Skip to main content

Lund University Publications

LUND UNIVERSITY LIBRARIES

Methods for barcode analysis in optical DNA mapping

Dvirnas, Albertas LU (2021)
Abstract
This thesis is composed of six papers, which all concern different methods and tools used for the analysis of barcodes in nanochannel-based Optical DNA Mapping (ODM). The first four papers consider densely-labeled barcodes while the last two consider sparsely-labeled barcodes.

Paper I presents a combinatorial auction algorithm for contig assembly ussing ODM barcodes as scaffolds.

Paper II concerns mapping of ODM barcodes on the human genome.

Paper III deals with bacterial typing.

Paper IV solves structural variation detection problem for competitive binding barcodes using Hidden Markov Models.

Paper V proposes the use of Sliding Frank-Wolfe methods for sparse-labeled single-frame... (More)
This thesis is composed of six papers, which all concern different methods and tools used for the analysis of barcodes in nanochannel-based Optical DNA Mapping (ODM). The first four papers consider densely-labeled barcodes while the last two consider sparsely-labeled barcodes.

Paper I presents a combinatorial auction algorithm for contig assembly ussing ODM barcodes as scaffolds.

Paper II concerns mapping of ODM barcodes on the human genome.

Paper III deals with bacterial typing.

Paper IV solves structural variation detection problem for competitive binding barcodes using Hidden Markov Models.

Paper V proposes the use of Sliding Frank-Wolfe methods for sparse-labeled single-frame ODM.

Paper VI extends the Sliding Frank-Wolfe methods from the analysis of single frame barcodes to multi-frame setting, where barcodes over multiple time-frames are averaged to improve the resolution.
(Less)
Please use this url to cite or link to this publication:
author
supervisor
opponent
  • Associate Professor Nyvold Pedersen, Jonas, Technical University of Denmark, DTU Nanotech/DTU Health Tech, Denmark
organization
publishing date
type
Thesis
publication status
published
subject
keywords
DNA Barcoding, Optical Mapping, Computational Biology
pages
219 pages
publisher
MediaTryck Lund
defense location
Lundmarksalen, Astronomihuset. Join via zoom: https://lu-se.zoom.us/j/64941727808?pwd=RUphOWZQMUhVVitwVFdZNUlwbk5ydz09 (Passcode: 2022)
defense date
2022-01-25 10:00:00
ISBN
978-91-8039-125-2
978-91-8039-126-9
language
English
LU publication?
yes
id
056d48a4-d656-4724-a7ac-836fe82c918e
date added to LUP
2021-12-13 23:52:19
date last changed
2021-12-20 10:22:10
@phdthesis{056d48a4-d656-4724-a7ac-836fe82c918e,
  abstract     = {{This thesis is composed of six papers, which all concern different methods and tools used for the analysis of barcodes in nanochannel-based Optical DNA Mapping (ODM). The first four papers consider densely-labeled barcodes while the last two consider sparsely-labeled barcodes.<br/><br/>Paper I  presents a combinatorial auction algorithm for contig assembly ussing ODM barcodes as scaffolds.<br/><br/>Paper II concerns mapping of ODM barcodes on the human genome.<br/><br/>Paper III deals with bacterial typing.<br/><br/>Paper IV solves structural variation detection problem for competitive binding barcodes using Hidden Markov Models.<br/><br/>Paper V proposes the use of Sliding Frank-Wolfe methods for sparse-labeled single-frame ODM.<br/><br/>Paper VI extends the Sliding Frank-Wolfe methods from the analysis of single frame barcodes to multi-frame setting, where barcodes over multiple time-frames are averaged to improve the resolution.<br/>}},
  author       = {{Dvirnas, Albertas}},
  isbn         = {{978-91-8039-125-2}},
  keywords     = {{DNA Barcoding; Optical Mapping; Computational Biology}},
  language     = {{eng}},
  month        = {{12}},
  publisher    = {{MediaTryck Lund}},
  school       = {{Lund University}},
  title        = {{Methods for barcode analysis in optical DNA mapping}},
  url          = {{https://lup.lub.lu.se/search/files/110913095/Albertas_Dvirnas_WEBB.pdf}},
  year         = {{2021}},
}