Search result: Catalogue data in Autumn Semester 2022

Biotechnology Master Information
Master Studies (Programme Regulations 2021)
Core Courses
Courses
Students need to acquire a total of 6 ECTS in lectures in this category.
The list of core courses is a closed list, no other course can be added to this category.
Students need to pass both lectures offered in this category.
NumberTitleTypeECTSHoursLecturers
636-0101-00LSystems GenomicsO4 credits3GB. Treutlein, C. Beisel, Z. He
AbstractThis course is an introduction to the wide field of Genomics. It addresses how fundamental questions in biological systems are studied using methods in genomics and how the resulting data is analysed to make quantitative interpretations of biological phenomena.
ObjectiveThe goal of this course is to get detailed insights in how state-of-the-art DNA sequencing technologies can be applied for a qualitative and quantitative description of molecular and cellular processes and function. Students will learn how to analyse RNA-seq / transcriptomics data and make biological interpretations in a quantitative manner.
ContentThis course will be a mix of lecture sessions, hands-on computational data analysis using public datasets and seminars discussing own results in the context of the published studies. In the lectures we will introduce current Next-Generation Sequencing technologies and their application to address basically all facets of modern biology and biomedical research. We will cover the major sample processing methods used for investigating functional genomic aspects like transcriptome and chromatin profiling, review recent advances in (cancer) genome sequencing and give an overview of public big data sequencing projects (ENCODE, GTEX, TCGA, ...).
For the computational data analysis we will focus on differential gene expression profiling (RNA-seq) experiments that have been selected from fascinating published biological studies. Data analysis based on R will follow a detailed tutorial describing all required steps of sequence read processing and will be conducted in small groups to enable every student hands-on experience.
Lecture notesThe PowerPoint presentations of the lectures as well as other course material relevant for an active participation will be made available online.
636-0102-10LAdvanced Bioengineering
Only for Biotechnologie Master, Programme Regulations 2021 or doctoral students of D-BSSE
O2 credits3SS. Panke, Y. Benenson, P. S. Dittrich, M. Fussenegger, A. Hierlemann, M. H. Khammash, A. Moor, D. J. Müller, M. Nash, R. Platt, J. Stelling, B. Treutlein
AbstractThis course provides an overview of modern concepts of bioengineering across different levels of complexity, from single molecules to systems, microscaled reactors to production environments, and across different fields of applications
ObjectiveStudents will be able to recognize major developments in bioengineering across different organisms and levels of complexity and be able to relate it to major technological and conceptual advances in the underlying sciences.
ContentMolecular and cellular engineering; Synthetic biology: Engineering strategies in biology; from single molecules to systems; downscaling bioengineering; Bioengineering in chemistry, pharmaceutical sciences, and diagnostics, personalized medicine.
Lecture notesHandouts during class
LiteratureWill be announced during the course
CompetenciesCompetencies
Subject-specific CompetenciesConcepts and Theoriesassessed
Techniques and Technologiesassessed
Personal CompetenciesCritical Thinkingassessed
Research Project and Industry Internship
Students can choose between Research Project OR Industry Internship. Duration: 12 weeks full-time min.
Must be carried out in a different research group/company than the master’s thesis.
NumberTitleTypeECTSHoursLecturers
636-0805-00LResearch Project
Only for Biotechnologie Master, Programme Regulations 2021.
W16 credits34AProfessors
AbstractIn a research project students extend their knowledge in a particular field, get acquainted with the scientific way of working, and learn to work on an actual research topic. Research projects are carried out in a core or optional subject area as chosen by the student.
Research Project duration: 12 weeks, completed with a written report.
ObjectiveStudents get acquainted with scientific working methods and deepen their knowledge in a particular research area
636-0806-00LIndustry Internship
Only for Biotechnologie Master, Programme Regulations 2021.
W16 credits34AProfessors
AbstractIndustry internship of at least 12 weeks, completed with a written report.
ObjectiveStudents gain experience in an industrial environment and an overview of different research areas by applying concepts taught in the courses.
Prerequisites / NoticeThe students look for a placement themselves.
Master's Thesis
NumberTitleTypeECTSHoursLecturers
636-0900-10LMaster's Thesis
Only for Biotechnologie Master, Programme Regulations 2021.

Students can only start with their master’s thesis if
a. The BSc programme has been completed successfully
b. Assigned additional requirements for the admission to the master’s degree programme have been passed
c. At least 64 ECTS have been acquired for the master’s degree programme, including 22 ECTS in the core course category and the 16 ECTS in the research projects and internships category
O44 credits91DSupervisors
AbstractIn the Master thesis students prove their ability to independent, structured and scientific working. The Master thesis is carried out under the supervision of a professor in a research group of the D-BSSE, usually at the D-BSSE. Students are free to choose the area.
ObjectiveIn the Master thesis students prove their ability to independent, structured and scientific working.
Master Studies (Programme Regulations 2017)
Core Courses
Students need to acquire a total of 8 ECTS in lectures in this category.
The list of core courses is a closed list, no other course can be added to this category.
Students need to pass both lectures offered in this category.
NumberTitleTypeECTSHoursLecturers
636-0102-00LAdvanced Bioengineering
Only for Biotechnologie Master, Programme Regulations 2017.
O4 credits3SS. Panke, Y. Benenson, P. S. Dittrich, M. Fussenegger, A. Hierlemann, M. H. Khammash, A. Moor, D. J. Müller, M. Nash, R. Platt, J. Stelling, B. Treutlein
AbstractThis course provides an overview of modern concepts of bioengineering across different levels of complexity, from single molecules to systems, microscaled reactors to production environments, and across different fields of applications
ObjectiveStudents will be able to recognize major developments in bioengineering across different organisms and levels of complexity and be able to relate it to major technological and conceptual advances in the underlying sciences.
ContentMolecular and cellular engineering; Synthetic biology: Engineering strategies in biology; from single molecules to systems; downscaling bioengineering; Bioengineering in chemistry, pharmaceutical sciences, and diagnostics, personalized medicine.
Lecture notesHandouts during class
LiteratureWill be announced during the course
CompetenciesCompetencies
Subject-specific CompetenciesConcepts and Theoriesassessed
Techniques and Technologiesassessed
Personal CompetenciesCritical Thinkingassessed
Research Projects and Internship
Students need to acquire a total of 20 ECTS in this category.
Either choose Research Project I (8 ECTS) and Research Project II (12 ECTS)
Or choose Research Project I (8 ECTS) and Industry Internship (12 ECTS)
Instead of Research Project I (8 ECTS) students may also choose Synthetic Biology II (8 ECTS)
Research Projects
NumberTitleTypeECTSHoursLecturers
636-0802-00LResearch Project I Restricted registration - show details
Only for Biotechnologie Master BSc, Programme Regulations 2017.
O8 credits23AProfessors
AbstractIn a research project students extend their knowledge in a particular field, get acquainted with the scientific way of working, and learn to work on an actual research topic. Research projects are carried out in a core or optional subject area as chosen by the student.
Research Project I duration: 8 weeks
ObjectiveStudents get acquainted with scientific working methods and deepen their knowledge in a particular research area
636-0803-00LResearch Project II Restricted registration - show details
Only for Biotechnologie Master BSc, Programme Regulations 2017.

Enrollment only for students that don`t do an industry internship but two research projects.
W12 credits34AProfessors
AbstractIn a research project students extend their knowledge in a particular field, get acquainted with the scientific way of working, and learn to work on an actual research topic. Research projects are carried out in a core or optional subject area as chosen by the student.
Research Project II duration: 12 weeks
ObjectiveStudents get acquainted with scientific working methods and deepen their knowledge in a particular research area
636-0507-00LSynthetic Biology II Restricted registration - show details
Does not take place this semester.
Students in the MSc Biotechnology (Programme Regulations 2017) may select Synthetic Biology II instead of the Research Project 1.
W8 credits4AS. Panke, Y. Benenson, J. Stelling
Abstract7 months biological design project, during which the students are required to give presentations on advanced topics in synthetic biology (specifically genetic circuit design) and then select their own biological system to design. The system is subsequently modeled, analyzed, and experimentally implemented. Results are presented at an international student competition at the MIT (Cambridge).
ObjectiveThe students are supposed to acquire a deep understanding of the process of biological design including model representation of a biological system, its thorough analysis, and the subsequent experimental implementation of the system and the related problems.
ContentPresentations on advanced synthetic biology topics (eg genetic circuit design, adaptation of systems dynamics, analytical concepts, large scale de novo DNA synthesis), project selection, modeling of selected biological system, design space exploration, sensitivity analysis, conversion into DNA sequence, (DNA synthesis external,) implementation and analysis of design, summary of results in form of scientific presentation and poster, presentation of results at the iGEM international student competition (Link).
Lecture notesHandouts during course
Prerequisites / NoticeThe final presentation of the project is typically at the MIT (Cambridge, US). Other competing schools include regularly Imperial College, Cambridge University, Harvard University, UC Berkeley, Princeton Universtiy, CalTech, etc.

This project takes place between end of Spring Semester and beginning of Autumn Semester. Registration in April.

Please note that the number of ECTS credits and the actual work load are disconnected.
Internship
NumberTitleTypeECTSHoursLecturers
636-0804-00LIndustry Internship Restricted registration - show details
Only for Biotechnologie Master BSc, Programme Regulations 2017.
W12 credits34AProfessors
AbstractIndustry internship of at least 12 weeks, completed with a written report.
ObjectiveStudents gain experience in an industrial environment and an overview of different research areas by applying concepts taught in the courses.
Prerequisites / NoticeThe students look for a placement themselves.
Master's Thesis
NumberTitleTypeECTSHoursLecturers
636-0900-00LMaster's Thesis Restricted registration - show details
Only for Biotechnologie Master BSc, Programme Regulations 2017.

Only students who fulfill the following criteria are allowed to begin with their master thesis:
a. successful completion of the bachelor programme;
b. fulfilling of any additional requirements necessary to gain admission to the master programme.
O40 credits91DSupervisors
AbstractIn the Master thesis students prove their ability to independent, structured and scientific working. The Master thesis is carried out under the supervision of a professor in a research group of the D-BSSE, usually at the D-BSSE. Students are free to choose the area.
ObjectiveIn the Master Thesis students prove their ability to independent, structured and scientific working.
Practical Training
All listed lab courses are mandatory.
For Students in Biotechnology Master, Programme Regulation 2021: 16 ECTS in this category are mandatory.
For Students in Biotechnology Master, Programme Regulation 2017: 14 ECTS in this category are mandatory.
NumberTitleTypeECTSHoursLecturers
636-0201-00LLab Course: Methods in Cell Analysis and Laboratory Automation Restricted registration - show details
The lab course is open for MSc Biotechnology students only.
O3 credits6PT. Horn
AbstractThe course Methods in Cell Analysis and Laboratory Automation introduces students to high-end cell analysis and sample preparation methods including image analysis. Students will be taught theoretical aspects and skills in Flow Cytometry, Light Microscopy, Image Analysis, and the use of Laboratory Automation.
Objective-to understand the technical and physical principles of light microscopes and flow cytometers
-to have hands-on experience in the use of these technologies to analyze/image real samples
-to be able to run a basic analysis of the data and images obtained with flow cytometers and microscopes
-to get introduced to liquid handling (pipetting) robotics and learn how to implement a basic workflow
ContentThe practical course will have five units at 2 days each (total 10 days):
1. Flow Cytometry:
a. Introduction to Flow Cytometry
b. Practical demonstration on flow cytometry analyzers and flow cytometry cell sorters
c. Flow cytometry sample preparation
d. Learn how to use flow cytometry equipment to analyze and sort fluorescence-labeled cells
2. Light microscopy
a. Learn how to build a microscope and understand the underlying physical principles
b. Learn how to use a modern automated wide field fluorescence microscope
c. Use this microscope to automatically acquire images of a cell culture assay to analyze the dose-dependent effect of a drug treatment
3. Image Analysis
a. Introduction to the fundamentals of image analysis
b. Learn the basics of the image analysis software Fiji/ImageJ
c. Use Fiji/ImageJ to analyze the images acquired during the microscopy exercise
4. Laboratory Automation
a. Introduction to the basics of automated liquid handling/ lab robotics
b. See examples on using lab automation for plasmid library generation and cell cultivation
c. Learn how to program and execute a basic pipetting workflow including liquid handling and labware transfers on Tecan and Hamilton robotic systems
5. Presentations
a. Each student will be assigned to an individual topic of the course and will have to prepare a presentation on it.
b. Presentations and discussion in form of a Colloquium
Lecture notesYou will find further information on the practical course and the equipment at:
Link
Link
LiteratureMicroscopy: Murphy and Davidson, Fundamentals of Light Microscopy and Electronic Imaging, John Wiley & Sons, 2012
Flow Cytometry: Shapiro, Practical Flow Cytometry, John Wiley & Sons, 2005
Image analysis: R. C. Gonzalez, R. E. Woods, Digital Image Processing (3rd Edition), Prentice Hall
Laboratory Automation: Design and construction of a first-generation high-throughput integrated robotic molecular biology platform for bioenergy applications (2011) J. Lab. Autom., 16(4), 292-307
Prerequisites / NoticeThe following knowledge is required for the course:
-basic laboratory methods
-basic physics of optics (properties of light, refraction, lenses, fluorescence)
-basic biology of cells (cell anatomy and physiology)
636-0203-00LLab Course: Microsystems and Microfluidics in Biology Restricted registration - show details
The lab course is open for MSc Biotechnology students only.
O3 credits5PP. S. Dittrich, A. Hierlemann
AbstractThis practical course is an introduction to microsystems technology and microfluidics for the life sciences. It includes basic concepts of microsystem design, fabrication, and assembly into an experimental setup. Biological applications include a variety of measurements of cellular and tissue signals and subsequent analysis.
ObjectiveThe students are introduced to the basic principles of microsystems technology. They get acquainted with practical scientific work and learn the entire workflow of (a) understanding the theoretical concept, (b) planning the experiment, (c) engineering of the needed device, (d) execution of the experiment and data acquisition, (e) data evaluation and analysis, and (f) reporting and discussion of the results.
ContentThe practical course will consist of a set of 4 experiments.
Lecture notesNotes and guidelines will be provided at the beginning of the course.
Literature- S.M. Sze, "Semiconductor Devices, Physics and Technology", 2nd edition, Wiley, 2002
- W. Menz, J. Mohr, O. Paul, "Microsystem Technology", Wiley-VCH, 2001
- G. T. A. Kovacs, "Micromachined Transducers Sourcebook", McGraw-Hill, 1998
- M. J. Madou, "Fundamentals of Microfabrication", 2nd ed., CRC Press, 2002
- N.-T. Nguyen and S. Wereley, "Fundamentals and Applications of Microfluidics", Artech House, ISBN 1-580-53343-4
- O. Geschke et al., "Microsystem Engineering for Chemistry and the Life Sciences", Wiley-VCH, ISBN 3-527-30733-8
Prerequisites / NoticeThe practical course will consist of a set of 4 experiments. For each experiment, the student will be required to
- understand the theoretical concept behind the experiment
- plan the experiment
- engineer the devices
- execute the experiments and acquire data
- evaluate and analyze the data
- report and discuss the results
A good quality of the final report will be expected and be an important criterion.
CompetenciesCompetencies
Subject-specific CompetenciesConcepts and Theoriesassessed
Techniques and Technologiesassessed
Method-specific CompetenciesAnalytical Competenciesassessed
Social CompetenciesCommunicationassessed
Cooperation and Teamworkassessed
Personal CompetenciesCritical Thinkingassessed
Self-direction and Self-management assessed
636-0204-00LLab Course: Microbial Biotechnology Restricted registration - show details
The lab course is open for MSc Biotechnology students only.
O2 credits5PM. Held
AbstractStudents will learn the foundations of monoseptic working practice and create and screen microbial libraries for identification of strains expressing different fluorescent protein (XFP) levels
ObjectiveStudents will learn the foundations of monoseptic working practice and create and screen microbial libraries for identification of strains expressing different fluorescent protein (XFP) levels
ContentBlock A: Handling and preparation and of microbial libraries
D1: Introduction to microbiological cultures and monoseptic working techniques.
D2: Plasmid-based expression systems and variation of XFP synthesis levels via site-directed RBS mutagenesis.
Block B: Library screening
D3: In vivo screening for XFP expression levels.
D4: Analysis of XFP levels via SDS-PAGE analysis. RBS-sequencing.
Block C: Hit recovery and validation
D5: In silico analysis of RBS variants.
D6: Cellular XFP content for selected variants at different culture conditions.
Block D: Data analysis and presentation
D7: Protein expression analysis. Q&A for reports and presentations.
D8: Final presentations and wrap-up.
Lecture notesMaterial will be provided during the course.
Literature(1) Reetz MT, Kahakeaw D, and Lohmer R. "Addressing the numbers problem in directed evolution." ChemBioChem 2008
(2) Jeschek M, Gerngross D, and Panke S. “Rationally reduced libraries for combinatorial pathway optimization minimizing experimental effort.” Nat. Commun. 2016
(3) Salis HM. “The ribosome binding site calculator.” Methods Enzymol. 2011
(4) Nienhaus G, Nienhaus K, and Wiedenmann J. "Structure–Function Relationships in Fluorescent Marker Proteins of the Green Fluorescent Protein Family." Fluorescent Proteins I. Springer Berlin Heidelberg, 2011

General introduction to microbiology:

(5) Schlegel HG, and Zaborosch C. “General Microbiology.” Cambridge University Press 1993
(6) Pirt JS. “Principles of microbe and cell cultivation.” Blackwell Scientific Publications 1975
Advanced Courses
Students need to aquire a total of 24 ECTS in this category.
The list of advanced courses is a closed list, no other course can be added to this category.
Biomelecular-Orientated
NumberTitleTypeECTSHoursLecturers
636-0103-00LMicrotechnologyW4 credits3GA. Hierlemann
AbstractStudents are introduced to the basics of microtechnology, cleanroom, semiconductor and silicon process technologies. They will get to know the fabrication of mostly silicon-based microdevices and -systems and all related microfabrication processes.
ObjectiveStudents are introduced to the basics of microtechnology, cleanroom, semiconductor and silicon process technologies. They will get to know the different fabrication methods for various microdevices and systems.
ContentIntroduction to microtechnology, semiconductors, and micro electro mechanical systems (MEMS)

- Fundamentals of semiconductors and band model
- Fundamentals of devices: transistor and diode.
- Silicon processing and fabrication steps
- Silicon crystal structure and manufacturing
- Thermal oxidation
- Doping via diffusion and ion implantation
- Photolithography
- Thin film deposition: dielectrics and metals
- Wet etching & bulk micromachining
- Dry etching & surface micromachining
- Microtechnological processing and fabrication sequence
- Optional: Packaging
Lecture notesHandouts in English
Literature- S.M. Sze, "Semiconductor Devices, Physics and Technology", 2nd edition, Wiley, 2002
- R.F. Pierret, "Semiconductor Device Fundamentals", Addison Wesley, 1996
- R. C. Jaeger, "Introduction to Microelectronic Fabrication", Prentice Hall 2002
- S.A. Campbell, "The Science and Engineering of Microelectronic Fabrication", 2nd edition, Oxford University Press, 2001
- W. Menz, J. Mohr, O. Paul, "Microsystem Technology", Wiley-VCH, 2001
- G. T. A. Kovacs, "Micromachined Transducers Sourcebook", McGraw-Hill, 1998
- M. J. Madou, "Fundamentals of Microfabrication", 2nd ed., CRC Press, 2002
Prerequisites / NoticeFundamentals in physics and physicochemistry (orbital models etc.) are required, a repetitorium of fundamental physics and quantum theory at the semester beginning can be offered.

The information on the web can be updated until the beginning of the semester.
CompetenciesCompetencies
Subject-specific CompetenciesConcepts and Theoriesassessed
Techniques and Technologiesassessed
Method-specific CompetenciesAnalytical Competenciesassessed
Social CompetenciesCommunicationassessed
Personal CompetenciesCritical Thinkingassessed
636-0104-00LBiophysical MethodsW4 credits3GD. J. Müller
AbstractStudents will be imparted knowledge in basic and advanced biophysical methods applied to problems in molecular biotechnology. The course is fundamental to applying the methods in their daily and advanced research routines. The students will learn the physical basis of the methods as well as their limitations and possibilities to address existing and future topics in molecular biotechnology.
ObjectiveGain of interdisciplinary competence in experimental and theoretical research, which qualifies for academic scientific work (master's or doctoral thesis) as well as for research in a biotechnology or a pharmaceutical company. The module is of general use in courses focused on modern biomolecular technologies, systems biology and systems engineering.
ContentThe students will learn basic and advanced knowledge in applying biophysical methods to address problems and overcome challenges in biotechnology, cell biology and life sciences in general. The biological and physical possibilities and limitations of the methods will be discussed and critically evaluated. By the end of the course the students will have assimilated knowledge on a portfolio of biophysical tools widening their research capabilities and aptitude.
The biophysical methods to be taught will include:
• Light microscopy: Resolution limit of light microscopy, fluorescence, GFP, fluorescence microscopy, DIC, phase contrast, difference between wide-field and confocal microscopy
• Super resolution optical microscopy: STED, PALM, STORM, other variations
• Electron microscopy: Scanning electron microscopy, transmission electron microscopy, electron tomography, cryo-electron microscopy, single particle analysis and averaging, tomography, sectioning, negative stain
• X-ray, electron and neutron diffraction
• MRI Imaging
• Scanning tunnelling microscopy and atomic force microscopy
• Patch clamp technologies: Principles of patch clamp analysis and application. Various patch clamp approaches used in research and industry
• Surface plasmon resonance-based biosensors
• Molecular pore-based sensors and sequencing devices
• Mechanical molecular and cellular assembly devices
• Optical and magnetic tweezers
• CD spectroscopy
• Optogenetics
• Molecular dynamics simulations
Lecture notesHand out will be given to students at lecture.
LiteratureMethods in Molecular Biophysics (5th edition), Serdyuk et al., Cambridge University Press
Biochemistry (5th edition), Berg, Tymoczko, Stryer; ISBN 0-7167-4684-0, Freeman
Bioanalytics, Lottspeich & Engels, Wiley VCH, ISBN-10: 3527339191
Cell Biology, Pollard & Earnshaw; ISBN:0-7216-3997-6, Saunder, Pennsylvania
Methods in Modern Biophysics, Nölting, 3rd Edition, Springer, ISBN-10: 3642030211
Prerequisites / NoticeThe module is composed of 3 SWS (3 hours/week): 2-hour lecture, 1-hour seminar. For the seminar, students will prepare oral presentations on specific in-depth subjects with/under the guidance of the teacher.
636-0105-00LIntroduction to Biological ComputersW4 credits3GY. Benenson
AbstractBiological computers are man-made biological networks that interrogate and control cells and organisms in which they operate. Their key features, inspired by computer science, are programmability, modularity, and versatility. The course will show how to rationally design, implement and test biological computers using molecular engineering, DNA nanothechnology and synthetic biology.
ObjectiveThe course has the following objectives:

* Familiarize students with parallels between theories in computer science and engineering and information-processing in live cells and organisms

* Introduce basic theories of computation

* Introduce approaches to creating novel biological computing systems in non-living environment and in living cells including bacteria, yeast and mammalian/human cells.

The covered approaches will include
- Nucleic acids engineering
- DNA and RNA nanotechnology
- Synthetic biology and gene circuit engineering
- High-throughput genome engineering and gene circuit assembly

* Equip the students with computer-aided design (CAD) tools for biocomputing circuit engineering. A number of tutorials will introduce MATLAB SimBiology toolbox for circuit design and simulations

* Foster creativity, research and communication skills through semester-long "Design challenge" assignment in the broad field of biological computing and biological circuit engineering.
ContentNote: the exact subjects can change, the details below should only serve for general orientation

Lecture 1. Introduction: what is molecular computation (part I)?

* What is computing in general?
* What is computing in the biological context (examples from development, chemotaxis and gene regulation)
* The difference between natural computing and engineered biocomputing systems

Lecture 2: What is molecular computation (part II) + State machines

1st hour

* Detailed definition of an engineered biocomputing system
* Basics of characterization
* Design challenge presentation

2nd hour

* Theories of computation: state machines (finite automata and Turing machines)

Lecture 3: Additional models of computation

* Logic circuits
* Analog circuits
* RAM machines

Basic approaches to computer science notions relevant to molecular computation. (i) State machines; (ii) Boolean networks; (iii) analog computing; (iv) distributed computing. Design Challenge presentation.

Lecture 4. Classical DNA computing

* Adleman experiment
* Maximal clique problem
* SAT problem

Lecture 5: Molecular State machines through self-assembly

* Tiling implementation of state machine
* DNA-based tiling system
* DNA/RNA origami as a spin-off of self-assembling state machines

Lecture 6: Molecular State machines that use DNA-encoded tapes

* Early theoretical work
* Tape extension system
* DNA and enzyme-based finite automata for diagnostic applications

Lecture 7: Introduction to cell-based logic and analog circuits

* Computing with (bio)chemical reaction networks
* Tuning computation with ultrasensitivity and cooperativity
* Specific examples

Lecture 8: Transcriptional circuits I

* Introducing transcription-based circuits
* General features and considerations
* Guidelines for large circuit construction

Lecture 9: Transcriptional circuits II

* Large-scale distributed logic circuits in bacteria
* Toward large-scale circuits in mammalian cells

Lecture 10: RNA circuits I

* General principles of RNA-centered circuit design
* Riboswitches and sRNA regulation in bacteria
* Riboswitches in yeast and mammalian cells
* General approach to RNAi-based computing

Lecture 11: RNA circuits II

* RNAi logic circuits
* RNAi-based cell type classifiers
* Hybrid transcriptional/posttranscriptional approaches

Lecture 12: In vitro DNA-based logic circuits

* DNAzyme circuits playing tic-tac-toe against human opponents
* DNA brain


Lecture 13: Advanced topics

* Engineered cellular memory
* Counting and sequential logic
* The role of evolution
* Fail-safe design principles

Lecture 14: Design challenge presentation
Lecture notesLecture notes will be available online
LiteratureAs a way of general introduction, the following two review papers could be useful:

Benenson, Y. RNA-based computation in live cells. Current Opinion in Biotechnology 2009, 20:471:478

Benenson, Y. Biocomputers: from test tubes to live cells. Molecular Biosystems 2009, 5:675:685

Benenson, Y. Biomolecular computing systems: principles, progress and potential (Review). Nature Reviews Genetics 13, 445-468 (2012).
Prerequisites / NoticeBasic knowledge of molecular biology is assumed.
636-0108-00LBiological Engineering and BiotechnologyW4 credits3VM. Fussenegger
AbstractBiological Engineering and Biotechnology will cover the latest biotechnological advances as well as their industrial implementation to engineer mammalian cells for use in human therapy. This lecture will provide forefront insights into key scientific aspects and the main points in industrial decision-making to bring a therapeutic from target to market.
ObjectiveBiological Engineering and Biotechnology will cover the latest biotechnological advances as well as their industrial implementation to engineer mammalian cells for use in human therapy. This lecture will provide forefront insights into key scientific aspects and the main points in industrial decision-making to bring a therapeutic from target to market.
Content1. Insight Into The Mammalian Cell Cycle. Cycling, The Balance Between Proliferation and Cancer - Implications For Biopharmaceutical Manufacturing. 2. The Licence To Kill. Apoptosis Regulatory Networks - Engineering of Survival Pathways To Increase Robustness of Production Cell Lines. 3. Everything Under Control I. Regulated Transgene Expression in Mammalian Cells - Facts and Future. 4. Secretion Engineering. The Traffic Jam getting out of the Cell. 5. From Target To Market. An Antibody's Journey From Cell Culture to The Clinics. 6. Biology and Malign Applications. Do Life Sciences Enable the Development of Biological Weapons? 7. Functional Food. Enjoy your Meal! 8. Industrial Genomics. Getting a Systems View on Nutrition and Health - An Industrial Perspective. 9. IP Management - Food Technology. Protecting Your Knowledge For Business. 10. Biopharmaceutical Manufacturing I. Introduction to Process Development. 11. Biopharmaceutical Manufacturing II. Up- stream Development. 12. Biopharmaceutical Manufacturing III. Downstream Development. 13. Biopharmaceutical Manufacturing IV. Pharma Development.
Lecture notesHandout during the course.
636-0107-00LMicrobial BiotechnologyW4 credits3GS. Panke
AbstractStudents of this course know and can evaluate modern methods of microbial biotechnology and enzyme technology and understand their relation to modern applications of microbial biotechnology.
ObjectiveStudents of this course know and can evaluate modern methods of microbial biotechnology and enzyme technology and understand their relation to modern applications of microbial biotechnology.
ContentThe course will cover in its main part selected fundamental and advanced topics and methodologies in microbial molecular biotechnology. Major topics include I) Microbial physiology of microbes (prokaryotes and selected fungi), II) Applications of Microbial Biotechnology, III) Enzymes - advanced kinetics and engineering, IV) Principles of in vivo directed evolution, V) System approaches to cell engineering/metabolic engineering, and VI) Trends in Microbial Biotechnology. The course is a mix of lectures and different exercise formats.
Lecture notesNotes will be provided in the forms of handouts.
LiteratureThe course will use selected parts of textbooks and then original scientific publications and reviews.
CompetenciesCompetencies
Subject-specific CompetenciesConcepts and Theoriesassessed
Techniques and Technologiesassessed
Method-specific CompetenciesAnalytical Competenciesassessed
Social CompetenciesCommunicationassessed
Cooperation and Teamworkassessed
Personal CompetenciesSelf-direction and Self-management assessed
636-0018-00LData Mining IW6 credits3G + 2AK. M. Borgwardt
AbstractData Mining, the search for statistical dependencies in large databases, is of utmost important in modern society, in particular in biological and medical research. This course provides an introduction to the key problems, concepts, and algorithms in data mining, and the applications of data mining in computational biology.
ObjectiveThe goal of this course is that the participants gain an understanding of data mining problems and algorithms to solve these problems, in particular in biological and medical applications.
ContentThe goal of the field of data mining is to find patterns and statistical dependencies in large databases, to gain an understanding of the underlying system from which the data were obtained. In computational biology, data mining contributes to the analysis of vast experimental data generated by high-throughput technologies, and thereby enables the generation of new hypotheses.

In this course, we will present the algorithmic foundations of data mining and its applications in computational biology. The course will feature an introduction to popular data mining problems and algorithms, reaching from classification via clustering to feature selection. This course is intended for both students who are interested in applying data mining algorithms and students who would like to gain an understanding of the key algorithmic concepts in data mining.

Tentative list of topics:

1. Distance functions
2. Classification
3. Clustering
4. Feature Selection
Lecture notesCourse material will be provided in form of slides.
LiteratureWill be provided during the course.
Prerequisites / NoticeBasic understanding of mathematics, as taught in basic mathematics courses at the Bachelor's level.
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