Titlebook: Comparative Genomics; International Worksh Francesca D. Ciccarelli,István Miklós Conference proceedings 2009 Springer-Verlag Berlin Heidelb

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Reconstructing Histories of Complex Gene Clusters on a Phylogeny, to functional analysis. These clusters are one of the major sources of evolutionary innovation, and they are linked to multiple diseases, including HIV and a variety of cancers. Understanding their evolutionary histories is a key to the application of comparative genomics methods in these regions o

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Co-evolutionary Models for Reconstructing Ancestral Genomic Sequences: Computational Issues and Biothe most parsimonious ancestral genomes usually include considerable error rates. In general, these errors cannot be abolished by utilizing more exhaustive computational approaches, by using longer genomic sequences, or by analyzing more taxa. In recent studies we showed that co-evolution is an impo

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Comparative Genomics and Extensive Recombinations in Phage Communities,to each genome. When several closely related genomes are compared, the unique sequences are likely to be shared with third genomes, leading to virus mosaic communities. Here we present comparative analysis of sets of . phages that share large identical sequences with up to three other genomes, and w

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Properties of Sequence Conservation in Upstream Regulatory and Protein Coding Sequences among Paralling pathways and has provided organisms a level of genetic robustness. We studied the long-term evolution and interrelationships of 5’ upstream regulatory sequences (URSs), protein coding sequences (CDSs) and expression correlations (EC) of duplicated gene pairs in Arabidopsis. Three distinct metho

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Transcription Factor Binding Probabilities in Orthologous Promoters: An Alignment-Free Approach to hm for assessing the conservation of predicted binding occupancy that does not rely on sequence alignment of promoters. The method, which we call ortholog-weighting, assesses the degree to which the predicted binding occupancy of a transcription factor in a reference gene is also predicted in the pr

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