Suchergebnis: Katalogdaten im Frühjahrssemester 2020

Rechnergestützte Wissenschaften Master Information
Vertiefungsgebiete
Biologie
NummerTitelTypECTSUmfangDozierende
636-0702-00LStatistical Models in Computational BiologyW6 KP2V + 1U + 2AN. Beerenwinkel
KurzbeschreibungThe course offers an introduction to graphical models and their application to complex biological systems. Graphical models combine a statistical methodology with efficient algorithms for inference in settings of high dimension and uncertainty. The unifying graphical model framework is developed and used to examine several classical and topical computational biology methods.
LernzielThe goal of this course is to establish the common language of graphical models for applications in computational biology and to see this methodology at work for several real-world data sets.
InhaltGraphical models are a marriage between probability theory and graph theory. They combine the notion of probabilities with efficient algorithms for inference among many random variables. Graphical models play an important role in computational biology, because they explicitly address two features that are inherent to biological systems: complexity and uncertainty. We will develop the basic theory and the common underlying formalism of graphical models and discuss several computational biology applications. Topics covered include conditional independence, Bayesian networks, Markov random fields, Gaussian graphical models, EM algorithm, junction tree algorithm, model selection, Dirichlet process mixture, causality, the pair hidden Markov model for sequence alignment, probabilistic phylogenetic models, phylo-HMMs, microarray experiments and gene regulatory networks, protein interaction networks, learning from perturbation experiments, time series data and dynamic Bayesian networks. Some of the biological applications will be explored in small data analysis problems as part of the exercises.
Skriptno
Literatur- Airoldi EM (2007) Getting started in probabilistic graphical models. PLoS Comput Biol 3(12): e252. doi:10.1371/journal.pcbi.0030252
- Bishop CM. Pattern Recognition and Machine Learning. Springer, 2007.
- Durbin R, Eddy S, Krogh A, Mitchinson G. Biological Sequence Analysis. Cambridge university Press, 2004
701-1708-00LInfectious Disease DynamicsW4 KP2VS. Bonhoeffer, R. D. Kouyos, R. R. Regös, T. Stadler
KurzbeschreibungThis course introduces into current research on the population biology of infectious diseases. The course discusses the most important mathematical tools and their application to relevant diseases of human, natural or managed populations.
LernzielAttendees will learn about:
* the impact of important infectious pathogens and their evolution on human, natural and managed populations
* the population biological impact of interventions such as treatment or vaccination
* the impact of population structure on disease transmission

Attendees will learn how:
* the emergence spread of infectious diseases is described mathematically
* the impact of interventions can be predicted and optimized with mathematical models
* population biological models are parameterized from empirical data
* genetic information can be used to infer the population biology of the infectious disease

The course will focus on how the formal methods ("how") can be used to derive biological insights about the host-pathogen system ("about").
InhaltAfter an introduction into the history of infectious diseases and epidemiology the course will discuss basic epidemiological models and the mathematical methods of their analysis. We will then discuss the population dynamical effects of intervention strategies such as vaccination and treatment. In the second part of the course we will introduce into more advanced topics such as the effect of spatial population structure, explicit contact structure, host heterogeneity, and stochasticity. In the final part of the course we will introduce basic concepts of phylogenetic analysis in the context of infectious diseases.
SkriptSlides and script of the lecture will be available online.
LiteraturThe course is not based on any of the textbooks below, but they are excellent choices as accompanying material:
* Keeling & Rohani, Modeling Infectious Diseases in Humans and Animals, Princeton Univ Press 2008
* Anderson & May, Infectious Diseases in Humans, Oxford Univ Press 1990
* Murray, Mathematical Biology, Springer 2002/3
* Nowak & May, Virus Dynamics, Oxford Univ Press 2000
* Holmes, The Evolution and Emergence of RNA Viruses, Oxford Univ Press 2009
Voraussetzungen / BesonderesBasic knowledge of population dynamics and population genetics as well as linear algebra and analysis will be an advantage.
262-0200-00LBayesian PhylodynamicsW4 KP2G + 2AT. Stadler, T. Vaughan
KurzbeschreibungHow fast was Ebola spreading in West Africa? Where and when did the epidemic outbreak start? How can we construct the phylogenetic tree of great apes, and did gene flow occur between different apes? At the end of the course, students will have designed, performed, presented, and discussed their own phylodynamic data analysis to answer such questions.
LernzielAttendees will extend their knowledge of Bayesian phylodynamics obtained in the “Computational Biology” class (636-0017-00L) and will learn how to apply this theory to real world data. The main theoretical concepts introduced are:
* Bayesian statistics
* Phylogenetic and phylodynamic models
* Markov Chain Monte Carlo methods
Attendees will apply these concepts to a number of applications yielding biological insight into:
* Epidemiology
* Pathogen evolution
* Macroevolution of species
InhaltIn the first part of the semester, in each week, we will first present the theoretical concepts of Bayesian phylodynamics. The presentation will be followed by attendees using the software package BEAST v2 to apply these theoretical concepts to empirical data. We use previously published datasets on e.g. Ebola, Zika, Yellow Fever, Apes, and Penguins for analysis. Examples of these practical tutorials are available on Link.
In the second part of the semester, the students choose an empirical dataset of genetic sequencing data and possibly some non-genetic metadata. They then design and conduct a research project in which they perform Bayesian phylogenetic analyses of their dataset. The weekly class is intended to discuss and monitor progress and to address students’ questions very interactively. At the end of the semester, the students present their research project in an oral presentation. The content of the presentation, the style of the presentation, and the performance in answering the questions after the presentation will be marked.
SkriptLecture slides will be available on moodle.
LiteraturThe following books provide excellent background material:
• Drummond, A. & Bouckaert, R. 2015. Bayesian evolutionary analysis with BEAST.
• Yang, Z. 2014. Molecular Evolution: A Statistical Approach.
• Felsenstein, J. 2003. Inferring Phylogenies.
The tutorials in this course are based on our Summer School “Taming the BEAST”: Link
Voraussetzungen / BesonderesThis class builds upon the content which we teach in the Computational Biology class (636-0017-00L). Attendees must have either taken the Computational Biology class or acquired the content elsewhere.
227-0973-00LTranslational Neuromodeling Information W8 KP3V + 2U + 1AK. Stephan
KurzbeschreibungThis course provides a systematic introduction to Translational Neuromodeling (the development of mathematical models for diagnostics of brain diseases) and their application to concrete clinical questions (Computational Psychiatry/Psychosomatics). It focuses on a generative modeling strategy and teaches (hierarchical) Bayesian models of neuroimaging data and behaviour, incl. exercises.
LernzielTo obtain an understanding of the goals, concepts and methods of Translational Neuromodeling and Computational Psychiatry/Psychosomatics, particularly with regard to Bayesian models of neuroimaging (fMRI, EEG) and behavioural data.
InhaltThis course provides a systematic introduction to Translational Neuromodeling (the development of mathematical models for diagnostics of brain diseases) and their application to concrete clinical questions (Computational Psychiatry/Psychosomatics). The first part of the course will introduce disease concepts from psychiatry and psychosomatics, their history, and clinical priority problems. The second part of the course concerns computational modeling of neuronal and cognitive processes for clinical applications. A particular focus is on Bayesian methods and generative models, for example, dynamic causal models for inferring neuronal processes from neuroimaging data, and hierarchical Bayesian models for inference on cognitive processes from behavioural data. The course discusses the mathematical and statistical principles behind these models, illustrates their application to various psychiatric diseases, and outlines a general research strategy based on generative models.

Lecture topics include:
1. Introduction to Translational Neuromodeling and Computational Psychiatry/Psychosomatics
2. Psychiatric nosology
3. Pathophysiology of psychiatric disease mechanisms
4. Principles of Bayesian inference and generative modeling
5. Variational Bayes (VB)
6. Bayesian model selection
7. Markov Chain Monte Carlo techniques (MCMC)
8. Bayesian frameworks for understanding psychiatric and psychosomatic diseases
9. Generative models of fMRI data
10. Generative models of electrophysiological data
11. Generative models of behavioural data
12. Computational concepts of schizophrenia, depression and autism
13. Model-based predictions about individual patients

Practical exercises include mathematical derivations and the implementation of specific models and inference methods. In additional project work, students are required to use one of the examples discussed in the course as a basis for developing their own generative model and use it for simulations and/or inference in application to a clinical question. Group work (up to 3 students) is permitted.
LiteraturSee TNU website:
Link
Voraussetzungen / BesonderesGood knowledge of principles of statistics, good programming skills (MATLAB or Python)
701-1418-00LModelling Course in Population and Evolutionary Biology Information Belegung eingeschränkt - Details anzeigen
Number of participants limited to 20.

Priority is given to MSc Biology and Environmental Sciences students.
W4 KP6PS. Bonhoeffer, V. Müller
KurzbeschreibungDieser Kurs ist eine praktische Einfuehrung in die mathematische/computerorientierte Modellierung biologischer Prozesse mit Schwerpunkt auf evolutionsbiologischen und populationsbiologischen Fragestellungen. Die Modelle werden in der Open Source software R entwickelt.
LernzielDen Teilnehmern soll der Nutzen der Modellierung als ein Hilfsmittel zur Untersuchung biologischer Fragestellungen vermittelt werden. Die einfacheren Module orientieren sich mehrheitlich an Beispielen aus der ehemaligen Vorlesung "Oekologie und Evolution: Populationen" (Skript von der Kurswebseite zugaenglich). Die fortgeschrittenen Module orientieren sich an aktuellen Forschungsthemen. Hierbei werden auch Fragestellungen untersucht, die zwar konzeptionell und methodisch auf Evolutions- und Populations-biologischen Ansaetzen beruhen, aber sich mit anderen Bereichen der Biologie befassen.
Inhaltsiehe Link
SkriptDetaillierte Handouts für alle Module sind an der Webseite des Kurses zu finden. Zusaetzlich ist das Skript für die frühere Vorlesung "Oekologie und Evolution: Populationen" auch zugaenglich, und enthaelt weitere relevante Informationen.
Voraussetzungen / BesonderesDer Kurs basiert auf der Open Source Software R. Programmiererfahrung in R ist nuetzlich, aber keine Voraussetzung. Ebenso ist der Kurs 701-1708-00L Infectious Disease Dynamics nützlich, aber keine Voraussetzung.
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