Publications

2009

• Lacson R, Pitzer E, Hinske C, Galante P, Ohno-Machado L. Evaluation of a large-scale biomedical data annotation initiative. BMC Bioinformatics. 2009; S10. [PubMed]
   
• da Cunha JP, Galante PA, de Souza JE, de Souza RF, Carvalho PM, Ohara DT, Moura RP, Oba-Shinja SM, Marie SK, Silva WA Jr, Perez RO, Stransky B, Pieprzyk M, Moore J, Caballero O, Gama-Rodrigues J, Habr-Gama A, Kuo WP, Simpson AJ, Camargo AA, Old LJ, de Souza SJ. Bioinformatics construction of the human cell surfaceome. Proc Natl Acad Sci U S A [PubMed]
   
• Pitzer E, Lacson R, Hinske C, Kim J, Galante PA, Ohno-Machado L. Towards large-scale sample annotation in gene expression repositories. BMC Bioinformatics [PubMed]
   
• Bettoni F, Filho FC, Grosso DM, Galante PA, Parmigiani RB, Geraldo MV, Henrique-Silva F, Oba-Shinjo SM, Marie SK, Soares FA, Brentani HP, Simpson AJ, de Souza SJ, Camargo AA. Identification of FAM46D as a novel Cancer/Testis antigen using EST data and serological analysis. Genomics. 2009 [PubMed]
   
• Pinheiro DG, Galante PA, de Souza SJ, Zago MA, Silva WA Jr. A score system for quality evaluation of RNA sequence tags: an improvement for gene expression profiling. BMC Bioinformatics. 2009 Jun 6;10(1):170 [Pubmed]
   
• Galante PA, Sandhu D, de Sousa Abreu R, Gradassi M, Slager N, Vogel C, de Souza SJ, Penalva LO. A comprehensive in silico expression analysis of RNA binding proteins in normal and tumor tissue: Identification of potential players in tumor formation. RNA Biol. 2009 Oct 24;6(4).[Pubmed]
   
• Zhao Q, Caballero OL, Levy S, Stevenson BJ, Iseli C, de Souza SJ, Galante PA, Busam D, Leversha MA, Chadalavada K, Rogers YH, Venter JC, Simpson AJ, Strausberg RL. Transcriptome-guided characterization of genomic rearrangements in a breast cancer cell line. Proc Natl Acad Sci U S A. 2009 106(6): 1886-91 [PubMed]

2008

• de Souza RF, Anantharaman V, de Souza SJ, Aravind L, Gueiros-Filho FJ. AMIN domains have a predicted role in localization of diverse periplasmic protein complexes. Bioinformatics [Epub ahead of print] [PubMed]
   
• da Cunha JP, Galante PA, de Souza SJ. Different Evolutionary Strategies for the Origin of Caspase-1 Inhibitors. J Mol Evol. 2008 [PubMed]
   
• Madeira L, Galante PA, Budu A, Azevedo MF, Malnic B, Garcia CR. Genome-wide detection of serpentine receptor-like proteins in malaria parasites. PLoS ONE. 2008; 3(3): e1889 [PubMed]
   
• Leoni SG, Galante PA, Ricarte-Filho JC, Kimura ET. Differential gene expression analysis of iodide-treated rat thyroid follicular cell line PCCl3. Genomics. 2008; 91(4): 356-66 [PubMed]
   
• Yamasaki C, Murakami K, Fujii Y, Sato Y, Harada E, et al. The H-Invitational Database (H-InvDB), a comprehensive annotation resource for human genes and transcripts. Nucleic Acids Res. 2008; 36: D793-9 [PubMed] 

2007

• Stransky B, Barrera J, Ohno-Machado L, De Souza SJ. Modeling cancer: integration of 'omics' information in dynamic systems. J Bioinform Comput Biol. 2007; 5 (4): 977-86 [PubMed]
   
• Ferreira EN, Galante PA, Carraro DM, de Souza SJ. Alternative splicing: a bioinformatics perspective. Mol Biosyst. 2007; 3(7): 473-7 [PubMed]
   
• Galante PA, Trimarchi J, Cepko CL, de Souza SJ, Ohno-Machado L, Kuo WP. Automatic correspondence of tags and genes (ACTG): a tool for the analysis of SAGE, MPSS and SBS data. Bioinformatics. 2007; 23(7): 903-5 [PubMed]
   
• Sakabe NJ, de Souza SJ. Sequence features responsible for intron retention in human. BMC Genomics. 2007; 8:59 [PubMed]
   
• Galante PA, Vidal DO, de Souza JE, Camargo AA, de Souza SJ. Sense-antisense pairs in mammals: functional and evolutionary considerations. Genome Biol. 2007; 8(3): R40 [PubMed]
   
• Parmigiani RB, Bettoni F, Vibranovski MD, Lopes MH, Martins WK, Cunha IW,Soares FA, Simpson AJ, de Souza SJ, Camargo AA. Characterization of a cancer/testis (CT) antigen gene family capable of eliciting humoral response in cancer patients. Proc Natl Acad Sci U S A. 2007; 103 (48): 18066-71[PubMed] 

2006

• Vibranovski MD, Sakabe NJ, de Souza SJ. A possible role of exon-shuffling in the evolution of signal peptides of human proteins. FEBS Lett. 2006; 580(6): 1621-4 [PubMed]
   
• Michaloski JS, Galante PA, Malnic B. Identification of potential regulatory motifs in odorant receptor genes by analysis of promoter sequences. Genome Res. 2006; 16(9): 1091-8 [PubMed] 

2005

• Vibranovski MD, Sakabe NJ, de Oliveira RS, de Souza SJ. Signs of ancient and modern exon-shuffling are correlated to the distribution of ancient and modern domains along proteins. J Mol Evol. 2005; 61(3): 341-50 [PubMed]
   
• Kirschbaum-Slager N, Parmigiani RB, Camargo AA, de Souza SJ. Identification of human exons overexpressed in tumors through the use of genome and expressed sequence data. Physiol Genomics. 2005; 21(3): 423-32 [PubMed]
   
• Brentani RR, Carraro DM, Verjovski-Almeida S, Reis EM, Neves EJ, de Souza SJ,Carvalho AF, Brentani H, Reis LF. Gene expression arrays in cancer research: methods and applications. Crit Rev Oncol Hematol. 2005; 54(2): 95-105 [PubMed]
   
• Tanino M, Debily MA, Tamura T, Hishiki T, Ogasawara O, Murakawa K, Kawamoto S, Itoh K, Watanabe S, de Souza SJ, Imbeaud S, Graudens E, Eveno E, Hilton P,Sudo Y, Kelso J, Ikeo K, Imanishi T, Gojobori T, Auffray C, Hide W, Okubo K. The Human Anatomic Gene Expression Library (H-ANGEL), the H-Inv integrative display of human gene expression across disparate technologies and platforms. Nucleic Acids Res. 2005; 33:D567-72 [PubMed]
   
• de Souza SJ, Galante PA, Soares R. Using ORESTES ESTs to mine gene cancer expression data. Encyclopedia of Genetics, Genomics, Proteomics and Bioinformatics. 2005; John Wiley & Sons, Ltd [PDF] 

2004

• Sakabe NJ, Vibranovski MD, de Souza SJ. A bioinformatics analysis of alternative exon usage in human genes coding for extracellular matrix proteins. Genet Mol Res. 2004; 3(4): 532-44[PubMed]
   
• Kirschbaum-Slager N, Lopes GM, Galante PA, Riggins GJ, de Souza SJ. Splicing factors are differentially expressed in tumors. Genet Mol Res. 2004; 3(4): 512-20 [PubMed]
   
• Ferreira EN, Pires LC, Parmigiani RB, Bettoni F, Puga RD, Pinheiro DG,Andrade LE, Cruz LO, Degaki TL, Faria M Jr, Festa F, Giannella-Neto D, Giorgi RR,Goldman GH, Granja F, Gruber A, Hackel C, Henrique-Silva F, Malnic B, Manzini CV,Marie SK,Martinez-Rossi NM, Oba-Shinjo SM, Pardini MI, Rahal P, Rainho CA,Rogatto SR, Romano CM, Rodrigues V, Sales MM, Savoldi M, da Silva ID, da Silva NP, de Souza SJ, Tajara EH, Silva WA Jr, Simpson AJ, Sogayar MC, Camargo AA, Carraro DM. Identification and complete sequencing of novel human transcripts through the use of mouse orthologs and testis cDNA sequences. Genet Mol Res. 2004; 3(4): 493-511 [PubMed]
   
• Parmigiani RB, Magalhães GS, Galante PA, Manzini CV, Camargo AA, Malnic B. A novel human G protein-coupled receptor is over-expressed in prostate cancer. Genet Mol Res. 2004; 3(4): 521-31 [PubMed]
   
• Silva AP, De Souza JE, Galante PA, Riggins GJ, De Souza SJ, Camargo AA. The impact of SNPs on the interpretation of SAGE and MPSS experimental data. Nucleic Acids Res. 2004; 32(20): 6104-10 [PubMed]
   
• Sogayar MC, Camargo AA, Bettoni F, Carraro DM, Pires LC, Parmigiani RB,Ferreira EN, de Sá Moreira E, do Rosário D de O Latorre M, Simpson AJ, Cruz LO, Degaki TL, Festa F, Massirer KB, Sogayar MC, Filho FC, Camargo LP, Cunha MA, De Souza SJ, Faria M Jr, Giuliatti S, Kopp L, de Oliveira PS, Paiva PB, Pereira AA, Pinheiro DG, Puga RD, S de Souza JE, Albuquerque DM, Andrade LE, Baia GS, Briones MR, Cavaleiro-Luna AM, Cerutti J, et al. A transcript finishing initiative for closing gaps in the human transcriptome. Genome Res. 2004; 14 (7): 1413-23 [PubMed]
   
• Imanishi T, Itoh T, Suzuki Y, ODonovan C, Fukuchi S, Koyanagi KO, Barrero RA, Tamura T, Yamaguchi-Kabata Y, Tanino M, Yura K, Miyazaki S, Ikeo K, Homma K, Kasprzyk A, Nishikawa T, Hirakawa M, Thierry-Mieg J, Thierry-Mieg D, Ashurst J, Jia L, Nakao M, Thomas MA, Mulder N, Karavidopoulou Y, Jin L, Kim S, Yasuda T, Lenhard B, Eveno E, Suzuki Y, Yamasaki C, Takeda J, Gough C, Hilton P, Fujii Y, Sakai H, Tanaka S, Amid C, Bellgard M, Bonaldo Mde F, Bono H, Bromberg SK, Brookes AJ, Bruford E, Carninci P, Chelala C, Couillault C, de Souza SJ, Debily MA, Devignes MD, Dubchak I, Endo T, Estreicher A, et al.Integrative annotation of 21,037 human genes validated by full-length cDNA clones. PLoS Biol. 2004; 2(6): e162 [PubMed]
   
• Galante PA, Sakabe NJ, Kirschbaum-Slager N, de Souza SJ. Detection and evaluation of intron retention events in the human transcriptome. RNA. 2004; 10(5): 757-65 [PubMed]
   
• Peres Lopes GM, de Souza SJ. Dissecting the human spliceosome through bioinformatics and proteomics approaches. J Bioinform Comput Biol. 2004; 1(4): 743-50 [PubMed] 

2003

• Sakabe NJ, de Souza JE, Galante PA, de Oliveira PS, Passetti F, Brentani H,Osório EC, Zaiats AC, Leerkes MR, Kitajima JP, Brentani RR, Strausberg RL,Simpson AJ, de Souza SJ. ORESTES are enriched in rare exon usage variants affecting the encoded proteins. C R Biol. 2003; 326 (10-11): 979-85[PubMed]
   
• Cerutti JM, Riggins GJ, de Souza SJ. What can digital transcript profiling reveal about human cancers?. Braz J Med Biol Res. 2003; 36(8): 975-85 [PubMed]
   
• de Souza SJ. The emergence of a synthetic theory of intron evolution. Genetica. 2003; 118(2-3): 117-21 [PubMed]
   
• Silva AP, Salim AC, Bulgarelli A, de Souza JE, Osório E, Caballero OL, Iseli C, Stevenson BJ, Jongeneel CV, de Souza SJ, Simpson AJ, Camargo AA. Identification of 9 novel transcripts and two RGSL genes within the hereditary prostate cancer region (HPC1) at 1q25. Gene. 2003; 310: 49-57[PubMed]
   
• Osório EC, de Souza JE, Zaiats AC, de Oliveira PS, de Souza SJ. pp-Blast: a 'pseudo-parallel' Blast. Braz J Med Biol Res. 2003; 36(4): 463-4 [PubMed]
   
• Brentani H, Caballero OL, Camargo AA, da Silva AM, da Silva WA Jr, Dias Neto E, Grivet M, Gruber A, Guimaraes PE, Hide W, Iseli C, Jongeneel CV, Kelso J, Nagai MA, Ojopi EP, Osorio EC, Reis EM, Riggins GJ, Simpson AJ, de Souza S, Stevenson BJ, Strausberg RL, Tajara EH, Verjovski-Almeida S, Acencio ML, Bengtson MH, Bettoni F, Bodmer WF, Briones MR, Camargo LP, Cavenee W, Cerutti JM, Coelho Andrade LE, Costa dos Santos PC, Ramos Costa MC, da Silva IT, Estécio MR, As Ferreira K, Furnari FB, Faria M Jr, Galante PA, , Guimaraes GS, Holanda AJ, Kimura ET, Leerkes MR, Lu X, et al. The generation and utilization of a cancer-oriented representation of the human transcriptome by using expressed sequence tags. Proc Natl Acad Sci U S A. 2003; 100(23): 13418-23 [PubMed]

2002

• Boon K, Osorio EC, Greenhut SF, Schaefer CF, Shoemaker J, Polyak K, Morin PJ,Buetow KH, Strausberg RL, De Souza SJ, Riggins GJ. An anatomy of normal and malignant gene expression. Proc Natl Acad Sci U S A. 2002; 99 (17): 11287-92 [PubMed]
   
• Iseli C, Stevenson BJ, de Souza SJ, Samaia HB, Camargo AA, Buetow KH, Strausberg RL, Simpson AJ, Bucher P, Jongeneel CV. Long-range heterogeneity at the 3 ends of human mRNAs. Genome Res. 2002; 12(7): 1068-74 [PubMed]
   
• Endo T, Fedorov A, de Souza SJ, Gilbert W. Do introns favor or avoid regions of amino acid conservation?. Mol Biol Evol. 2002; 19(4): 521-252 [PubMed]
   
• Camargo AA, de Souza SJ, Brentani RR, Simpson AJ. Human gene discovery through experimental definition of transcribed regions of the human genome. Curr Opin Chem Biol. 2002; 6(1): 13-6 [PubMed]
   
• Leerkes MR, Caballero OL, Mackay A, Torloni H, OHare MJ, Simpson AJ, de Souza SJ. In silico comparison of the transcriptome derived from purified normal breast cells and breast tumor cell lines reveals candidate upregulated genes in breast tumor cells. Genomics. 2002; 79 (2): 257-65 [PubMed]
   
• Sakharkar M, Passetti F, de Souza JE, Long M, de Souza SJ. ExInt: an Exon Intron Database. Nucleic Acids Res. 2002; 30(1): 191-4 [PubMed]
   
• Strausberg RL, Camargo AA, Riggins GJ, Schaefer CF, de Souza SJ, Grouse LH, Lal A, Buetow KH, Boon K, Greenhut SF, Simpson AJ. An international database and integrated analysis tools for the study of cancer gene expression. Pharmacogenomics J. 2002; 2 (3): 156-64 [PubMed]

2001

• Fedorov A, Cao X, Saxonov S, de Souza SJ, Roy SW, Gilbert W. Intron distribution difference for 276 ancient and 131 modern genes suggests the existence of ancient introns. Proc Natl Acad Sci U S A. 2001; 98 (23): 13177-82 [PubMed]
   
• Camargo AA, Samaia HP, Dias-Neto E, Simão DF, Migotto IA, Briones MR, Costa FF, Nagai MA, Verjovski-Almeida S, Zago MA, Andrade LE, Carrer H, El-Dorry HF, Espreafico EM, Habr-Gama A, Giannella-Neto D, Goldman GH, Gruber A, Hackel C, Kimura ET, Maciel RM, Marie SK, Martins EA, Nobrega MP, Paco-Larson ML, Pardini MI, Pereira GG, Pesquero JB, Rodrigues V, Rogatto SR, da Silva ID, Sogayar MC, Sonati MF, Tajara EH, Valentini SR, Alberto FL, Amaral ME, Aneas I, Arnaldi LA, de Assis AM, Bengtson MH, Bergamo NA, Bombonato V, de Camargo ME, Canevari RA, Carraro DM, Cerutti JM, Correa ML, Correa RF, Costa MC, Curcio C, Hokama PO, Ferreira AJ, Furuzawa GK, Gushiken T, Ho PL, Kimura E, Krieger JE, Leite LC, Majumder P, Marins M, Marques ER, Melo AS, Melo MB, Mestriner CA, Miracca EC, Miranda DC, Nascimento AL, Nobrega FG, Ojopi EP, Pandolfi JR, Pessoa LG, Prevedel AC, Rahal P, Rainho CA, Reis EM, Ribeiro ML, da Ros N, de Sa RG, Sales MM, Santanna SC, dos Santos ML, da Silva AM, da Silva NP, Silva WA Jr, da Silveira RA, Sousa JF, Stecconi D, Tsukumo F, Valente V, Soares F, Moreira ES, Nunes DN,Correa RG, Zalcberg H, Carvalho AF, Reis LF, Brentani RR, Simpson AJ, de Souza SJ. The contribution of 700,000 ORF sequence tags to the definition of the human transcriptome. Proc Natl Acad Sci U S A. 2001; 98(21): 12103-8 [PubMed]
   
• Sakharkar MK, Tan TW, de Souza SJ. Generation of a database containing discordant intron positions in eukaryotic genes (MIDB). Bioinformatics. 2001; 17 (8): 671-5 [PubMed]
   
• Correa RG, Sasahara RM, Bengtson MH, Katayama ML, Salim AC, Brentani MM, Sogayar MC, de Souza SJ, Simpson AJ. Human semaphorin 6B (HSA)SEMA6B, a novel human class 6 semaphorin gene: alternative splicing and all-trans-retinoic acid-dependent downregulation in glioblastoma cell lines. Genomics. 2001; 73 (3): 343-8 [PubMed]
   
• Caballero OL, de Souza SJ, Brentani RR, Simpson AJ. Alternative spliced transcripts as cancer markers. Dis Markers. 2001; 17(2): 67-75 [PubMed] 

2000 

• Sakharkar MK, Kangueane P, Woon TW, Tan TW, Kolatkar PR, Long M, de Souza SJ. IE-Kb: intron exon knowledge base. Bioinformatics. 2000; 16 (12): 1151-2 [PubMed]
   
• de Souza SJ, Camargo AA, Briones MR, Costa FF, Nagai MA, Verjovski-Almeida S, Zago MA, Andrade LE, Carrer H, El-Dorry HF, Espreafico EM, Habr-Gama A, Giannella-Neto D, Goldman GH, Gruber A, Hackel C, Kimura ET, Maciel RM, Marie SK, Martins EA, Nobrega MP, Paco-Larson ML, et al.Identification of human chromosome 22 transcribed sequences with ORF expressed sequence tags. Proc Natl Acad Sci U S A. 2000; 97 (23): 12690-3 [PubMed]
   
• Correa RG, de Carvalho AF, Pinheiro NA, Simpson AJ, de Souza SJ. NABC1 (BCAS1): alternative splicing and downregulation in colorectal tumors. Genomics. 2000; 65 (3): 299-302 [PubMed]
   
• Dias Neto E, Correa RG, Verjovski-Almeida S, Briones MR, Nagai MA, da Silva W Jr, Zago MA, Bordin S, Costa FF, Goldman GH, Carvalho AF, Matsukuma A, Baia GS, Simpson DH, Brunstein A, de Oliveira PS, Bucher P, Jongeneel CV, OHare MJ, Soares F, Brentani RR, Reis LF, de Souza SJ, Simpson AJ. Shotgun sequencing of the human transcriptome with ORF expressed sequence tags. Proc Natl Acad Sci U S A. 2000; 97 (7): 3491-6 [PubMed]
   
• Sakharkar M, Long M, Tan TW, de Souza SJ. ExInt: an Exon/Intron database. Nucleic Acids Res. 2000; 28 (1): 191-2 [PubMed]