Systems Biology for Industrial Biotechnology
ERASysAPP workshop combined with the DLN Volterra lecture.
Open for everyone - no registration required.
Session 1 – LeanProt ERASysAPP project partners’ perspective
|08.30-08.35||Welcome by Agnieszka Gawin (LeanProt ERASysAPP, NTNU, Norway)|
|08.35-09.00||Peter Neubauer (Head of Department of Bioprocess Engineering, TU Berlin, Germany)
Title: Towards a computation-based bioprocess development: Clearing the hurdle of parameter estimation by combining high throughput systems with model based Design of Experiments
|09.00-09.25||Raivo Vilu (Director of R&D at the Center of Food and Fermentation Technologies, Estonia)
Title: Trial-and-error vs “first time right” in design of cell factories
|09.25-09.50||Klaus Bensch (Head of R&D and Production at Biotechrabbit GmbH, Henningsdorf, Germany)
Title: Recombinant protein production in Escherichia coli
|09.50-10.15||Egils Stalidzans (Head of Biosystems Group, University of Agriculture, Latvia)
Title: Automation of COPASI based optimization workflow of kinetic models
|10.15-10.30||Karl Peebo (Researcher at the Center of Food and Fermentation Technologies, Estonia)
Title: Quantitative proteomics of biotechnology workhorses
10.30-10.45: Coffee break
(warm drinks and refreshments will be provided for all participants)
Session 2 – Implementation of computational models and omics data
|10.45-11.00||Fernando Pérez-Garcia (Postdoc at Department of Chemical Process Technology, NTNU, Norway)
Title: Real time automatic control of industrial bioprocesses for production of high value
|11.00-11.15||Simone Balzer (Researcher at the Department of Biotechnology, SINTEF, Norway)
Title: BioZEment - Understanding and improving bacterial processes in the production of bio-concrete for construction purposes
|11.15-11.30||Marta Irla (Researcher at Department of Biotechnology and Food Sciences, NTNU, Norway)
Title: Genome and transcriptome based metabolic engineering of Bacillus methanolicus
|11.30-11.50||Eivind Almaas (Professor at the Department of Biotechnology and Food Sciences, NTNU, Norway)
Title: Differential network analysis as approach to study human disease
12.00-13.00: Lunch break
13.00-14.00: Volterra lecture by Professor Bonnie Berger
(Professor of Applied Mathematics and Head of Computation and Biology at the Massachusetts Institute of Technology (MIT), USA)
Title: Biomedical data sharing with privacy
Abstract: The last two decades have seen an exponential increase in genomic and biomedical data. Extracting new science from these massive datasets will require efficient cryptographic techniques that can help overcome the privacy barriers to biomedical data sharing. Leveraging and adapting tools from modern cryptography, we present the first scalable, end-to-end pipeline for secure genome-wide association studies (GWAS), which obtains accurate results while ensuring no information about the underlying data is leaked to any entity, including the researchers. Our approach enables secure genome crowdsourcing at the scale of a million genomes, allowing the individuals to contribute their genomes to a study without compromising their privacy.
Also, we introduce a protocol for securely training a neural network model of drug-target interaction (DTI) that newly ensures the confidentiality of all underlying drugs, targets, and observed interactions. Our protocol scales to a real dataset of more than a million interactions, and is more accurate than state-of-the-art (plaintext) DTI prediction methods. Using our protocol, we discover novel DTIs that we experimentally validated via targeted assays. Our work lays a foundation for more effective and cooperative biomedical research.