Phd thesis on bioinformatics pdf

Calculating and Visualizing Sequence Statistics Aligning Pairs of Sequences Working with Whole Genome Data Comparing Whole Genomes Assessing the Significance of an Alignment Building a Phylogenetic Tree for the Hominidae Species Analyzing the Origin of the Human Immunodeficiency Virus Analyzing Synonymous and Nonsynonymous Substitution Rates Investigating the Bird Flu Virus Bootstrapping Phylogenetic Trees Exploring Primer Design Identifying Over-Represented Regulatory Motifs Nucleotide sequence and analysis 6.

Structural analysis 7. Phylogenetic analysis 8. SNP Analysis 9. Gene Silencing Protein Sequence Analysis Comparative Genomics. Arsenic, a naturally occurring metalloid, is widely spread in the environment and is toxic to living organisms. Its pollution, caused mostly by mining, industrial and agricultural uses, has become a global problem. To elucidate arsenic resistance mechanisms evolved in diverse organisms has been an active research area which will help combat the threatening pollutant.

We have the necessary skills, knowledge, and experience to complete virtually any …. Couto April, Outline 1 Substance 2 Structure 3 Style. You must start your 30 ECTS thesis no later than February 1 or September 1 a year and a half after commencement of your studies i.

February for students admitted in summer , or September for students admitted in winter Third semester Master thesis, 30 ECTS Each student works on an individual research thesis in one of the research groups, thus specializing in a chosen area. The master thesis can also be carried out in collaboration with one of the affiliated institutes, e. Mux-seq is becoming increasingly popular for performing large-scale scRNA-seq experiments in a cost-effective manner.

However, the existing statistical method, demuxlet, requires external genotypes to be collected by array genotyping or DNA sequencing, limiting the ability to apply the method when it is not feasible to obtain genotypes such as in model organisms or cancer cells.

Furthermore, the additional steps to obtain, process, and impute the external genotypes in addition to scRNA-seq experiment become a substantial bottleneck to analyze the data within a rapid turnaround time. Freemuxlet defines the distances between a pair of cell barcodes as Bayes Factors BF to determine statistical confidence between possible hypotheses of genetic identities of each cell barcodes. The iterative procedure of multi-class clustering guided by BF distances simultaneously estimates the consensus genotypes of each individual while detecting multiplets and deconvoluting the sample provenances of singlets.

I apply these methods to the 7-sample mixture dataset and observe high concordance of estimated droplets identities between freemuxlet and other methods cell hashing, demuxlet with external genotypes. I further demonstrate that freemuxlet can successfully deconvolute multiplexed scRNA-seq of cancer cell lines, where demuxlet could not deconvolute the droplet identities due to the difficulty of accurately genotyping cancer cell lines.

Our results suggest that genotyping-free multiplexing of scRNA-seq experiment will facilitate a more wide range of population-scale single cell studies including cancer cells and model organisms.

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