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Bioinformatica 29-09-2011-t1-bioinformatics
 

Bioinformatica 29-09-2011-t1-bioinformatics

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    Bioinformatica 29-09-2011-t1-bioinformatics Bioinformatica 29-09-2011-t1-bioinformatics Presentation Transcript

    • FBW
      29-09-2011
      Wim Van Criekinge
    • 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 ?
    • Promises of genomics and bioinformatics
      Medicine (Pharma)
      Genome analysis allows the targeting of genetic diseases
      The effect of a disease or of a therapeutic on RNA and protein levels can be elucidated
      Knowledge of protein structure facilitates drug design
      Understanding of genomic variation allows the tailoring of medical treatment to the individual’s genetic make-up
      The same techniques can be applied to crop (Agro) and livestock improvement (Animal Health)
    • Bioinformatics: What’s in a name ?
      Begin 1990’s
      “Bio-informatics”:
      Computing Power
      Genbank
      (Log)
      Time (years)
    • Bioinformatics: What’s in a name ?
      Begin 1990’s
      “Bio-informatics”:
      convergence of explosive growth in biotechnology, paralled by the explosive growth in information technology
      Not new: > 30 years that people use “computers” in biology
      In silico biology, database biology, ...
    • Time (years)
    • Happy Birthday …
    • PCR + dye termination
      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)
    • Math
      Theoretical Biology
      Computer Science
      (Molecular)
      Biology
      Informatics
      Computational Biology
      Bioinformatics, a scientific discipline …
      Bioinformatics
    • Math
      Algorithm Development
      Theoretical Biology
      Computer Science
      AI, Image Analysis
      structure prediction (HTX)
      NP
      Datamining
      Interface Design
      Expert Annotation
      Sequence Analysis
      (Molecular)
      Biology
      Informatics
      Computational Biology
      Bioinformatics, a scientific discipline …
      Bioinformatics
    • Math
      Algorithm Development
      Theoretical Biology
      Computer Science
      AI, Image Analysis
      structure prediction (HTX)
      NP
      Datamining
      Interface Design
      Expert Annotation
      Sequence Analysis
      (Molecular)
      Biology
      Informatics
      Computational Biology
      Bioinformatics, a scientific discipline …
      Bioinformatics
      Discovery Informatics – Computational Genomics
    • Doel van de cursus
      Meer 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.
    • Inhoud Lessen: Bioinformatica
      don 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 Alignments
      don 10-11-2011: 5 Database Searching Fasta/Blast
      don 17-11-2011: 6 Phylogenetics
      don 24-11-2011: 7 Protein Structure
      don 01-12-2011: 8 Gene Prediction, Gene Ontologies & HMM
      don 08-12-2011: 9 ncRNA, Chip Data Analysis, AI
      don 15-12-2011: 10 Bio- & Cheminformatics in Drug Discovery (inhaalweek)
      Opgelet: Geen les op don 13-10-2010 en don 3-11-2010
    • Examen
      Theorie
      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 veronderstellen
      Puntenverdeling 50/50
    • Timelin: Magaret Dayhoff …
    • Nexus > FAQ > Bioinformatics Milestones
    • http://www.sciencemag.org/cgi/content/full/291/5507/1195
      Printed version in cursus
    • nature
      the
      Human
      genome
      Setting the stage …
    • Genome Meters
      Genomes Online Database (GOLD 1.0)
      http://geta.life.uiuc.edu/~nikos/genomes.html
      http://www.ebi.ac.uk/research/cgg/genomes.html
      NCBI
      http://www.ncbi.nlm.nih.gov/PMGifs/Genomes/bact.html
      INFOBIOGEN
      http://www.infobiogen.fr/doc/data/complete_genome.html
    • Genome Size
      E. coli = 4.2 x 106
      Yeast = 18 x 106
      Arabidopsis = 80 x 106
      C.elegans = 100 x 106
      Drosophila = 180 x 106
      Human/Rat/Mouse = 3000 x 106
      Lily = 300 000 x 106
      With ... : 99.9 %
      To primates: 99%
      DOGS: Database Of Genome Sizes
    • Biological Research
      Adapted from John McPherson, OICR
    • And this is just the beginning ….
      Next Generation Sequencing is here
    • Basics of the “old” technology
      Clone 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 long
      1 machine generates 57,000 nucleotides/run
      Assemble all strings into a genome.
    • Basics of the “new” technology
      Get 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 long
      Multiple 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.
    • Next Generation Technologies
      454
      Emulsion PCR
      Polymerase
      Natural Nucleotides
      20-100Mb for 5-15k
      1% error rate
      Homopolymers
    • One additional insight ...
    • Read Length is Not As Important For Resequencing
      Jay Shendure
    • Two Short Read Techologies
      Illumina GA
      ABI SOLID
    • Technology Overview: Solexa/Illumina Sequencing
    • ABI Solid
      Dressman 2003
    • ABI SOLID
    • ABI SOLID
    • Paired End Reads are Important!
      Known Distance
      Read 1
      Read 2
      Repetitive DNA
      Unique DNA
      Paired read maps uniquely
      Single read maps to
      multiple positions
    • Single Molecule Sequencing
      Adapted from: Barak Cohen, Washington University, Bio5488 http://tinyurl.com/6zttuq http://tinyurl.com/6k26nh
      Microscope slide
      *
      *
      *
      Single DNA
      molecule
      Super-cooled
      TIRF microscope
      primer
      dNTP-Cy3
      *
      Helicos Biosciences Corp.
    • IntroducingNXT GNT DXSNextGenerationDiagnostics
      18th september 2009
      Wim Van Criekinge
    • develop in shortest time frame best assay for most relevant clinical application
    • NXT GNT DXS
      • GNT
      • Dedicated Team & Network
      • Operational: Location
      • Professionalized
      • DXS
      • Content engine
      • Product 1 established
      • Pipeline for n+1
      • NXT
      • Workflow management
      • Bioinformatics
      • Epigenetics
    • Next next generation sequencing
      Third generation sequencing
      Now sequencing
    • Complete genomics
    • Complete genomics
    • Pacific Biosciences: A Third Generation Sequencing Technology
      Eid et al 2008
    • Pacific Biosciences: A Third Generation Sequencing Technology
    • Nanopore Sequencing
    • NCBI (educational resources)
    • Weblems
      What ?
      Web-based problemes (over de huidige les en/of voorbereiding op volgende les)
      When ?
      Einde van elke les
      How ?
      Oplossingen online via screencasts
      Practicum
      Voorbedereiding op het practicum examen ... Niet alle problemen vereisen noodzakelijk programmacode ...
    • Weblems
      W1.1: To which phyla do the following species belong (a) starfish (b) ginko tree (c) scorpion
      W1.2: What are the common names for the following species (a) Orycterophus afer (b) Beta vulagaris (c) macrocystis pyrifera
      W1.3: What species has the smallest known genome ? And is genome size related to number of genes ?
      W1.4: What are the 5 latest genomes published ? How complete is “coverage” ?
      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 ?