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Master's thesis

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.

Fields of Interest

Master’s Thesis at Partner University

Partner University Contact Topics / Field
Bioinformatics and System Biology University of Giessen, Germany

Exchange Programme
With the University of Giessen we have
a SEMP contract (Swiss-European Mobility
Programme) where you get financial
support for the exchange.
Jochen Blum
Theo Smits
Maria Anisimova
  • Microbial Bioinformatics:
    Genome annotation,
    Comparative genomics
  • High-throughput data analysis:
    Cloud-Computing / Big Data- Pipeline / Workflow-Development,
    Research data management
  • Algebraic dynamic programming:
    Microbiome data analysis
  • Data Science Departement Worcester Polytechnic Institute WPI, USA

    Exchange Programme
    The WPI is an official partner university of ZHAW.
    Elke A. Rundensteiner
    Claus Horn
  • Data Science and Big Data Analytics,
    Big Data Infrastructures and
    Data Management
  • Artificial Intelligence, Machine Learning
    and Data Mining
  • Visual and Interactive Analytics
  • Fair Artificial Intelligence and Decision Making
  • Digital Health:
    Leveraging Smart Digital Technology
    for addressing Wellness & …
  • For more information, please visit our website for the international exchange options or contact Dr. Matthias Nyfeler, the head of the ACLS Master's programme.


    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) Olivier Merlo
  • Chromatography, when biology goes quantum
  • Biotechnological Processes

    Research Group Contact Topics / Field
    Biosystems Technology (ICBT) Christin Peters
  • Enzyme cascades
  • Biocatalysis
  • Biotransformations
  • Centre for Analytical Chemistry (ICBT) Caspar Demuth
  • Development and application of sensors)
    for bioprocesses
  • Online bioprocess analytics
  • Characterisation of sensor components
  • Centre for Biocatalysis, Environmental-
    and Process-Technology (ICBT)
    Rebecca Buller
  • Biocatalysis
  • Biotransformation
  • Process Development
  • Process Scale-Up
  • Enzyme Engineering
  • Directed Evolution
  • 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
  • Applications in Environment and Agriculture

    Research Group Contact Topics / Field
    Geoinformatics research group (IUNR) Patrick Laube
  • GIS, Geographic information Science and Geoinformatics
  • Computational Movement Analysis and Mobility Analytics
  • Remote Sensing (Satellite – Airplane - Drone)
  • Landscape Analytics / Dynamics
  • Spatial algorithms
  • Spatio-temporal data science
  • Spatio-temporal Environment Analysis
  • Spatio-temporal Environment Analysis
  • Natural Hazard Assessment
  • Cognitive Computing in Life Sciences (ICLS)
    Collaboration with Intel
    Yulia Sandamirskaya
  • Brain-inspired robotics and AI
  • Real-time 3D vision
  • Neuromorphic computing
  • Computational Environment (ICLS) Martin Schüle
  • Data science, machine & deep learning
  • Natural language processing
  • Complex system modelling
  • Cellular automata, application focus in
    environmental sciences and finance
  • Institute of Computational Life Sciences (ICLS) Thomas Ott
  • Bio-inspired algorithms, complex system dynamics
  • Forecasting
  • Seed classification using pattern recognition
  • Institute of Computational Life Sciences (ICLS) Ivo Kaelin
  • Statistical data analysis
  • Mathematical modeling
  • Identification and quantification of estrogenic
    activity in freshwater samples
  • Advanced Signal Analytics (ICLS) Matthias Nyfeler
  • Deep learning in signal- and image-processing
    as well as time-series data
  • Bioacoustics, rockfall
  • modelling, data analysis and machine learning of
    environmental and financial impacts of urban
    landscape architecture in Zurich in
    collaboration with Landsale AG
  • Autonomous Learning Systems (ICLS) Claus Horn
  • Build the next generation of AI solutions by integrating
    deep learning and reinforcement learning techniques
    to create autonomous AI agents
  • Develop AI solutions for protein engineering
  • Agricultural and Resource Economics
    Group (IUNR)
    Raushan Bokusheva
  • Application of statistical approaches for
    assessing the impact of climate change
    in agriculture
  • Climate change economics
  • Adaptation to climate change in agriculture
    (supervisor has access to large panel dataset
    from Europe and Eastern and Southern Africa)
  • Trade and environment
  • Environmental Biotechnology (ICBT) Hans-Joachim Nägele
  • Biogas simulation data analysis
  • Process simulation in bioengineering and biotechnology
  • Analysis and optimization of real plant processes
  • Application focus in life science, environmental science
    and production of bioenergy
  • Research Group Ecotechnology (IUNR) Andreas Schönborn
  • Thin-layer chromatography with AI in
    collaboration with a startup for the evaluation
    of microcontaminants in food, plastics and
    the environment
  • Edge Computing & Interfaces (ICLS) Christian Glahn
  • Connecting dynamic physical infrastructures
    with digital environments and processes
  • Linking IoT, Edge and Cloud Computing to support automation
    and decentral smart data processing in the life sciences
  • Aquaculture Systems (IUNR) Dominik Refardt
  • Research projects at the interface of computer science
    and biology/engineering
  • Model technical and biological aspects of aquaculture
    facilities or photobioreactors to improve their design and construction
  • Development of software prototypes that use machine
    and deep learning to automatically assess the health
    of fish using computer vision
  • Development of a customized software solution
    for recirculating aquaculture and hydroponic production
  • 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.

    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)
    2023 Baiges Samuel Polypharmacy Analysis in Delirium ICU Patients Stefan Glüge (ZHAW, ICLS)
    2023 Benvenga Vanni Food Pathogen Metagenomics Theo Smits (ZHAW, IUNR)
    2023 Berger Thomas Advanced Spectroscopic Analysis and Data Exploitation Concepts in Bioprocessing Lukas Neutsch (ZHAW, ICBT)
    2023 Bertoz Marc Oliver Deep Learning for Vortex Detection and Tracking in Cardiac MRI Robert Vorburger (ZHAW, ICLS)
    2023 Biland Julien Exploratory Analysis of Peripheral Neuropathy Patient Biomarker and Symptom Characteristics Norman Juchler (ZHAW, ICLS)
    2023 Bourtzos Anastasuios Bayesian inference for skeletal muscle structure and perfusion estimation from magnetic resonance imaging Georg Spinner (ZHAW, ICLS)
    2023 Breitenmoser Linus Automatic creation and selection of mechanistic models of cell culture processes in bioprocess engineering Lukas Neutsch (ZHAW, ICBT)
    2023 Bürkli Tim Electric Power prediction of a waste incineration plant using machine & deep learning Robert Vorburger (ZHAW, ICLS)
    2023 Gericke Eric Flood Modeling With Neural Cellular Automata Martin Schüle (ZHAW, ICLS)
    2023 Graber David Protein Interaction Prediction with Graph Convolutional Networks and AlphaFold-predicted Protein Structures Claus Horn (ZHAW, ICLS)
    2023 Grossmann Leonie Automated Quantification of Histological Constituents in Thrombosed Aneurysms Norman Juchler (ZHAW, ICLS)
    2023 Imstepf Nicolas Re-Programming of Fe(II)/α-Ketoglutarate-Dependent Hydroxylases to Halogenases Rebecca Buller (ZHAW, ICBT)
    2023 Koch Kilian Deep learning assisted X-ray photoelectron spectroscopy analysis Martin Schüle (ZHAW, ICLS)
    2023 Kunz Domink AI-based patient identity verification for radio-therapeutic 3D cone beam computed tomography Norman Juchler (ZHAW, ICLS)
    2023 Maslov Dmitry Federated Learning for Speech Processing on the Edge: Practical Implementation and Considerations for Reducing Network Bandwidth Requirements of Voice-Aware Edge Computing Applications Christian Glahn (ZHAW, ICLS)
    2023 Maurer Manuel Data driven analysis of Fluorescence Spectroscopy of Algae as a compound monitoring tool in Bioprocesses Lukas Neutsch (ZHAW, ICBT)
    2023 Medici Milo Data Framework to Characterize and Identify Wildlife Corridors Robert Vorburger (ZHAW, ICLS)
    2023 Mohammad Yar Kevin Machine-learning assisted engineering of a Fe(II)/αKG-dependent Hydroxylase to accept lignin derivatives Rebecca Buller (ZHAW, ICBT)
    2023 Orbeanu Georgiana Evaluation of Deep Neural Networks for Haematology Image Classification Stefan Glüge (ZHAW, ICLS)
    2023 Rey Phil Automatic spinal canal segmentation on axial spine MRI images using a U-Net CNN Georg Spinner (ZHAW, ICLS)
    2023 Rieder Jonathan Applied Machine Learning Algorithms for automated Flow Cytometry Data Evaluation Lukas Neutsch (ZHAW, ICBT)
    2023 Saxer Jasmin Ontology-Aware Biomedical Text Classification Ahmad Aghaebrahimian (ZHAW, ICLS)
    2023 Schittly Timo Dynamic modelling of nitrogen flow through fish gut to estimate nitrogen excretions Dominik Refardt (ZHAW, IUNR)