Advanced Course

Integrated Multi-Omics approaches for Improvement of Industrial Microbes

Course description

The advanced course Integrated Multi-Omics approaches for Improvement of Industrial Microbes aims to offer a coherent overview of current state of the art omics technologies, bridging the different cellular levels, i.e. metabolomics, fluxomics, transcriptomics and proteomics. It will be shown how integrated application of these technologies provides holistic, quantitative insights in cellular physiology. Finally, it will be demonstrated how targets for (further) improvement of industrial microbes can be identified through integration of omics data with modelling approaches.

22 – 26 May 2023

Delft University of Technology, the Netherlands

A limited number of fellowships is available for PhD students (reduced fee).

Register
THE COURSE

Advanced Course Integrated Multi-Omics approaches for Improvement of Industrial Microbes

This intensive, activating, one-week course aims at providing fundamental and applied knowledge in the field. To this end, the course is set up as an alternating program of expert lectures and exercises.

Especially, the course offers a coherent overview of current state of the art omics technologies, bridging the different cellular levels, i.e. metabolomics, fluxomics, transcriptomics and proteomics. It will be shown how integrated application of these technologies provides holistic, quantitative insights in cellular physiology. Finally, it will be demonstrated how targets for (further) improvement of industrial microbes can be identified through integration of omics data with modelling approaches.

The day themes are:
Day 1 – Omics technologies: Overview and state of the art.
Day 2 – Mass spectrometry based proteomics & metabolomics techniques
Day 3 – Fluxomics & Modelling approaches
Day 4 – Integration of omics data & Modelling approaches
Day 5 – Future perspectives

Lectures

Attention will be on a variety of themes:

  • Genome sequencing and analysis
  • Transcriptomics (incl. RNA sequencing)
  • Proteomics
  • Bioinformatics
  • Novel molecular tools and automated strain construction
  • Rapid sampling and quantitative analysis
  • Metabolite quantification and validation using
  • Isotope Dilution Mass Spectrometry, IDMS
  • Estimation of extra- and intracellular rates from experimental data
  • Kinetic modeling and approaches to handle parameter identification problems
  • Genomics in strain improvement (incl. metabolic and evolutionary engineering)

Exercises

Several exercises will be performed to familiarize the participants with the theory and practice and to illustrate the utility and utilization of bioinformatics, quantitative metabolomics and metabolic modeling. Especially, the participants will focus on analysis of next-generation sequence data, massive data handling, statistics, interpretation and visualisation of multi-omics data.

Study load

The course (including preparatory materials) is valued 41 hours of work.

Who should attend?

This Advanced Course is aimed at participants from industry, universities and research institutions who want to update and extend their theoretical knowledge and practical insight in multi-omics and modeling. The course is intended for postgraduates (MSc, PDEng, PhD), with a sound background in microbiology, microbial physiology, biotechnology, biochemistry or biochemical engineering, with a basic working knowledge in some of the other disciplines and an affinity to applied mathematics.

Course registration

Please register clicking the tab Register to attend the course. Deadline for application is 11 October 2021. Applicants will be handled in order of the date of receipt.

PROGRAMME

Programme 2023

Monday, 22 May 2023
Theme: Omics technologies: Overview and state of the art
08.45 Registration
09.00 Short introduction on Surfaces and BioTech Delft Vincent Renken
09.10 Introduction, including motivation for multi-omix analysis Aljoscha Wahl
09.30 Genome insights in plant, microbial and fungal genomes using long-read sequencing technologies Alexander Wittenberg
10.30 Break
10.45 Introduction to genome analyses Marcel van den Broek, Raúl A. Ortiz-Merino
11.45 Genome analyses I Marcel van den Broek, Raúl A. Ortiz-Merino
12:30 Group picture and lunch
13.30 Genome analyses II Marcel van den Broek, Raúl A. Ortiz-Merino
17.30 RNA sequencing and transcriptomics Eduard Kerkhoven
18.30 Social drink and buffet
 
Tuesday, 23 May 2023
Theme: Mass spectrometry based proteomics & metabolomics techniques
09.00 Genome analyses III Marcel van den Broek, Raúl A. Ortiz-Merino
12.30 Lunch
13.30 Technology – Mass Spectrometry Martin Pabst
14.30 High resolution proteomics approaches Martin Pabst
15.30 Break
15.45 State-of-the-art metabolomics Walter van Gulik
16.45 Break
17.00 Experimental design for quantitative metabolomics (with tracer stories) Aljoscha Wahl
Wednesday, 24 May 2023
Theme: Fluxomics & Modelling approaches
09.00 Exercise with open source tools Aljoscha Wahl
11.15  Break
11.30 Genome-scale modelling for in-silico analysis of metabolism Bas Teusink
12.30 Lunch
13.30 Continuation: Exercise with open source tools Aljoscha Wahl
14.30 Industrial applications (including 13 MFA) Aljoscha Wahl
15:30 Break
15:45 E. Coli resource allocation  (experimental) Greg Bokinsky
16:45 Resource allocation modelling (S. cerevisiae, E. coli) Aljoscha Wahl
Thursday, 25 May 2023
Theme: Integration of omics data & Modelling approaches
09.00 Regulatory functions of the metabolomics network Frank Bruggeman
10.00 Break
10.15 Kinetic modelling approaches – open source tools (Copasi) Aljoscha Wahl, Walter van Gulik
12.30 Lunch
13.30 Continuation: Kinetic modelling approaches – open source tools Aljoscha Wahl
15.15 Break
15:30 Multi omics in industrial environment (with examples) Liang Wu, Maurien Oudshoorn
16:30 Systems bioengineering for renewable chemicals production Gionata Scalcinati
17:30 Evolution of Orbitrap mass spectrometry instrumentation Peter Mowlds
19:00 Course dinner
Friday, 26 May 2023
Theme: Future perspectives
09.30 Machine learning for industrial biotechnology Hector Garcia Martin
10.30 Break
10.40 Leveraging cell-to-cell heterogeneity to gain functional insight into microbial metabolism and physiology Aljoscha Wahl
11.30 Ex vivo expansion of erythroblasts: Media and culture condition optimization using untargeted metabolomics Joan Sebastián Gallego Murillo
12.30 Lunch
13.30 Cell culture proteomics Jeroen Demmers
14.30 Single cell proteomics To Be Announced Peter Mowlds
15.30 Panel discussion, Evaluation, Drinks
LOCATION

The course will be held at:

Faculty of Applied Sciences (building 58)
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
W https://www.biotechnologycourses.nl

FEE

Deadline for registration is 1 May 2023

The course fee is:

Early Bird €2.500,-*
Regular Fee €2.750,-
Small and medium-sized enterprises (SME/Startups/scaleups) €1.750,-**
Small and medium-sized enterprises (SME/Startups/scaleups) of Biotech Campus Delft €1.250,-**
PhD Students €1.250,-**

*To be eligible for the reduced early bird fee you need to register before 13 March 2023 If this date is exceeded, the regular fee applies.

**A limited number of fellowships is available for PhD students and SME’s (small/medium enterprise). Fellowships will be available on a first-come-first-serve basis. To apply as to one of these fellowships, please include a copy either of your registration as a PhD student from your university or a proof of the SME-status of the company you work at.

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 27 March 2023, 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

Dr. Walter van Gulik

Cell Systems Engineering, Department of Biotechnology, Delft University of Technology, the Netherlands

Dr. Martin Pabst

Cell Systems Engineering, Delft University of Technology, Department of Biotechnology, Delft, the Netherlands

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).

Guest lecturers

Greg Bokinsky

Department of Bionanoscience Delft University of Technology
Delft, the Netherlands

Marcel van den Broek

Industrial Microbial Biotechnology
Delft University of Technology
Delft, the Netherlands

Raúl A. Ortiz Merino

Laboratory for Genetics and Genomics, Leuven Institute for Beer Research
KU Leuven
Leuven, Belgium

Eduard Kerkhoven

Stefan de Kok

Zymergen
Emeryvill, USA

Hector Garcia Martin

Joan Gallego Murillo

Bioprocess Engineering
Delft University of Technology
Delft, the Netherlands

Maurien Olsthoorn

Corporate Science Fellow, Analysis & Characterization
DSM, Delft, the Netherlands

Jeroen Demmers

Bas Teusink

Vrije Universiteit Amsterdam
Systems Bioinformatics group (AIMMS)
Amsterdam, the Netherlands

Liang Wu

DSM, Delft, The Netherlands

Alexander Wittenberg

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    testimonials

    Multi-Omics 2021

    Working with fermentation and bacterial cell physiology, my interest naturally shifted towards the ‘omics technologies which are essential state-of-the-art tools for intelligent microbial host design. I participated on this course to deepen my knowledge on the ‘omics approaches and to find further inspiration for their applications within my own research project. Without a doubt, this was one of the best courses I have taken during my PhD education – the organization and execution of the course was spotless. High-quality lectures were spiced with interesting exercises, relevant examples and talks by industry. Additionally, the course provided a great platform for social networking. I would recommend this course to those who are working on the development/improvement of industrial microbes and would like to have a coherent overview of the state-of-the-art ‘omics tools with hands on experience and relevant examples. This course requires some prior knowledge on Python and working in a terminal.

    Greta Gecse
    Industrial PhD student at DSM and DTU (Technical University of Denmark)

    Multi-Omics 2021

    In my career so far I have mostly worked with genome-scale metabolic model to improve industrial microorganisms. I decided to follow the advanced multi-omics course to get a broader overview also about the different -omic techniques and how to integrate them into my work. The course exceeded my expectations and I gained state of the art insights that are going to help me a lot. The entry-level of the course is quite high, but with the preparatory materials you will become familiar with the topics. I highly recommend candidates that are less familiar to work them through. The course itself had a nice balance of lectures, practical exercises and talks about different applications of the techniques. The organisation of the course left no room for improvement and I can recommend it to everyone who wants to get an overview of this emerging field.

    Tim Krempel
    Modelling Analyst at EV-Biotech

    Multi-Omics 2021

    I applied to the multi-omics course to get a better understanding of the techniques that exist to unravel the mysterious world of microorganisms and their capabilities. The course provided a great overview of each -omic technique to someone like me with more of an engineering background. The course itself had a good combination of theoretical background lectures as well as practical exercises to gain a better grasp of concepts. Although some of the techniques covered are too in depth for my project, it gave me a lot of ideas to consider for future research.

    Kestral Johnston
    PhD Candidate at Wetsus/Wageningen University

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