. ; LEVERSHA, M. ; CHADALAVADA, K. ; ROGERS, Y. ; VENTER, J. ; SIMPSON, A. J. G. ; STRAUSBERG, Robert L . Transcriptome-guided characterization of genomic rearrangements in a breast cancer cell line. PNAS. Proceedings of the National Academy of Sciences of the United States of America, v. 106, p. 1886-1891, 2009.
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  • da Cunha, J. P. C. ; Galante, P. A. F. ; de Souza, J. E. ; de Souza, R. F. ; Carvalho, P. M. ; Ohara, D. T. ; Moura, R. P. ; Oba-Shinja, S. M. ; Marie, S. K. N. ; Silva, W. A. ; Perez, R. O. ; Stransky, B. ; Pieprzyk, M. ; Moore, J. ; Caballero, O. ; Gama-Rodrigues, J. ; Habr-Gama, A. ; Kuo, W. P. ; Simpson, A. J. ; Camargo, A. A. ; Old, L. J. ; de Souza SJ . Bioinformatics construction of the human cell surfaceome. Proceedings of the National Academy of Sciences of the United States of America,
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  • de Souza, Sandro J ; Stransky, Beatriz ; CAMARGO, Anamaria A . Insights into gliomagenesis: systems biology unravels key pathways. Genome Medicine, v. 1, p. 101, 2009.
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  • SUGANO, Sumio ; FUJII, Yasuyuki ; TANINO, Motohiko ; KOYANAGI, Kanako O ; HANAOKA, Hideki ; KANEKO, Yayoi ; de Souza SJ ; NAGATA, Naoki ; SAKAI, Hiroaki ; SHIBA, Rie ; SUZUKI, Mami ; TAKAHASHI, Aiko ; IMANISHI, T ; GOJOBORI, Takashi . The H-Invitational Database (H-InvDB), a comprehensive annotation resource for human genes and transcripts.. Nucleic Acids Research, v. 36, p. D793-D799, 2008.
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  • SOUZA, Robson Francisco de ; Anatharaman, V. ; de Souza SJ ; Aravind, L. ; GUEIROS FILHO, Frederico José . AMIN domains have a predicted role in localization of diverse periplasmic protein complexes. Bioinformatics (Oxford), v. 24, p. 2423-2426, 2008.
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  • FERREIRA, Elisa Napolitano e ; Rangel, M.C. ; Pineba, P.B. ; Daniel O Vidal ; CAMARGO, Anamaria A ; de Souza SJ ; CARRARO, Dirce M. Heteroduplex formation and S1 digestion for mapping alternative splicing sites. Genetics and Molecular Research, v. 7, p. 958-969, 2008.
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  • da Cunha, J ; GALANTE, Pedro A F ; de Souza SJ . Different evolutionary strategies for the origin of caspase-1 inhibitors. Journal of Molecular Evolution, v. 66, p. 591-597, 2008.
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  • FERREIRA, B. S. ; BARRERA, Junior ; Lucila Ohno Machado ; de Souza SJ . Modeling cancer: integration of. Journal of Bioinformatics and Computational Biology, v. 5, p. 977-986, 2007.
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  • FERREIRA, Elisa Napolitano e ; GALANTE, Pedro Alexandre Favoretto ; CARRARO, Dirce Maria ; de Souza SJ . Alternative splicing: a bioinformatics perspective.. Molecular Biosystems, v. 3, p. 473-477, 2007.
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  • GALANTE, Pedro Alexandre Favoretto ; Daniel O Vidal ; SOUZA, Jorge Estefano Santana de ; CAMARGO, Anamaria Aranha ; de Souza SJ . Sense-antisense pairs in mammals: functional and evolutionary considerations.. Genome Biology, v. 8, p. R40, 2007. 
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  • SAKABE, Noboru Jô ; de Souza SJ . Sequence features responsible for intron retention in human.. BMC Genomics, v. 8, p. 1-14, 2007.
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  • GALANTE, Pedro Alexandre Favoretto ; TRIMARCH, J. ; Constance L Cepko ; de Souza SJ ; Lucila Ohno Machado ; Winston P Kuo . Automatic correspondence of tags and genes (ACTG): a tool for the analysis of SAGE, MPSS and SBS data.. Bioinformatics (Oxford), v. 23, p. 903-905, 2007.
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  • MAIA, Rafaela M ; VALENTE, Valeria ; CUNHA, Marco A V ; Joseane F Souza ; ARAUJO, Daniela D ; SILVA JR, Wilson A ;ZAGO, M. A. ; DIAS NETO, Emmanuel ; de Souza SJ ; SIMPSON, Andrew Jonh George ; MONESI, Nadia ; Ricardo GP Ramos ; ESPREAFICO, Enilza M ; LARSON, M. L. P. . Identification of unannotated exons of low abundance transcripts in Drosophila melanogaster and cloning of a new serine protease gene upregulated upon injury.. BMC Genomics, v. 8, p. 1-9, 2007.
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  • PARMIGIANI, Raphael Bessa ; BETTONI, Fabiana ; VIBRANOVSKI, Maria Dulcetti ; Marilene H Lopes ; MARTINS, Waleska K ; Isabela W Cunha ; SIMPSON, Andrew John George ; de Souza SJ ; CAMARGO, Anamaria Aranha. Characterization of a cancer/testis (CT) antigen gene family capable of eliciting humoral response in cancer patients.. PNAS. Proceedings of the National Academy of Sciences of the United States of America, v. 28, p. 18066-18071, 2006. 
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  • VIBRANOVSKI, Maria Dulcetti ; SAKABE, Noboru Jô ; de Souza SJ . A possible role of exon-shuffling in the evolution of signal peptides of human proteins.. FEBS Letters, v. 580, p. 1621-1624, 2006.
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  • TANINO, Motohiko ; DEBILY, Marie Anne ; TAMURA, Takuro ; HISHIKI, Teruyoshi ; OGASAWARA, Osamu ; MURAKAWA, Katsuji ; KAWAMOTO, Shoko ; ITOH, Kouichi ; WATANABE, Shinya ; de Souza SJ ; IMBEAUD, Sandrine ; GRAUDENS, Esther ; EVENO, Eric ; HILTON, Phillip ; SUDO, Yukio ; KELSO, Janet ; IKEO, Kazuho ; IMANISHI, Tadashi ; GOJOBORI, Takashi ; AUFFRAY, Charles ; HIDE, Winston ; OKUBO, Kousaku . The Human Anatomic Gene Expression Library (H-ANGEL), the H-Inv Integrative Display of Human Gene Expression across Disparate Technologies and Platforms.. Nucleic Acids Research, v. 33, p. D567-D572, 2005.
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  • VIBRANOVSKI, Maria Dulcetti ; SAKABE, Noboru Jô ; SOARES, Rodrigo ; de Souza SJ . Signs of ancient and modern exon shuffling are correlated to the distribution of ancient and modern domains along proteins.. Journal of Molecular Evolution, v. 60, p. 1-10, 2005.
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  • MARTINS, Vilma Regina ; BRENTANI, Ricardo Renzo ; de Souza SJ . Chasing the elusive cellular prion receptor.. Protein Discovery, 2005.
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  • BRENTANI, Ricardo Renzo ; CAMARGO, Anamaria Aranha ; BRENTANI, Helena Paula ; de Souza SJ . The FAPESP/LICR Human Cancer Genome Project: perspectives on integration.. Cancer Bioinformatics, 2005.
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  • SLAGER, Natanja Sara Kirschbaum ; PARMIGIANI, Raphael Bessa ; CAMARGO, Anamaria Aranha ; de Souza SJ . Identification of human exons over-expressed in tumors through the use of genome and expressed sequence data.. Physiological Genomics, v. 21, p. 423-432, 2005.
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  • de Souza SJ ; GALANTE, Pedro Alexandre F ; SOARES, Rodrigo . Using ORESTES ESTs to mine gene cancer expression data. In: Encyclopedia of Genetics, Genomics, Proteomics and Bioinformatics.. John Wiley And Sons Ltd, 2005.
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  • BRENTANI, Ricardo Renzo ; CARRARO, Dirce Maria ; ALMEIDA, Sérgio Verjovski ; REIS, Eduardo M ; NEVES, e Jordão ; de Souza SJ ; CARVALHO, Alex Fiorini ; BRENTANI, Helena Paula ; REIS, Luiz Fernando Lima . Gene expression arrays in Cancer Research: Methods and Applications.. Critical Reviews in Oncology/Hematology, v. 54, p. 95-105, 2005.
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  • SAKHARKAR, Meena K ; KANGUEANE, Pandjassarame ; WOO, Tong W ; TAN, Tin W ; KOLATKAR, Prasanna R ; LONG, Manyuan ; de Souza SJ . ExInt - An Exon Intron database.. Encyclopediaof Medical Genomics Proteomics Emgp Marcel Dekker, v. 16, n. 12 2000, p. 1151-1152, 2005.
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  • SOGAYAR, Mari Cleide ; CAMARGO, Anamaria A ; de Souza SJ . A transcript finishing initiative for closing gaps in the human transcriptome.. Genome Research, v. 14, p. 1413-1423, 2004.
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  • NUNES, Francis M F VALENTE, Valeria SOUSA, Josane F CUNHA, Marco A V PINHEIRO, Daniel G MAIA, Rafaela M ARAUJO, Daniela D COSTA, Maria C R MARTINS, Waleska K CARVALHO, Alex F MONESI, Nadia NASCIMENTO, Adriana M PEIXOTO, Pablo M V SILVA, Maria F R RAMOS, Ricardo G P REIS, Luis Fernando Lima DIAS NETO, Emmanuel de Souza SJ SIMPSON, Andrew J G ZAGO, Marco Antonio SOARES, Ademilson e e BITONDI, Marcia M G ESPREAFICO, Enilza M ESPINDOLA, Foued LARSON, Maria L Paco , et al. ; The use of Open Reading Frame ESTs (ORESTES) for analysis of the honeybee transcriptome.. BMC Genomics, v. 5, p. 84-96, 2004.
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  • FERREIRA, Elisa Napolitano e PIRES, Lilian C PARMIGIANI, Raphael Bessa BETTONI, Fabiana PUGA, Renato D PINHEIRO, Daniel G ANDRADE, Luís Eduardo C CRUZ, Luciana O DEGAKI, Theri L FARIA JR, Milton FESTA, Fernanda GIANELLA NETO, Daniel GIORGI, Ricardo R GOLDMAN, Gustavo H GRANJA, Fabiana GRUBER, Artur HACKEL, Christine SILVA, Flávio Henrique MALNIC, Bettina MANZINI, Carina V B MARIE, Suely K N ROSSI, Nilce M Martinez SHINJO, Sueli M Oba PARDINI, Maria Ines M C RAHAL, Paula , et al. ; Identification and characterization of new human genes through the use of mouse orthologs and testis cDNA sequences.. Genetics and Molecular Research, v. 3, n.4, p. 493-511, 2004.
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  • SLAGER, Natanja S Kirschbaum ; LOPES, Graziela M P ; GALANTE, Pedro A F ; RIGGINS, Gregory ; de Souza SJ . Splicing factors are differentially expressed in tumors. . Genetics and Molecular Research, v. 3, n. 4, p. 512-520, 2004.
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  • LOPES, Graziela Miê Peres ; de Souza SJ . Dissecting the Human Spliceosome Through Bioinformatics and Proteomics Approaches. IEEE/ACM Transactions on Computational Biology and Bioinformatics, v. 1, n. 4, p. 743-750, 2004.
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  • SAKABE, Noboru Jô ; VIBRANOVSKI, Maria Dulcetti ; de Souza SJ . A bioinformatics analysis of alternative exon usage in human genes coding for extracellular matrix proteins.. Genetics and Molecular Research, v. 3, n. 4, p. 532-544, 2004.
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  • GALANTE, Pedro Alexandre Favoretto ; SAKABE, Noboru Jô ; SALGER, Natanja Sara Kirschbaum ; de Souza SJ . Detection and evaluation of intron retention events in the human transcriptome. RNA. Ribonucleic Acid, v. 10, p. 757-765, 2004.
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  • SILVA, Ana Paula M ; SOUZA, Jorge e S de ; GALANTE, Pedro A F ; RIGGINS, Gregory ; de Souza SJ ; CAMARGO, Anamaria A . The impact of SNPs on the interpretation of SAGE and MPSS experimental data.. Nucleic Acids Research, v. 32, n. 20, p. 6104-6110, 2004.
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  • IMANISHI, Tadashi ITOH, Takeshi SUZUKI, Yutaka DONOVAN, Claire O FUKUCHI, Satoshi KOYANAGI, Kanako O BARRERO, Roberto A TAMURA, Takuro KABATA, Yumi Yamaguchi TANINO, Motohiko YURA, Kei MIYAZAKI, Satoru IKEO, Kazuho HOMMA, Keiichi KASPRZYK, Arek NISHIKAWA, Tetsuo HIRAKAWA, Mika MIEG, Jean Thierry MIEG, Danielle Thierry ASHURST, Jennifer JIA, Linbin NAKAO, Mitsuteru THOMAS, Michael A MULDER, Nicola KARAVIDOPOULOU, Youla , et al. ; Integrative Annotation of 21,037 Human Genes Validated by Full-Length cDNA Clones.. PLoS Biology, v. 2, p. 856-875, 2004.
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  • OSORIO, E. C. ; SOUZA, Jorge Estefano Santana de ; ZAIATS, A. C. ; OLIVEIRA, P. S. L. ; de Souza SJ . pp-Blast: a pseudo-parallel Blast.. Brazilian Journal of Medical and Biological Research, v. 36, p. 463-464, 2003.
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  • de Souza SJ . The emergence of a synthetic theory of intron evolution.. Genetica (The Hague), USA, v. 118, p. 117-121, 2003.
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  • SILVA, Ana Paula M ; SALIM, A. C. M. ; BULCARELLI, A. ; SOUZA, J. E. S. ; OSÓRIO, Elisson Campos ; CABALLERO, O. L. D. ; ISELI, C. ; STEVENSON, Brian J ; JONGENEEL, C Victor ; de Souza SJ ; SIMPSON, Andrew J G ; CAMARGO, Anamaria A . Identification of 9 novel transcripts and two RGSL gene within the hereditary prostate cancer region (HPC1) at 1q25. Gene (Amsterdam), v. 310, p. 49-57, 2003.
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  • SAKABE, Noboru Jô ; SOUZA, Jorge Estefano Santana de ; GALANTE, Pedro Alexandre Favoretto ; OLIVEIRA, Paulo Sérgio L de ; PASSETTI, Fábio ; BRENTANI, Helena Paula ; OSÓRIO, Elisson Campos ; ZAIATS, André Celso ; LEERKES, Maarten Rudolph ; KITAJIMA, João Paulo ; BRENTANI, Ricardo Renzo ; STRAUSBERG, Roberto L ; SIMPSON, Andrew John George ; de Souza SJ . ORESTES are enriched in rare exon usage variants affecting the encoded proteins. Comptes Rendus. Biologies, v. 326, p. 979-985, 2003.
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  • BRENTANI, Helena Paula ; CABALLERO, Otavia L ; CAMARGO, Anamaria A ; SILVA, Aline M da ; SILVA JR, Wilson Araujo da ; DIAS NETO, Emmanuel ; GRIVET, Marco ; GRUBER, Arthur ; GUIMARAES, Pedro Edson Moreira ; HIDE, Winston ; ISELI, Chistian ; JONGENEEL, C Victor ; KELSO, Janete ; NAGAI, Maria Aparecida ; OJOPI, Elida Paula Benquique ; OSORIO, Elisson C ; REIS, Eduardo M R ; RIGGINS, Gregory J ; SIMPSON, Andrew J G ; de Souza SJ ; STEVENSON, Brian J ; STRAUSBERG, Robert L ; TAJARA, Eloiza H ; ALMEIDA, Sergio Verjovski . The generation and utilization of a cancer oriented representation of the human transcriptome using expressed sequence tags.. PNAS. Proceedings of the National Academy of Sciences of the United States of America, USA, v. 100, n.23, p. 13418-13423, 2003.
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  • LEERKES, Maarten Rudolph ; CABALLERO, O. L. ; MACKAY, A. ; TORLONI, H. ; HARE, M. J. O. ; SIMPSON, Andrew Jonh George ; de Souza SJ . In Silico Comparison of the Ttranscriptome Derived from Purified Normal Breast Cells and Breast Tumor Cell Lines Reveals Candidate Upreguated Genes in Breast Tumor Cells.. Genomics (San Diego), Estados Unidos, v. 79, n. 2, p. 257-265, 2002.
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  • ENDO, Toshinori ; FEDOROV, A. ; de Souza SJ ; GILBERT, W. . Do introns favor or avoid regions of amino acid conservation?. Mol Biol Evol, Estados Unidos, v. 19, p. 521-522, 2002.
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  • STRAUSBERG, Robert L ; CAMARGO, Anamaria Aranha ; RIGGINS, Gregory ; SCHAEFER, C F ; de Souza SJ ; GROUSE, L H ; LAL, A ; BUETOW, K. H. ; BOOM, K. ; GREENHUT, S F ; SIMPSON, A. J. G. . An international database and integrated analysis tools for the study of cancer gene expression.. Pharmacogenomics, USA, v. 2, p. 156-164, 2002.
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  • REYMOND, A. ; CAMARGO, Anamaria Aranha ; DEUTSCH, S. ; STEVENSON, Brian J ; PARMIGIANI, Raphael Bessa ; UCLA, C. ;BETTONI, Fabiana ; ROSSIER, C. ; LYLE, R. ; GUIPPONI, M. ; de Souza SJ ; ISELI, C. ; JONGENEEL, C Victor ; BUCHER, P. ; SIMPSON, A. J. G. ; ANTONARAKIS, S. E. . Nineteen Additional Unpredicted Transcripts from Human Chromosome 21.. Genomics (San Diego), USA, v. 79, n. 6, p. 824-832, 2002.
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  • ISELI, C. ; STEVENSON, Brian J ; de Souza SJ ; SAMAIA, H. B. ; CAMARGO, Anamaria Aranha ; BUETOW, K. H. ; STRAUSBERG, Robert L ; SIMPSON, A. J. G. ; BUCHER, P. ; JONGENEEL, C Victor . Long-Range Heterogeneity at the 3´ Ends of Human mRNAs. . Genome Research, USA, v. 12, p. 1068-1074, 2002.
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  • SAKHARKAR, Meena K ; PASSETTI, Fábio ; SOUZA, Jorge Estefano Santana de ; LONG, Manyuan ; de Souza SJ . ExInt: an Exon intron Database.. Nucleic Acids Research, Estados Unidos, v. 30, n. 1, p. 191-194, 2002.
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  • BOOM, K. ; OSORIO, E. C. ; GREENHUT, S. F. ; SCHAEFER, C. F. ; SHOEMAKER, J. ; POLYAK, K. ; MORIN, P. J. ; BUETOW, K. H. ; STRAUSBERG, Robert L ; de Souza SJ ; RIGGINS, Gregory J . An anatomy of normal and malignant gene expression.. PNAS. Proceedings of the National Academy of Sciences of the United States of America, USA, v. 99, n. 17, p. 11287-11292, 2002.
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  • CAMARGO, Anamaria Aranha ; de Souza SJ ; BRENTANI, Ricardo Renzo ; SIMPSON, Andrew John George . Human gene discovery through experimental definition of transcribed regions of the human genome.. Current Opinion in Chemical Biology, Estados Unidos, v. 6, p. 13-16, 2002.
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  • SAKARKHAR, M. K. ; TAN, T. W. ; de Souza SJ . Geration of a database cotainning discordant intron positions in euKaryotic gene (MIDB). Bioinformatics, Estados Unidos, v. 17, p. 671-675, 2001.
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  • CORREA, R. G. ; SASAHARA, R M ; BENGSTON, M. H. ; KATAYAMA, M L H ; SALIM, A. C. M. ; BRENTANI, M. M. ; SOGAYAR, Mari C ; de Souza SJ ; SIMPSON, Andrew John George . Human Semaphorin 6B [(HSA) SEMAB], A Novel Human Class 6 Semaphorin Gene: Alternative Splicing and All-Trans-Retinoic Acid-Dependent Downregulation in Glioblastoma Cell Lines. Genomics (San Diego), Estados Unidos, v. 73, p. 343-348, 2001.
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  • SIMPSON, Andrew John George ; de Souza SJ ; CAMARGO, Anamaria Aranha ; BRENTANI, Ricardo Renzo . Definition of the gene content of the human genome: the need for deep experimental verification. . Comparative And Funcional Genomics, Estados Unidos, v. 2, p. 169-175, 2001.
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  • CABALLERO, O. L. ; de Souza SJ ; BRENTANI, Ricardo Renzo ; SIMPSON, Andrew John George . Alternative spliced transcriptas cancer markers.. Disease Markers, Estados Unidos, v. 17, p. 67-75, 2001.
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  • FEDOROV, A. ; CAO, X. ; SAXONOV, S. ; de Souza SJ ; ROY, S. W. ; GILBERT, W. . Intron distribution difference for 276 ancient and 131 modern genes suggests the existence of ancient introns.. PNAS. Proceedings of the National Academy of Sciences of the United States of America, Estados Unidos, v. 98, n. 23, p. 13177-13182, 2001.
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  • CAMARGO, Anamaria A SAMAIA, H. P. B. DIAS NETO, Emmanuel SIMÃO, D. F. MIGOTTO, I. A. BRIONES, M. R. S. COSTA, F. F. NAGAI, Maria Aparecida ALMEIDA, Sérgio Verjovski ZAGO, M. A. ANDRADE, L. E. C. CARRER, H. DORRY, H. F. A. E. ESPREÁFICO, E. M. GAMA, A. H. GIANELLA NETO, Daniel GOLDMAN, Gustavo H GRUBER, Arthur RACKEL, C. KIMURA, E. T. MACIEL, R. M. B. MARIE, Suely K N MARTINS, E. A. L. NOBREGA, M. P. LARSON, M. L. P. , et al. ; The Contribution of 700,000 ORF Sequence tags to the definition of the human transcriptome. PNAS. Proceedings of the National Academy of Sciences of the United States of America, v. 98, p. 12103-12108, 2001.
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  • SAKHARKAR, M. ; LONG, Manyuan ; TAN, T. W. ; de Souza SJ . ExInt: an Exon/Intron database.. Nucleic Acids Research, Estados Unidos, v. 28, p. 191-192, 2000.
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  • DIAS NETO, E. ; CORREA, R. G. ; ALMEIDA, Sérgio Verjovski ; BRIONES, M. R. S. ; NAGAI, Maria Aparecida ; SILVA JUNIOR, W. ; ZAGO, M. A. ; BORDIM, S. ; COSTA, F. F. ; GOLDMAN, G. H. ; CARVLAHO, A. F. ; MATSUKUMA, A. ; BAIA, G. S. ; SIMPSON, D. H. ; BRUNSTEIN, A. ; OLIVEIRA, P. S. L. ; BUCHER, P. ; JONGENELL, C. V. ; HARE, M. J. O. ; SOARES, F. ; BRENTANI, Ricardo Renzo ; REIS, Luiz Fernando Lima ; de Souza SJ ; SIMPSON, A. J. G. . Shotgun sequencing of the human transcriptome with Open ORF expressed sequence tags.. PNAS. Proceedings of the National Academy of Sciences of the United States of America, Estados Unidos, v. 97, p. 3491-3496, 2000.
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  • CORREA, R. G. ; CARVALHO, Alex F ; PINHEIRO, N. A. ; SIMPSON, Andrew Jonh George ; de Souza SJ . NABC1 (BCAS1): Alternative Splicing and Downregulation in Colorectal Tumors.. Genomics (San Diego), Estados Unidos, v. 65, p. 299-302, 2000.
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  • SAKHARKAR, M. ; LONG, Manyuan ; TAN, T W ; de Souza SJ . IEKb- An Exon intron Knowledge base from database.. Bioinformatics, Estados Unidos, v. 16, p. 1151-1152, 2000.
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  • de Souza SJ; de Souza SJ CAMARGO, Anamaria A BRIONES, M. R. S. COSTA, F. F. NAGAI, Maria Aparecida ALMEIDA, S. V. ZAGO, M. A. ANDRADE, L. E. C. CARRER, H. DORRY, H. F. A. E. ESPREAFICO, Enilza M GAMA, A. H. GIANELLA NETO, Daniel GOLDMAN, Gustavo H GRUBER, Arthur HACKEL, Christine KIMURA, E. T. MACIEL, R. M. B. MERIE, S. K. N. MARTINS, E. A. L. NOBREGA, M. P. LARSON, M. L. P. PARDINI, Maria Ines M C PEREIRA, G. G. PESQUERO, J. B. , et al. ; Identification of human chromosome 22 trascribed sequences with ORF expressed sequence tags.. Proceedings of the National Academy of Sciences of the United States of America, Estados Unidos, v. 97, p. 12690-12693, 2000.
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  • ROY, S. ; NOSAKA, Michiko ; de Souza SJ ; GILBERT, W. . Centripetal modules and ancient introns.. Gene (Amsterdam), Estados Unidos, v. 238, p. 85-91, 1999.
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  • GILBERT, W. ; de Souza SJ . Introns and the RNA World. Cshl Press, p. 221-231, 1999.
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  • LONG, Manyuan ; de Souza SJ ; ROSENBERG, C. ; GILBERT, W. . Relationship between proto-splice sites and intron phase: Evidence from dicodon analysis.. PNAS. Proceedings of the National Academy of Sciences of the United States of America, Estados Unidos, v. 95, p. 219-223, 1998.
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  • de Souza SJ ; LONG, Manyuan ; KLEIN, R. J. ; ROY, S. ; LIN, S. ; GILBERT, W. . Toward a resolution of the introns early / late debate: Only phase zero introns are correlated with the structure of ancient proteins.. PNAS. Proceedings of the National Academy of Sciences of the United States of America, Estados Unidos, v. 95, p. 5094-5099, 1998.
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  • LONG, Manyuan ; de Souza SJ . Intron-Exon Strutures: From Molecular to Population Biology. Advance In Genome Biology, USA, v. 5A, p. 143-178, 1998.
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  • LONG, Manyuan ; de Souza SJ ; GILBERT, W. . The yeast splice site revisited: A new exon consensus from genome analysis.. Cell, Estados Unidos, v. 91, p. 739-740, 1997.
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  • de Souza SJ ; LONG, Manyuan ; SCHOENBACH, L. ; ROY, S. W. ; GILBERT, W. . The correlation between introns and the three-dimensional structure of proteins.. Gene (Amsterdam), Estados Unidos, v. 205, p. 141-144, 1997.
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  • de Souza SJ . The origin and evolution of introns: a debate. . A Biomednet Publication, Estados Unidos, v. 1, 1997.
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  • LONG, Manyuan ; de Souza SJ ; GILBERT, W. . Delta- Interacting Protein A and the Origin of Hepatitis Delta Antigen. Science, Estados Unidos, v. 276, p. 824-825, 1997.
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  • GILBERT, W. ; de Souza SJ ; LONG, Manyuan . Origin of Genes. PNAS. Proceedings of the National Academy of Sciences of the United States of America, Estados Unidos, v. 94, p. 7698-7703, 1997.
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  • MARTINS, Vilma Regina ; GRANER, E. ; ABREU, J. G. ; de Souza SJ ; MERCADANTE, A. F. ; VEIGA, S. S. ; ZANATA, S. M. ; MOURA NETO, V. ; BRENTANI, Ricardo Renzo . Complementary hydropathy identifies a cellular prion protein receptor.. Nature Med, Estados Unidos, v. 3, n. 12, p. 1376-1382, 1997.
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  • de Souza SJ ; LONG, Manyuan ; SCHOENBACH, L. ; ROY, S. W. ; GILBERT, W. . Intron positions correlate with module bondaries in anciet proteins. PNAS. Proceedings of the National Academy of Sciences of the United States of America, Estados Unidos, v. 93, p. 14632-14636, 1996.
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  • de Souza SJ ; PEREIRA, H. M. ; JACCHIERI, S. ; BERNTANI, R. R. . Colagen/ collagenase interaction: Does the enzyme mimic the conformation of its own substrate?. The FASEB Journal, Estados Unidos, v. 10, p. 927-930, 1996.
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  • SANTOS, M. A. V. ; de Souza SJ ; BRENTANI, Ricardo Renzo ; SOUZA, W. . Polymorphonuclear Leukocytes Present Laminin Peptides in Endocytic Compartments.. Biochemical and Biophysical Research Communications, Estados Unidos, v. 221, p. 837-842, 1996.
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  • LONG, Manyuan ; de Souza SJ ; ROSENBERG, C. ; GILBERT, W. . Exon shuffing and the origin of the mitochondrial targenting function in plant cytochrome c1 precursor.. PNAS. Proceedings of the National Academy of Sciences of the United States of America, Estados Unidos, v. 93, p. 7727-7731, 1996.
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  • de Souza SJ ; LONG, Manyuan ; GILBERT, W. . Introns and gene evolution.. Genes To Cells, Estados Unidos, v. 1, p. 493-505, 1996.
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  • LONG, Manyuan ; de Souza SJ ; GILBERT, W. . Evolution of the intron-exon structure of euKaryotic gene.. Curr Opin Genet Develop, Estados Unidos, v. 5, p. 774-778, 1995.
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  • de Souza SJ ; BRENTANI, Ricardo Renzo. On the struture / function relationship of polymorphonuclear-leukocyte collagenase.. Biochemical Journal (London), Estados Unidos, v. 300, p. 605-607, 1994.
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  • de Souza SJ ; MADAIO, M. P. ; JULIANO NETO, L. ; BRENTANI, Ricardo Renzo . A monoclonal Autoantibody against a Complementary Peptide Recognizes Interstitial Collagenase.. Immunomethods, Estados Unidos, v. 5, p. 172-176, 1994.
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  • de Souza SJ ; M, Pacheco M ; S, Sonohara ; BRENTANI, M. M. ; BRENTANI, Ricardo Renzo . Regulation of extracellular matrix-degrading proteases.. Ciência e Cultura (SBPC), Brasil, v. 45, n. 5, p. 313-318, 1993.
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  • de Souza SJ ; BRENTANI, Ricardo Renzo . Sequence Homology Between a Bacterial Metalloproteinase and Eukaryotic Matrix Metalloproteinases. Journal of Molecular Evolution, New York, v. 36, p. 596-598, 1993.
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  • VIEIRA, J. L. ; CHAMMAS, Roger ; VERDE, D. M. S. V. ; SANTOS, M. A. V. ; COELHO, V. M. ; de Souza SJ ; BRENTANI, Ricardo Renzo ;SAVINO, W. . Extracellular matrix components of the mouse thymic microenviroment, III Thymic epithelial cells express the VLA6 complex that is involved in laminin-mediated interactions with thymocytes.. International Immunology, Estados Unidos, v. 5, n. 11, p. 1421-1430, 1993.
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  • de Souza SJ ; SABAGA, J. ; AMICO, e D ; PASQUALINI, R. ; BRENTANI, Ricardo Renzo . Anti-platelets auto-antibodies from ITP patients recognize an epitope in GP IIb/IIIa deduced by complementary hydropathy. . Immunology (Oxford), v. 7, p. 17-22, 1992.
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  • de Souza SJ ; BRENTANI, Ricardo Renzo . Collagen-binding site in collagenase can be determined using the concept of sense-antisense peptide interactions.. The Journal of Biological Chemistry, v. 267, n. 19, p. 13763-13767, 1992.
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  • PASQUALINI, R. ; LEVI, J. E. ; AZUL, M. I. S. ; FARIA, M. ; de Souza SJ ; BRENTANI, Ricardo Renzo . IID510g52, a monoclonal antibody against platelet membrane glycoprotein IIIa is a suitable tool for the determination of functional domains within integrin cell surface receptors.. Hybridoma (New York) (Cessou em 2001. Cont. 1554-0014 Hybridoma [Larchmont]), v. 11, n. 6, p. 741-755, 1992.
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