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Documents authored by Apostolico, Alberto

Document
DOI: 10.4230/DagRep.2.7.92
Structure Discovery in Biology: Motifs, Networks & Phylogenies (Dagstuhl Seminar 12291)

Authors: Alberto Apostolico, Andreas Dress, and Laxmi Parida

Published in: Dagstuhl Reports, Volume 2, Issue 7 (2013)

Abstract
From 15.07.12 to 20.07.12, the Dagstuhl Seminar 12291 "Structure Discovery in Biology: Motifs, Networks & Phylogenies" was held in Schloss Dagstuhl -- Leibniz Center for Informatics. The seminar was in part a follow-up to Dagstuhl Seminar 10231, held in June 2010, this time with a strong emphasis on large data. Both veterans and new participants took part in this edition. During the seminar, several participants presented their current research, and ongoing work and open problems were discussed. Abstracts of the presentations given during the seminar, as well as abstracts of seminar results and ideas, are put together in this report. The first section describes the seminar topics and goals in general. Links to extended abstracts or full papers are provided, if available.
Cite as

Alberto Apostolico, Andreas Dress, and Laxmi Parida. Structure Discovery in Biology: Motifs, Networks & Phylogenies (Dagstuhl Seminar 12291). In Dagstuhl Reports, Volume 2, Issue 7, pp. 92-117, Schloss Dagstuhl – Leibniz-Zentrum für Informatik (2012)

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@Article{apostolico_et_al:DagRep.2.7.92,
  author =	{Apostolico, Alberto and Dress, Andreas and Parida, Laxmi},
  title =	{{Structure Discovery in Biology: Motifs, Networks \& Phylogenies (Dagstuhl Seminar 12291)}},
  pages =	{92--117},
  journal =	{Dagstuhl Reports},
  ISSN =	{2192-5283},
  year =	{2012},
  volume =	{2},
  number =	{7},
  editor =	{Apostolico, Alberto and Dress, Andreas and Parida, Laxmi},
  publisher =	{Schloss Dagstuhl -- Leibniz-Zentrum f{\"u}r Informatik},
  address =	{Dagstuhl, Germany},
  URL =		{https://drops.dagstuhl.de/entities/document/10.4230/DagRep.2.7.92},
  URN =		{urn:nbn:de:0030-drops-37509},
  doi =		{10.4230/DagRep.2.7.92},
  annote =	{Keywords: mathematical biology, computational biology, algorithmic bioinformatics, pattern discovery, networks, phylogenetics, stringology}
}
Document
DOI: 10.4230/DagSemProc.10231.1
10231 Abstracts Collection – Structure Discovery in Biology: Motifs, Networks & Phylogenies

Authors: Alberto Apostolico, Andreas Dress, and Laxmi Parida

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

Abstract
From 06.06. to 11.06.2010, the Dagstuhl Seminar 10231 ``Structure Discovery in Biology: Motifs, Networks & Phylogenies '' was held in Schloss Dagstuhl~--~Leibniz Center for Informatics. During the seminar, several participants presented their current research, and ongoing work and open problems were discussed. Abstracts of the presentations given during the seminar as well as abstracts of seminar results and ideas are put together in this paper. The first section describes the seminar topics and goals in general. Links to extended abstracts or full papers are provided, if available.
Cite as

Alberto Apostolico, Andreas Dress, and Laxmi Parida. 10231 Abstracts Collection – Structure Discovery in Biology: Motifs, Networks & Phylogenies. In Structure Discovery in Biology: Motifs, Networks & Phylogenies. Dagstuhl Seminar Proceedings, Volume 10231, pp. 1-20, Schloss Dagstuhl – Leibniz-Zentrum für Informatik (2010)

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@InProceedings{apostolico_et_al:DagSemProc.10231.1,
  author =	{Apostolico, Alberto and Dress, Andreas and Parida, Laxmi},
  title =	{{10231 Abstracts Collection – Structure Discovery in Biology: Motifs, Networks \& Phylogenies}},
  booktitle =	{Structure Discovery in Biology: Motifs, Networks \& Phylogenies},
  pages =	{1--20},
  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.10231.1},
  URN =		{urn:nbn:de:0030-drops-26910},
  doi =		{10.4230/DagSemProc.10231.1},
  annote =	{Keywords: Mathematical biology, computational biology, algorithmic bioinformatics, pattern discovery, phylogenetics, networks}
}
Document
DOI: 10.4230/DagSemProc.06201.1
06201 Abstracts Collection – Combinatorial and Algorithmic Foundations of Pattern and Association Discovery

Authors: Rudolf Ahlswede, Alberto Apostolico, and Vladimir I. Levenshtein

Published in: Dagstuhl Seminar Proceedings, Volume 6201, Combinatorial and Algorithmic Foundations of Pattern and Association Discovery (2006)

Abstract
From 15.05.06 to 20.05.06, the Dagstuhl Seminar 06201 ``Combinatorial and Algorithmic Foundations of Pattern and Association Discovery'' was held in the International Conference and Research Center (IBFI), Schloss Dagstuhl. During the seminar, several participants presented their current research, and ongoing work and open problems were discussed. Abstracts of the presentations given during the seminar as well as abstracts of seminar results and ideas are put together in this paper. The first section describes the seminar topics and goals in general. Links to extended abstracts or full papers are provided, if available.
Cite as

Rudolf Ahlswede, Alberto Apostolico, and Vladimir I. Levenshtein. 06201 Abstracts Collection – Combinatorial and Algorithmic Foundations of Pattern and Association Discovery. In Combinatorial and Algorithmic Foundations of Pattern and Association Discovery. Dagstuhl Seminar Proceedings, Volume 6201, pp. 1-15, Schloss Dagstuhl – Leibniz-Zentrum für Informatik (2006)

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@InProceedings{ahlswede_et_al:DagSemProc.06201.1,
  author =	{Ahlswede, Rudolf and Apostolico, Alberto and Levenshtein, Vladimir I.},
  title =	{{06201 Abstracts Collection – Combinatorial and Algorithmic Foundations of Pattern and Association Discovery}},
  booktitle =	{Combinatorial and Algorithmic Foundations of Pattern and Association Discovery},
  pages =	{1--15},
  series =	{Dagstuhl Seminar Proceedings (DagSemProc)},
  ISSN =	{1862-4405},
  year =	{2006},
  volume =	{6201},
  editor =	{Rudolf Ahlswede and Alberto Apostolico and Vladimir I. Levenshtein},
  publisher =	{Schloss Dagstuhl -- Leibniz-Zentrum f{\"u}r Informatik},
  address =	{Dagstuhl, Germany},
  URL =		{https://drops.dagstuhl.de/entities/document/10.4230/DagSemProc.06201.1},
  URN =		{urn:nbn:de:0030-drops-7873},
  doi =		{10.4230/DagSemProc.06201.1},
  annote =	{Keywords: Data compression, pattern matching, pattern discovery, search, sorting, molecular biology, reconstruction, genome rearrangements}
}
Document
DOI: 10.4230/DagSemProc.06201.2
06201 Executive Summary – Combinatorial and Algorithmic Foundations of Pattern and Association Discovery

Authors: Rudolf Ahlswede, Alberto Apostolico, and Vladimir I. Levenshtein

Published in: Dagstuhl Seminar Proceedings, Volume 6201, Combinatorial and Algorithmic Foundations of Pattern and Association Discovery (2006)

Abstract
The goals of this seminar have been (1) to identify and match recently developed methods to specific tasks and data sets in a core of application areas; next, based on feedback from the specific applied domain, (2) to fine tune and personalize those applications, and finally (3) to identify and tackle novel combinatorial and algorithmic problems, in some cases all the way to the development of novel software tools.
Cite as

Rudolf Ahlswede, Alberto Apostolico, and Vladimir I. Levenshtein. 06201 Executive Summary – Combinatorial and Algorithmic Foundations of Pattern and Association Discovery. In Combinatorial and Algorithmic Foundations of Pattern and Association Discovery. Dagstuhl Seminar Proceedings, Volume 6201, pp. 1-2, Schloss Dagstuhl – Leibniz-Zentrum für Informatik (2006)

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@InProceedings{ahlswede_et_al:DagSemProc.06201.2,
  author =	{Ahlswede, Rudolf and Apostolico, Alberto and Levenshtein, Vladimir I.},
  title =	{{06201 Executive Summary – Combinatorial and Algorithmic Foundations of Pattern and Association Discovery}},
  booktitle =	{Combinatorial and Algorithmic Foundations of Pattern and Association Discovery},
  pages =	{1--2},
  series =	{Dagstuhl Seminar Proceedings (DagSemProc)},
  ISSN =	{1862-4405},
  year =	{2006},
  volume =	{6201},
  editor =	{Rudolf Ahlswede and Alberto Apostolico and Vladimir I. Levenshtein},
  publisher =	{Schloss Dagstuhl -- Leibniz-Zentrum f{\"u}r Informatik},
  address =	{Dagstuhl, Germany},
  URL =		{https://drops.dagstuhl.de/entities/document/10.4230/DagSemProc.06201.2},
  URN =		{urn:nbn:de:0030-drops-7926},
  doi =		{10.4230/DagSemProc.06201.2},
  annote =	{Keywords: Data compression, pattern matching, pattern discovery, search, sorting, molecular biology, reconstruction, genome rearrangements}
}
Document
DOI: 10.4230/DagSemProc.06201.5
On the Monotonicity of the String Correction Factor for Words with Mismatches

Authors: Alberto Apostolico and Cinzia Pizzi

Published in: Dagstuhl Seminar Proceedings, Volume 6201, Combinatorial and Algorithmic Foundations of Pattern and Association Discovery (2006)

Abstract
The string correction factor is the term by which the probability of a word $w$ needs to be multiplied in order to account for character changes or ``errors'' occurring in at most $k$ arbitrary positions in that word. The behavior of this factor, as a function of $k$ and of the word length, has implications on the number of candidates that need to be considered and weighted when looking for subwords of a sequence that present unusually recurrent replicas within some bounded number of mismatches. Specifically, it is seen that over intervals of mono- or bi-tonicity for the correction factor, only some of the candidates need be considered. This mitigates the computation and leads to tables of over-represented words that are more compact to represent and inspect. In recent work, expectation and score monotonicity has been established for a number of cases of interest, under {em i.i.d.} probabilistic assumptions. The present paper reviews the cases of bi-tonic behavior for the correction factor, concentrating on the instance in which the question is still open.
Cite as

Alberto Apostolico and Cinzia Pizzi. On the Monotonicity of the String Correction Factor for Words with Mismatches. In Combinatorial and Algorithmic Foundations of Pattern and Association Discovery. Dagstuhl Seminar Proceedings, Volume 6201, pp. 1-9, Schloss Dagstuhl – Leibniz-Zentrum für Informatik (2006)

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@InProceedings{apostolico_et_al:DagSemProc.06201.5,
  author =	{Apostolico, Alberto and Pizzi, Cinzia},
  title =	{{On the Monotonicity of the String Correction Factor for Words with Mismatches}},
  booktitle =	{Combinatorial and Algorithmic Foundations of Pattern and Association Discovery},
  pages =	{1--9},
  series =	{Dagstuhl Seminar Proceedings (DagSemProc)},
  ISSN =	{1862-4405},
  year =	{2006},
  volume =	{6201},
  editor =	{Rudolf Ahlswede and Alberto Apostolico and Vladimir I. Levenshtein},
  publisher =	{Schloss Dagstuhl -- Leibniz-Zentrum f{\"u}r Informatik},
  address =	{Dagstuhl, Germany},
  URL =		{https://drops.dagstuhl.de/entities/document/10.4230/DagSemProc.06201.5},
  URN =		{urn:nbn:de:0030-drops-7899},
  doi =		{10.4230/DagSemProc.06201.5},
  annote =	{Keywords: Pattern discovery, Motif, Over-represented word, Monotone score, Correction Factor}
}
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