Pedro A F Galante

Summary

Country: Brazil

Publications

  1. ncbi request reprint Alternative splicing: a bioinformatics perspective
    Elisa Napolitano Ferreira
    Ludwig Institute for Cancer Research, Sao Paulo Branch, Hospital A C Camargo, Sao Paulo, Brazil
    Mol Biosyst 3:473-7. 2007
  2. pmc Systematic detection of putative tumor suppressor genes through the combined use of exome and transcriptome sequencing
    Qi Zhao
    Ludwig Collaborative Group, Department of Neurosurgery, Johns Hopkins University, 1550 Orleans Street, Baltimore, MD 21231, USA
    Genome Biol 11:R114. 2010
  3. pmc Sense-antisense pairs in mammals: functional and evolutionary considerations
    Pedro A F Galante
    Ludwig Institute for Cancer Research, Sao Paulo Branch, Hospital Alemao Oswaldo Cruz, Sao Paulo, SP, Brazil
    Genome Biol 8:R40. 2007
  4. doi request reprint Comprehensive evaluation of the effectiveness of gene expression signatures to predict complete response to neoadjuvant chemoradiotherapy and guide surgical intervention in rectal cancer
    Camila Lopes-Ramos
    Centro de Oncologia Molecular, Hospital Sirio Libanes, Sao Paulo, Brazil
    Cancer Genet 208:319-26. 2015
  5. pmc SPLOOCE: a new portal for the analysis of human splicing variants
    José Eduardo Kroll
    Laboratory of Computational Biology, Ludwig Institute for Cancer Research São Paulo, Brazil Inter institutional Program on Bioinformatics, University of Sao Paulo, Sao Paulo, Brazil
    RNA Biol 9:1339-43. 2012
  6. pmc A comprehensive in silico expression analysis of RNA binding proteins in normal and tumor tissue: Identification of potential players in tumor formation
    Pedro A F Galante
    Ludwig Institute for Cancer Research Sao Paulo Branch, Sao Paulo, Brazil
    RNA Biol 6:426-33. 2009
  7. pmc PVALB, a new Hürthle adenoma diagnostic marker identified through gene expression
    Janete M Cerutti
    Genetic Bases of Thyroid Tumor Laboratory, Federal University of Sao Paulo, Sao Paulo, SP, Brazil
    J Clin Endocrinol Metab 96:E151-60. 2011
  8. pmc Alternative splicing and genetic diversity: silencers are more frequently modified by SNVs associated with alternative exon/intron borders
    Jorge E S De Souza
    Ludwig Institute for Cancer Research at Hospital Alemão Oswaldo Cruz, Sao Paulo, SP, 01509 010, Brasil
    Nucleic Acids Res 39:4942-8. 2011
  9. doi request reprint Identification of FAM46D as a novel cancer/testis antigen using EST data and serological analysis
    Fabiana Bettoni
    Ludwig Institute for Cancer Research, Hospital Alemao Oswaldo Cruz, Sao Paulo, SP, Brazil
    Genomics 94:153-60. 2009
  10. pmc The use of personalized biomarkers and liquid biopsies to monitor treatment response and disease recurrence in locally advanced rectal cancer after neoadjuvant chemoradiation
    Paola Carpinetti
    Ludwig Institute for Cancer Research, Sao Paulo, SP, Brazil
    Oncotarget 6:38360-71. 2015

Collaborators

Detail Information

Publications26

  1. ncbi request reprint Alternative splicing: a bioinformatics perspective
    Elisa Napolitano Ferreira
    Ludwig Institute for Cancer Research, Sao Paulo Branch, Hospital A C Camargo, Sao Paulo, Brazil
    Mol Biosyst 3:473-7. 2007
    ..In this review, we discuss several issues related to alternative splicing with a special emphasis on identification strategies based on bioinformatics...
  2. pmc Systematic detection of putative tumor suppressor genes through the combined use of exome and transcriptome sequencing
    Qi Zhao
    Ludwig Collaborative Group, Department of Neurosurgery, Johns Hopkins University, 1550 Orleans Street, Baltimore, MD 21231, USA
    Genome Biol 11:R114. 2010
    ..The analysis was conducted on the breast cancer cell line HCC1954, and a lymphoblast cell line from the same individual, HCC1954BL...
  3. pmc Sense-antisense pairs in mammals: functional and evolutionary considerations
    Pedro A F Galante
    Ludwig Institute for Cancer Research, Sao Paulo Branch, Hospital Alemao Oswaldo Cruz, Sao Paulo, SP, Brazil
    Genome Biol 8:R40. 2007
    ..A significant number of genes in mammalian genomes are being found to have natural antisense transcripts (NATs). These sense-antisense (S-AS) pairs are believed to be involved in several cellular phenomena...
  4. doi request reprint Comprehensive evaluation of the effectiveness of gene expression signatures to predict complete response to neoadjuvant chemoradiotherapy and guide surgical intervention in rectal cancer
    Camila Lopes-Ramos
    Centro de Oncologia Molecular, Hospital Sirio Libanes, Sao Paulo, Brazil
    Cancer Genet 208:319-26. 2015
    ....
  5. pmc SPLOOCE: a new portal for the analysis of human splicing variants
    José Eduardo Kroll
    Laboratory of Computational Biology, Ludwig Institute for Cancer Research São Paulo, Brazil Inter institutional Program on Bioinformatics, University of Sao Paulo, Sao Paulo, Brazil
    RNA Biol 9:1339-43. 2012
    ..Here we present SPLOOCE, a portal for the analysis of human splicing variants. SPLOOCE uses a method based on regular expressions for retrieval of ASEs. We propose a simple syntax that is able to capture the complexity of ASEs...
  6. pmc A comprehensive in silico expression analysis of RNA binding proteins in normal and tumor tissue: Identification of potential players in tumor formation
    Pedro A F Galante
    Ludwig Institute for Cancer Research Sao Paulo Branch, Sao Paulo, Brazil
    RNA Biol 6:426-33. 2009
    ..This later list contains potential candidates to be explored as diagnostic and prognostic markers as well as putative targets for cancer therapy approaches...
  7. pmc PVALB, a new Hürthle adenoma diagnostic marker identified through gene expression
    Janete M Cerutti
    Genetic Bases of Thyroid Tumor Laboratory, Federal University of Sao Paulo, Sao Paulo, SP, Brazil
    J Clin Endocrinol Metab 96:E151-60. 2011
    ..One lingering problem with these markers was that false positives occurred with Hürthle cell adenomas (HCA) which lowered test specificity...
  8. pmc Alternative splicing and genetic diversity: silencers are more frequently modified by SNVs associated with alternative exon/intron borders
    Jorge E S De Souza
    Ludwig Institute for Cancer Research at Hospital Alemão Oswaldo Cruz, Sao Paulo, SP, 01509 010, Brasil
    Nucleic Acids Res 39:4942-8. 2011
    ..Our results establish a clear association between genetic diversity and alternative splicing involving ESSs...
  9. doi request reprint Identification of FAM46D as a novel cancer/testis antigen using EST data and serological analysis
    Fabiana Bettoni
    Ludwig Institute for Cancer Research, Hospital Alemao Oswaldo Cruz, Sao Paulo, SP, Brazil
    Genomics 94:153-60. 2009
    ..Due to its restricted expression pattern and immunogenicity FAM46D represents a novel target for cancer immunotherapy...
  10. pmc The use of personalized biomarkers and liquid biopsies to monitor treatment response and disease recurrence in locally advanced rectal cancer after neoadjuvant chemoradiation
    Paola Carpinetti
    Ludwig Institute for Cancer Research, Sao Paulo, SP, Brazil
    Oncotarget 6:38360-71. 2015
    ..Our study supports the use of personalized biomarkers and liquid biopsies to tailor the management of rectal cancer patients, however, replication in a larger cohort is necessary to introduce this strategy into clinical practice. ..
  11. doi request reprint ICRmax: an optimized approach to detect tumor-specific interchromosomal rearrangements for clinical application
    Elisa R Donnard
    Centro de Oncologia Molecular, Hospital Sirio Libanes, Sao Paulo, Brazil Departamento de Bioquímica, Instituto de Quimica, Universidade de Sao Paulo, Sao Paulo, Brazil
    Genomics 105:265-72. 2015
    ..ICRmax identifies ICRs from low-coverage sequenced tumors, eliminates the need to sequence a matched normal tissue and significantly reduces the costs that limit the utilization of personalized biomarkers in the clinical setting...
  12. pmc A score system for quality evaluation of RNA sequence tags: an improvement for gene expression profiling
    Daniel G Pinheiro
    Departamento de Genetica, Faculdade de Medicina de Ribeirao Preto, Universidade de Sao Paulo, Ribeirao Preto, SP, Brazil
    BMC Bioinformatics 10:170. 2009
    ..This is made through a series of evaluations based on a defined rule set. S3T allows the identification/selection of tags, considered more reliable for further gene expression analysis...
  13. ncbi request reprint A novel human G protein-coupled receptor is over-expressed in prostate cancer
    Raphael B Parmigiani
    Ludwig Institute for Cancer Research, Rua Professor Antonio Prudente, 109, 4th Floor, Sao Paulo, SP, Brasil
    Genet Mol Res 3:521-31. 2004
    ....
  14. pmc Common promoter elements in odorant and vomeronasal receptor genes
    Jussara S Michaloski
    Departamento de Bioquimica, Instituto de Quimica, Universidade de Sao Paulo, Sao Paulo, Sao Paulo, Brazil
    PLoS ONE 6:e29065. 2011
    ..Analysis of these motifs and of the proteins that bind to these motifs should reveal important aspects of the mechanisms of OR/V1R gene regulation...
  15. ncbi request reprint Splicing factors are differentially expressed in tumors
    Natanja Kirschbaum-Slager
    Ludwig Institute for Cancer Research, Sao Paulo Branch, Sao Paulo, SP, Brazil
    Genet Mol Res 3:512-20. 2004
    ..We discuss that this supports the notion of a broader association between alternative splicing and cell transformation, and that splicing factors may be involved in oncogenic pathways...
  16. pmc Identification of potential regulatory motifs in odorant receptor genes by analysis of promoter sequences
    Jussara S Michaloski
    Departamento de Bioquimica, Instituto de Quimica, Universidade de Sao Paulo, C P 26077 CEP 05513 970, Sao Paulo, Brazil
    Genome Res 16:1091-8. 2006
    ..Our results show that the OR genes share common promoter elements. The present strategy should provide information on the role played by cis-regulatory sequences in OR gene regulation...
  17. pmc Distinct patterns of somatic alterations in a lymphoblastoid and a tumor genome derived from the same individual
    Pedro A F Galante
    Ludwig Institute for Cancer Research, São Paulo Branch at Hospital Alemão Oswaldo Cruz, São Paulo 01323 903, Brazil
    Nucleic Acids Res 39:6056-68. 2011
    ....
  18. pmc Functional genomics analyses of RNA-binding proteins reveal the splicing regulator SNRPB as an oncogenic candidate in glioblastoma
    Bruna R Correa
    Centro de Oncologia Molecular, Hospital Sirio Libanes, Sao Paulo, Brazil
    Genome Biol 17:125. 2016
    ..To further our knowledge of novel regulatory pathways that could contribute to gliomagenesis, we have conducted a systematic study of RBPs in GBM...
  19. ncbi request reprint Automatic correspondence of tags and genes (ACTG): a tool for the analysis of SAGE, MPSS and SBS data
    Pedro A F Galante
    Departamento de Bioquimica, Instituto de Quimica, Universidade de Sao Paulo, Sao Paulo, Brazil
    Bioinformatics 23:903-5. 2007
    ..We developed ACTG, a web-based application that allows a large-scale tag-to-gene mapping using several reference datasets. ACTG can annotate SAGE (14 or 21 bp), MPSS (17 or 20 bp) and SBS (16 bp) data for both human and mouse organisms...
  20. pmc Signaling transcript profile of the asexual intraerythrocytic development cycle of Plasmodium falciparum induced by melatonin and cAMP
    Wânia Rezende Lima
    Departamento de Fisiologia, Instituto de Biociencias, Universidade de Sao Paulo, Sao Paulo, Brazil Instituto de Ciências Exatas e Naturais ICEN Medicina, Universidade Federal do Mato Grosso Campus Rondonópolis, Brazil
    Genes Cancer 7:323-339. 2016
    ..Our results highlight P. falciparum's perception of the external milieu through the signaling molecules MEL and cAMP, which are able to drive to changes in gene expression in the parasite...
  21. pmc A Genome-Wide Landscape of Retrocopies in Primate Genomes
    Fábio C P Navarro
    Centro de Oncologia Molecular, Hospital Sirio Libanes, Sao Paulo, Brazil Dep de Bioquímica, Universidade de Sao Paulo, Brazil
    Genome Biol Evol 7:2265-75. 2015
    ....
  22. pmc Mutational analysis of genes coding for cell surface proteins in colorectal cancer cell lines reveal novel altered pathways, druggable mutations and mutated epitopes for targeted therapy
    Elisa Donnard
    Centro de Oncologia Molecular, Hospital Sirio Libanes, Sao Paulo, Brazil Programa de Pós Graduação do Departamento de Bioquímica, Instituto de Quimica, Universidade de Sao Paulo, Sao Paulo, Brazil These authors contributed equally to this work
    Oncotarget 5:9199-213. 2014
    ..Notwithstanding, 92% of these epitopes were expressed in cell lines with the mutator phenotype, opening new venues for the use of "general" immune checkpoint drugs in this subset of patients. ..
  23. doi request reprint Different evolutionary strategies for the origin of caspase-1 inhibitors
    Julia P C da Cunha
    Ludwig Institute for Cancer Research, Sao Paulo Branch, Sao Paulo, Brazil
    J Mol Evol 66:591-7. 2008
    ..Surprisingly, stop codons originated independently in all duplicated copies to generate CARD-only proteins with inhibitory activity. We discuss this evolutionary model in the context of both neo- and subfunctionalization...
  24. pmc The impact of SNPs on the interpretation of SAGE and MPSS experimental data
    Ana Paula M Silva
    Laboratory of Molecular Biology, Ludwig Institute for Cancer Research, 01509 010, Sao Paulo, SP, Brazil
    Nucleic Acids Res 32:6104-10. 2004
    ..The availability of our SNP-associated alternative tag database will certainly improve the interpretation of SAGE and MPSS experiments...
  25. ncbi request reprint ORESTES are enriched in rare exon usage variants affecting the encoded proteins
    Noboru Jo Sakabe
    Ludwig Institute for Cancer Research, Sao Paulo Branch, Rua Prof Antonio Prudente 109, 4 o andar, 01509 010, Sao Paulo, Brazil
    C R Biol 326:979-85. 2003
    ..It is shown here that ORESTES probe low abundant messages more efficiently. In addition, most of the variants detected by ORESTES affect the structure of the corresponding proteins...
  26. pmc The generation and utilization of a cancer-oriented representation of the human transcriptome by using expressed sequence tags
    Helena Brentani
    Laboratório de Genética Molecular do Câncer, Departmento de Radiologia, Universidade de Sao Paulo, Travessa da Rua Dr Ovídeo Pires de Campos S N, 4deg, Brazil
    Proc Natl Acad Sci U S A 100:13418-23. 2003
    ....