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Journals and Conferences
We prove that sorting by reciprocal translocations can be done in O(n p log(n)) for an n-gene genome. Our algorithm is an adaptation of the Tannier et. al algorithm for sorting by reversals. This improves over the O(n) algorithm for sorting by reciprocal translocations given by Bergeron et al.
Chronic diseases constitute the leading cause of mortality in the western world, have a major impact on the patients' quality of life, and comprise the bulk of healthcare costs. Nowadays, healthcare data management systems integrate large amounts of medical information on patients, including diagnoses, medical procedures, lab test results, and more.… (More)
A central problem in genome rearrangement is finding a most parsimonious rearrangement scenario using certain rearrangement operations. An important problem of this type is sorting a signed genome by reversals and translocations (SBRT). Hannenhalli and Pevzner presented a duality theorem for SBRT which leads to a polynomial time algorithm for sorting a… (More)
Genomes undergo changes in organization as a result of gene duplications, chromosomal rearrangements and local mutations, among other mechanisms. In contrast to prokaryotes, in which genes of a common function are often organized in operons and reside contiguously along the genome, most eukaryotes show much weaker clustering of genes by function, except for… (More)
Chromosomal aneuploidy, that is to say the gain or loss of chromosomes, is the most common abnormality in cancer. While certain aberrations, most commonly translocations, are known to be strongly associated with specific cancers and contribute to their formation, most aberrations appear to be non-specific and arbitrary, and do not have a clear effect. The… (More)
We prove that sorting by reciprocal translocations can be done in O(n3/2 √ log(n)) for an n-gene genome. Our algorithm is an adaptation of the algorithm of Tannier, Bergeron and Sagot for sorting by reversals. This improves over the O(n3) algorithm for sorting by reciprocal translocations given by Bergeron, Mixtacki and Stoye.
The understanding of genome rearrangements is an important endeavor in comparative genomics. A major computational problem in this field is finding a shortest sequence of genome rearrangements that “sorts” one genome into another. In this paper we focus on sorting a multi-chromosomal genome by translocations. We reveal new relationships between this problem… (More)
The availability of electronic health records creates fertile ground for developing computational models of various medical conditions. We present a new approach for detecting and analyzing patients with unexpected responses to treatment, building on machine learning and statistical methodology. Given a specific patient, we compute a statistical score for… (More)
Since the discovery of the "Philadelphia chromosome" in chronic myelogenous leukemia in 1960, there has been ongoing intensive research of chromosomal aberrations in cancer. These aberrations, which result in abnormally structured genomes, became a hallmark of cancer. Many studies provide evidence for the connection between chromosomal alterations and… (More)
Chromosomal instability is a hallmark of cancer. The results of this instability can be observed in the karyotypes of many cancerous genomes, which often contain a variety of aberrations. In this study we introduce a new approach for analyzing rearrangement events in carcinogenesis. This approach builds on a new effective heuristic for computing a short… (More)