Research Topics
Genomes and Genes | Sergio Verjovski-AlmeidaSummaryCountry: Brazil Publications
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Publications
Systems medicine and integrated care to combat chronic noncommunicable diseasesJean Bousquet
Department of Respiratory Diseases, Arnaud de Villeneuve Hospital, CHU Montpellier, INSERM CESP U1018, Villejuif, France
Genome Med 3:43. 2011..This systems medicine strategy, which will take a holistic approach to disease, is designed to allow the results to be used globally, taking into account the needs and specificities of local economies and health systems...- Evaluation of reference-based two-color methods for measurement of gene expression ratios using spotted cDNA microarraysBernardo R Peixoto
Departamento de Matematica, Universidade dos Acores, 9501 801 Ponta Delgada, Acores, Portugal
BMC Genomics 7:35. 2006..Here we evaluated the precision and accuracy of reconstructed ratios from three indirect methods relative to ratios obtained from direct hybridizations, herein considered as the gold-standard... - Transcriptome analysis of the acoelomate human parasite Schistosoma mansoniSergio Verjovski-Almeida
Departamento de Bioquimica, Instituto de Quimica, Universidade de Sao Paulo, 05508 900 Sao Paulo, SP, Brazil
Nat Genet 35:148-57. 2003.... - Zerg: a very fast BLAST parser libraryApua C M Paquola
Departamento de Bioquimica, Instituto de Quimica, Universidade de São Paulo 05508 900, Sao Paulo, SP, Brazil
Bioinformatics 19:1035-6. 2003..It is optimized for speed, being especially useful for large-scale genomic analysis. Benchmark tests show that Zerg is over two orders of magnitude faster than some widely used BLAST parsers. AVAILABILITY: http://bioinfo.iq.usp.br/zerg.. - Use of a 44k oligoarray to explore the transcriptome of Schistosoma mansoni adult wormsSergio Verjovski-Almeida
Laboratory of Gene Expression in Eukaryotes, Departamento de Bioquimica, Instituto de Quimica, Universidade de Sao Paulo, Av Prof Lineu Prestes, 748, 05508 000 Sao Paulo, SP, Brazil
Exp Parasitol 117:236-45. 2007..Moreover, detection of bi-directional transcription for 7% of the active "no match" genes in adults leads us to hypothesize a widespread production of antisense RNA in S. mansoni, with possible regulatory roles... - Current developments on Schistosoma proteomicsSergio Verjovski-Almeida
Departamento de Bioquimica, Instituto de Quimica, Universidade de Sao Paulo, 05508 900 Sao Paulo, SP, Brazil
Acta Trop 108:183-5. 2008..Here we review the development of schistosome proteomic research around the world and provide an appreciation on the future opportunities in Brazil... - Schistosome transcriptome: insights and perspectives for functional genomicsSergio Verjovski-Almeida
Instituto de Quimica, , , SP, Brazil
Trends Parasitol 20:304-8. 2004 - Gene structure and splicing in schistosomesSergio Verjovski-Almeida
Departamento de Bioquimica, Instituto de Quimica, Universidade de Sao Paulo, 05508 900 Sao Paulo, SP, Brazil
J Proteomics 74:1515-8. 2011..Complete description of the functions of these variable proteins will greatly contribute to our understanding of host-parasite interactions... - RASL11A, member of a novel small monomeric GTPase gene family, is down-regulated in prostate tumorsRodrigo Louro
Departamento de Bioquimica, Instituto de Quimica, Universidade de Sao Paulo, 05508 900 Sao Paulo, SP, Brazil
Biochem Biophys Res Commun 316:618-27. 2004..These results highlight a previously uncharacterized subfamily of Ras-related genes that may have a tumor suppressor role in prostate cancer... - Curupira-1 and Curupira-2, two novel Mutator-like DNA transposons from the genomes of human parasites Schistosoma mansoni and Schistosoma japonicumDaniele S Jacinto
Departamento de Fisica e Informatica, Instituto de Fisica de Sao Carlos, Universidade de Sao Paulo, 13566 590 Sao Carlos, SP, Brazil
Parasitology 138:1124-33. 2011..Description of these novel schistosome transposons provides new insights in the evolution of transposable elements in schistosomes... - Bursts of transposition from non-long terminal repeat retrotransposon families of the RTE clade in Schistosoma mansoniThiago M Venancio
Departamento de Bioquimica, Instituto de Quimica, Universidade de Sao Paulo, 05508 900 Sao Paulo, SP, Brazil
Int J Parasitol 40:743-9. 2010..We hypothesise that these bursts could be a consequence of the evolutionary pressure resulting from migration of Schistosoma from Asia to Africa and their establishment in this new environment, helping both speciation and adaptation... - Large-scale transcriptome analyses reveal new genetic marker candidates of head, neck, and thyroid cancerEduardo M Reis
, Faculdade de Medicina, , Brazil
Cancer Res 65:1693-9. 2005..Similar analysis is warranted for a number of other tumors for which large EST data sets are available... - Androgen responsive intronic non-coding RNAsRodrigo Louro
Departamento de Bioquimica, Instituto de Quimica, Universidade de Sao Paulo, 05508 900 Sao Paulo, Brazil
BMC Biol 5:4. 2007.... - Genome mapping and expression analyses of human intronic noncoding RNAs reveal tissue-specific patterns and enrichment in genes related to regulation of transcriptionHelder I Nakaya
Departamento de Bioquimica, Instituto de Quimica, Universidade de Sao Paulo, Sao Paulo, SP, Brazil
Genome Biol 8:R43. 2007..However, the complement of human genes in which introns are transcribed, and the number of intronic transcriptional units and their tissue expression patterns are not known... - Conserved tissue expression signatures of intronic noncoding RNAs transcribed from human and mouse lociRodrigo Louro
Departamento de Bioquimica, Instituto de Quimica, Universidade de Sao Paulo, 05508 900 Sao Paulo, Brasil
Genomics 92:18-25. 2008..Altogether, these results support an evolutionarily conserved role of intronic ncRNAs in human and mouse, which are likely to be involved in the fine tuning of gene expression regulation in different mammalian tissues... - Identification of the Schistosoma mansoni TNF-alpha receptor gene and the effect of human TNF-alpha on the parasite gene expression profileKatia C Oliveira
Laboratory of Gene Expression in Eukaryotes, Departamento de Bioquimica, Instituto de Quimica, Universidade de Sao Paulo, Sao Paulo, Brazil
PLoS Negl Trop Dis 3:e556. 2009.... - Identification of protein-coding and intronic noncoding RNAs down-regulated in clear cell renal carcinomaGlauber Costa Brito
Departamento de Bioquimica, Instituto de Quimica, Universidade de Sao Paulo, SP, Brazil
Mol Carcinog 47:757-67. 2008..Our results indicate a novel set of tumor suppressor gene candidates, including noncoding intronic RNAs, which may play a significant role in malignant transformations of normal renal cells... - Saci-1, -2, and -3 and Perere, four novel retrotransposons with high transcriptional activities from the human parasite Schistosoma mansoniRicardo DeMarco
Laboratorio de Bioinformatica. Departamento de Bioquimica, Instituto de Quimica, , , Brazil
J Virol 78:2967-78. 2004..mansoni target gene transcripts. The data presented here suggest a role for these elements in the dynamics of this complex human parasite genome... - Screening the Schistosoma mansoni transcriptome for genes differentially expressed in the schistosomulum stage in search for vaccine candidatesLeonardo P Farias
Centro de Biotecnologia, Instituto Butantan, Av Vital Brasil 1500, 05503 900 Sao Paulo, Sao Paulo, Brazil
Parasitol Res 108:123-35. 2011.... - As antisense RNA gets intronicEduardo M Reis
Department of Biochemistry, Institute of Chemistry, , , Brazil
OMICS 9:2-12. 2005.... - A quantitative view of the transcriptome of Schistosoma mansoni adult-worms using SAGEElida P B Ojopi
Laboratório de Neurociências LIM27, Instituto de Psiquiatria, Faculdade de Medicina da Universidade de Sao Paulo, Sao Paulo, SP, Brazil
BMC Genomics 8:186. 2007..By using SAGE (Serial Analysis of Gene Expression) we describe here the first large-scale quantitative analysis of the Schistosoma mansoni transcriptome, one of the most epidemiologically relevant species of this genus... - Gender biased differential alternative splicing patterns of the transcriptional cofactor CA150 gene in Schistosoma mansoniRicardo DeMarco
Laboratory of Gene Expression in Eukaryotes, , , , Brazil
Mol Biochem Parasitol 150:123-31. 2006..Due to the role of CA150 in RNA transcription and processing, we hypothesize that these differential expression events may be important in the generation and maintenance of the different phenotypes between male and female... - SmTRC1, a novel Schistosoma mansoni DNA transposon, discloses new families of animal and fungi transposons belonging to the CACTA superfamilyRicardo DeMarco
Laboratory of Gene Expression in Eukaryotes Departamento de Bioquímica, Instituto de Quimica, Universidade de Sao Paulo, Brazil
BMC Evol Biol 6:89. 2006..Despite the extensive description of retroelements in S. mansoni, just a single DNA-only transposon belonging to the Merlin family has so far been reported in this organism... - Splice variants of TLE family genes and up-regulation of a TLE3 isoform in prostate tumorsHelder I Nakaya
Departamento de Bioquimica, Instituto de Quimica, Universidade de Sao Paulo, 05508 900 Sao Pau lo, SP, Brazil
Biochem Biophys Res Commun 364:918-23. 2007..These results demonstrate that different isoforms of TLE genes are commonly transcribed in human tissues and suggest that TLE3 could be involved in prostate cancer development... - Gene expression profile of mesenchymal stem cells from paired umbilical cord units: cord is different from bloodMariane Secco
Human Genome Research Center, Department of Genetic and Evolutive Biology, University of Sao Paulo, 106 Cidade Universitária, 05508 090 São Paulo, SP, Brazil
Stem Cell Rev 5:387-401. 2009..In addition, these findings reinforce our previous suggestion on the importance of banking the whole umbilical cord unit for research or future therapeutic use... - Identification of protein-coding and non-coding RNA expression profiles in CD34+ and in stromal cells in refractory anemia with ringed sideroblastsMariana O Baratti
Department of Internal Medicine, School of Medical Science, Hematology and Hemotherapy Center, University of Campinas, 13083 970 Campinas, SP, Brazil
BMC Med Genomics 3:30. 2010..Characterization of ncRNAs in progenitor cells and stromal cells of MDS patients could be strategic for understanding gene expression regulation in this disease... - Analysis of Schistosoma mansoni genes shared with Deuterostomia and with possible roles in host interactionsThiago M Venancio
Laboratory of Bioinformatics Departamento de Bioquímica, Instituto de Quimica, Universidade de Sao Paulo, 05508 900 Sao Paulo, SP, Brazil
BMC Genomics 8:407. 2007.... - Characterization of Schistosoma mansoni ATPDase2 gene, a novel apyrase family memberJulio Levano Garcia
Departamento de Bioquimica, Instituto de Quimica, Universidade de Sao Paulo, 05508 900 Sao Paulo, SP, Brazil
Biochem Biophys Res Commun 352:384-9. 2007..Taken together these data suggest a non-redundant role for SmATPDase2 in the parasite-host interplay... - Non-coding RNAs in schistosomes: an unexplored worldKatia C Oliveira
Departamento de Bioquimica, Instituto de Quimica, Universidade de Sao Paulo, SP, Brasil
An Acad Bras Cienc 83:673-94. 2011..Exploring this world is a challenge for the scientists under a new molecular perspective of host-parasite interactions and parasite development... - Identification of 18 new transcribed retrotransposons in Schistosoma mansoniRicardo DeMarco
Departamento de Bioquimica, Instituto de Quimica, , Brazil
Biochem Biophys Res Commun 333:230-40. 2005..These results allow for a comprehensive description of the transcribed retrotransposon diversity of this complex human parasite... - Schistosomes--proteomics studies for potential novel vaccines and drug targetsRicardo DeMarco
Departamento de Fisica e Informatica, Instituto de Fisica de Sao Carlos, Universidade de Sao Paulo, 13560 970 Sao Carlos, SP, Brazil
Drug Discov Today 14:472-8. 2009..Successful preliminary trials of two vaccine candidates that have been detected at the parasite surface by proteomics give grounds for believing that such an approach may provide a fresh start for the field... - Apert p.Ser252Trp mutation in FGFR2 alters osteogenic potential and gene expression of cranial periosteal cellsRoberto D Fanganiello
Departamento de Genética e Biologia Evolutiva, Instituto de Biociencias, Universidade de Sao Paulo, Brazil
Mol Med 13:422-42. 2007.... - Mapping transposon insertion sites by touchdown PCR and hybrid degenerate primersJulio Levano-Garcia
, , SP, Brazil
Biotechniques 38:225-9. 2005..citri mutants. Restriction mapping and Southern blot analysis confirmed the insertion sites for eight randomly chosen mutants. This method is a very useful tool for large-scale characterization of mutants in functional genomics studies... - Molecular characterization and immunolocalization of Schistosoma mansoni ATP-diphosphohydrolaseRicardo DeMarco
, , , , SP, Brazil
Biochem Biophys Res Commun 307:831-8. 2003..The presence of an ATPDase ortholog on the surface of S. mansoni suggests that the enzyme might play a role in the escape from host defenses that would involve platelet activation... - Antisense intronic non-coding RNA levels correlate to the degree of tumor differentiation in prostate cancerEduardo M Reis
, , , , SP, Brasil
Oncogene 23:6684-92. 2004..024) between the low/high degrees of tumor differentiation and antisense intronic RASSF1 transcript levels. The need to use intron arrays to reveal the transcriptome profile of antisense intronic RNA in cancer has clearly emerged... - DNA microarray-based genome comparison of a pathogenic and a nonpathogenic strain of Xylella fastidiosa delineates genes important for bacterial virulenceTie Koide
, , , SP, Brazil
J Bacteriol 186:5442-9. 2004..These results provide the first detailed comparison between a nonpathogenic strain and a pathogenic strain of X. fastidiosa, constituting an important step towards understanding the molecular basis of the disease... - Gene expression arrays in cancer research: methods and applicationsRicardo R Brentani
Ludwig Institute for Cancer Research, Sao Paulo, Brazil
Crit Rev Oncol Hematol 54:95-105. 2005..Hence, we shall also highlight some of the already available and promising applications of array technology on the day-to-day practice of oncology... - Gene expression profiling reveals molecular marker candidates of laryngeal squamous cell carcinomaJucimara Colombo
UNESP Universidade Estadual Paulista, Instituto de Biociencias, Letras e Ciências Exatas IBILCE, Departamento de Biologia, Sao Paulo, Brazil
Oncol Rep 21:649-63. 2009..0001). The set of genes identified here contribute to a better understanding of the molecular basis of larynx cancer, and provide candidate markers for improving diagnosis, prognosis and treatment of this carcinoma... - Long intronic noncoding RNA transcription: expression noise or expression choice?Rodrigo Louro
Departamento de Bioquimica, Instituto de Quimica, Universidade de Sao Paulo, 05508 900 Sao Paulo, SP, Brazil
Genomics 93:291-8. 2009..Deciphering nature's choice of different types of messages conveyed by ncRNAs will shed light on the RNA-based layer of regulatory processes in eukaryotic cells... - Transcriptional regulation differs in affected facioscapulohumeral muscular dystrophy patients compared to asymptomatic related carriersPatricia Arashiro
Human Genome Research Center, Department of Genetics and Evolutive Biology, Institute of Biosciences, University of Sao Paulo, 05508 090, Sao Paulo, Brazil
Proc Natl Acad Sci U S A 106:6220-5. 2009.... - Schistosomiasis--a century searching for chemotherapeutic drugsGabriela Ribeiro-dos-Santos
Centro de Biotecnologia, Instituto Butantan, 05503 900, Sao Paulo, SP, Brazil
Parasitol Res 99:505-21. 2006.... - Effect of human TGF-? on the gene expression profile of Schistosoma mansoni adult wormsKatia C Oliveira
Departamento de Bioquimica, Instituto de Quimica, Universidade de Sao Paulo, 05508 900 Sao Paulo, SP, Brazil
Mol Biochem Parasitol 183:132-9. 2012..These datasets offer potential targets to be explored in order to understand the molecular mechanisms behind the possible role of hTGF-? effects on parasite biology... - Long noncoding intronic RNAs are differentially expressed in primary and metastatic pancreatic cancerAna C Tahira
Departamento de Bioquimica, Instituto de Quimica, Universidade de Sao Paulo, 05508 900, Sao Paulo, SP, Brasil
Mol Cancer 10:141. 2011..abstract:.. - The generation and utilization of a cancer-oriented representation of the human transcriptome by using expressed sequence tagsHelena Brentani
, Departmento de Radiologia, , , 4deg, Brazil
Proc Natl Acad Sci U S A 100:13418-23. 2003.... - Perspectives of Long Non-Coding RNAs in Cancer DiagnosticsEduardo M Reis
Departamento de Bioquimica, Instituto de Quimica, Universidade de São Paulo São Paulo, Brasil
Front Genet 3:32. 2012..Annotation and functional characterization of the lncRNA complement of the cancer transcriptome will conceivably provide new venues for early diagnosis and treatment of the disease... - Human malaria parasites display a receptor for activated C kinase orthologLuciana Madeira
Departamento de Parasitologia, , , 05508-900, , SP, Brazil
Biochem Biophys Res Commun 306:995-1001. 2003.... - Schistosoma mansoni TGF-beta receptor II: role in host ligand-induced regulation of a schistosome target geneAhmed Osman
Department of Microbiology and Immunology, School of Medicine and Biomedical Sciences, State University of New York at Buffalo, Buffalo, New York, USA
PLoS Pathog 2:e54. 2006..The results also provide additional evidence for a role for the TGF-beta signaling pathway in male-induced female reproductive development... - Genome sequence of Aedes aegypti, a major arbovirus vectorVishvanath Nene
Institute for Genomic Research, 9712 Medical Center Drive, Rockville, MD 20850, USA
Science 316:1718-23. 2007..An increase in genes encoding odorant binding, cytochrome P450, and cuticle domains relative to An. gambiae suggests that members of these protein families underpin some of the biological differences between the two mosquito species... - Cloning the genes and DNA binding properties of High Mobility Group B1 (HMGB1) proteins from the human blood flukes Schistosoma mansoni and Schistosoma japonicumFrancisco Meirelles Bastos de Oliveira
, , Universidade Federal do Rio de Janeiro, , Brazil
Gene 377:33-45. 2006.... - Use of degenerate primers and touchdown PCR for construction of cDNA librariesJuliana L R Fietto
, Brasil
Biotechniques 32:1404-8, 1410-1. 2002..20-40 sequences/ mini-library). The optimized high-throughput approach described here is likely to help in the discovery of expressed genes in any complex organism... - The tegument surface membranes of the human blood parasite Schistosoma mansoni: a proteomic analysis after differential extractionSimon Braschi
Department of Biology, University of York, York, UK
Proteomics 6:1471-82. 2006..The proteins identified were categorised by their function and putative location on the basis of their homology with annotated proteins in other organisms...