Advisors
Now showing items 1-15 of 15
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Algorithms for the discovery of large genomic inversions using pooled clone sequencing
(Bilkent University, 2015)An inversion is a chromosomal rearrangement in which an internal segment of a chromosome has been broken twice, flipped 180 degrees, and rejoined. Most known examples of large inversions were found indirectly from studies ... -
Assessment and correction of errors in DNA sequencing technologies
(Bilkent University, 2017-12)Next Generation Sequencing technologies differ by several parameters where the choice to use whether short or long read sequencing platforms often leads to trade-offs between accuracy and read length. In this thesis, I ... -
Bias correction in finding copy number variation with using read depth-based methods in exome sequencing data
(Bilkent University, 2014)Medical research has striven for identifying the causes of disorders with the ultimate goal of establishing therapeutic treatments and finding cures since its early years. This aim is now becoming a reality thanks to ... -
Breakpoint refinement of genomic structural variation using split read analysis
(Bilkent University, 2019-09)Genomic variations that vary from single nucleotide polymorphisms (SNPs), small INDELs to structural variations (SVs) are discovered to have significant phenotypic effects on individuals. Among these genomic variations, ... -
Characterization of large structural variation using linked-reads
(Bilkent University, 2018-08)Many algorithms aimed at characterizing genomic structural variation (SV) have been developed since the inception of high-throughput sequencing. However, the full spectrum of SVs in the human genome is not yet assessed. ... -
Characterization of short tandem repeats using local assembly
(Bilkent University, 2017-03)Tandem repeats are pieces of DNA where a pattern has multiple consecutive copies adjacent to itself. If the repeat unit (pattern) consists of 2 to 6 nucleotides, it can be referred to as a short tandem repeat or a ... -
A cryptocurrency incentivized voluntary grid computing platform for DNA read alignment
(Bilkent University, 2019-09)The main computational bottleneck of High Throughput Sequencing (HTS) data analysis is to map the reads to a reference genome, for which clusters are typically used. However, building clusters large enough to handle ... -
Distributed stream-processing framework for graph-based sequence alignment
(Bilkent University, 2020-01)Optimized the sequence alignment pipelines are needed to minimize the time required to complete processing the short-read genomic data. Today there are many sequence alignment tools exist, yet few of them are capable of ... -
GateKeeper-GPU: accelerated pre-alignment filtering in short read mapping
(Bilkent University, 2020-08)Recent advances in high throughput sequencing (HTS) facilitate fast production of short DNA fragments (reads) in numerous amounts. Although the production is becoming inexpensive everyday, processing the present data for ... -
Genome scaffolding using poled clone sequencing
(Bilkent University, 2014)The DNA sequencing technologies hold great promise in generating information that will guide scientists to learn more about how the genome affects human health, organismal evolution, and genetic relationships between ... -
High throughput udp-based peer-to-peer secure data transfer
(Bilkent University, 2018-05)High throughput sequencing (HTS) platforms have been developed in recent years. These technologies enable researchers to answer a wide range of biological questions by obtaining whole or targeted segments of genomes of ... -
Identification of protein-protein interaction bridges for multiple sclerosis
(Bilkent University, 2022-12)Identifying and prioritizing disease-related proteins is an important scientific problem to understand disease etiology. Network science has become an important discipline to prioritize such proteins. Multiple sclerosis ... -
Large structural variation discovery using long reads with several degrees of error
(Bilkent University, 2020-12)Genomic structural variations (SVs) are briefly defined as large-scale alterations of DNA content, copy, and organization. Although significant progress has been made since the introduction of high throughput sequencing (HTS) ... -
Paralog-specific gene copy number discovery within segmental duplications
(Bilkent University, 2019-09)With the advancing technology in genome sequencing and analysis, it has become evident that the structural variations are the main source of alteration in human genome. Despite their signi cance in understanding disease ... -
Read mapping methods optimized for multiple GPGPU
(Bilkent University, 2016-07)DNA sequence alignment problem can be broadly defined as the character-level comparison of DNA sequences obtained from one or more samples against a database of reference (i.e., consensus) genome sequence of the same or a ...
