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The checkpoint kinases Chk1 and ATR are broadly known for their role in the response to the accumulation of damaged DNA. Because Chk1 activation requires its phosphorylation by ATR, it is expected that ATR or Chk1 down-regulation should cause similar alterations in the signals triggered by DNA lesions. Intriguingly, we found that Chk1, but not ATR, promotes(More)
The notion of DNA motif is a mathematical abstraction used to model regions of the DNA (known as Transcription Factor Binding Sites, or TFBSs) that are bound by a given Transcription Factor to regulate gene expression or repression. In turn, DNA structured motifs are a mathematical counterpart that models sets of TFBSs that work in concert in the gene(More)
We present a tool for detecting long similar fragments that occur two or more times in a set of biological sequences. The problem has interesting applications in the analysis of biological sequences and their correlation, and becomes computationally challenging when a certain non negligible number of insertions, deletions and substitutions are allowed. For(More)
Finding motifs in biological sequences is one of the most intriguing problems for string algorithms designers due to, on the one hand, the numerous applications of this problem in molecular biology and, on the other hand, the challenging aspects of the computational problem. Indeed, when dealing with biological sequences it is necessary to work with(More)
We present an algorithm for detecting long similar fragments occurring at least twice in a set of biological sequences. The problem becomes computationally challenging when the frequency of a repeat is allowed to increase and when a non-negligible number of insertions, deletions and substitutions are allowed. We introduce in this paper an algorithm, Rime1(More)
After UV irradiation, DNA polymerases specialized in translesion DNA synthesis (TLS) aid DNA replication. However, it is unclear whether other mechanisms also facilitate the elongation of UV-damaged DNA. We wondered if Rad51 recombinase (Rad51), a factor that escorts replication forks, aids replication across UV lesions. We found that depletion of Rad51(More)
This paper presents new optimizations designed to improve an algorithm at the state-of-the-art for filtering sequences as a preprocessing step to the task of finding multiple repeats allowing a given pairwise edit distance between pairs of occurrences. The target application is to find possibly long repeats having two or more occurrences, such that each(More)
With a growing number of online videos, many producers feel the need to use video captions in order to expand content accessibility and face two main issues: production and alignment of the textual transcript. Both activities are expensive either for the high labor of human resources or for the employment of dedicated software. In this paper, we focus on(More)
Radiation therapy (RT) is a component of the treatment of patients with head and neck malignancies. This therapy may damage the nearby carotid arteries, thereby initiating or accelerating the atherosclerotic process (atheroma formation). Dentists treating patients who have been irradiated should examine the patient's panoramic radiograph for evidence of(More)