Labpib:Ricardo Z.N. Vencio
<wikionly>Click here to see the *official* version of this page</wikionly> <wikionly>Clique aqui para ver a versão *oficial* desta página</wikionly>
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
Education | Formação
Publications | PublicaçõesDue 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 | MétodosUsing credibility intervals instead of hypothesis tests in SAGE analysis Bayesian model accounting for within-class biological variability in Serial Analysis of Gene Expression (SAGE) HTself: self-self based statistical test for low-replication microarray studies BayGO: Bayesian analysis of ontology term enrichment in microarray data SpotWhatR: an user-friendly microarray data analysis system BayBoots: a model-free Bayesian tool to identify class markers from gene expression data Simcluster: clustering enumeration gene expression data on the simplex space ProbCD: enrichment analysis accounting for categorization uncertainty ProbFAST: Probabilistic functional analysis system tool Combining p-values to improve classification of differential gene expression in the HTself software
Applied | AplicaçõesDNA microarray-based genome comparison of a pathogenic and a nonpathogenic strain of Xylella fastidiosa delineates genes important for bacterial virulence DNA microarrays for comparative genomics and analysis of gene expression in Trypanosoma cruzi Gene discovery and expression profile analysis through EST sequencing from different developmental stages of the chytridiomycete Blastocladiella emersonii Transcription profiling of signal transduction-related genes in sugarcane tissues Whole-genome expression profiling of Xylella fastidiosa in response to growth on glucose Gene expression profile associated to response to doxorubicin based therapy in breast cancer Evaluation of reference-based two-color methods for measurement of gene expression ratios using spotted cDNA microarrays Global gene expression analysis of the heat shock response in the phytopathogen Xylella fastidiosa Differential transcription profiles in Trypanosoma cruzi associated with clinical forms of Chagas disease: maxicircle NADH dehydrogenase subunit 7 gene truncation in asymptomatic patient isolates Signal transduction-related responses to phytohormones and environmental challenges in sugarcane Common molecular pathways involved in human CD133+ / CD34+ progenitor cell expansion and cancer Multisite fMRI reproducibility of a motor task using identical MR systems Comparative transcriptome analysis of Listeria monocytogenes strains of the two major lineages reveals differences in virulence, cell wall and stress response The SUCEST-FUN project: identifying genes that regulate sucrose content in sugarcane plants The Iron Stimulon of Xylella fastidiosa Includes Genes for Type IV Pilus and Colicin V-Like Bacteriocins Systems biology approach predicts immunogenicity of the yellow fever vaccine in humans Age-dependent signature of metallothionein expression in primary CD4 T cell responses is due to sustained zinc signaling Global gene expression analysis during germination in the chytridiomycete Blastocladiella emersonii Sugarcane genes associated with sucrose content Expression profile of signal transduction components in a sugarcane population segregating for sugar content Temporal expression profiling of the effects of secreted factors from prostate stromal cells on embryonal carcinoma stem cells Gene expression down-regulation in CD90+ prostate tumor-associated stromal cells involves potential organ-specific gene Differential inductive signaling of CD90+ prostate cancer-associated fibroblasts compared to normal tissue stromal mesenchyme cells Insights on PRAME and osteosarcoma by means of gene expression profiling Lineage relationship of prostate cancer cell types based on gene expression. Combining P-values to improve classification of differential gene expression in the HTself software. In silico identification of conserved intercoding sequences in Leishmania genomes: Unraveling putative cis-regulatory elements. Reprogramming of prostate cancer-associated stromal cells to embryonic stem-like.
Other | OutrasIntellectual property and public research in biotechnology: the scientists opinion Biology and Physics integration: building genetic regulatory networks using differential equations (in Portuguese) Chapter 11 - Statistical Methods in Serial Analysis of Gene Expression (SAGE) Chapter 2 - Constructing probabilistic genetic networks of Plasmodium falciparum from dynamical expression signals of the intraerythrocytic development cycle. Plasmodium vivax and the importance of the subtelomeric multigene vir superfamily Stromal-epithelial interactions in early neoplasia
Contributions to Wikipedia | Contribuições a Wikipédia
Patents | PatentesGenes associated to sucrose content 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 New transgenic plant e.g. sugarcane plant useful for producing ethanol, comprises recombinant expression vector containing polynucleotide
Contact Information | Informações para ContatoProf. Dr. Ricardo Zorzetto Nicoliello Vêncio |
