Bioinformatica 29-09-2011-t1-bioinformatics

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Bioinformatica 29-09-2011-t1-bioinformatics

  1. 1.
  2. 2. FBW<br />29-09-2011<br />Wim Van Criekinge<br />
  3. 3.
  4. 4. What is Bioinformatics ?<br />Application of information technology to the storage, management and analysis of biological information (Facilitated by the use of computers)<br />Sequence analysis?<br />Molecular modeling (HTX) ?<br />Phylogeny/evolution?<br />Ecology and population studies?<br />Medical informatics?<br />Image Analysis ?<br />Statistics ? AI ?<br />Sterkstroom of zwakstroom ?<br />
  5. 5. Promises of genomics and bioinformatics<br />Medicine (Pharma)<br />Genome analysis allows the targeting of genetic diseases<br />The effect of a disease or of a therapeutic on RNA and protein levels can be elucidated<br />Knowledge of protein structure facilitates drug design<br />Understanding of genomic variation allows the tailoring of medical treatment to the individual’s genetic make-up<br />The same techniques can be applied to crop (Agro) and livestock improvement (Animal Health)<br />
  6. 6. Bioinformatics: What’s in a name ?<br />Begin 1990’s<br />“Bio-informatics”:<br />Computing Power<br />Genbank<br />(Log)<br />Time (years)<br />
  7. 7. Bioinformatics: What’s in a name ?<br />Begin 1990’s<br />“Bio-informatics”:<br />convergence of explosive growth in biotechnology, paralled by the explosive growth in information technology<br />Not new: > 30 years that people use “computers” in biology<br />In silico biology, database biology, ...<br />
  8. 8. Time (years)<br />
  9. 9. Happy Birthday …<br />
  10. 10. PCR + dye termination<br />Suddenly, 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)<br />
  11. 11. Math<br />Theoretical Biology<br />Computer Science<br />(Molecular)<br />Biology<br />Informatics<br />Computational Biology<br />Bioinformatics, a scientific discipline …<br />Bioinformatics<br />
  12. 12. Math <br />Algorithm Development<br />Theoretical Biology<br />Computer Science<br />AI, Image Analysis<br />structure prediction (HTX)<br />NP<br />Datamining<br />Interface Design<br />Expert Annotation<br />Sequence Analysis<br />(Molecular)<br />Biology<br />Informatics<br />Computational Biology<br />Bioinformatics, a scientific discipline …<br />Bioinformatics<br />
  13. 13. Math <br />Algorithm Development<br />Theoretical Biology<br />Computer Science<br />AI, Image Analysis<br />structure prediction (HTX)<br />NP<br />Datamining<br />Interface Design<br />Expert Annotation<br />Sequence Analysis<br />(Molecular)<br />Biology<br />Informatics<br />Computational Biology<br />Bioinformatics, a scientific discipline …<br />Bioinformatics<br />Discovery Informatics – Computational Genomics<br />
  14. 14. Doel van de cursus<br />Meer dan een inleiding tot ... het is de bedoeling van de cursus een onderliggend inzicht te verschaffen achter de verschillende technieken. <br />Naast het gebruik van recepten, wat terug te vinden is in delen van de syllabus laat een inzicht in <br />de werking van databanken <br />en de achterliggende algoritmen <br />toe <br />om wisselende interfaces op nieuwe problemen toe te passen.<br />
  15. 15. Inhoud Lessen: Bioinformatica<br />don 29-09-2011: 1* Bioinformatics (practicum 8.30-11.00) <br />don 06-10-2011: 2* Biological Databases (practicum 9.00-11.30) <br />don 20-10-2011: 3 Sequence Similarity (Scoring Matrices)<br />don 27-10-2011: 4 Sequence Alignments<br />don 10-11-2011: 5 Database Searching Fasta/Blast<br />don 17-11-2011: 6 Phylogenetics<br />don 24-11-2011: 7 Protein Structure <br />don 01-12-2011: 8 Gene Prediction, Gene Ontologies & HMM<br />don 08-12-2011: 9 ncRNA, Chip Data Analysis, AI<br />don 15-12-2011: 10 Bio- & Cheminformatics in Drug Discovery (inhaalweek)<br />Opgelet: Geen les op don 13-10-2010 en don 3-11-2010<br />
  16. 16. Examen<br />Theorie <br />Deel rond een zelf te kiezen publicatie die in verband staat met de cursus <br />Bv Bioinformatics of Computational Biology <br />Drie inzichtsvragen over de cursus (inclusief  !!)<br />Practicum (“open-book”)<br />Viertal oefeningen die meestal het schrijven van een programma veronderstellen<br />Puntenverdeling 50/50<br />
  17. 17.
  18. 18. Timelin: Magaret Dayhoff …<br />
  19. 19. Nexus > FAQ > Bioinformatics Milestones<br />
  20. 20. http://www.sciencemag.org/cgi/content/full/291/5507/1195<br />Printed version in cursus<br />
  21. 21. nature<br />the<br />Human<br />genome<br />Setting the stage …<br />
  22. 22.
  23. 23.
  24. 24.
  25. 25. Genome Meters<br />Genomes Online Database (GOLD 1.0)<br />http://geta.life.uiuc.edu/~nikos/genomes.html<br />http://www.ebi.ac.uk/research/cgg/genomes.html<br />NCBI<br />http://www.ncbi.nlm.nih.gov/PMGifs/Genomes/bact.html<br />INFOBIOGEN<br />http://www.infobiogen.fr/doc/data/complete_genome.html<br />
  26. 26. Genome Size<br />E. coli = 4.2 x 106<br />Yeast = 18 x 106<br />Arabidopsis = 80 x 106<br />C.elegans = 100 x 106<br />Drosophila = 180 x 106<br />Human/Rat/Mouse = 3000 x 106<br />Lily = 300 000 x 106<br />With ... : 99.9 %<br />To primates: 99%<br />DOGS: Database Of Genome Sizes<br />
  27. 27.
  28. 28. Biological Research<br />Adapted from John McPherson, OICR<br />
  29. 29. And this is just the beginning ….<br />Next Generation Sequencing is here<br />
  30. 30. Basics of the “old” technology<br />Clone the DNA.<br />Generate a ladder of labeled (colored) molecules that are different by 1 nucleotide.<br />Separate mixture on some matrix.<br />Detect fluorochrome by laser.<br />Interpret peaks as string of DNA.<br />Strings are 500 to 1,000 letters long<br />1 machine generates 57,000 nucleotides/run<br />Assemble all strings into a genome. <br />
  31. 31. Basics of the “new” technology<br />Get DNA.<br />Attach it to something.<br />Extend and amplify signal with some color scheme.<br />Detect fluorochrome by microscopy.<br />Interpret series of spots as short strings of DNA.<br />Strings are 30-300 letters long<br />Multiple images are interpreted as 0.4 to 1.2 GB/run (1,200,000,000 letters/day). <br />Map or align strings to one or many genome. <br />
  32. 32. Next Generation Technologies<br />454<br />Emulsion PCR<br />Polymerase<br />Natural Nucleotides<br />20-100Mb for 5-15k <br />1% error rate<br />Homopolymers<br />
  33. 33.
  34. 34.
  35. 35.
  36. 36.
  37. 37.
  38. 38. One additional insight ...<br />
  39. 39. Read Length is Not As Important For Resequencing<br />Jay Shendure<br />
  40. 40. Two Short Read Techologies<br />Illumina GA<br />ABI SOLID<br />
  41. 41. Technology Overview: Solexa/Illumina Sequencing<br />
  42. 42.
  43. 43.
  44. 44.
  45. 45.
  46. 46.
  47. 47. ABI Solid<br />Dressman 2003<br />
  48. 48. ABI SOLID<br />
  49. 49. ABI SOLID<br />
  50. 50.
  51. 51.
  52. 52.
  53. 53. Paired End Reads are Important!<br />Known Distance<br />Read 1<br />Read 2<br />Repetitive DNA<br />Unique DNA<br />Paired read maps uniquely<br />Single read maps to <br />multiple positions<br />
  54. 54. Single Molecule Sequencing<br />Adapted from: Barak Cohen, Washington University, Bio5488 http://tinyurl.com/6zttuq http://tinyurl.com/6k26nh<br />Microscope slide<br />*<br />*<br />*<br />Single DNA <br />molecule<br />Super-cooled<br />TIRF microscope<br />primer<br />dNTP-Cy3<br />*<br />Helicos Biosciences Corp.<br />
  55. 55. IntroducingNXT GNT DXSNextGenerationDiagnostics<br />18th september 2009<br />Wim Van Criekinge<br />
  56. 56. develop in shortest time frame best assay for most relevant clinical application<br />
  57. 57.
  58. 58. NXT GNT DXS<br /><ul><li>GNT
  59. 59. Dedicated Team & Network
  60. 60. Operational: Location
  61. 61. Professionalized
  62. 62. DXS
  63. 63. Content engine
  64. 64. Product 1 established
  65. 65. Pipeline for n+1
  66. 66. NXT
  67. 67. Workflow management
  68. 68. Bioinformatics
  69. 69. Epigenetics</li></li></ul><li>Next next generation sequencing<br />Third generation sequencing<br />Now sequencing<br />
  70. 70. Complete genomics<br />
  71. 71. Complete genomics<br />
  72. 72. Pacific Biosciences: A Third Generation Sequencing Technology<br />Eid et al 2008<br />
  73. 73. Pacific Biosciences: A Third Generation Sequencing Technology<br />
  74. 74. Nanopore Sequencing<br />
  75. 75. NCBI (educational resources)<br />
  76. 76. Weblems<br />What ?<br />Web-based problemes (over de huidige les en/of voorbereiding op volgende les)<br />When ?<br />Einde van elke les<br />How ?<br />Oplossingen online via screencasts<br />Practicum<br />Voorbedereiding op het practicum examen ... Niet alle problemen vereisen noodzakelijk programmacode ...<br />
  77. 77. Weblems<br />W1.1: To which phyla do the following species belong (a) starfish (b) ginko tree (c) scorpion<br />W1.2: What are the common names for the following species (a) Orycterophus afer (b) Beta vulagaris (c) macrocystis pyrifera<br />W1.3: What species has the smallest known genome ? And is genome size related to number of genes ?<br />W1.4: What are the 5 latest genomes published ? How complete is “coverage” ?<br />W1.5: For approximately 10% of europeans, the painkiller codeine is ineffective because the patients lack the enzyme that converts codeine into the active molecule, morphine. What is the most common mutation that causes this condition ?<br />
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