Maria Federico

Learn More
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)
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)
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)
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)
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)