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DNA Is a Puzzle Enthusiast

Authors: Roberto Marangoni

Published in: OASIcs, Volume 132, From Strings to Graphs, and Back Again: A Festschrift for Roberto Grossi's 60th Birthday (2025)

Abstract

This article presents a concise summary of research projects in which Roberto Grossi participated, yielding interesting results that were never previously published in research papers. At the time, these studies were deemed too limited and in need of further extensions and generalizations, which were never realized due to a lack of resources. The researches focused on methods for inferring possible three-dimensional DNA conformations based on nucleotide sequence characteristics. Specifically, two key approaches were investigated: the identification of structured motifs for detecting Transcription Factor Binding Sites (TFBS) and the study of nested permutations using PQ-trees. This article describes the obtained results in selected case studies, their potential implications, and the current state of the art in these research areas.

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Roberto Marangoni. DNA Is a Puzzle Enthusiast. In From Strings to Graphs, and Back Again: A Festschrift for Roberto Grossi's 60th Birthday. Open Access Series in Informatics (OASIcs), Volume 132, pp. 18:1-18:8, Schloss Dagstuhl – Leibniz-Zentrum für Informatik (2025)

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@InProceedings{marangoni:OASIcs.Grossi.18,
  author =	{Marangoni, Roberto},
  title =	{{DNA Is a Puzzle Enthusiast}},
  booktitle =	{From Strings to Graphs, and Back Again: A Festschrift for Roberto Grossi's 60th Birthday},
  pages =	{18:1--18:8},
  series =	{Open Access Series in Informatics (OASIcs)},
  ISBN =	{978-3-95977-391-1},
  ISSN =	{2190-6807},
  year =	{2025},
  volume =	{132},
  editor =	{Conte, Alessio and Marino, Andrea and Rosone, Giovanna and Vitter, Jeffrey Scott},
  publisher =	{Schloss Dagstuhl -- Leibniz-Zentrum f{\"u}r Informatik},
  address =	{Dagstuhl, Germany},
  URL =		{https://drops.dagstuhl.de/entities/document/10.4230/OASIcs.Grossi.18},
  URN =		{urn:nbn:de:0030-drops-238172},
  doi =		{10.4230/OASIcs.Grossi.18},
  annote =	{Keywords: DNA, 3D structure, PQ trees, structural motifs}
}

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DNA Is a Puzzle Enthusiast

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