Industrial PhD student at DSM and DTU (Technical University of Denmark)
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
Attention will be on a variety of themes:
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.
The course (including preparatory materials) is valued 41 hours of work.
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.
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.
|Monday, 22 May 2023
Theme: Omics technologies: Overview and state of the art
|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|
|10.45||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|
|13.30||Technology – Mass Spectrometry||Martin Pabst|
|14.30||High resolution proteomics approaches||Martin Pabst|
|15.45||State-of-the-art metabolomics||Walter van Gulik|
|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|
|11.30||Genome-scale modelling for in-silico analysis of metabolism||Bas Teusink|
|13.30||Continuation: Exercise with open source tools||Aljoscha Wahl|
|14.30||Industrial applications (including 13 MFA)||Aljoscha Wahl|
|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|
|10.15||Kinetic modelling approaches – open source tools (Copasi)||Aljoscha Wahl, Walter van Gulik|
|13.30||Continuation: Kinetic modelling approaches – open source tools||Aljoscha Wahl|
|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|
|Friday, 26 May 2023
Theme: Future perspectives
|09.30||Machine learning for industrial biotechnology||Hector Garcia Martin|
|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|
|13.30||Cell culture proteomics||Jeroen Demmers|
|14.30||Single cell proteomics To Be Announced||Peter Mowlds|
|15.30||Panel discussion, Evaluation, Drinks|
|Small and medium-sized enterprises (SME/Startups/scaleups)||€1.750,-**|
|Small and medium-sized enterprises (SME/Startups/scaleups) of Biotech Campus Delft||€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.
Industrial Microbiology, Department of Biotechnology, Delft University of Technology, the Netherlands
Cell Systems Engineering, Department of Biotechnology, Delft University of Technology, the Netherlands
Cell Systems Engineering, Delft University of Technology, Department of Biotechnology, Delft, the Netherlands
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).
Department of Bionanoscience Delft University of Technology
Delft, the Netherlands
Industrial Microbial Biotechnology
Delft University of Technology
Delft, the Netherlands
Laboratory for Genetics and Genomics, Leuven Institute for Beer Research
Delft University of Technology
Delft, the Netherlands
Corporate Science Fellow, Analysis & Characterization
DSM, Delft, the Netherlands
Vrije Universiteit Amsterdam
Systems Bioinformatics group (AIMMS)
Amsterdam, the Netherlands
DSM, Delft, The Netherlands