VL Algorithmische BioInformatik (19710) WS2013/2014 Woche 16 - Mittwoch
VL Algorithmische BioInformatik (19710)
Transcript of VL Algorithmische BioInformatik (19710)
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VL Algorithmische BioInformatik (19710)
WS2013/2014
Woche 16 - Mittwoch
Annkatrin Bressin
Freie Universität Berlin
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Vorlesungsthemen
Part 1: Background Basics (4)
1. The Nucleic Acid World
2. Protein Structure
3. Dealing with Databases
Part 2: Sequence Alignments (3)
4. Producing and Analyzing Sequence Alignments
5. Pairwise Sequence Alignment and Database Searching
6. Patterns, Profiles, and Multiple Alignments
Part 3: Evolutionary Processes (3)
7. Recovering Evolutionary History
8. Building Phylogenetic Trees
Part 4: Genome Characteristics (4)
9. Revealing Genome Features
10. Gene Detection and Genome Annotation
Part 5: Secondary Structures (4) 11. Obtaining Secondary Structure from Sequence 12. Predicting Secondary Structures Part 6: Tertiary Structures (4) 13. Modeling Protein Structure 14. Analyzing Structure-Function Relationships Part 7: Cells and Organisms (6) 15. Proteome and Gene Expression Analysis 17. Systems Biology
Tim Conrad, VL Algorithmische Bioinformatik, WS2013/2014 2
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Tim Conrad, VL Algorithmische Bioinformatik, WS2013/2014
• Wiederholung der Vorlesungsthemen
• Gliederung
• Blöcke: • Part 1: Background Basics
• Part 2: Sequence Alignments
• Part 3: Evolutionary Processes
• Part 4: Genome Characteristics
• Part 5: Secondary Structures
• Part 6: Tertiary Structures
• Part 7: Cells and Organisms
• Pro Block: • Themen / Mind-Maps der zugrundeliegenden Buchkapitel
• Wichtigste Stichwörter der jeweiligen Vorlesungen als Word-Cloud
• Beispiel-Fragen der Probeklausur
Heute
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Block 1
Background Basics
Topics: 1. The Nucleic Acid World 2. Protein Structure 3. Dealing with Databases
Kapitel 1,2,3
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Tim Conrad, VL Algorithmische Bioinformatik, WS2013/2014
Kapitel 1 - Themen
Nicht alle Themen kamen in der VL dran!
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Tim Conrad, VL Algorithmische Bioinformatik, WS2013/2014
Kapitel 2 - Themen
Nicht alle Themen kamen in der VL dran!
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Tim Conrad, VL Algorithmische Bioinformatik, WS2013/2014
Kapitel 3 - Themen
Nicht alle Themen kamen in der VL dran!
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Woche 1 - Montag
Tim Conrad, VL Algorithmische Bioinformatik, WS2013/2014 8
Einführung
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Woche 1 - Mittwoch
Tim Conrad, VL Algorithmische Bioinformatik, WS2013/2014 9
Wiederholung: Molekular-Biologische Grundlagen
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Woche 2 - Montag
Tim Conrad, VL Algorithmische Bioinformatik, WS2013/2014 10
Wiederholung: Proteinstrukturen, Einführung (biologische) Datenbanken
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Woche 2 - Mittwoch
Tim Conrad, VL Algorithmische Bioinformatik, WS2013/2014 11
Vertiefung: (Biologische) Datenbanken, Webservices, BioJava
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Block 2
Sequence Alignments
Topics: 4. Producing and Analyzing Sequence Alignments 5. Pairwise Sequence Alignment and Database Searching 6. Patterns, Profiles, and Multiple Alignments
Kapitel 4,6
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Tim Conrad, VL Algorithmische Bioinformatik, WS2013/2014
Kapitel 4 - Themen
Nicht alle Themen kamen in der VL dran!
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Tim Conrad, VL Algorithmische Bioinformatik, WS2013/2014
Kapitel 6 - Themen
Nicht alle Themen kamen in der VL dran!
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Woche 3 - Montag
Tim Conrad, VL Algorithmische Bioinformatik, WS2013/2014 16
Wiederholung: Sequence Alignment
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Woche 3 - Mittwoch
Tim Conrad, VL Algorithmische Bioinformatik, WS2013/2014 17
Einführung: Patterns & Profiles
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Block 3
Evolutionary Processes
Topics: 7. Recovering Evolutionary History 8. Building Phylogenetic Trees
Kapitel 7,8
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Tim Conrad, VL Algorithmische Bioinformatik, WS2013/2014
Kapitel 7 - Themen
Nicht alle Themen kamen in der VL dran!
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Tim Conrad, VL Algorithmische Bioinformatik, WS2013/2014
Kapitel 8 - Themen
Nicht alle Themen kamen in der VL dran!
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Woche 4 - Mittwoch
Tim Conrad, VL Algorithmische Bioinformatik, WS2013/2014 22
Einführung: Phylogenetische Bäume
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Woche 5 - Montag
Tim Conrad, VL Algorithmische Bioinformatik, WS2013/2014 23
Vertiefung: Phylogenetische Bäume Evolutionary Distances, Generating Single Trees
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Woche 5 - Mittwoch
Tim Conrad, VL Algorithmische Bioinformatik, WS2013/2014 24
Vertiefung: Phylogenetische Bäume Generating Multiple Tree Topologies, Tree Evaluation
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Woche 5 - 3
Tim Conrad, VL Algorithmische Bioinformatik, WS2013/2014 25
Vertiefung: Phylogenetische Bäume Statistical Methods for Tree Evaluation
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Block 4
Genome Characteristics
Topics: 9. Revealing Genome Features 10. Gene Detection and Genome Annotation
Kapitel 9,10
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Tim Conrad, VL Algorithmische Bioinformatik, WS2013/2014
Kapitel 9 - Themen
Nicht alle Themen kamen in der VL dran!
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Tim Conrad, VL Algorithmische Bioinformatik, WS2013/2014
Kapitel 10 - Themen
Nicht alle Themen kamen in der VL dran!
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Woche 6 - Montag
Tim Conrad, VL Algorithmische Bioinformatik, WS2013/2014 30
Einführung: Gene Finding
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Woche 6 - Mittwoch
Tim Conrad, VL Algorithmische Bioinformatik, WS2013/2014 31
Vertiefung: Gene Detection in Prokaryotes
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Woche 7 - Montag
Tim Conrad, VL Algorithmische Bioinformatik, WS2013/2014 32
Vertiefung: Gene Detection in Eukaryotes
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Woche 7 - Donnerstag
Tim Conrad, VL Algorithmische Bioinformatik, WS2013/2014 33
Einführung: Genome Sequencing, Assembly and Comparison
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Block 5
Secondary Structures
Topics: 11. Obtaining Secondary Structure from Sequence 12. Predicting Secondary Structures
Kapitel 11,12
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Tim Conrad, VL Algorithmische Bioinformatik, WS2013/2014
Kapitel 11 - Themen
Nicht alle Themen kamen in der VL dran!
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Tim Conrad, VL Algorithmische Bioinformatik, WS2013/2014
Kapitel 12 - Themen
Nicht alle Themen kamen in der VL dran!
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Woche 8 - Montag
Tim Conrad, VL Algorithmische Bioinformatik, WS2013/2014 38
Einführung: Secondary Structure from Sequence
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Woche 8 - Mittwoch
Tim Conrad, VL Algorithmische Bioinformatik, WS2013/2014 39
Vertiefung: Statistical Methods for Secondary Structure Prediction
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Woche 9 - Montag
Tim Conrad, VL Algorithmische Bioinformatik, WS2013/2014 40
Guest Lecture: Repeat Resolution for Genome Assembly (Prof. Reinert)
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Woche 9 - Mittwoch
Tim Conrad, VL Algorithmische Bioinformatik, WS2013/2014 41
Vertiefung: Neural Networks for Secondary Structure Prediction
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Woche 10 - Montag
Tim Conrad, VL Algorithmische Bioinformatik, WS2013/2014 42
Vertiefung: Neural Networks for Secondary Structure Prediction, Prediction Methods for Special Secondary Structures
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Woche 10 - Mittwoch
Tim Conrad, VL Algorithmische Bioinformatik, WS2013/2014 43
Vertiefung: RNA Secondary Structure Prediction
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Block 6
Tertiary Structures
Topics: 13. Modeling Protein Structure 14. Analyzing Structure-Function Relationships
Kapitel 13,14
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Tim Conrad, VL Algorithmische Bioinformatik, WS2013/2014
Kapitel 13 - Themen
Nicht alle Themen kamen in der VL dran!
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Tim Conrad, VL Algorithmische Bioinformatik, WS2013/2014
Kapitel 14 - Themen
Nicht alle Themen kamen in der VL dran!
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Woche 11 - Montag
Tim Conrad, VL Algorithmische Bioinformatik, WS2013/2014 48
Einführung: Modeling Protein Structures, Potential Energy, Force Fields, Threading Homology Modeling
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Woche 11 - Mittwoch
Tim Conrad, VL Algorithmische Bioinformatik, WS2013/2014 49
Vertiefung: Homology Modeling
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Woche 12 - Montag
Tim Conrad, VL Algorithmische Bioinformatik, WS2013/2014 50
Vertiefung: Threading
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Woche 12 - Mittwoch
Tim Conrad, VL Algorithmische Bioinformatik, WS2013/2014 51
Vertiefung: Structure Comparison
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Woche 13 - Montag
Tim Conrad, VL Algorithmische Bioinformatik, WS2013/2014 52
Vertiefung: Binding Site Detection, Docking
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Block 7
Cells and Organisms
Topics: 15. Proteome and Gene Expression Analysis 17. Systems Biology
Kapitel 15,17
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Tim Conrad, VL Algorithmische Bioinformatik, WS2013/2014
Kapitel 15 - Themen
Nicht alle Themen kamen in der VL dran!
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Tim Conrad, VL Algorithmische Bioinformatik, WS2013/2014
Kapitel 17 - Themen
Nicht alle Themen kamen in der VL dran!
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Woche 13 - Mittwoch
Tim Conrad, VL Algorithmische Bioinformatik, WS2013/2014 57
Einführung: Gene / Microarray Expression Analysis
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Woche 14 - Montag
Tim Conrad, VL Algorithmische Bioinformatik, WS2013/2014 58
Vertiefung: Gene / Microarray Expression Analysis; Quality Control, Preprocessing, Normalization, Self-organizing Maps for clustering and classification
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Woche 14 - Mittwoch
Tim Conrad, VL Algorithmische Bioinformatik, WS2013/2014 59
Einführung: Protein Expression Analysis, 2D GE, Mass Spectrometry
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Woche 15 - Montag
Tim Conrad, VL Algorithmische Bioinformatik, WS2013/2014 60
Vertiefung: Protein Expression Analysis; Mass Spectrometry, Algorithms for analysing MS data
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Woche 15 - Mittwoch
Tim Conrad, VL Algorithmische Bioinformatik, WS2013/2014 61
Vertiefung: Protein Expression Analysis, Peptide Mass Fingerprinting; Einführung: Systems Biology
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Woche 16 - Montag
Tim Conrad, VL Algorithmische Bioinformatik, WS2013/2014 62
Vertiefung: Systems Biology
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