Nanobiology student
I am Matthijs Leenders, currently a second-year MSc Nanobiology student. While following some elective courses, I found my interest in the data sciences and modeling of biophysical processes. Therefore, I am happy to do my master’s thesis at the Arjen Jakobi lab. I will simulate cryo-EM data with advanced motion models to mimic empirical data. Besides studying, I currently work as a data scientist at Genescape, a startup that aims to provide robust patient estimates and models for rare diseases. In my free time, I like to do sports (running and football) and play board games. Furthermore, I spend too much time watching sports and Netflix. I am eager to apply my data science and biophysical modeling skills to contribute meaningfully to my academic and professional endeavors while continuing to enjoy the balance that my hobbies and interests bring to my life.
Nanobiology student
Hi, my name is Birgit and I am a second year master student Nanobiology. I will be working with Alok on time resolved cryo-EM. We are trying to create a setup which can freeze proteins at small intervals. Outside of the lab I enjoy theatre and I am participating in a 100km rowing competition.
Nanobiology student
I am Phuong Nguyen, a second-year MSc Nanobiology student. I am from Vietnam, as you can tell from my name, and I am always excited to share with everyone about my heritage and culture. I also enjoy trying out new Asian restaurants in Rotterdam, so you can come to me if you need any recommendations. I have been really interested in structural studies using cryo-EM since my MEP, thus I am really happy to be able to learn the basics of cryo-EM and image processing during my internship. I hope that I will produce some useful data for the structural study of interactions between nanobodies and GBPs.
Nanobiology student
My name is Alex van Tol and I am a third-year Nanobiology BSc student. My passions lie in the fields of applied physics, computer science, and optics. For this reason, I am doing my bachelor end thesis at the Jakobi lab as it perfectly combines these subjects. My thesis is on simulating cryo-EM data with different motion models to mimic empirical data as best as possible.
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Applied Physics student
I am Mats Lenes, a BSc Applied Physics student. I love trying to solve useless math problems with interesting solutions. I also do a lot of rock climbing at the local bouldering gym. At the Jakobi lab, I am developing an AI model for simulating noise from cryo-EM images using a generative adversarial (GAN) network, this involves doing a lot of data analysis and preprocessing.
Nanobiology student
I am Lotte Veerbeek and I am a third-year Nanobiology BSc student. I am working on my bachelor end project under the supervision of Alok. This end project regards deep-learning based segmentation of detergent belts in cyro-EM maps. Where traditional methods struggle to segment these, I will be employing transformer and convolutional neural networks to segment out the lipid belt.
Nanobiology student
My name is Ana and I am currently a 3rd-year BSc Nanobiology student. Previous to that I studied Chemical Engineering in Croatia before a change of interest occured.
Apart from studying, I work as a production engineer at a company that automates graphene liquid cell assembly to improve high-resolution liquid phase TEM imaging. Although a lot more technical than my current studies, I very much enjoy constantly learning about this field.
During my free time, one of my favorite things to do is collecting and listening to records, as well as playing table football, which I never say no to!
Nanobiology & Econometrics student (September 2022 - July 2023)
Subsequently: Junior specialist at Jamie Fraser’s lab at UCSF
I am Flip Jansen, a third-year MSc Nanobiology student with an MSc in Econometrics from the Erasmus University Rotterdam. Generally, I seek projects and interests at the intersection of these disciplines; therefore, I am joyous to be able to pursue an MEP which involves machine learning and statistical analysis at the Jakobi lab.
During my MEP, I will try to improve gas vesicles’ structural and biogenesis model by analysing Cryo-EM images.
Through my studies, I came to appreciate the considerable effort that can go into obtaining a structural model of the smallest components of life. I am, therefore, very excited that I might be able to contribute to this effort with my MEP.
Nanobiology student
I am a BSc Applied Physics and BSc Applied Mathematics student with an interest in machine learning. For my bachelor thesis I will try implement deep learning networks to predict signatures of biological macromolecule structures determined by cryo-EM without the use of atomic models.
Applied Physics student (February 2021 - June 2022)
Subsequently: Data Scientist at BCG X
I am Reinier de Bruin, a second year MSc Applied Physics student, enrolled in the Health and Life track. After doing a few extracurricular computer science courses, I got excited about doing a MSc thesis project that lies at the junction of biophysics and computer science.
At the Jakobi lab, I will try to develop new algorithms to improve interpretation of three-dimensional (3D) volumes of protein complexes obtained by cryo-EM imaging. This will consist of coming up with suitable 3D map metrics, designing and training a deep neural network and benchmarking this network against a phyiscs-based contrast restoration procedure. By doing this, we hope to improve the reliability of interpretation for cryo-EM maps.
Outside the lab, I like following societal developments, while having the tendency to let myself believe that I would do a better job than the currently employed politicians at solving them. Given the very low chances of me being a rare undiscovered political talent, we can safely assume that that’s not true. While being fed up about that rather undisputable conclusion, I enjoy going out for a run or do other sports. Like most, I like hanging out with people I find interesting and fun, because in the end, people are amazing: that’s where it’s all about.
Nanobiology & Computer Science student (February 2021 - June 2022)
Subsequently: Sofware Developer at IVO
I am a Nanobiology bachelor student, doing my BEP at the Jakobi lab. I will look at algorithms from small angle x-ray scattering as a potential new way to produce initial models that are usable for cryo-EM structure determination.
Nanobiology student (February 2020 - February 2021)
Subsequently: PhD student at Wageningen University
My name is Anna Daamen and I am a Nanobiology master student. The High Resolution Imaging course during my first year as a master student is what got me excited about electron microscopy, so in February I started my Master End Project in the Jakobi lab. During my project I will try to reconstitute the lipid modification of proteins in intracellular immunity in vitro and in vivo. The lipid modification of these proteins is what enables them to interact with the membrane and assemble in large molecular machineries. I will study their assemblies on liposomes and the interactions with the membrane using Cryo-EM.
Nanobiology & Computer Science student (February 2020 - February 2021)
Subsequently: Medical Physics Engineer at Holland PTC
As a Nanobiology master student, I am doing my academic internship in the [Jakobi Lab]https://cryoem.tudelft.nl(). The group focuses on cellular auto-immunity, but the mechanisms the key proteins carry out are still quite unknown. Therefore I will look into the interactions between these proteins as this could give more insight in their different functions. I am curious to see what we will find out!
Nanobiology student (September 2019 - November 2020)
Subsequently: Application specialist at Delmic
As part of my masters Nanobiology, I am doing my final project in the Jakobi lab. I will be working on the development of a new correlative imaging and nanomanipulation setup for cryo-EM sample preparation. With this setup, we will be able to investigate processes of cell-autonomous immunity in an entirely new way.
Nanobiology student (September 2019 - August 2020)
Subsequently: PhD student with our friends in the Jacob Hoogenboom Lab at ImPhys
I am a Nanobiology student doing my MEP project in the Jakobi lab. I am interested in high-resolution imaging, image processing and data science. Therefore I took on the challenge to develop new methods that aim to utilize machine learning tools to automate data collection and analysis of electron diffraction data from macromolecular crystals. These tools will hopefully contribute to accelerating structural analysis of biomacromolecules using electron diffraction. When I am not analyzing data I like to play songs on my guitar or swim some lanes in the pool.
Applied Physics student (September 2019 - November 2019)
Subsequently: Junior Consultant Energy Transition at BDH
I am a 3rd year bachelor student in Applied Physics and currently doing my final BEP project in the Jakobi lab. I am working on the data processing of electron diffraction patterns from crystals. From these patterns the orientation and structure of a crystal can be determined. In my project I try making data analysis of these patterns easier and more automated.
Nanobiology student September 2018 - July 2019)
Subsequently: PhD student at Debye Institute for Nanomaterial Research
I am a Nanobiology student doing my master thesis at Jakobi lab and Brouns lab. I will study recombinant phages with using cryo-EM and (hopefully!) resolve a high-resolution 3D structure of the phages to gain more insight into phage evolution. My project will consist of the optimization of the sample preparation, finding the best imaging technique and the image analysis of the microscopy data.
Nanobiology student (April 2019 - July 2019)
Subsequently: PhD student at Erasmus Medical Center
I’m a third year Nanobiology student and I’m doing my BEP at Jakobi Lab. I will be working on the contrast enhancement in the image analysis of the electron microscopy. The current program needs an initial atomic model for contrast enhancement and I will try to get rid of this. With this we could get a better look at proteins we don’t know anything of yet.
Nanobiology student (April 2019 - July 2019)
Subsequently: Research Associate at Genmab
I am a bachelor student in the Nanobiology programme working on my BEP in the Jakobi Lab. I am trying to develop co-expression systems for lipid modification of intracellular immune effectors.
Nanobiology student (April 2019 - July 2019)
Subsequently: Consultant at ttopstart
As a Nanobiology Bachelor’s student, I am working on my Bachelor End Project in the Jakobi Lab. I will be working on in vivo biotinylation of intracellular immune effectors. This will eventually enable me to study the interactions between these effectors in higher-order assemblies and to visualize these interactions using cryo-EM.
Nanobiology student (April 2018 - August 2018)
I am third year student in the Nanobiology program and I am currently doing my BEP in the Electron Nanoscopy group at the Bionanoscience department. In this project I will be working on faciltiating the interpretability of single particle cryo-EM maps by further developing local sharpening as implemented in the LocScale method.
Life Science and Technology student (April 2018 - August 2018)
I am currently in my third year of the Life Science & Technology program. For my BEP, I joined the Electron Nanoscopy group at the Kavli Institute in Delft. For this project, I will focus on the isolation and characterization of proteins involved in the cellular response against viral or bacterial attacks.
Kavli Institute of Nanoscience
Department of Bionanosciene
Delft University of Technology
Van der Maasweg 9, 2629 HZ Delft
