arXiv subjects

F. Di Cunto

Publications and source records attributed to F. Di Cunto.

4 recordsLinked to original sources

arXiv2018

Automatic microtubule tracking in fluorescence images of cells doped with increasing concentrations of taxol and nocodazole

The purpose of this paper is to provide an algorithm for detecting and tracking astral MTs in a fully automated way and supply a description of their dynamic behaviour. For the algorithm testing, a dataset of stacks (i.e. time-lapse image sequences), acquired with a confocal microscope, has been employed. Cells were treated with two different drugs, nocodazole and taxol, in order to explore their effect on microtubule dynamic instability.

q-bio.BM↗

arXiv2003

A computational approach to regulatory element discovery in eukaryotes

Gene regulation in Eukaryotes is mainly effected through transcription factors binding to rather short recognition motifs generally located upstream of the coding region. We present a novel computational method to identify regulatory elements in the upstream region of Eukaryotic genes. The genes are grouped in sets sharing an overrepresented short motif in their upstream sequence. For each set, the average expression level from a microarray experiment is determined: if this level is significantly higher or lower than the average taken over the whole genome, then the overrepresented motif shared by the genes in the set is likely to play a role in their regulation. We illustrate the method by applying it to the genome of {\it S. cerevisiae}, for which many datasets of microarray experiments are publicly available. Several known binding motifs are correctly recognized by our algorithm, and a new candidate is suggested for experimental verification.

cond-mat.dis-nn↗

arXiv2002

Correlating overrepresented upstream motifs to gene expression: a computational approach to regulatory element discovery in eukaryotes

Gene regulation in eukaryotes is mainly effected through transcription factors binding to rather short recognition motifs generally located upstream of the coding region. We present a novel computational method to identify regulatory elements in the upstream region of eukaryotic genes. The genes are grouped in sets sharing an overrepresented short motif in their upstream sequence. For each set, the average expression level from a microarray experiment is determined: If this level is significantly higher or lower than the average taken over the whole genome, then the overerpresented motif shared by the genes in the set is likely to play a role in their regulation. The method was tested by applying it to the genome of Saccharomyces cerevisiae, using the publicly available results of a DNA microarray experiment, in which expression levels for virtually all the genes were measured during the diauxic shift from fermentation to respiration. Several known motifs were correctly identified, and a new candidate regulatory sequence was determined.

physics.bio-ph↗

arXiv2002

Finding regulatory sites from statistical analysis of nucleotide frequencies in the upstream region of eukaryotic genes

We discuss two new approaches to extract relevant biological information on the Transcription Factors (and in particular to identify their binding sequences) from the statistical distribution of oligonucleotides in the upstream region of the genes. Both the methods are based on the notion of a ``regulatory network'' responsible for the various expression patterns of the genes. In particular we concentrate on families of coregulated genes and look for the simultaneous presence in the upstream regions of these genes of the same set of transcription factor binding sites. We discuss two instances which well exemplify the features of the two methods: the coregulation of glycolysis in Drosophila melanogaster and the diauxic shift in Saccharomyces cerevisiae.

physics.bio-ph↗