Papers by Dunarel Badescu
An Evolutionary Study of the Human Papillomavirus Genomes
In this article, we undertake a study of the evolution of Human Papillomaviruses (HPV), whose pot... more In this article, we undertake a study of the evolution of Human Papillomaviruses (HPV), whose potential to cause cervical cancer is well known. First, we found that the existing HPV groups are monophyletic and that the high-risk carcinogenicity taxa are usually clustered together. Then, we present a new algorithm for analyzing the information content of multiple sequence alignments in relation to epidemiologic carcinogenicity data to identify regions that would warrant additional experimental analyses. The new algorithm is based on a sliding window procedure looking for genomic regions being responsible for disease. Examination of the genomes of 83 HPVs allowed us to identify specific regions that might be influenced by insertions, deletions, or simply by mutations, and that may be of interest for further analyses.
Journal of Computational Biology, 2009
In this article, we undertake a study of the evolution of human papillomaviruses (HPV), whose pot... more In this article, we undertake a study of the evolution of human papillomaviruses (HPV), whose potential to cause cervical cancer is well known. First, we found that the existing HPV groups are monophyletic and that the high risk of carcinogenicity taxa are usually clustered together. Then, we present a new algorithm for analyzing the information content of multiple sequence alignments in relation to epidemiologic carcinogenicity data to identify regions that would warrant additional experimental analyses. The new algorithm is based on a sliding window procedure and a p-value computation to identify genomic regions that are specific to HPVs causing disease. Examination of the genomes of 83 HPVs allowed us to identify specific regions that might be influenced by insertions, by deletions, or simply by mutations, and that may be of interest for further analyses. Supplementary Material is provided (see online Supplementary Material at www.libertonline.com).
Classification of the Human Papilloma Viruses
In this study we present a whole-genome phylogenetic classification of the human papilloma viruse... more In this study we present a whole-genome phylogenetic classification of the human papilloma viruse (HPV) family. We found that the high risk of carcinogenicity taxa are clustered together. The most likely insertion and deletion (indel) scenarios of HPV nucleotides were computed. We also searched for relationships between the number of indels which occurred during the evolution of the HPV family and the degree of carcinogenicity of considered taxa. Linear and polynomial redundancy analyses (RDA) were carried out to relate the HPV carcinogenicity with the number of insertions, deletions and conservations.
Identification of Specific Genomic Regions Responsible for the Invasivity of Neisseria Meningitidis
In this article, we present four distance-based discrimination functions for the identification o... more In this article, we present four distance-based discrimination functions for the identification of relevant genomic segments that distinguish between two groups of data. These discrimination functions are designed for the detection of genomic regions responsible for disease. One of them was previously employed for the analysis of the Human Papilloma Virus family in relation to carcinogenicity (Diallo et al. 2009). Here, we used an improved version of the algorithm described in Badescu et al. (2008) and Diallo et al. (2009) for analyzing the information content of a multiple sequence alignments (MSA) in relation to epidemiologic data. In this study, those functions have been applied to identify specific genomic regions responsible for the hyperinvasivity of Neisseria Meningitidis. Neisseria Meningitidis is a major causal agent of meningitis and septicaemia worldwide. This study suggests that the tested functions permit to identify relevant regions and known molecular features. We found that one of the new functions tested is specifically well correlated with surface-exposed loops, regions important in vaccine design.
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Papers by Dunarel Badescu