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Documents authored by Utro, Filippo

Document
DOI: 10.4230/LIPIcs.WABI.2018.14
Essential Simplices in Persistent Homology and Subtle Admixture Detection

Authors: Saugata Basu, Filippo Utro, and Laxmi Parida

Published in: LIPIcs, Volume 113, 18th International Workshop on Algorithms in Bioinformatics (WABI 2018)

Abstract
We introduce a robust mathematical definition of the notion of essential elements in a basis of the homology space and prove that these elements are unique. Next we give a novel visualization of the essential elements of the basis of the homology space through a rainfall-like plot (RFL). This plot is data-centric, i.e., is associated with the individual samples of the data, as opposed to the structure-centric barcodes of persistent homology. The proof-of-concept was tested on data generated by SimRA that simulates different admixture scenarios. We show that the barcode analysis can be used not just to detect the presence of admixture but also estimate the number of admixed populations. We also demonstrate that data-centric RFL plots have the potential to further disentangle the common history into admixture events and relative timing of the events, even in very complex scenarios.
Cite as

Saugata Basu, Filippo Utro, and Laxmi Parida. Essential Simplices in Persistent Homology and Subtle Admixture Detection. In 18th International Workshop on Algorithms in Bioinformatics (WABI 2018). Leibniz International Proceedings in Informatics (LIPIcs), Volume 113, pp. 14:1-14:10, Schloss Dagstuhl – Leibniz-Zentrum für Informatik (2018)

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@InProceedings{basu_et_al:LIPIcs.WABI.2018.14,
  author =	{Basu, Saugata and Utro, Filippo and Parida, Laxmi},
  title =	{{Essential Simplices in Persistent Homology and Subtle Admixture Detection}},
  booktitle =	{18th International Workshop on Algorithms in Bioinformatics (WABI 2018)},
  pages =	{14:1--14:10},
  series =	{Leibniz International Proceedings in Informatics (LIPIcs)},
  ISBN =	{978-3-95977-082-8},
  ISSN =	{1868-8969},
  year =	{2018},
  volume =	{113},
  editor =	{Parida, Laxmi and Ukkonen, Esko},
  publisher =	{Schloss Dagstuhl -- Leibniz-Zentrum f{\"u}r Informatik},
  address =	{Dagstuhl, Germany},
  URL =		{https://drops.dagstuhl.de/entities/document/10.4230/LIPIcs.WABI.2018.14},
  URN =		{urn:nbn:de:0030-drops-93166},
  doi =		{10.4230/LIPIcs.WABI.2018.14},
  annote =	{Keywords: population admixture, topological data analysis, persistent homology, population evolution}
}
Document
DOI: 10.4230/DagSemProc.10231.6
Functional Information, Biomolecular Messages and Complexity of BioSequences and Structures

Authors: Raffaele Giancarlo, Davide Corona, Valeria Di Benedetto, Alessandra Gabriele, and Filippo Utro

Published in: Dagstuhl Seminar Proceedings, Volume 10231, Structure Discovery in Biology: Motifs, Networks & Phylogenies (2010)

Abstract
In the quest for a mathematical measure able to capture and shed light on the dual notions of information and complexity in biosequences, Hazen et al. have introduced the notion of Functional Information (FI for short). It is also the result of earlier considerations and findings by Szostak and Carothers et al. Based on the experiments by Charoters et al., regarding FI in RNA binding activities, we decided to study the relation existing between FI and classic measures of complexity applied on protein-DNA interactions on a genome-wide scale. Using classic complexity measures, i.e, Shannon entropy and Kolmogorov Complexity as both estimated by data compression, we found that FI applied to protein-DNA interactions is genuinely different from them. Such a fact, together with the non-triviality of the biological function considered, contributes to the establishment of FI as a novel and useful measure of biocomplexity. Remarkably, we also found a relationship, on a genome-wide scale, between the redundancy of a genomic region and its ability to interact with a protein. This latter finding justifies even more some principles for the design of motif discovery algorithms. Finally, our experiments bring to light methodological limitations of Linguistic Complexity measures, i.e., a class of measures that is a function of the vocabulary richness of a sequence. Indeed, due to the technology and associated statistical preprocessing procedures used to conduct our studies, i.e., genome-wide ChIP-chip experiments, that class of measures cannot give any statistically significant indication about complexity and function. A serious limitation due to the widespread use of the technology. References J.M. Carothers, S.C. Oestreich, J.H. Davis, and J.W. Szostack. Informational complexity and functional activity of RNA structures. J. AM. CHEM. SOC., 126 (2004), pp. 5130-5137. R.M. Hazen, P.L. Griffin, J.M. Carothers, and J.W. Szostak. Functional Information and the emergence of biocomplexity. Proc. of Nat. Acad. Sci, 104 (2007), pp. 8574-8581. J.W. Szostak. Functional Information: molecular messages, Nature, 423 (2003).
Cite as

Raffaele Giancarlo, Davide Corona, Valeria Di Benedetto, Alessandra Gabriele, and Filippo Utro. Functional Information, Biomolecular Messages and Complexity of BioSequences and Structures. In Structure Discovery in Biology: Motifs, Networks & Phylogenies. Dagstuhl Seminar Proceedings, Volume 10231, pp. 1-13, Schloss Dagstuhl – Leibniz-Zentrum für Informatik (2010)

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@InProceedings{giancarlo_et_al:DagSemProc.10231.6,
  author =	{Giancarlo, Raffaele and Corona, Davide and Di Benedetto, Valeria and Gabriele, Alessandra and Utro, Filippo},
  title =	{{Functional Information, Biomolecular Messages and Complexity of BioSequences and Structures}},
  booktitle =	{Structure Discovery in Biology: Motifs, Networks \& Phylogenies},
  pages =	{1--13},
  series =	{Dagstuhl Seminar Proceedings (DagSemProc)},
  ISSN =	{1862-4405},
  year =	{2010},
  volume =	{10231},
  editor =	{Alberto Apostolico and Andreas Dress and Laxmi Parida},
  publisher =	{Schloss Dagstuhl -- Leibniz-Zentrum f{\"u}r Informatik},
  address =	{Dagstuhl, Germany},
  URL =		{https://drops.dagstuhl.de/entities/document/10.4230/DagSemProc.10231.6},
  URN =		{urn:nbn:de:0030-drops-26884},
  doi =		{10.4230/DagSemProc.10231.6},
  annote =	{Keywords: Functional activity, sequence complexity, combinatorics on words, protein-DNA interaction.}
}
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