Sharif Digital Repository

DNA sequence is the lifetime private information of each individual: it can reveal personal traits, health status, and medical risk of that individual, it can be abused by entities such as insurance companies, it can be used for identity theft, etc. Unfortunately, due to cost, regulations, or some restrictions, we may not be able to complete DNA sequencing in-house and have to outsource it to some unreliable companies in some foreign countries.This would compromise the DNA privacy from the beginning. This would raise the question that how we can guarantee the DNA privacy in the process of sequencing.Here we propose a solution for private DNA sequencing by exploiting the fact that the process... 

Humans, as a diploid species, have two nucleotide sequences of homologous chromosomes in their genomes, where one set is inherited from the mother, and the other comes from the father. The Single Individual Haplotype assembly problem (SIH) refers to the reconstruction of these two distinct nucleotide sequences of a chromosome from the sequencing reads, and it is currently considered one of the most important issues in the field of computational genomics, which plays an essential role in solving various genetic and medical problems.Nowadays direct experimental methods are not welcomed due to their high cost, and labor intensity, and are limited to certain regions of the genome, therefore,... 

The field of Genome-Wide Asocciation Studies (GWAS) plays a vital role in understanding the genetic basis of complex traits and diseases. In this thesis, the focus is on investigating the effectiveness of two approaches combining Differential Evolution (DE) with Random Forest (RF) and support vector machine (SVM) for feature selection in the context of GWAS. Arabidopsois Thaliana dataset is used as experimental dataset for comparative analysis. The main goal is to achieve more efficient feature selection while maintaining competitive accuracy compared to RF and SVM without using DE. This research includes conducting experiments using DE with RF and DE with SVM followed by a comprehensive... 

Human is diploid specie that inherits a set of chromosomes from their mother and a set from their father. The process of separating the nucleotide content of a set of extracted maternal and paternal chromosomes for an individual or a population is called phasing the genome of the individual or the population. The placement of any two variants relative to each other in diploid species is possible in two forms: cis (placement of both variants on one chromosome), and trans (placement of variants on different chromosomes). Each of these conditions leads to different phenotypes. Thus, understanding how variants are placed relative to each other is a crucial problem in human biology which is... 

One of the branches of genetic studies is population genetics. Each population has its own characteristics due to its evolutionary history, cultural characteristics and geography, which distinguish it from other populations. Scientific and technological advances in recent decades have led to the production of new generation sequencing machines and the creation of large genetic data. These data contain important genetic information and answers to many questions about the origin of humans, the history of populations and their evolutionary process. More and better understanding of the human genome and the distance between populations can help to better understand biological mechanisms and deal... 

Development of DNA sequencing technologies in the recent years magnifies the need for computational tools in genomic data processing, and thus has attracted inten- sive research interest to this area. Among them, Genome-Wide Association Study (GWAS) refers to discovering of causal relationships among genetic sequences of living organisms and the macroscopic phenotypes present in their physiological structure. Chosen phenotypes for genomic association studies are mostly vulnerability or im- munity to common genetic diseases. Conventional methods in GWAS consists of statistical hypothesis testing algorithms in case/control approaches; Most of which are based upon single-locus analysis and... 

Startups mostly originated from creating an idea and introduced themselves as a new plan for optimization and development in societies. Being exquisite foreclosed any prediction of their future for their owners. On the other hand, the destination of an idea to be a product needs a solution. If the solution matches the structural behavior of the society, it will survive. Simulation of the structural behavior of society through genetic science creates a suitable gadget for the investigation of genetic logic. It accumulated the response of stakeholders of society in that subject according to the standard index in the format of information and database completely and meticulously. It depicts the... 

Recent advances in genome sequencing technologies have provided a wide variety of completely sequenced genomes. This opened up the opportunity to study genomic sequences, using pairwise or multiple alignment of the whole-genomes. The aim is to explore the similarities and differences between genomes for further comparative studies. This task is challenging because genomes of different species have undergone not only small mutations but also many large-scale evolutionary events such as insertion, deletion and inversion.There has been a lot of research on developing whole-genome alignment algorithms. Having an optimal trade-off between sensitivity, accuracy and computational expense are very... 

In this research, an optical processing method for DNA classification is presented in order to overcome the problems in the previous methods. With improving in the operational capacity of the sequencing process, which has increased the number of genomes, comparing sequences with a complete database of genomes is a serious challenge to computational methods. Most current classification programs suffer from either slow classification speeds, large memory requirements, or both. To achieve high speed and accuracy at the same time, we suggest using optical processing methods. The performance of electronic processing-based computing, especially in the case of large data processing, is usually...