Labpib:Ricardo Z.N. Vencio

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Introduction | Introdução


BSc. in Physics, MSc. in Statistics and PhD. in Bioinformatics by the University of São Paulo (USP), I have been working on the creation of mathematical and computational methods for the solution of problems in Biology and Medicine. In late 2008 I joined the University of São Paulo's Medical School at Ribeirão Preto (FMRP-USP) as Assistant Professor to conduct research and teaching activities on bioinformatics at the Genetics Department. At that moment I founded the LabPIB (acronym that stands for Biological Information Processing Lab, in Portuguese http://labpib.openwetware.org). In late 2010 I moved from the Medical School, along with LabPIB, to the newly created Department of Computation and Mathematics (DCM) at University of Sao Paulo's Ribeirao Preto campus. Questions or reprint requisitions of my published works or even random comments are always welcome: rvencio@usp.br

Graduado em Física pelo IF-USP, mestre em Estatística pelo IME-USP e doutor em Bioinformática pela USP - Universidade de São Paulo; venho trabalhando na criação de métodos matemáticos e computacionais para solução de problemas em Biologia e em Medicina. Em meados de 2008 integrei-me ao corpo docente da Faculdade de Medicina de Ribeirão Preto - Universidade de São Paulo (FMRP-USP) como Professor Doutor MS-3 para atuar na área de Bioinformática do Departamento de Genética. Neste momento, fundei então o LabPIB - Laboratório de Processamento de Informação Biológica (http://labpib.openwetware.org). Desde o fim de 2010, me tranferi, junto com o LabPIB, para o recém criado Departamento de Computação e Matemática (DCM) dentro da Faculdade de Filosofia Ciências e Letras de Ribeirão Preto (FFCLRP-USP). Questões, pedido de cópias dos trabalhos publicados e comentários diversos são sempre bem-vindos: rvencio@usp.br

Education | Formação

 * 2006 - 2008, Post-doctorate | Pós-doutorado, Institute for Systems Biology
 * 2005 - 2006, PhD Bioinformatics | Doutorado em Bioinformática, Universidade de São Paulo
 * 2002 - 2004, MSc Statistics | Mestrado em Estatística, Instituto de Matemática e Estatística da Universidade de São Paulo
 * 1998 - 2001, BSc Physics | Graduação em Física, Instituto de Física da Universidade de São Paulo

Publications | Publicações
Due to some evil copyright issues, I can't make available here all papers I co-authored. Please download them at our server.

Devido a algumas questões malígnas de direitos autorais, eu não posso deixar disponíveis aqui todos os artigos em que fui co-autor. Eles estão no nosso servidor.

Methods | Métodos
Using credibility intervals instead of hypothesis tests in SAGE analysis Vêncio, et al. (2003) Bioinformatics, 19, 2461-2464.

Bayesian model accounting for within-class biological variability in Serial Analysis of Gene Expression (SAGE) Vêncio, et al. (2004) BMC Bioinformatics, 5, 119.

HTself: self-self based statistical test for low-replication microarray studies Vêncio and Koide (2005) DNA Research, 12, 211-214

BayGO: Bayesian analysis of ontology term enrichment in microarray data Vêncio, et al. (2006) BMC Bioinformatics, 7, 86

SpotWhatR: an user-friendly microarray data analysis system Koide, et al. (2006) Genetics and Molecular Research, 5, 93-107

BayBoots: a model-free Bayesian tool to identify class markers from gene expression data Vêncio, et al. (2006) Genetics and Molecular Research, 5, 138-142

Simcluster: clustering enumeration gene expression data on the simplex space Vêncio and Varuzza, et al. (2007) BMC Bioinformatics, 8, 246

ProbCD: enrichment analysis accounting for categorization uncertainty Vêncio and Shmulevich (2007) BMC Bioinformatics, 8, 383

ProbFAST: Probabilistic functional analysis system tool Silva, et al. (2010) BMC Bioinformatics, 11, 161

Applied | Aplicações
DNA microarray-based genome comparison of a pathogenic and a nonpathogenic strain of Xylella fastidiosa delineates genes important for bacterial virulence Koide and Zaini, et al. (2004) Journal of Bacteriology, 186, 5442-5449.

DNA microarrays for comparative genomics and analysis of gene expression in Trypanosoma cruzi Baptista, et al. (2004) Molecular and Biochemical Parasitology, 138, 183-194.

Gene discovery and expression profile analysis through EST sequencing from different developmental stages of the chytridiomycete Blastocladiella emersonii Ribichich, et al. (2005) Eukaryotic Cell, 4, 455-464. Transcription profiling of signal transduction-related genes in sugarcane tissues Papini-Terzi, et al. (2005) DNA Research, 12, 27-38.

Whole-genome expression profiling of Xylella fastidiosa in response to growth on glucose Pashalidis, Zaini and Moreira, et al. (2005) OMICS, 9, 77-90.

Gene expression profile associated to response to doxorubicin based therapy in breast cancer Folgueira, et al. (2005) Clinical Cancer Research, 11, 7434-7443

Evaluation of reference-based two-color methods for measurement of gene expression ratios using spotted cDNA microarrays Peixoto, et al. (2006) BMC Genomics, 7, 35

Global gene expression analysis of the heat shock response in the phytopathogen Xylella fastidiosa Koide, et al. (2006) Journal of Bacteriology, 188, 5821-5830

Differential transcription profiles in Trypanosoma cruzi associated with clinical forms of Chagas disease: maxicircle NADH dehydrogenase subunit 7 gene truncation in asymptomatic patient isolates Baptista, et al. (2006) Molecular and Biochemical Parasitology,150, 236-248

Signal transduction-related responses to phytohormones and environmental challenges in sugarcane Rocha, et al. (2007) BMC Genomics, 8, 71

Common molecular pathways involved in human CD133+ / CD34+ progenitor cell expansion and cancer Okamoto, et al. (2007) Cancer Cell International, 7, 11

Multisite fMRI reproducibility of a motor task using identical MR systems Costafreda, et al. (2007) Journal of Magnetic Resonance Imaging, 26, 1122-1126

Comparative transcriptome analysis of Listeria monocytogenes strains of the two major lineages reveals differences in virulence, cell wall and stress response Severino, et al. (2007) Applied and Environmental Microbiology, 73, 6078-6088

The SUCEST-FUN project: identifying genes that regulate sucrose content in sugarcane plants Papini-Terzi, et al. (2008) Sugar Cane International, 26, 25-29

The Iron Stimulon of Xylella fastidiosa Includes Genes for Type IV Pilus and Colicin V-Like Bacteriocins Zaini, et al. (2008) Journal of Bacteriology, 190, 2368-2378

Systems biology approach predicts immunogenicity of the yellow fever vaccine in humans Querec, et al. (2008) Nature Immunology, 10, 116-125.

Age-dependent signature of metallothionein expression in primary CD4 T cell responses is due to sustained zinc signaling Lee, et al. (2009) Rejuvenation Research, 11, 1001-1011.

Global gene expression analysis during germination in the chytridiomycete Blastocladiella emersonii Salem-Izacc, et al. (2009) Eukaryot Cell, 8, 170-80.

Sugarcane genes associated with sucrose content Papini-Terzi, et al. (2009) BMC Genomics, 21, 10:120.

Expression profile of signal transduction components in a sugarcane population segregating for sugar content Felix, et al. (2009) Tropical Plant Biology, 2, 98:109.

Temporal expression profiling of the effects of secreted factors from prostate stromal cells on embryonal carcinoma stem cells Pascal, et al. (2009) Prostate, 69, 1353-65.

Gene expression down-regulation in CD90+ prostate tumor-associated stromal cells involves potential organ-specific gene Pascal, et al. (2009) BMC Cancer, 9, 317.

Differential inductive signaling of CD90+ prostate cancer-associated fibroblasts compared to normal tissue stromal mesenchyme cells Pascal, et al. (2011) Cancer Microenvironment, 4, 51.

Insights on PRAME and osteosarcoma by means of gene expression profiling Toledo, et al. (2011) Journal of Orthopaedic Science, 4, ?.

Other | Outras
Intellectual property and public research in biotechnology: the scientists opinion Coutinho, et al. (2003) Scientometrics, 58, 641-656.

Biology and Physics integration: building genetic regulatory networks using differential equations (in Portuguese) Vêncio and Oliveira (2006) Revista Brasileira de Ensino de Bioquímica e Biologia Molecular, 1/2006

Chapter 11 - Statistical Methods in Serial Analysis of Gene Expression (SAGE) Vêncio and Brentani (2006) in Computational and Statistical Approaches to Genomics - 2nd edition (eds: Zhang and Shmulevich), Springer, ISBN:0-387-26287-3

Chapter 2 - Constructing probabilistic genetic networks of Plasmodium falciparum from dynamical expression signals of the intraerythrocytic development cycle. Barrera, et al. (2006) in Methods of Microarray Data Analysis V (eds: McConnell, Lin and Hurban), Springer, ISBN: 978-0-387-34568-0

Genes associated to sucrose content Mendes, et al. (2007) United States Patent Application 20070292874

Plasmodium vivax and the importance of the subtelomeric multigene vir superfamily Fernandez-Becerra, et al. (2009) Trends in Parasitology, 25, 44-51

Contributions to Wikipedia | Contribuições a Wikipédia
in Portuguese | em português

in English | em inglês

Contact Information | Informações para Contato
Prof. Dr. Ricardo Zorzetto Nicoliello Vêncio University of Sao Paulo | Universidade de São Paulo Department of Computing and Mathematics FFCLRP | Departamento de Computação e Matemática FFCLRP Av. Bandeirantes, 3900 - Monte Alegre Ribeirão Preto - SP CEP: 14040-901 Fone: +55 (16) 3602 3718 Fax: +55 (16) 3602 4887 rvencio@usp.br Email me through OpenWetWare