Genomes and Genes
Pedro A F Galante
- Alternative splicing: a bioinformatics perspectiveElisa 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...
- Systematic detection of putative tumor suppressor genes through the combined use of exome and transcriptome sequencingQi 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...
- Sense-antisense pairs in mammals: functional and evolutionary considerationsPedro 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...
- Comprehensive evaluation of the effectiveness of gene expression signatures to predict complete response to neoadjuvant chemoradiotherapy and guide surgical intervention in rectal cancerCamila Lopes-Ramos
Centro de Oncologia Molecular, Hospital Sirio Libanes, Sao Paulo, Brazil
Cancer Genet 208:319-26. 2015....
- SPLOOCE: a new portal for the analysis of human splicing variantsJosé 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...
- A comprehensive in silico expression analysis of RNA binding proteins in normal and tumor tissue: Identification of potential players in tumor formationPedro 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...
- PVALB, a new Hürthle adenoma diagnostic marker identified through gene expressionJanete 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...
- Alternative splicing and genetic diversity: silencers are more frequently modified by SNVs associated with alternative exon/intron bordersJorge 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...
- Identification of FAM46D as a novel cancer/testis antigen using EST data and serological analysisFabiana 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...
- The use of personalized biomarkers and liquid biopsies to monitor treatment response and disease recurrence in locally advanced rectal cancer after neoadjuvant chemoradiationPaola 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. ..
- ICRmax: an optimized approach to detect tumor-specific interchromosomal rearrangements for clinical applicationElisa 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...
- A score system for quality evaluation of RNA sequence tags: an improvement for gene expression profilingDaniel 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...
- A novel human G protein-coupled receptor is over-expressed in prostate cancerRaphael 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....
- Common promoter elements in odorant and vomeronasal receptor genesJussara 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...
- Splicing factors are differentially expressed in tumorsNatanja 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...
- Identification of potential regulatory motifs in odorant receptor genes by analysis of promoter sequencesJussara 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...
- Distinct patterns of somatic alterations in a lymphoblastoid and a tumor genome derived from the same individualPedro 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....
- Functional genomics analyses of RNA-binding proteins reveal the splicing regulator SNRPB as an oncogenic candidate in glioblastomaBruna 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...
- Automatic correspondence of tags and genes (ACTG): a tool for the analysis of SAGE, MPSS and SBS dataPedro 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...
- Signaling transcript profile of the asexual intraerythrocytic development cycle of Plasmodium falciparum induced by melatonin and cAMPWânia 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...
- A Genome-Wide Landscape of Retrocopies in Primate GenomesFábio 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....
- 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 therapyElisa 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. ..
- Different evolutionary strategies for the origin of caspase-1 inhibitorsJulia 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...
- The impact of SNPs on the interpretation of SAGE and MPSS experimental dataAna 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...
- ORESTES are enriched in rare exon usage variants affecting the encoded proteinsNoboru 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...
- The generation and utilization of a cancer-oriented representation of the human transcriptome by using expressed sequence tagsHelena 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....