Ivan Costa

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Josiah Heyman

University of Texas at El Paso (UTEP)

David Moffette

University of Ottawa | Université d'Ottawa

Raquel Augustin

Universidade Federal de Pelotas (Federal University of Pelotas)

Tomás Mantecón

Universidad de Cantabria

Lorena Córdoba

National Scientific and Technical Research Council

martinho almeida

Universidade de São Paulo

Carlos Guardado da Silva

Universidade de Lisboa

Nilton Dantas

UFBA - Federal University of Bahia

Henrique Costa

CEBRAP

Adriana Sansão

Universidade Federal do Rio de Janeiro (UFRJ)

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Papers by Ivan Costa

Comparative Analysis of Clustering Methods for Gene Expression Data

ABSTRACT Large scale approaches, namely proteomics and transcriptomics, will play the most import... more ABSTRACT Large scale approaches, namely proteomics and transcriptomics, will play the most important role of the so-called post-genomics. These approaches allow experiments to measure the expression of thousands of genes from a cell in distinct time points. The analysis of this data can allow the understanding of gene function and gene regulatory networks [3].

Epigenetic age predictions based on buccal swabs are more precise in combination with cell type-specific DNA methylation signatures

Aging, Jan 31, 2016

Aging is reflected by highly reproducible DNA methylation (DNAm) changes that open new perspectiv... more Aging is reflected by highly reproducible DNA methylation (DNAm) changes that open new perspectives for estimation of chronological age in legal medicine. DNA can be harvested non-invasively from cells at the inside of a person's cheek using buccal swabs - but these specimens resemble heterogeneous mixtures of buccal epithelial cells and leukocytes with different epigenetic makeup. In this study, we have trained an age predictor based on three age-associated CpG sites (associated with the genesPDE4C, ASPA, and ITGA2B) for swab samples to reach a mean absolute deviation (MAD) between predicted and chronological age of 4.3 years in a training set and of 7.03 years in a validation set. Subsequently, the composition of buccal epithelial cells versus leukocytes was estimated by two additional CpGs (associated with the genes CD6 and SERPINB5). Results of this "Buccal-Cell-Signature" correlated with cell counts in cytological stains (R2 = 0.94). Combination of cell type-speci...

Analysis of computational footprinting methods for DNase sequencing experiments

Nature Methods, 2016

DNase-seq allows nucleotide-level identification of transcription factor binding sites on the bas... more DNase-seq allows nucleotide-level identification of transcription factor binding sites on the basis of a computational search of footprint-like DNase I cleavage patterns on the DNA. Frequently in high-throughput methods, experimental artifacts such as DNase I cleavage bias affect the computational analysis of DNase-seq experiments. Here we performed a comprehensive and systematic study on the performance of computational footprinting methods. We evaluated ten footprinting methods in a panel of DNase-seq experiments for their ability to recover cell-specific transcription factor binding sites. We show that three methods-HINT, DNase2TF and PIQ-consistently outperformed the other evaluated methods and that correcting the DNase-seq signal for experimental artifacts significantly improved the accuracy of computational footprints. We also propose a score that can be used to detect footprints arising from transcription factors with potentially short residence times.

DNA methylation levels at individual age-associated CpG sites can be indicative for life expectancy

Aging, Jan 25, 2016

DNA-methylation (DNAm) levels at age-associated CpG sites can be combined into epigenetic aging s... more DNA-methylation (DNAm) levels at age-associated CpG sites can be combined into epigenetic aging signatures to estimate donor age. It has been demonstrated that the difference between such epigenetic age-predictions and chronological age is indicative for of all-cause mortality in later life. In this study, we tested alternative epigenetic signatures and followed the hypothesis that even individual age-associated CpG sites might be indicative for life-expectancy. Using a 99-CpG aging model, a five-year higher age-prediction was associated with 11% greater mortality risk in DNAm profiles of the Lothian Birth Cohort 1921 study. However, models based on three CpGs, or even individual CpGs, generally revealed very high offsets in age-predictions if applied to independent microarray datasets. On the other hand, we demonstrate that DNAm levels at several individual age-associated CpGs seem to be associated with life expectancy - e.g., at CpGs associated with the genesPDE4C and CLCN6. Our r...

Polysomnographic monitoring of difficult-to-control asthma patients

European Respiratory Journal, Sep 1, 2013

Number: 4199 Publication Number: P2122 Abstract Group: 1.1. Clinical Problems

Ivan Costa

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