Methods for barcode analysis in optical DNA mapping

Summary, in English

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.

• Author: Albertas Dvirnas
• Department/s: Computational Biology and Biological Physics - Has been reorganised
• Publishing year: 2021-12-13
• Language: English
• Full text: - 1 MB; Download statistics
• Document type: Dissertation
• Publisher: MediaTryck Lund
• Topic: Biophysics
• Keywords: DNA Barcoding; Optical Mapping; Computational Biology
• Status: Published
• Supervisor: Tobias Ambjörnsson
• ISBN/ISSN/Other: ISBN: 978-91-8039-126-9; ISBN: 978-91-8039-125-2
• Defence date: 25 January 2022
• Defence time: 10:00
• Defence place: Lundmarksalen, Astronomihuset. Join via zoom: https://lu-se.zoom.us/j/64941727808?pwd=RUphOWZQMUhVVitwVFdZNUlwbk5ydz09 (Passcode: 2022)
• Opponent: Jonas Nyvold Pedersen (Associate Professor)