2 Search Results for "Abd-El-Malek, Michael"

Document
DOI: 10.4230/LIPIcs.WABI.2021.15
BISER: Fast Characterization of Segmental Duplication Structure in Multiple Genome Assemblies

Authors: Hamza Išerić, Can Alkan, Faraz Hach, and Ibrahim Numanagić

Published in: LIPIcs, Volume 201, 21st International Workshop on Algorithms in Bioinformatics (WABI 2021)

Abstract
The increasing availability of high-quality genome assemblies raised interest in the characterization of genomic architecture. Major architectural parts, such as common repeats and segmental duplications (SDs), increase genome plasticity that stimulates further evolution by changing the genomic structure. However, optimal computation of SDs through standard local alignment algorithms is impractical due to the size of most genomes. A cross-genome evolutionary analysis of SDs is even harder, as one needs to characterize SDs in multiple genomes and find relations between those SDs and unique segments in other genomes. Thus there is a need for fast and accurate algorithms to characterize SD structure in multiple genome assemblies to better understand the evolutionary forces that shaped the genomes of today. Here we introduce a new tool, BISER, to quickly detect SDs in multiple genomes and identify elementary SDs and core duplicons that drive the formation of such SDs. BISER improves earlier tools by (i) scaling the detection of SDs with low homology (75%) to multiple genomes while introducing further 8-24x speed-ups over the existing tools, and by (ii) characterizing elementary SDs and detecting core duplicons to help trace the evolutionary history of duplications to as far as 90 million years.
Cite as

Hamza Išerić, Can Alkan, Faraz Hach, and Ibrahim Numanagić. BISER: Fast Characterization of Segmental Duplication Structure in Multiple Genome Assemblies. In 21st International Workshop on Algorithms in Bioinformatics (WABI 2021). Leibniz International Proceedings in Informatics (LIPIcs), Volume 201, pp. 15:1-15:18, Schloss Dagstuhl – Leibniz-Zentrum für Informatik (2021)

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@InProceedings{iseric_et_al:LIPIcs.WABI.2021.15,
  author =	{I\v{s}eri\'{c}, Hamza and Alkan, Can and Hach, Faraz and Numanagi\'{c}, Ibrahim},
  title =	{{BISER: Fast Characterization of Segmental Duplication Structure in Multiple Genome Assemblies}},
  booktitle =	{21st International Workshop on Algorithms in Bioinformatics (WABI 2021)},
  pages =	{15:1--15:18},
  series =	{Leibniz International Proceedings in Informatics (LIPIcs)},
  ISBN =	{978-3-95977-200-6},
  ISSN =	{1868-8969},
  year =	{2021},
  volume =	{201},
  editor =	{Carbone, Alessandra and El-Kebir, Mohammed},
  publisher =	{Schloss Dagstuhl -- Leibniz-Zentrum f{\"u}r Informatik},
  address =	{Dagstuhl, Germany},
  URL =		{https://drops.dagstuhl.de/entities/document/10.4230/LIPIcs.WABI.2021.15},
  URN =		{urn:nbn:de:0030-drops-143681},
  doi =		{10.4230/LIPIcs.WABI.2021.15},
  annote =	{Keywords: genome analysis, fast alignment, segmental duplications, core duplicons, sequence decomposition}
}
Document
DOI: 10.4230/DagSemProc.06371.5
Towards bounded wait-free PASIS

Authors: Michael Abd-El-Malek, Gregory R. Ganger, Garth R. Goodson, Michael K. Reiter, and Jay J. Wylie

Published in: Dagstuhl Seminar Proceedings, Volume 6371, From Security to Dependability (2007)

Abstract
The PASIS read/write protocol implements a Byzantine fault-tolerant erasure-coded atomic register. The prototype PASIS storage system implementation provides excellent best-case performance. Writes require two round trips and contention- and failure-free reads require one. Unfortunately, even though writes and reads are wait-free in PASIS, Byzantine components can induce correct clients to perform an unbounded amount of work. In this extended abstract, we enumerate the avenues by which Byzantine servers and clients can induce correct clients to perform an unbounded amount of work in PASIS. We sketch extensions to the PASIS protocol and Lazy Verification that bound the amount of work Byzantine components can induce correct clients to perform. We believe that the extensions provide bounded wait-free reads and writes. We also believe that an implementation that incorporates these extensions will preserve the excellent best-case performance of the original PASIS prototype.
Cite as

Michael Abd-El-Malek, Gregory R. Ganger, Garth R. Goodson, Michael K. Reiter, and Jay J. Wylie. Towards bounded wait-free PASIS. In From Security to Dependability. Dagstuhl Seminar Proceedings, Volume 6371, pp. 1-4, Schloss Dagstuhl – Leibniz-Zentrum für Informatik (2007)

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@InProceedings{abdelmalek_et_al:DagSemProc.06371.5,
  author =	{Abd-El-Malek, Michael and Ganger, Gregory R. and Goodson, Garth R. and Reiter, Michael K. and Wylie, Jay J.},
  title =	{{Towards bounded wait-free PASIS}},
  booktitle =	{From Security to Dependability},
  pages =	{1--4},
  series =	{Dagstuhl Seminar Proceedings (DagSemProc)},
  ISSN =	{1862-4405},
  year =	{2007},
  volume =	{6371},
  editor =	{Christian Cachin and Felix C. Freiling and Jaap-Henk Hoepman},
  publisher =	{Schloss Dagstuhl -- Leibniz-Zentrum f{\"u}r Informatik},
  address =	{Dagstuhl, Germany},
  URL =		{https://drops-dev.dagstuhl.de/entities/document/10.4230/DagSemProc.06371.5},
  URN =		{urn:nbn:de:0030-drops-8488},
  doi =		{10.4230/DagSemProc.06371.5},
  annote =	{Keywords: Byzantine fault-tolerant, erasure-coded storage, bounded wait-free, non-skipping timestamps}
}
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