• Biotechnology Sciences Delft Leiden
Advanced Course

Genomics in Industrial Biotechnology

Course description

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.

31 October – 4 November 2016

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.

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

The course fee is:

Early bird fee: € 2500 if payment is received before 19 September 2016.
Regular fee: € 2750 if payment is received on or after 19 September 2016.

To facilitate enrollment of PhD students, a limited number of fellowships is available covering part of the course fee. In that case the reduced fee is € 1250. To apply, please include proof of your university registration as a PhD student.

The fee includes course materials, meals (5 lunches and 4 dinners). The fee does not include hotel accommodation. Hotel accommodation can be arranged at your request. Preparatory texts will be sent after receipt of the course fee. The complete course book will be supplied at the start of the course. In the event of cancellation before 19 September 2016 a full refund will be granted. After this date, a 25% fee charge will be made.

The complete course book will be supplied at the start of the course.

Course fees can be paid by bank transfer or credit card (we are required to charge extra costs for this option; please contact us). TU Delft employees can use their internal (project) code. Customers are requested to pay the course fee within 30 days after the invoice date, but at the latest six weeks before the course starts. In case of payment before this date, the reduced course fee applies. After this date, we charge the full course fee. The course fees need to be on our bank account before the course starts.

DOWNLOADS
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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