Methods for barcode analysis in optical DNA mapping
(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:
https://lup.lub.lu.se/record/056d48a4-d656-4724-a7ac-836fe82c918e
- author
- Dvirnas, Albertas LU
- supervisor
- opponent
-
- Associate Professor Nyvold Pedersen, Jonas, Technical University of Denmark, DTU Nanotech/DTU Health Tech, Denmark
- organization
- publishing date
- 2021-12-13
- 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
- 978-91-8039-126-9
- 978-91-8039-125-2
- 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 = {{978-91-8039-126-9}}, 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}}, }