Renato Paro: Katalogdaten im Herbstsemester 2016

NameHerr Prof. em. Dr. Renato Paro
Professur für Biophysik
ETH Zürich, BSS H 41
Klingelbergstrasse 48
4056 Basel
BeziehungProfessor emeritus

626-0003-AALMolecular Biology
Belegung ist NUR erlaubt für MSc Studierende, die diese Lerneinheit als Auflagenfach verfügt haben.

Alle anderen Studierenden (u.a. auch Mobilitätsstudierende, Doktorierende) können diese Lerneinheit NICHT belegen.
4 KP9RR. Paro
KurzbeschreibungThis lecture course gives an in-depth view into molecular mechanisms controlling basic biological processes, ranging from genetic regulatory networks, the internal functional organization of a cell to the signaling events controlling cells in their social context. An additional focus is on methods and techniques used in molecular biology to solve problems in biotechnology and medicine.
LernzielThe goal is to achieve a high level knowledge of basic biological processes, to learn the methodology to tackle questions in molecular biology and to interpret experimental molecular data. Emphasis is given to cellular processes amenable to studies in systems and synthetic biology.
InhaltMolecular Biology of the Cell (Alberts et al.) Sixth Edition (ISBN 978-0-8153-4464-3)

Chapter 4 DNA, Chromosomes, and Genomes
p. 173-216

Chapter 5 DNA Replication, Repair, and Recombination
p. 237-286

Chapter 6 How Cells Read the Genome: From DNA to Protein
p. 299-362

Chapter 7 Control of Gene Expression
p. 369-436

Chapter 8 Analyzing Cells, Molecules, and Systems
p. 439-508

Chapter 9 Visualizing Cells
p. 529-562

Chapter 10 Membrane Structure
p. 565-594

Chapter 11 Membrane Transport of Small Molecules and the Electrical Properties of Membranes
p. 597-638

Chapter 12 Intracellular Compartments and Protein Sorting
p. 641-691

Chapter 13 Intracellular Membrane Traffic
p. 695-750

Chapter 15 Cell Signaling
p. 813-880

Chapter 17 The Cell Cycle
p. 963-1018

Chapter 18 Cell Death
p. 1021-1034

Chapter 20 Cancer
p. 1091-1141

Chapter 22 Stem Cells and Tissue Renewal
p. 1217-1260
SkriptUse the respective end-of-chapter problems section ("Which statements are true?") to test your knowledge and prepare for exam.
LiteraturMolecular Biology of the Cell (Alberts et al.) Sixth Edition (ISBN 978-0-8153-4464-3)
Book Summary
As the amount of information in biology expands dramatically, it becomes increasingly important for textbooks to distill the vast amount of scientific knowledge into concise principles and enduring concepts. As with previous editions, Molecular Biology of the Cell, Sixth Edition accomplishes this goal with clear writing and beautiful illustrations. The Sixth Edition has been extensively revised and updated with the latest research in the field of cell biology, and it provides an exceptional framework for teaching and learning.
The entire illustration program has been greatly enhanced. Protein structures better illustrate structure-function relationships, icons are simpler and more consistent within and between chapters, and micrographs have been refreshed and updated with newer, clearer, or better images. As a new feature, each chapter now contains intriguing open-ended questions highlighting "What We Don´t Know" introducing students to challenging areas of future research. Updated end-of-chapter problems reflect new research discussed in the text, and these problems have been expanded to all chapters by adding questions on developmental biology, tissues and stem cells, pathogens, and the immune system.
Voraussetzungen / BesonderesDuring the semester two half days will be offered to discuss the content and allow questions to the lecturer.
636-0005-00LSystems Biology Information 6 KP3GR. Paro, N. Beerenwinkel
KurzbeschreibungThis lecture course is an introduction to systems biology. It explores how complex biological networks are experimentally studied and how the resulting data is mathematically evaluated in order to derive predictive models. The biology of selected cellular processes, ranging from protein interaction networks to gene controlling systems and signaling cascades will be discussed in detail.
LernzielThe goal of this course is to learn how a detailed quantitative description of complex biological processes can be employed for a better understanding of molecular interactions, the power and efficiency of regulatory networks, and the evolution of biological complexity. Students will learn how to identify techniques producing quantitative data and how to develop mathematical models and efficient statistical inference algorithms to recognize patterns, molecular interrelationships and systems behavior.
InhaltSessions will alternate between a thorough introduction into the basic biology of defined cellular processes and a corresponding mathematical and statistical analysis of the experimental data. Selected complex biological systems and the respective experimental tools for a quantitative analysis will be presented. Examples include the identification of protein interaction networks required for specific physiological processes in yeast based on graph theoretic methods, including the identification of network motifs and the global statistical analysis of graph properties (power laws); the comparative analysis of gene expressions data from cancer and normal cells involving data normalization techniques, multiple testing procedures, clustering algorithms, Bayesian networks, and linear dynamical systems; the definition of hierarchies of kinase signaling cascades employing Bayesian networks and their causal interpretation and nested effects models for the analysis of perturbed systems; analysis of deep sequencing data derived from studies of chromatin control and gene expression.

- Control of Gene Expression: DNA binding proteins, gene activation in chromatin, posttranscriptional control
- Genetic Switches: combinatorial gene control, transcriptional circuits, transcriptional noise/robustness
- Analysis of Gene Expression Data: normalization, differential gene expression, multiple testing, PCA, clustering
- Large-scale Genomic Profiling: mapping genomes/epigenomes, high throughput sequencing technologies
- Analysis of Deep Sequencing Data: quality control, genome assembly, read mapping, RNA-seq, ChIP-seq
- Biological Networks: signaling networks and protein-protein interaction networks
- Network Biology: basic graph theory, motifs, dense subgraphs, power laws
- Boolean Network Dynamics: Boolean algebra, Boolean networks, random Boolean networks, yeast cell cycle
- Cellular Communication: signal transduction cascades, regulatory mechanisms
- Probabilistic Graphical Models: probabilities, statistical inference, Bayesian networks, nested effects models
- Evolutionary Mechanisms: RNA world, origin of life, ribozyme selection, genome evolution, SNP mapping, evolution & development
- Genome-wide association studies

As part of the tutorial you will work on a real set of data, elaborate the experimental strategy to produce the data and use bioinformatics tools to analyze the data.
SkriptThe Powerpoint presentations of the lectures as well as other course material relevant for an active participation will be made available online.
Literatur- Alberts B et al. (2008) Molecular Biology of the Cell, Fifth Edition, Garland Science

- Klipp E. et al (2009) Systems Biology, Wiley-Blackwell

- Alon U (2007) An Introduction to Systems Biology, Chapman & Hall

- Wolkenhauer O (2008) Systems Biology: Dynamic Pathway Modeling

- Zvelebil M & Baum JO (2008) Understanding Bioinformatics, Garland Science
636-0301-00LCurrent Topics in Biosystems Science and Engineering2 KP1ST. Stadler, N. Beerenwinkel, Y. Benenson, K. M. Borgwardt, P. S. Dittrich, M. Fussenegger, A. Hierlemann, D. Iber, M. H. Khammash, D. J. Müller, S. Panke, P. Pantazis, R. Paro, R. Platt, S. Reddy, T. Schroeder, J. Stelling
KurzbeschreibungThis seminar will feature invited lectures about recent advances and developments in systems biology, including topics from biology, bioengineering, and computational biology.
LernzielTo provide an overview of current systems biology research.
InhaltThe final list of topics will be available at