Course description
*** This course has been last organised in 2020. It has been replaced by the Multi-Omics course. Please check the course information there for an up-to-date overview of the course.***
The Advanced Course on Genomics in Industrial Biotechnology aims at familiarizing industrial and academic research professionals (i.e. MSc, PhD, or equivalent experience) with modern concepts in genomics, their use in microbial research and development, and their utility in contemporary biotechnological industry.
This course focuses on the singular and combined utilization of the modern molecular research tools genome sequencing, transcriptomics, proteomics, and metabolomics to elucidate cellular regulatory mechanisms of sensing and signalling, metabolic flux and physiology. Mathematical tools and computer algorithms are indispensable to analyze, interpret and model this experimental data. In combined approaches, these tools offer unprecedented possibilities for industrial biotechnology research.
Experts will present lectures on genome analysis and -interpretation, genome-wide mRNA expression analysis (transcriptomics), whole-organism protein expression and activity analysis (proteomics), and metabolic pathway analysis (metabolomics). Data handling and bioinformatics are key to the successful application of genomics and hence, will be an integral part of the course. The necessary links between theory and practice will be provided in interactive case studies and demo-workshops. Implementation of these technologies in industrial R&D will be illustrated with real-life examples.
Planned for November 2020
Delft University of Technology, the Netherlands
A limited number of fellowships is available for PhD students (reduced fee).
THE COURSE
Advanced Course Genomics in Industrial Biotechnology
This intensive, high-diversity, one-week course provides a full overview of the possibilities and challenges of genomics in the field of industrial biotechnology. A combination of expert lectures and hands-on activities ensures active participation. The participants will receive the course book, including the presentations of the lecturers, on the first day. The course will be taught in English.
Lectures
Expert lectures are taught by renowned scientists from both Delft University of Technology as well as other universities and companies from all over the world. They will focus on a variety of themes:
- Genome sequencing and analysis
- Transcriptomics (incl. RNA sequencing)
- Proteomics
- Metabolomics
- Bioinformatics
- Systems Biology
- Genomics in strain improvement (incl. metabolic and evolutionary engineering)
- Regulation, legislation and patents
- Biodiversity
- Novel molecular tools and automated strain construction
- Examples from biotechnology industry
Hands-on
Two afternoons are reserved for hands-on activities in bioinformatics. These will focus on analysis of next-generation sequence data, massive data handling, statistics, interpretation and visualisation of genomics data.
Study load
The course (including preparatory materials) is valued 45 hours of work.
Who should attend?
This Advanced Course is aimed both at participants from industry, who want to update and extend their theoretical knowledge and practical insight in this field and at participants from universities and research institutions with a wish to evaluate practical implications of their research.
It is intended for postgraduates (MSc, PhD level, or equivalent experience), with a sound background in microbiology, microbial physiology, molecular cell biology, biochemistry or biochemical engineering, and a basic working knowledge in some of the other disciplines. Having some basic insight into one or more of the genomics technologies or in bioinformatics is not compulsory, but certainly is an advantage.
PROGRAMME
Programme 2016
| Monday, October 31, 2016 Theme Genome Sequencing & Analysis |
||
| 08.45 | Registration | |
| 09.00 | Introduction | Jean-Marc Daran |
| 09.30 | Technology Review I: Microbial genome sequencing | Derek Butler |
| 10.45 | From raw data to assembled genome | Thomas Abeel |
| 12.00 | Genome annotation | Ken Wolfe |
| 14.00 | Interactive case: Analysis of next-generation sequencing data |
Marcel van den Broek/Thomas Abeel |
| 18.00 | Dinner | |
| 19.30 | Introduction to genome-scale metabolic models | Bas Teusink |
| Tuesday, November 1, 2016 Theme Analytical Tools |
||
| 09.00 | Technology Review II: Transcriptomics | Jean-Marc Daran |
| 10.15 | Technology Review III: Proteomics | To be announced |
| 11.30 | Technology Review IV : Metabolomics | Aljoscha Wahl |
| 13.30 | Introductory lecture: Bioinformatics, datahandling & visualization |
Thomas Abeel |
| 14.45 | Computer demo’s: Bioinformatics: massive data handling, statistics, interpretation and visualization |
Marcel van den Broek/Thomas Abeel |
| 18.00 | Dinner | |
| 19.30 | Functional genomics of plant biomass utilization by fungi | Ronald de Vries |
| Wednesday, November 2, 2016 Theme Systems Biology |
||
| 09.00 | Model-based design of metabolic networks | To be announced |
| 10.15 | Metabolic Flux Analysis | Aljoscha Wahl |
| 11.30 | Metagenomics of the intestinal microbiome | Hauke Smidt |
| 13.30 | Linking the -omes | Pascale Daran-Lapujade |
| 14.45 | Allosteric regulation of metabolism | Hannes Link |
| 16.00 | Application of systems biology in the biotech industry | Ralf Takors |
| 17.00 | Genomics of wine yeast | Sylvie Dequin |
| 18.15 | Dinner | |
| Thursday, November 3, 2016 Theme Genomics & Strain Improvement |
||
| 09.00 | Introduction to Metabolic Engineering | Walter van Gulik |
| 10.15 | Exploring biodiversity: QTL analysis | Giani Liti |
| 11.30 | Application of genomics in evolutionary engineering | Jack Pronk |
| 13.30 | Strain improvement and regulatory constraints: experiences from the food industry |
Eric Johansen |
| 14.45 | (Intellectual) Property Rights | Bram de Jonge |
| 16.00 | Patenting genes and genomes | Mark Chadwick |
| 17.00 | Metagenomics of mixed-culture processes | Sacha van Hijum |
| 19.00 | Course dinner | |
| Friday, November 4, 2016 Theme Outlook |
||
| 09.00 | Novel molecular tools in strain construction | Jean-Marc Daran |
| 10.15 | High-throughput microbe construction & phenotype testing | Stefan de Kok |
| 11.30 | Heterogeneity in pure cultures | Matthias Heinemann |
| 13.00 | Lunch |
LOCATION
The course will be held at:
Department of Biotechnology
Delft University of Technology
Van der Maasweg 9
2629 HZ Delft
The Netherlands
P +31 (0)15 278 1922
F +31 (0)15 278 2355
E BiotechDelft@tudelft.nl
FEE
Deadline for registration is 7 November 2019
The course fee is:
| Early Bird | €2.500,-* |
| Regular Fee | €2.750,- |
| PhD Students | €1.250,-** |
*To be eligible for the reduced early bird fee you need to register before 19th of September 2019. If this date is exceeded, the regular fee applies.
**A limited number of fellowships is available for PhD students. To apply, please include a copy of your registration as a PhD student from your university.
The fee includes course materials, lunches and the buffets and the course dinners as indicated on the program. The fee does not cover other meals or lodging. Hotel accommodation can be arranged at your request.
The course fee is preferably paid by bank transfer. Payment by PayPal is possible. TU Delft employees can use their internal (project) code.
Preparatory texts will be sent one month before start of the course and after receipt of the course fee. The complete set of course books will be supplied at the start of the course.
In the event of your cancellation before 3 October 2019, a full refund will be granted. After this date, a 25% fee charge can be made.
Delay of payment past the final deadline as indicated on the invoice may result in cancellation of entry to the course. Re-entry is only possible in case of vacancies and the regular fee will be applied. Payment terms and deadlines will be indicated on the invoice and/or provided in an e-mail after registration, but the course fee should always be paid before the start of the course.
When the number of participants is too low to have a fruitful course, the Institute BioTech Delft will cancel the event no later than six weeks before the start of the course. The course fee will be reimbursed within three weeks after cancellation. In case a speaker will not be able to present his/her lecture, due to unforeseen circumstances, BioTech Delft will arrange an equivalent replacement.
BROCHURES
LECTURERS
Course board
Dr. Jean-Marc Daran
Industrial Microbiology, Department of Biotechnology, Delft University of Technology, the Netherlands
Faculty staff
Dr. Thomas Abeel
Bioinformatics group, Delft University of Technology, the Netherlands
Dr. Pascale Daran-Lapujade
Pascale Daran-Lapujade is assistant professor at the TU Delft Department of Biotechnology in the Industrial Microbiology section. Her research investigates the physiology of the yeast Saccharomyces cerevisiae, to unravel the molecular mechanisms that drive its response to diverse environmental stimuli and to identify the evolutionary circumstances that have shaped their genomes. Although many of her research questions are inspired by industrial applications of yeasts, she also seeks to contribute to a deeper understanding of fundamental aspects of cellular physiology and metabolism, using S. cerevisiae as a model. In addition she is editor of the journal FEMS Yeast Research and member of the board of the Microbial Biotechnology section of the Dutch Society for Microbiology (KNVM).
Dr. Walter van Gulik
Cell Systems Engineering, Department of Biotechnology, Delft University of Technology
Prof. Jack Pronk
Jack Pronk holds an MSc (Plant Molecular Biology) from Leiden University and a PhD (Microbiology) from the Delft University of Technology (TU Delft). In 1991, he joined the Delft Industrial Microbiology Section, first as assistant professor and later as full professor. Since 2002, prof. Pronk leads the TU Delft’s Industrial Microbiology section. From 2002-2013, he was director of the Kluyver Centre for Genomics of Industrial Fermentation, a national Centre of Excellence in which 140 researchers collaborated. His research aims to understand metabolism and its regulation in industrial microorganisms, with a focus on the yeast Saccharomyces cerevisiae. Improvement of the performance of industrial microorganisms by targeted genetic modification and laboratory evolution is a second key topic in his research. Prof. Pronk is (co)author of over 200 scientific publications, co-inventor on 20 patent applications and has supervised more than 20 PhD students. Prof. Pronk enjoys teaching and is (besides his teaching activities for BSDL) actively involved in the Delft-Leiden ‘Life Science and Technology’ programme (BSc/MSc), both as teacher and as coordinator of the MSc profile ‘Cell Factory’.
Dr. Aljoscha Wahl
Aljoscha Wahl is assistant professor at TU Delft with a focus on fluxomics and metabolomics in eukaryotic microorganisms. He studies the interactions of metabolism and its regulation under dynamic environmental conditions. Dr. Wahl contributes to experimental and computational approaches for (1) 13C flux analysis under metabolic dynamic conditions, (2) compartmentalized fluxomics and metabolomics using intracellular sensor reactions, (3) transport system studies. He teaches several master courses at TUD and was active in the iGEM competition (supervisor of the TUD team and organization of the European Jamboree). In addition, he is member of the editorial board of Applied and Environmental Microbiology (AEM)
Coordinator computer exercises
Marcel van den Broek
Department of Biotechnology, Delft University of Technology, the Netherlands
Guest lecturers
Mr. Anthony Burgard
Genomatica, San Diego, CA, USA
Dr. Derek Butler
BaseClear, Leiden, the Netherlands
Mark Chadwick, PhD
DSM, Delft, the Netherlands
Dr. Sylvie Dequin
INRA, Montpellier, France
Prof. Matthias Heinemann
Matthias Heinemann is full professor and group leader of the Molecular Systems Biology Group at the University of Groningen. After his studies in Biochemical/Environmental Engineering at the University of Stuttgart (Germany) and University of Western Ontario (London, Canada), he completed his PhD thesis in Biochemical Engineering at RWTH Aachen University. After a postdoc at ETH Zurich in the Bioprocess Lab he became Research group leader at the Institute of Molecular Systems Biology at the same university. In 2009, prof. Heinemann moved to Groningen. In his research, he combines systems biology with classical approaches to biological research to get quantitative understanding of microbial metabolism with a special focus on single cell behaviour.
Dr. Sacha van Hijum
Radboud Nijmegen Medical Center and NIZO, the Netherlands
Dr. Eric Johansen
Christian Hansen A/S, Hørsholm, Denmark
Dr. Bram de Jonge
Law & Governance group, Wageningen University, the Netherlands
Dr. Stefan de Kok
Stefan de Kok obtained his PhD from Delft University of Technology by studying “metabolic engineering of free-energy (ATP) conserving reactions in Saccharomyces cerevisiae”. Afterwards, he moved to Amyris Inc. in California, where he worked for 2 years on high-throughput, automated strain engineering. Dr. De Kok led a project to optimize ligase cycling reaction (LCR) as a method for rapid and reliable assembly of up to 20 DNA parts into DNA constructs up to 20 kb. In addition, he was involved in metabolic engineering of yeast strains for farnesene production. Currently, Dr. de Kok works as scientist and project leader at Zymergen Inc. in California, where he utilizes robotic strain engineering technologies to develop microbes producing novel molecules, and to improve the performance of microbes used in industrial fermentation.
Dr. Hannes Link
MPI für terrestrische Mikrobiology, LOEWE-Zentrum für Synthetische Mikrobiologi (SYNMIKRO), Marburg, Germany
Dr. Giani Liti
National Center for Scientific Research (CNRS), Nice, France
Dr. Hanna Schebesta
Law & Governance group, Wageningen University, the Netherlands
Prof. Hauke Smidt
Laboratory of Microbiology, Wageningen University, the Netherlands
Prof. Ralf Takors
Ralf Takors is a process engineer by training and had received his diploma at RWTH Aachen in 1993. At 1997 he got PhD in Biochemical Engineering and succeeded to finish his ‚Habilitation‘ in 2004, at RWTH Aachen having performed research at the Institute of Biotechnology, Forschungszentrum Jülich GmbH. He joined Evonik Industries AG being responsible for metabolic engineering, biochemical engineering and systems biology covering lab- and production scale. At July 2009 he took over the responsibility of the Institute of Biochemical Engineering (IBVT) at University of Stuttgart as the successor of Prof. Matthias Reuss. He is (co-) author of >50 peer-reviewed articles and member of several journal editorial (advisory) boards.
Prof. Bas Teusink
Vrije Universiteit Amsterdam, the Netherlands
Dr. Ronald de Vries
Utrecht University and CBS Fungal Biodiversity Centre, the Netherlands
Prof. Ken Wolfe
University College Dublin, Ireland
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