Advanced Phylogenetics

1. Phylogeny Enumeration (Tue 16.01.2018 11am) – Preparatory material / Lecture
2. Tree Generating Process (Wed 17.01.2018 10am) – Preparatory material / Lecture
3. Compatibility (Tue 23.01.2018 11am) –  Preparatory material / Lecture
4. Statistical Alignment (Wed 24.01.2018 10am) – Preparatory material / Lecture

Problem Sheet (Statistical Alignment. Hand-in: Tue 23.01.2018 by 2pm. Session:  Thur 25.01.2018 10am – 11.30am)

Comparative Biology

1. Complex Evolutionary Objects (Tue 30.01.2018 11am) – Preparatory material / Lecture
2. Comparative Method (Wed 31.01.2018 10am) –  Preparatory material / Lecture
3. Networks (Tue 06.02.2018 11am) –  Preparatory material / Lecture
4. Proteins (Wed 07.02.2018 10am) – Preparatory material / Lecture

Problem Sheet (The Comparative Method. Hand-in: Tue 06.02.2018 by 2pm. Session:  Thur 08.02.2018 10am – 11.30am)

Molecular Dynamics

1. Physics of Molecules (Tue 13.02.2018 11am) –  Preparatory material / Lecture
2. Integrators (Wed 14.02.2018 10am)  Lecture
3. History and Applications of MD (Tue 20.02.2018 11am) Preparatory material / Lecture
4. Protein Folding (Wed 21.02.2018 10am) Preparatory material / Lecture

Problem Sheet (Molecular Dynamics. Hand-in: Tue 20.02.2018 by 2pm. Session:  Thur 22.02.2018 10am – 11.30am)
Solutions (code: ipython/jupyter notebook, or pure python)

Chemoinformatics

1. Mathematical Models of Origins of Life   (Tue 27.02.2018 11am) Lecture
2. Polya Enumeration  (Wed 28.02.2018 10am)  Lecture Preparatory material
3. Chemical Space  (Tue 06.03.2018 11am) Lecture Preparatory material
4. Chemical Reactions (Wed 07.06.2018 10am) Lecture

Problem Sheet (Molecular Combinatorics. Hand-in: Tue 6.03.2018 by 2pm. Session:  Thur 8.03.2018 10am – 11.30am)
Solutions (Python code for Pólya counting: polya_python.py)

This course is examined by mini-projects. Anything that legitimately could be called COMPUTATIONAL BIOLOGY is acceptable as a topic.  Mini-projects will be released to student March 9th 2018.  They will include examples of what could be a topic, but also the possibility of chosing your own topic. Reports should be handed in April 30th at noon 2018

Examples of reports from an earlier similar course can be found here:

• Stochastic Context Free Grammars in RNA Secondary Structure Prediction                                        
• Substitution Models with Rate Heterogeneity       
• Clustering Biological Networks
• Quantum algorithms for Protein folding    
• Probability Theory of Networks                                          
• Inference of Gene Regulatory Networks using Differential Equations                                                    
• Hidden Markov Models and their Applications to Bioinformatics
• Computational Models for Gene prediction
• Alignment-based De Novo Prediction of Non-coding RNA
• Automated Annotation of Genes                                           
• Network flow and its applications to the analysis  
• Identification of Regulatory Elements – Phylogenetic Footprinting
• Probable and Improbable Paths in Sequence Evolution            
• Simulative Approach to Alignment    
• Sequence RAFs                   
• Birth and Death Processes
• Haplotype Imputation