Genome Rearrangement Algorithms

UNLABELLED: Recent years have witnessed an increase in research activity for the detection of structural variants (SVs) and their association to human disease. The advent of next-generation sequencing technologies make it possible to extend the scope of structural variation studies to a point previously unimaginable a…

• CAN ALKAN

MOTIVATION: The high throughput sequencing (HTS) platforms generate unprecedented amounts of data that introduce challenges for the computational infrastructure. Data management, storage and analysis have become major logistical obstacles for those adopting the new platforms. The requirement for large investment for t…

• CAN ALKAN

MOTIVATION: High throughput DNA sequencing (HTS) technologies generate an excessive number of small DNA segments -called short reads- that cause significant computational burden. To analyze the entire genome, each of the billions of short reads must be mapped to a reference genome based on the similarity between a rea…

• CAN ALKAN

Motivation: Segmental duplications (SDs) or low-copy repeats, are segments of DNA > 1 Kbp with high sequence identity that are copied to other regions of the genome. SDs are among the most important sources of evolution, a common cause of genomic structural variation and several are associated with diseases of genomic…

• CAN ALKAN

Variable clinical presentations of patients with chromosomally detected deletions in the distal long arm (q) of chromosome 4 have been reported. The lack of molecular characterization of the deletion sizes and deleted genes hinders further genotype-phenotype correlation. Using a validated oligonucleotide array compara…

• HANDE KAYMAKÇALAN ÇELEBİLER

MOTIVATION: The increasing availability of high-quality genome assemblies raised interest in the characterization of genomic architecture. Major architectural elements, such as common repeats and segmental duplications (SDs), increase genome plasticity that stimulates further evolution by changing the genomic structur…

• CAN ALKAN

Özet henüz yok.

• MEHMET ALİ ERGÜN

BACKGROUND: 14q duplications caused by parental pericentric inversion of chromosome 14 are rarely reported and no clear genotype-phenotype correlation has been determined yet. CASE PRESENTATION: Here we reported a 7 years old female patient with recombinant chromosome characterized by 14 q duplication and originated f…

• MALİK EJDER YILDIRIM

Abstract Motivation Despite recent advances in algorithms design to characterize structural variation using high-throughput short read sequencing (HTS) data, characterization of novel sequence insertions longer than the average read length remains a challenging task. This is mainly due to both computational difficulti…

• CAN ALKAN
• TUNGA GÜNGÖR

BACKGROUND: Although many algorithms are now available that aim to characterize different classes of structural variation, discovery of balanced rearrangements such as inversions remains an open problem. This is mainly due to the fact that breakpoints of such events typically lie within segmental duplications or commo…

• CAN ALKAN

Spectroscopy is an experimental technique which exploits the magnetic properties of specific nuclei and enables the study of proteins in solution. The key bottleneck of NMR studies is to map the NMR peaks to corresponding nuclei, also known as the assignment problem. Structure-Based Assignment (SBA) is an approach to…

• BÜLENT ÇATAY
• MEHMET SERKAN APAYDIN

BACKGROUND: Understanding the evolution of biological networks can provide insight into how their modular structure arises and how they are affected by environmental changes. One approach to studying the evolution of these networks is to reconstruct plausible common ancestors of present-day networks, allowing us to an…

• EMRE SEFER