Master's thesis | ZHAW Life Sciences and Facility Management

Applied Computational Life Sciences

The Master’s thesis is the scientific core of your studies. Through the thesis you not only demonstrate your knowledge and skills, but also the ability to successfully integrate into a research group and expand your knowledge in your specific field of scientific expertise.

You choose your specialist courses with a view to the topic of your thesis, which you determine before starting your studies.
Based on the theoretical foundations of the study programme, you answer a specific question in this research field.
You work out solutions that are relevant for research, industry and society, often in co-operation with national and international partners.
Depending on your topic, you work in a research group at the ZHAW in Wädenswil or externally with an industrial or research partner.

Choose your field of interest

The Master’s thesis is the scientific core of your studies. Through the thesis you not only demonstrate your knowledge and skills, but also the ability to successfully integrate into a research group and expand your knowledge in your specific field of scientific expertise.

You choose your specialist courses with a view to the topic of your thesis, which you determine before starting your studies.
Based on the theoretical foundations of the study programme, you answer a specific question in this research field.
You work out solutions that are relevant for research, industry and society, often in co-operation with national and international partners.
Depending on your topic, you work in a research group at the ZHAW in Wädenswil or externally with an industrial or research partner.

Fields of Interest

Bioinformatics

Research Group	Contact	Topics / Field
Computatinal Genomics (ICLS)	Maria Anisimova	Stochastic modeling and simulation Gene and protein family evolution and phylogeny Classification, prediction and hypothesis testing Algorithms for genomic sequence analysis Computational genomics with medical applications
Environmental Genomics and Systems Biology (IUNR)	Theo Smits	Genomics, transcriptomics Population genetics Phylogenomics Taxonomy Antibiotic resistances Plasmids Source-tracking of plant pathogenic bacteria Applications in biotechnology, food science, environment and agriculture
Biomedical String Analysis (ICLS)	Manuel Gil	Computational genomics, phylogenetics Biomedical natural language processing Semantic web technologies, data integration Modelling, developing algorithms, programming Pipelining, simulation study, data analysis
Applied Mathematical Biology (ICLS)	Victor Garcia	Population genetics Codon usage bias modeling Mathematical modeling of cancer immunotherapies Mathematical and statistical analysis of data Modelling, hypothesis testing, applied computational genomics

Computational Chemistry

Research Group	Contact	Topics / Field
Section for Organic and Medicinal Chemistry (ICBT)	Stefan Höck	Cheminformatics Pure functional programming Type-driven development Developing algorithms and designing abstractions in cheminformatics in tactically typed, purely functional programming languages (i.e. Haskell)
Applied Mathematics and Physics (IAMP)	Manuel Dömer	Cheminformatics
Computational Environment (ICLS)	Martin Schüle	Automatic interpretation of NMR Spectra using Neural Networks
Environmental Analytics (ICBT)	Susanne Kern	Chromatography Mass Spectrometry Trace analysis of environmental sample
Advanced Signal Analytics (ICLS)	Matthias Nyfeler	Chromatography, when biology goes quantum

Biotechnological Processes

Research Group	Contact	Topics / Field
Biosystems Technology (ICBT)	Christin Peters	Enzyme cascades Biocatalysis Biotransformations
Centre vor Analytical Chemistry (ICBT)	Caspar Demuth	Development and application of sensors) for bioprocesses Online bioprocess analytics Characterisation of sensor components
Bioprocess Technology Research Group (ICBT)	Lukas Neutsch	Data-driven models (Python 3.7, Matlab) and soft-sensors for real-time bioprocess control and optimization Multivariate analysis (SIMCA) of physiology-related process data for quality assurance in biopharmaceutical production Implementation of fully integrated data processing environments and workflows (R Studio, programmable process control systems) in life science laboratories Automated image analysis for cell monitoring with fluorescence microscopy and atomic force microscopy
Chemical Engineering (ICBT)	Judith Krautwald	Process simulation in bioengineering and biotechnology Analysis and optimization of real plant processes Application focus in life science, environmental science and production of bioenergy Modelling and simulation of biological methanation processes Downscaling towards microfluidic devices
Biomedical Simulation (ICLS)	Sven Hirsch	Crystallization process modelling and simulation Process optimization
Microbiology and Molecular Biology (ICBT)	Martin Sievers	Genome mining

Digital Health, Biology and Neuroscience

Research Group	Contact	Topics / Field
Biomedical Simulation (ICLS)	Sven Hirsch	Understanding biomedical phenomena Medical imaging analysis & diagnostics systems Data assimilation and machine intelligence Sensor and time series analysis Simulations of brain aneurysms
Medical Image Analysis & Data Modeling (ICLS)	Georg Spinner	Medical image analysis 3D visualization & shape analysis Machine learning & deep learning Clinical prediction models Causal disease models Bayesian inference & Bayesian networks
Cognitive Computing in Life Sciences (ICLS) Collaboration with Intel	Yulia Sandamirskaya	Brain-inspired robotics and AI Real-time 3D vision Neuromorphic computing
Autonomous Learning Systems (ICLS)	Claus Horn	Next-generation of AI systems by integrating deep learning and reinforcement learning techniques to create autonomous AI agents Development of AI solutions for protein engineering
Medical Physics (Dep. T)	Stephan Scheidegger	Impact of anti-cancer treatment on ecosystem dynamics of cancer Model-based data analysis of anti-cancer Treatments in vitro and in vivo Model-based data analysis in medical imaging
Hospitality Management Competency Group (IFM)	Nicole Gerber	Visualisation of complex business process interpendencies in hospitals and healthcare organisations
Institute of Computational Life Sciences (ICLS)	Thomas Ott	Bio-inspired algorithms neuroinformatics, (machine) learning systems Computer models and simulations of biological dynamics
Data Management & Visualization (ICLS)	Robert Vorburger	Data processing Data pipeline automation App development
Predictive Analytics (ICLS)	Krzysztof Kryszczuk	Non-invasive wearable core body temperature sensor Antimicrobial resistance prediction Medical image analysis Classification of bone marrow cell images
Biomedical Engineering (Dept. T)	Daniel Baumgartner	Biomechanical engineering Finite elemente analysis Ergonomics & rehabilitation Data bases Clinical study design Experimental test design of medical products
Applied Complex Systems Science (Dept. T)	Ruedi Füchslin	Theory, modeling and simulation of complex systems Information processing in biological and life-like systems
Biosignal Analysis & Digital Health (ICLS)	Samuel Wehrli	Monitoring patient health with Wearables Activity tracking for hospital patients to improve fitness Feedback on writing skills for children with smart watches and activity recognition Brainwave analysis with EEG data to improve meditation skills

Applications in Food Industry

Research Group	Contact	Topics / Field
Simulation & Optimization (ICLS)	Lukas Hollenstein	Modelling, simulation and optimization of complex processes in production Logistics, supply-chain, business, facilities, etc. using discrete-event simulation and data analytics
Food Microbiology Research Group (ILGI)	Lars Fieseler	Phylogenetic analyses of bacteriophage genome sequences and phage derived proteins
Center for Food Processing and Packaging (ILGI)	Selçuk Yildirim	Modelling and simulation of shelf life of food and packaged food
Research Group Food Technology (ILGI)	Nadina Müller	Modelling of food processes and their impact of end product quality Creation of forecast models for the digitalisation of food processing
Coffee Exellence Center (ICBT)	Chahan Yeretzian	Computational (multivariante) data analysis using advanced statistical methods Analysis of time resolved analytical data Data visualization

Master Thesis Topics with Full Description

The table above lists thesis supervisors and their fields of interest. All these supervisors provide thesis topics. You can get in touch with them to learn more about their topics. In the following you find a small selection of topics with full description:

Antimicrobial resistance prediction from MALDI-TOF mass spectra,(PDF 174,2 KB) Supervisor: Stefan Glüge (ICLS)

Differentiation of bone marrow cell morphologies using deep neural networks(PDF 179,0 KB), Supervisor: Stefan Glüge (ICLS)

Effect-based Trace Analytics of Toxic Substances leveraging Native Cloud Computing Services (Cognitive Services, AI and ML)(PDF 499,9 KB), Supervisor: Andreas Schönborn (INUR)

Exploring the effectiveness of cancer-immunotherapies for non-small lung cancer(PDF 527,0 KB), Supervisor: Victor Garcia (ICLS)

How does an ancient protein expression regulation mechanism affect how the choice of codons in DNA(PDF 502,5 KB), Supervisor: Victor Garcia (ICLS)

Industry Collaborations

Depending on your topic, you work in a research group at the ZHAW in Wädenswil or externally with an industrial or research partner. In any case, you have a local thesis advisor at ZHAW. Ask our advisors about possible industry collaborations. In the thesis Market-Place you find a list with some possible thesis topics and collaboration partners.

Partners

Participating institutes

Affiliated partners

Completed Master Theses

Year of Graduation	Student	Title	Advisor
2019	Delucchi Matteo	Tandem Repeat Variation in Genomic Databases	Maria Anisimova (ZHAW, ICLS)
2019	Gygax Gregory	Smart Algorithms for Efficient Yield Forecasting	Thomas Ott (ZHAW, ICLS)
2019	Kaufmann Moritz	Evolution of multidrug resistance in pEL60 plasmids	Theo Smits (ZHAW, IUNR)
2019	Meier Patrick	A mathematical model to describe the relationship between the unfolded protein response (UPR) and production of recombinant proteins in the yeast Pichia pastoris	Sven Hirsch (ZHAW, ICLS)
2019	Naef Paulina	Optimizing of the Tandem Repeat Annotation Library (TRAL) and Copy Number Variations of Tandem Repeats in RNAseq Illumina Data	Maria Anisimova (ZHAW, ICLS)
2019	Peechatt Jithin Mathew	Characterisation of Bias and Variance of Progressive Sequence Alignment	Manuel Gil (ZHAW, ICLS)
2019	Schiling Daniel	Geoinformatics methods for a better understanding of wildlife-caused traffic accidents in the Cantons of Zurich (Switzerland)	Patrick Laube (ZHAW, IUNR)
2019	Selvaratnam Laksathan	Understanding cerebrovascular pathologies within the Circle of Willis using 0D flow network simulations	Sven Hirsch (ZHAW, ICLS)
2019	Siegrist Jonas Aaron	Genome mining of polyketide and nonribosomal peptide synthases in actinomycetes	Martin Sievers (ZHAW, ICBT)
2019	Ta Cam Phuong	Estimating Insertion and Deletion Parameters from Pairwise Sequence Alignments	Manuel Gil (ZHAW, ICLS)
2019	Weichart Sonja	Continued development of an online application for the use in microbial batch cultures: Planning and simulation of experiments and data analysis and management	Robert Vorburger (ZHAW, ICLS)
2020	Atilgan Cahit	Synthetic health data generation with pre- and intraoperative Total Knee Arthroplasty (TKA) parameters for ligament balancing and subsequent outcome analysis	Daniel Baumgartner (ZHAW)
2020	Joseph Abel Thomson	Design of Algorithms to study the property of Reversibility in TKF91 Model	Manuel Gil (ZHAW, ICLS)
2020	Mikos Alexander	A Perception-based Adaptive Immune System Model to describe the Effect of Anticancer Radiation Therapy In-Silico	Stefan Scheidegger (ZHAW, SoE)
2020	Müller Georg	Simulation of Renewable and Self-Sufficient Building Energy	Ivo Kälin (ZHAW, ICLS)
2020	Nüesch Manuel	Simulation of separation tasks using vacuum distillation	Simone Ulzega (ZHAW, ICLS)
2020	Poulose Eldhose	A study of dynamics of Indels using ProPIP, PRANK and MAFFT	Manuel Gil (ZHAW, ICLS)
2020	Seidel Stefan	Gas bubble simulation for the computation of oxygen supply for cells	Werner Sören (ZHAW, ICBT)
2020	Brühwiler Robin	Stochastic Optimization of Time-Dose-Fractionation Schemes in Cancer Radiation Therapy	Sven Hirsch (ZHAW, ICLS)
2021	Antalfy Imre Istvàn	A Data Science Approach to Solid Waste Biogas Plats Data Pre-processing and Modelling with Neural Networks	Martin Schüle (ZHAW, ICLS)
2021	Chandra Saurabh	Analysis of health conditions of cancer patients in palliative care based on movement data tracked by wearable devices	Thomas Ott (ZHAW, ICLS)
2021	Mauch Ueli	Modelling tick risk from uncertain citizen science data. Exploring the benefits of irregular spatial tessellations	Patrick Laube (ZHAW, ICLS)
2021	Krayer Patricia	Modelling Environmental and Nutritional Impacts of Vegan Agriculture	Matthias Nyfeler (ZHAW, ICLS)
2021	Rey Sofia	Health Status Analysis from Wearable Children Patient Data	Sven Hirsch (ZHAW, ICLS)
2021	Roth Sandro	AngioSynth - Cross-modality synthesis of cerebral angiographies using CycleGANs	Norman Juchler (ZHAW, ICLS)
2021	Schmutz Stefan	Characterizing undetermined sequences from metagenomic sequencing	Maria Anisimova (ZHAW, ICLS)
2021	Von Gunten Cédric	Public sequencing data mining and in silico protein masses prediction for improving accurate subspecies determination in Bacillus cereus using MALDI-TOF MS	Jöel Pothier (ZHAW, IUNR)
2021	Von Rotz Sebastian	Evaluation and development of a bioinformatics workflow for amplicon sequencing with nanopore long read technology	Jöel Pothier (ZHAW, IUNR)
2021	Wegmann Thomas	Computer Vision for the Automated Validation of Cancer Drugs	Robert Vorburger (ZHAW, ICLS)
2021	Wrobel Anna	Prediction of parturition in mares based on body sensor data	Thomas Ott (ZHAW, ICLS)
2022	Amacker Julian Martin	Analysis of brain connectivity using phase transfer entropy and deep learning based causal inference	Sven Hirsch (ZHAW, ICLS)
2022	Bajka Daniel	Extraction and Provision of Tacit Knowledge from Institutions Data Repositories on Energy Research	Christian Glahn (ZHAW, ICLS)
2022	Gees Marco	Investigation of the Gene Expression Level for CODON Optimized Heterologous Genes	Christin Peters (ZHAW, ICLS)
2022	Graf Dominik	Automatic interpretation of NMR Spectra using Neural Networks	Martin Schüle (ZHAW, ICLS)
2022	Grossenbacher Amira	Transition analysis of small-scale and at-scale Chromatography Columns	Olivier Merlo (ZHAW, ICLS)
2022	Höhener Rebecca Juliette	Applying Reinforcement Learning to a Production Scheduling Problem	Lukas Hollenstein (ZHAW, ICLS)
2022	Iglhaut Clara Ev Andrea	Indel-Aware Parsimony Methods for Phylogenetic Inferences	Manuel Gil (ZHAW, ICLS)
2022	Joos Matthias	Optimization of the Delirium Algorithm Workflow of the University Hospital of Zurich with Data Analytics and Machine Learning	Thomas Ott (ZHAW, ICLS)
2022	Jordan Sara	Community analysis of methanogenic microbiomes in biogas reactors	Theo Smits (ZHAW, IUNR)
2022	Keel Thomas	Modeling the aging behavior of electrochemical sensors	Caspar Demuth (ZHAW, ICLS)
2022	Memeti Nurdzane	The CRISPR region analysis program (CRAP)	Theo Smits (ZHAW, IUNR)
2022	Schaub Lukas	Cell growth and lifelines analysis CFD Solver Implementation	Dieter Eibl (ZHAW, ICLS)
2022	Senn Saskia	Ensemble of BERT Variants for Depression Detection	Claus Horn (ZHAW, ICLS)
2022	Thomas Chirayil Harry	Evaluation of Transfer Learning for Protein Function Prediction	Claus Horn (ZHAW, ICLS)
2022	Von Däniken Kim	Generating synthetic order data from clinical laboratories using classical methods of statistics and machine learning	Lukas Hollenstein (ZHAW, ICLS)
2022	Walder Tim	Application of data exploration algorithms on a labelled property graph	Robert Vorburger (ZHAW, ICLS)