A Biology Introduction for Bioinformatics

1. A Biology Introduction for Bioinformatics Lecture #1 By Dr. Emad Nabil Faculty of Computers and Information, Cairo University Spring 2019

2. Agenda • Bioinformatics definition • Why you should be a Bioinformatician?! • Syllabus • Resources • Introduction to Biology

3. Course Page http://www.acadox.com/class/56661#resources

4. Grading Scheme Course work(40%) • Individual • Programming Assignments • Groups: • Pick Interesting Research Topic Survey and Presentation Final Exam (60%)

5. Bioinformatics

6. Bioinformatics

7. Computational Biology It involves the development and application of: • data-analytical and theoretical methods, • mathematical modeling and computational simulation techniques to the study of biological, behavioral, and social systems. • It includes foundations in:

8. Why you might be Bioinformatician? • Inter-disciplinary field… • Staff and researchers needed worldwide • Contribution to health, agriculture, … etc • Contemplation of how creatures were created The future of medicine Ex: Gene therapy, personalized medicine, CRISPR CRISPR technology is a simple yet powerful tool for editing genomes. It allows researchers to easily alter DNA sequences and modify gene function. Its many potential applications include correcting genetic defects, treating and preventing the spread of diseases and improving crops. However, its promise also raises ethical concerns.

9. Interdisciplinary Terminologies/Techniques for Genomics How do we (get/process/store) genome-based biological data? • Genome Sequencing (based on whole genome) • Compressionalgorithms used for genome compression • Graphalgorithms used for genome assembly • HeuristicSearch techniques used for Motif Finding • Dynamic programming used for sequence alignment • Microarray (Based on genes) • Machine Learning techniques used for Microarray data analysis: • Feature Selection Selection of candidate data items from huge data • Classification Finding Classification boundaries between selected data items that allow classifying new data

10. Introduction to biology

11. Human Body Human Organs Tissues Cells Genome

12. Genome A genome is the collection of an organism's hereditary information as encoded in its DNA. For most life forms, DNA is assembled into chromosomes; the 23 pairs of chromosome pairs making up a human genome form 3.2 billion base pairs. Humans share about 99.9% of our genome  In 2001, the human genome was finally sequenced by taking an average case (consensus) genome from 12 individuals, thus completing a 3 billion dollar project. The median size of a protein-coding gene is 26,288 bp. mean = 66,577 bp

13. Human genome project • The Human Genome Project was an international research effort to determine the sequence of the human genome and identify the genes that it contains. • The Project was coordinated by the National Institutes of Health and the U.S. Department of Energy. • Additional contributors included universities across the United States and international partners in the United Kingdom, France, Germany, Japan, and China. • The Human Genome Project formally began in 1990 and was completed in 2003, 2 years ahead of its original schedule. thus completing a 3 billion dollar project • As researchers learn more about the functions of genes and proteins, this knowledge will have a major impact in the fields of medicine, biotechnology, and the life sciences. https://ghr.nlm.nih.gov/primer/hgp/description

14. Human genome project Goals The main goals of the Human Genome Project were to provide a complete and accurate sequence of the 3 billion DNA base pairs that make up the human genome. to find all of the estimated 20,000 to 25,000 human genes. sequence the genomes of several other organisms that are important to medical research, such as the mouse and the fruitfly. to develop new tools to obtain and analyze the data and to make this information widely available. to explore the consequences of genomic research through its Ethical, Legal, and SocialImplications(ELSI) program. https://ghr.nlm.nih.gov/primer/hgp/goals

15. Length of Genome If the DNA in all the person’s cells is stretched out, end to end, it'd reach the sun and back about four times!

16. Chromosomes There are an estimated 19,000-20,000 human protein-coding genes

17. DNA • The sugar and phosphate group make up the backbone of the DNA double helix, while the bases are located in the middle

18. DNA Nucleotides ˈn(y)o͞oklēəˌtīd A nucleotide is the basic structural unit and building block for DNA. A nucleotide is composed of 3 parts: * five-sided sugar* phosphate group* nitrogenous base (nitrogen containing) there are 4 bases Single Nucleotide

19. DNA

20. DNA nitrogenous base • There are four types of bases in DNA. They are called: • Adenine (A)* Cytosine (C)* Guanine (G)* Thymine (T) • Bases are the part of DNA that stores information and gives DNA the ability to encode phenotype • phenotype: the observable or physical characteristics of an individual, as a result of genetic expression and environment Single Nucleotide