Algorithms and procedures in genomics and transcriptomics

Bioinformatics has evolved to a scientific discipline that is central for discoveries in genetics, molecular biology, biotechnology and medicine. Over the last decades a huge set of databases, data structures, methods and algorithms has been developed in this scientific field.
In this work, we provide a comprehensive overview of the underlying biotechnologies, such as microarrays and next generation sequencing, the data types, approaches, methodology and algorithms. The aim of this master thesis is to provide those topics in the form of a textbook that can serve as a basis of a University lecture.
There are at least two aspects that make this effort challenging:
1. The interdisciplinary nature of Bioinformatics. Bioinformatics can be considered as a science in the intersection of computer science, molecular biology and mathematics. Thus, inhomogeneous prior knowledge about the subject has to be taken into account when content such as algorithms, the programming language R, statistics, biotechnologies, is presented.
2. A high amount of technical details. There is a certain danger that the content loses itself into “not seeing the woods from all the trees”. On the other hand, each of the presented concepts has a wide scope and many details are necessary to get an understanding.
This work uses a pedagogical concept that separates the details as much as possible from the “big picture”. Boxes with explanations, footnotes for further details, code snippets to explain an algorithm, pictures, illustrations and graphics to make it understandable are an integral part of both the script and the slides that are developed from it. Difficult concepts are explained in two or three separate ways, so that they can be understood by as many readers as possible. Things are always put into context (both within this lecture and across others), so that the knowledge that builds up with the reader is not a collection of seemingly unrelated bits and pieces.
Overall, this work presents a new, comprehensive overview of methods from two main bioinformatics areas - genomics and transcriptomics - in the form of a textbook with a focus on pedagogical presentation of the content.