The document discusses the field of bioinformatics, which involves applying computational techniques and building tools to solve biological problems, such as analyzing genetic sequences and modeling molecular structures. It outlines several applications of bioinformatics, including in medicine for disease research and drug design, as well as in agriculture and animal health. The emergence of bioinformatics is attributed to the convergence of rapid growth in fields like biotechnology and information technology.

2. FBW29-09-2011Wim Van Criekinge

4. What is Bioinformatics ?Application of information technology to the storage, management and analysis of biological information (Facilitated by the use of computers)Sequence analysis?Molecular modeling (HTX) ?Phylogeny/evolution?Ecology and population studies?Medical informatics?Image Analysis ?Statistics ? AI ?Sterkstroom of zwakstroom ?

5. Promises of genomics and bioinformaticsMedicine (Pharma)Genome analysis allows the targeting of genetic diseasesThe effect of a disease or of a therapeutic on RNA and protein levels can be elucidatedKnowledge of protein structure facilitates drug designUnderstanding of genomic variation allows the tailoring of medical treatment to the individual’s genetic make-upThe same techniques can be applied to crop (Agro) and livestock improvement (Animal Health)

6. Bioinformatics: What’s in a name ?Begin 1990’s“Bio-informatics”:Computing PowerGenbank(Log)Time (years)

7. Bioinformatics: What’s in a name ?Begin 1990’s“Bio-informatics”:convergence of explosive growth in biotechnology, paralled by the explosive growth in information technologyNot new: > 30 years that people use “computers” in biologyIn silico biology, database biology, ...

8. Time (years)

9. Happy Birthday …

10. PCR + dye terminationSuddenly, a flash of insight caused him to pull the car off the road and stop. He awakened his friend dozing in the passenger seat and excitedly explained to her that he had hit upon a solution - not to his original problem, but to one of even greater significance. Kary Mullis had just conceived of a simple method for producing virtually unlimited copies of a specific DNA sequence in a test tube - the polymerase chain reaction (PCR)

11. MathTheoretical BiologyComputer Science(Molecular)BiologyInformaticsComputational BiologyBioinformatics, a scientific discipline …Bioinformatics

12. Math Algorithm DevelopmentTheoretical BiologyComputer ScienceAI, Image Analysisstructure prediction (HTX)NPDataminingInterface DesignExpert AnnotationSequence Analysis(Molecular)BiologyInformaticsComputational BiologyBioinformatics, a scientific discipline …Bioinformatics

13. Math Algorithm DevelopmentTheoretical BiologyComputer ScienceAI, Image Analysisstructure prediction (HTX)NPDataminingInterface DesignExpert AnnotationSequence Analysis(Molecular)BiologyInformaticsComputational BiologyBioinformatics, a scientific discipline …BioinformaticsDiscovery Informatics – Computational Genomics

14. Doel van de cursusMeer dan een inleiding tot ... het is de bedoeling van de cursus een onderliggend inzicht te verschaffen achter de verschillende technieken. Naast het gebruik van recepten, wat terug te vinden is in delen van de syllabus laat een inzicht in de werking van databanken en de achterliggende algoritmen toe om wisselende interfaces op nieuwe problemen toe te passen.

15. Inhoud Lessen: Bioinformaticadon 29-09-2011: 1* Bioinformatics (practicum 8.30-11.00) don 06-10-2011: 2* Biological Databases (practicum 9.00-11.30) don 20-10-2011: 3 Sequence Similarity (Scoring Matrices)don 27-10-2011: 4 Sequence Alignmentsdon 10-11-2011: 5 Database Searching Fasta/Blastdon 17-11-2011: 6 Phylogeneticsdon 24-11-2011: 7 Protein Structure don 01-12-2011: 8 Gene Prediction, Gene Ontologies & HMMdon 08-12-2011: 9 ncRNA, Chip Data Analysis, AIdon 15-12-2011: 10 Bio- & Cheminformatics in Drug Discovery (inhaalweek)Opgelet: Geen les op don 13-10-2010 en don 3-11-2010

16. ExamenTheorie Deel rond een zelf te kiezen publicatie die in verband staat met de cursus Bv Bioinformatics of Computational Biology Drie inzichtsvragen over de cursus (inclusief  !!)Practicum (“open-book”)Viertal oefeningen die meestal het schrijven van een programma veronderstellenPuntenverdeling 50/50

18. Timelin: Magaret Dayhoff …

19. Nexus > FAQ > Bioinformatics Milestones

20. http://www.sciencemag.org/cgi/content/full/291/5507/1195Printed version in cursus

21. naturetheHumangenomeSetting the stage …

25. Genome MetersGenomes Online Database (GOLD 1.0)http://geta.life.uiuc.edu/~nikos/genomes.htmlhttp://www.ebi.ac.uk/research/cgg/genomes.htmlNCBIhttp://www.ncbi.nlm.nih.gov/PMGifs/Genomes/bact.htmlINFOBIOGENhttp://www.infobiogen.fr/doc/data/complete_genome.html

26. Genome SizeE. coli = 4.2 x 106Yeast = 18 x 106Arabidopsis = 80 x 106C.elegans = 100 x 106Drosophila = 180 x 106Human/Rat/Mouse = 3000 x 106Lily = 300 000 x 106With ... : 99.9 %To primates: 99%DOGS: Database Of Genome Sizes

28. Biological ResearchAdapted from John McPherson, OICR

29. And this is just the beginning ….Next Generation Sequencing is here

30. Basics of the “old” technologyClone the DNA.Generate a ladder of labeled (colored) molecules that are different by 1 nucleotide.Separate mixture on some matrix.Detect fluorochrome by laser.Interpret peaks as string of DNA.Strings are 500 to 1,000 letters long1 machine generates 57,000 nucleotides/runAssemble all strings into a genome.

31. Basics of the “new” technologyGet DNA.Attach it to something.Extend and amplify signal with some color scheme.Detect fluorochrome by microscopy.Interpret series of spots as short strings of DNA.Strings are 30-300 letters longMultiple images are interpreted as 0.4 to 1.2 GB/run (1,200,000,000 letters/day). Map or align strings to one or many genome.

32. Next Generation Technologies454Emulsion PCRPolymeraseNatural Nucleotides20-100Mb for 5-15k 1% error rateHomopolymers

38. One additional insight ...

39. Read Length is Not As Important For ResequencingJay Shendure

40. Two Short Read TechologiesIllumina GAABI SOLID

41. Technology Overview: Solexa/Illumina Sequencing

47. ABI SolidDressman 2003

48. ABI SOLID

49. ABI SOLID

53. Paired End Reads are Important!Known DistanceRead 1Read 2Repetitive DNAUnique DNAPaired read maps uniquelySingle read maps to multiple positions

54. Single Molecule SequencingAdapted from: Barak Cohen, Washington University, Bio5488 http://tinyurl.com/6zttuq http://tinyurl.com/6k26nhMicroscope slide***Single DNA moleculeSuper-cooledTIRF microscopeprimerdNTP-Cy3*Helicos Biosciences Corp.

55. IntroducingNXT GNT DXSNextGenerationDiagnostics18th september 2009Wim Van Criekinge

56. develop in shortest time frame best assay for most relevant clinical application

58. NXT GNT DXSGNT

59. Dedicated Team & Network

60. Operational: Location

61. Professionalized

62. DXS

63. Content engine

64. Product 1 established

65. Pipeline for n+1

66. NXT

67. Workflow management