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 transferi, 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

Combining p-values to improve classification of differential gene expression in the HTself software
Cortez, et al. (2011) Genetics and Molecular Research, 10, 5.5


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.

Gene expression relationship between prostate cancer cells of Gleason 3, 4 and normal epithelial cells as revealed by cell type-specific transcriptomes
Pascal, et al. (2009) BMC Cancer, 9, 452.

Differential inductive signaling of CD90+ prostate cancer-associated fibroblasts compared to normal tissue stromal mesenchyme cells
Pascal, et al. (2011) Cancer Microenvironment, 4, 51-59.

Insights on PRAME and osteosarcoma by means of gene expression profiling
Toledo, et al. (2011) Journal of Orthopaedic Science, 16, 458-466.

Lineage relationship of prostate cancer cell types based on gene expression.
Pascal, et al. (2011) BMC Medical Genomics, 4, 46.

In silico identification of conserved intercoding sequences in Leishmania genomes: Unraveling putative cis-regulatory elements.
Vasconcelos, et al. (2012) Mol. Biochem. Parasitology, 183, 140

Bladder expression of CD cell surface antigens and cell-type-specific transcriptomes
Liu, et al. (2012) Cell and Tissue Research, 348, 589

Reprogramming of prostate cancer-associated stromal cells to embryonic stem-like.
Vêncio , et al. (2012) Prostate pubmed


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

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

Stromal-epithelial interactions in early neoplasia
Liu, et al. (2011) Cancer Biomarkers, 9, 141-55

A “molecularização” do câncer de próstata: reflexões sobre o chip de DNA
Monteiro and Vêncio (2012) in Identidades Emergentes, Genética e Saúde: Perspectivas Antropológicas (eds: Santos, Gibbon, S. and Beltrão), Editora Garamond e Editora Fiocruz, ISBN:xxxxxxx

Contributions to Wikipedia | Contribuições a Wikipédia

in Portuguese | em português

in English | em inglês


Patents | Patentes

Genes associated to sucrose content
Souza, et al. (2010) United States Patent US7732664B2

Determining ability of plant to accumulate sugar comprises measuring the expression level a polynucleotide or its encoded polypeptide associated with sucrose content in a plant sample
Souza, et al. (2008) Patent Application, Derwent Primary Accession: 2008-A47420

New transgenic plant e.g. sugarcane plant useful for producing ethanol, comprises recombinant expression vector containing polynucleotide
Buckeridge, et al. (2010) Patent Application, Derwent Primary Accession: 2010-H36216


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 0429
Fax: +55 (16) 3602 0407

rvencio@usp.br
Email me through OpenWetWare

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