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Bioinformatics Theory and Practice

Bioinformatics Theory and Practice. So.. What is Bioinformatics? What is it used for?. So.. What is Bioinformatics? And what is it used for?. Wikipedia: “Bioinformatics is an interdisciplinary field that develops methods and software tools for understanding biological data”

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Bioinformatics Theory and Practice

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  1. BioinformaticsTheory and Practice

  2. So.. What is Bioinformatics?What is it used for?

  3. So.. What is Bioinformatics?And what is it used for? Wikipedia: “Bioinformatics is an interdisciplinary field that develops methods and software tools for understanding biological data” Why study bioinformatics? Why don’t we study biology and take programming lessons? Using our knowledge in computer science, we can develop efficient algorithms and methods. Using our knowledge in biology, we can understand what we are doing 

  4. מה נלמד בקורס? • ביואינפורמטיקה זה נושא מאוד רחב, שאי אפשר לכסות בקורס אחד. • ביואינפורמטיקה יכולה לשלב כמעט כל תחום במדעי המחשב. • בקורס זה תלמדו אלגוריתמים שמהווים בסיס בתחומים חשובים ונחקרים מאוד בביואינפורמטיקה • תלמדו את האלגוריתמים מאחורי כלים שכל ביולוג מכיר

  5. The future of bioinformatics

  6. Personalized medicine • The use of genomic information – in addition to family history, lifestyle, and environmental factors – to customize health management. • Combining genomic and clinical information to predict a person’s • Susceptibility of developing disease • Course of disease • Response to treatment

  7. Personalized medicine - Ovarian cancer • Hard to treat: • The tumors are different from patient to patient because of different mutations in their particular tumor • The mutations can determine the response to treatment • Can we improve treatment outcomes by giving the right drug to the right patient?

  8. Personalized medicine - Ovarian cancer BRCA Mutation

  9. DNA sequencing cost of human genome

  10. DNA sequencing cost of human genome

  11. Personalized medicine - Ovarian cancer • A “silent killer” • Ovarian cancer's early stages are difficult to diagnose because most symptoms are nonspecific • It is rarely diagnosed until it spreads and advances to later stages • Early diagnosis is crucial!

  12. Ovarian cancer – biomarker CA125 • Low sensitivity: • ~80% of patients with advanced ovarian cancer have raised levels of CA 125 • < 50% of patients with stage I disease have raised CA 125 levels • Nonspecific test - also raised in other conditions • There is a need to find more biomarkers for early discovery

  13. Biomarkers discovery

  14. Bioinformatics in treating leukemia • In leukemia – abnormal white blood cells are created • Leukemia cells divide to produce many copies and they don’t die • This results in low level of normal blood cells, and makes it harder for the body to: • Get oxygen to tissues • Control bleeding • Fight infections • In Chronic myelogenous leukemia (CML) patients, abnormal white blood cell production is caused by the Bcr-Abl, a protein formed by a chromosomal defect found in 90% of CML patients. 

  15. Bioinformatics in treating leukemia This image shows Gleevec (imatinib mesylate) interrupting the normal pathway of Bcr-Abl. It bonds to Bcr-Abl instead of ATP so the signal (making cancer cells) cannot be carried out http://kohnpharmaceuticals.weebly.com/biochemical-pathways.html

  16. Bioinformatics in treating leukemia http://www.dnalc.org/resources/3d/32-how-gleevec-works.html

  17. Machine learning • Can be used for finding biomarkers in blood, tissue etc. • Can also be used for other areas in bioinformatics like clustering and classification. • Will not be covered in out course. • Machine learning in general • Genomic Data Science and Clustering

  18. Big Data

  19. Every bioinformatician should know statistics • After creating a fancy algorithm, we often have to evaluate the significance of the results • Statistics for Genomic Data Science

  20. C Finding ordered gene teams D B E C G D F E F F G A

  21. Finding ordered gene teams - algorithm

  22. פרטים טכניים • אתר הקורס: • http://www.cs.bgu.ac.il/~tabio172 • חשוב: לעקוב אחרי ה-Announcements • שעות קבלה: • בניין 34 חדר 312 • רביעי 10:00-12:00, עדיף בתיאום מראש • dinasv@post.bgu.ac.il • כל החומר שיופיע בהרצאות ובתרגולים יכול להיות במבחן

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