Simona E. Rombo

TCS Journal 2019 Journal Article

DNA combinatorial messages and Epigenomics: The case of chromatin organization and nucleosome occupancy in eukaryotic genomes

• Raffaele Giancarlo
• Simona E. Rombo
• Filippo Utro

Epigenomics is the study of modifications on the genetic material of a cell that do not depend on changes in the DNA sequence, since those latter involve specific proteins around which DNA wraps. The end result is that Epigenomic changes have a fundamental role in the proper working of each cell in Eukaryotic organisms. A particularly important part of Epigenomics concentrates on the study of chromatin, that is, a fiber composed of a DNA-protein complex and very characterizing of Eukaryotes. Understanding how chromatin is assembled and how it changes is fundamental for Biology. In more than thirty years of research in this area, Mathematics and Theoretical Computer Science have gained a prominent role, in terms of modeling and mining, regarding in particular the so-called 10 nm fiber. Starting from some very basic notions of Biology, we briefly illustrate the recent advances obtained via laboratory experiments on the organization and dynamics of chromatin. Then, we mainly concentrate our attention on the contributions given by Combinatorial and Informational Methodologies, that are at the hearth of Theoretical Computer Science, to the understanding of mechanisms determining the 10 nm fiber. We conclude highlighting several directions of investigation that are perceived as important and where Theoretical Computer Science can provide high impact results.

TCS Journal 2017 Journal Article

Foreword: Algorithms, Strings and Theoretical Approaches in the Big Data Era – Special Issue in Honor of the 60th Birthday of Professor Raffaele Giancarlo

• Simona E. Rombo
• Filippo Utro

TCS Journal 2014 Journal Article

Irredundant tandem motifs

• Laxmi Parida
• Cinzia Pizzi
• Simona E. Rombo

Eliminating the possible redundancy from a set of candidate motifs occurring in an input string is fundamental in many applications. The existing techniques proposed to extract irredundant motifs are not suitable when the motifs to search for are structured, i. e. , they are made of two (or several) subwords that co-occur in a text string s of length n. The main effort of this work is studying and characterizing a compact class of tandem motifs, that is, pairs of substrings 〈 m 1, m 2 〉 occurring in tandem within a maximum distance of d symbols in s, where d is an integer constant given in input. To this aim, we first introduce the concept of maximality, related to four specific conditions that hold only for this class of motifs. Then, we eliminate the remaining redundancy by defining the notion of irredundancy for tandem motifs. We prove that the number of non-overlapping irredundant tandem motifs is O ( d 2 n ) which, considering d as a constant, leads to a linear number of tandems in the length of the input string. This is an order of magnitude less than previously developed compact indexes for tandem extraction. The notions and bounds provided for tandem motifs are generalized for the case r ⩾ 2, if r is the number of subwords composing the motifs. Finally, we also provide an algorithm to extract irredundant tandem motifs.

TCS Journal 2012 Journal Article

Extracting string motif bases for quorum higher than two

• Simona E. Rombo

Bases of generators of motifs consisting of strings in which some positions can be occupied by a don’t care provide a useful conceptual tool for their description and a way to reduce the time and space involved in the discovery process. In the last few years, a few algorithms have been proposed for the extraction of a basis, building in large part on combinatorial properties of strings and their autocorrelations. Currently, the most efficient techniques for binary alphabets and quorum q = 2 require time quadratic in the length of the host string. The present paper explores properties of motif bases for quorum q ≥ 2, both with binary and general alphabets, by also showing that important results holding for quorum q = 2 cannot be extended to this, more general, case. Furthermore, the extraction of motifs in which a bound is set on the maximum allowed number of don’t cares is addressed, and suitable algorithms are proposed whose computational complexity depends on the fixed bound.

TCS Journal 2008 Journal Article

Motif patterns in 2D

• Alberto Apostolico
• Laxmi Parida
• Simona E. Rombo

Motif patterns consisting of sequences of intermixed solid and don’t-care characters have been introduced and studied in connection with pattern discovery problems of computational biology and other domains. In order to alleviate the exponential growth of such motifs, notions of maximal saturation and irredundancy have been formulated, whereby more or less compact subsets of the set of all motifs can be extracted, that are capable of expressing all others by suitable combinations. In this paper, we introduce the notion of maximal irredundant motifs in a two-dimensional array and develop initial properties and a combinatorial argument that poses a linear bound on the total number of such motifs. The remainder of the paper presents approaches to the discovery of irredundant motifs both by offline and incremental algorithms.