PhD programme

The NAD PhD programme presents almost endless opportunities for expanding your scientific horizon during the pre-PhD year. At the same time, it is an intense year that makes demands on fellows to reflect on what they learn and make decisions accordingly.  After having finished her first lab rotation, Ginevra Matilde Dall’Ò is still deep in the process of collecting input and scoping out a direction for her PhD project.

For her first rotation, Ginevra joined the Paludan Lab at the Department of Biomedicine, Aarhus University, led by Professor Søren Paludan. Working at the intersection of immunology/virology and neuroscience, the group is interested in how the immune system detects viral infection as well as immune defense mechanisms, with a special interest in the virus-infected brain and its immune defense.  Professor Søren Paludan is also spearheading the Center for Immunology of Viral Infections (CiViA), consisting of five research groups from Aarhus University and the Technical University of Munich. The center aims to address major unanswered questions within virology and immunology and was established in 2022 with a DKK 60 million grant from the Danish National Research Foundation.

New perspectives on the neuroscience field

With a BSc in Cognitive Psychology and an MSc in Cognitive Neuroscience, Ginevra would like to challenge and broaden her understanding of the neuroscience field during the pre-PhD year. She specifically chose the Paludan lab in order to gain familiarity with the (neuro)immunology field as well as neurobiological methods:

“I am thinking about neuroscience and the brain informed by my background in psychology and cognitive neuroscience whereas (…) here, I gain a new perspective on neuroscience from another field, namely immunology. I had the chance to explore how the immune system and the brain interacts and it provided me with a fresh outlook to understand the inner mechanisms of the brain,” Ginevra says.

During her rotation, Ginevra has been involved in a new project in the lab:

“My project has involved a little bit of neuroscience, as I have studied how the metabolite itaconate is involved in (…) the brain’s immune response. It has been previously shown that itaconate is upregulated in the virus-infected brain, so the underlying question was: how might itaconate impact the innate immune responses, and how could the molecular mechanisms involved be deciphered? I started this project working with mixed brain cells from mice, which was really interesting. It was my first time working with cell cultures, so I got the chance to learn new skills and gain valuable experience. It has been quite challenging because the background of this lab is completely different from mine,” Ginevra explains. 

Putting the puzzle pieces together

A lot of work lies ahead for Ginevra and the other NAD fellows when it comes to making sense of the many insights from the pre-PhD year, culminating in drafting and presenting a PhD project proposal later in the year. During her rotation in the lab, Ginevra had the chance to be part of a new project during her rotation in the Paludan lab, and she emphasises how being involved in the early stages and idea-generation phase of a research project is valuable experience leading up to working on her own PhD proposal:

“It has been really nice to see how new projects develop and start, how you get new ideas, and how you direct your research. Now, we have some preliminary data, and things are getting interesting and exciting – and I have to leave,” Ginevra says.

Ginevra has also used these first few months of the pre-PhD year to reflect on how to form a good and translational research question:

”It is really important to me to always take the bigger picture into consideration and keep it in the back of my mind, as you are usually working with a small fraction of larger mechanisms. In this project, the question was more of a basic research question, but it arose from an observation in virus-infected and pathological brains,” Ginevra explains.

In her second rotation at the Department of Neurology at Bispebjerg Hospital with PI Sanne Simone Kaalund, Ginevra is interested in exploring clinical aspects of neuroscience further. In this rotation, she will be working with post-mortem brains of patients diagnosed with multiple system atrophy (MSA), analysing Lewy bodies. While the research itself will not be clinical, she will have the opportunity to shadow a clinician and be part of a hospital environment.

Ginevra is determined to get the most out of the pre-PhD year. This means that she is still very open, both when it comes to her third lab rotation and her future PhD project:

“Here in the Paludan Lab, I work with molecular and cellular systems. Next rotation will be more focused on stereology with a hint of clinical perspective, so maybe the third rotation will be something that combines those two, a bridge. I would also like to get more experience within animal models, so that might be something that I would like to take into consideration.”

The pre-PhD year is a process, and Ginevra is constantly working to pave the way for her future PhD project:

“I think it is just like a puzzle. Currently, I am putting all the pieces together – let us see how the final picture will turn out.”

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The field of computational neuroscience is in rapid development, and data analysis and machine learning methods are of great interest to neuroscientists around the world as they can help make sense of large and complex data sets and provide new ways of approaching a scientific question.

Both Marta Tataryn (MSc in Neuroscience, University of Trieste) and Emma Kragelund Christensen (MSc in Neuroscience, University of Copenhagen) are trained as experimenters – however, they both came into the NAD PhD programme with a profound interest in computational neuroscience and data analysis methods. This led them to choose to do their first rotation at the Analysis Group with PI Associate Professor Diego Vidaurre, a part of the Center of Functionally Integrative Neuroscience (CFIN) at Aarhus University.

The Analysis Group develops computational models for brain activity across a range of data modalities; invasive and non-invasive electrophysiological data as well as neuroimaging data. They strive to characterise and understand the brain’s spontaneous activity and how this activity shapes perception and, most generally, our relation to the world. Since the way our brain works is in certain ways unique to each of us, these models are fitted at the individual level, which in turn allows the group to study how these subject-specific models relate to and predict behavioral traits and clinical variables.

The group works with datasets generated by a wide range of collaborators from all over the world.

From experiments to analysis

While both fellows share an interest in the data analysis field, their projects during the first rotation have been quite different.

Marta’s main research interests center around perception, memory and learning, and her project during the rotation focused on working with human data sets and improving her skills within coding and machine learning:

“My project was based on investigating spontaneous activity in the brain and especially how this spontaneous activity influences human tactile perception. For my investigation I used an MEG dataset, previously acquired in Dusseldorf University. It was based on a tactile discrimination task designed to be ambiguous. This means that that there were two closely related tactile stimuli in time, so it was difficult for each subject to say whether they perceived one or two stimuli. It was my first time working with a human data set and applying machine learning, which is a computational neuroscience method used to decode brain activity. During my project I decoded behavioral outcomes, so the correctness of the perception in this case, from the spontaneous brain activity.”

Marta feels like this rotation has helped her learn things on two different levels. One is the big picture: as it was Marta’s first time working with a human data set, she feels like she had some exposure to the complex questions that you can ask based on this type of data sets. The other level is the small details: Marta dramatically improved her coding skills, and she learned how to structure human data sets.

One thing that proved challenging for Marta was the lack of ownership over the experiments that data were based on:

“It was a new experience because I was trained as an experimenter, so it was my first time not doing experiments myself. Analysing that dataset was challenging for me as I am new to both cognitive science and machine learning. Without daily discussions with the experimenters to clarify the data structure and their research goals, I encountered some difficulties in understanding the context of the data,” she explains

At the same time, this provided her with valuable time to dive into the complex methods:

“I am happy I started my rotations this way because, being new to my project, I had to spend a lot of time reviewing literature and going through online tutorials to understand it better. This gave me the perfect chance to begin formulating my research question. During this rotation, I acquired a broad perspective of what could be feasible or not. It offered me the tools to move forward in the direction that I want to go. Also, working with human data sets helped me understand what types of questions I could ask,” Marta explains.

With her pre-NAD work centering on spinal cord injuries and spasticity in mouse models, the field of data analysis is also quite new to Emma. For her project in the first rotation, she has been focused on pseudotime analysis:

“Pseudotime is […] latent temporal information that you extract from a data set. Most typically […] single cell data sets, gene expression data. You try to look at the data and find a pattern that can tell you what is going on in the biological process of this particular cell. So you order the cells by the state that they are in,” Emma explains.

During her rotation, Emma has done work based on findings from a paper by Campbell and Yao, who have developed a pseudotime algorithm called Phenopath:

“The authors have developed a pseudotime algorithm for heterogeneous datasets by incorporating covariates to account for their interaction effects on the biological process. By doing this, they suggest that it may be possible to use this algorithm on different kind of data that is not single cell or gene expression data. I tried using it on structural MRI data, focusing on gray matter volumes. Conditions like Alzheimer’s disease are characterized by a large loss of gray matter volume, but gray matter loss also naturally occurs with age. I was trying to implement this algorithm to see if there was a way to find a pseudo-temporal trajectory in the data that allowed me to distinguish healthy subjects from Alzheimer’s disease subjects. The goal was to see whether it could be used as a diagnostic tool,” Emma explains.

Her preliminary results show that there is definitely something to build upon.

Building a basis for a PhD project

Overall, this first rotation has given the two fellows a unique opportunity to dive head-first into the field of data analysis and computational neuroscience, an avenue they are both going to explore further during the pre-PhD year. Both of them expect to use data analysis techniques and computational methods extensively in their PhD projects.

Emma is currently conducting her second rotation at the Danish Research Centre for Magnetic Resonance with PI Kristoffer Hougaard Madsen. She is working with resting state functional MRI data and decomposing the data using ICA (independent component analysis).

Marta is carrying out her second rotation at the Neurobiology Research Unit at Rigshospitalet in the group of Cyril Pernet:

“During my second rotation, I am focusing on developing a paradigm and implementing it to map reward circuits using fMRI within a reinforcement learning framework. I feel that this rotation is laying the groundwork for any project I might undertake during my PhD. I am in the process of defining my scientific question and trying to span between the most methods and perspectives I can, both to refine the question and to identify the best approach to study it. I am exploring, and I am really happy about what is coming out of it,” Marta concludes.

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When you first meet Carolyn, you are taken aback by her passion for what she does; she has a natural and infectious curiosity that drives her in her work. Carolyn did not go into the NAD programme with a clear idea of what topic she would like to investigate for her PhD project. Instead, she has been very method-focused when scoping out potential rotation labs:

“I was looking at methods a lot because I wanted to see what I want to use in the future. I knew from the beginning that omics was going to be a part of my PhD project because I like that type of data analysis, especially the breadth and the multi-applicability of it, so I am using the rotation process to dive into this approach. In addition, I really wanted to do at least one rotation involving surgical procedures.”

This led her to approach Professor Winnie Jensen of the Neural Engineering and Neurophysiology Group at Aalborg University Hospital for her first rotation. Winnie’s group works within the field of electrophysiology and electrophysiological animal models:

“I have been working interfacing the nervous system ever since I was a PhD student. I have an engineering background, so my unique approach and one of the things we are strong at here in Aalborg is electrophysiology. I use implantable devices that you could say are comparable to a pacemaker for the peripheral or central nervous system,” Winnie explains.

Winnie is currently occupied with developing chronic pain models of Danish farm pigs, and this is also the project that Carolyn has been involved in.

Making new connections

During her rotation, Carolyn has been broadly involved in the lab’s work: she has done animal behavior, attended surgery courses and observed surgical procedures. She has also been involved in dissecting pigs in addition to preserving and processing samples.

While getting involved in the lab’s current project, Carolyn saw an opportunity to build upon the lab’s existing work. Drawing on her previous experience with mass spectrometry, Carolyn suggested that the samples preserved from the pig dissections were sent for further analysis in order to piece together a map of the adult pig brain:

“I brought up the possibility of bringing some of these tissue samples over to process full RNA sequencing for transcriptomic analysis because the proteome is so spotty. It is quite difficult to put together, but if we could pair it with a transcriptomic analysis, that is a whole project right there. Then you would be piecing together something like a neural atlas of the adult pig”, Carolyn explains.

This project could potentially be highly translatable as pigs have crucial similarities in neurotransmitter systems to humans: “We know very little about the different brain regions in adult pigs, especially the peripheral nervous system and spinal cord. Lots of studies are done in fetal pigs, and with so many industries now coming up with more pig studies, mapping the adult pig brain is going to be extremely relevant”, Carolyn says.

Carolyn’s fresh perspectives has led Winnie to think about the possibility of establishing a collaboration with another lab with expertise within mass spectrometry – a great example of how the rotation process can also set new collaborations between labs in motion:

“I think that is why it is actually nice to have Carolyn come in and be open because proteomics is not my expertise at all. I think it is a really nice example of complementing each other so that we can actually add on to what we do.”

Prior to starting her rotation, Carolyn went to Aalborg for two days to visit Winnie’s lab. She had the opportunity to see the behavior and the surgery, and she was introduced to people working in the lab.

“We were lucky with the timing. We talked in October, and I told Carolyn that we had a surgery going on in November. I think the visit was really good because Carolyn could see what environment she would be heading into, and we also got to explore directions for the rotation project”, Winnie says.

Carolyn, who has done her MSc in Human Biology at the University of Copenhagen, is definitely excited about the research community in Aalborg:

“I have moved around a lot and been to many different cities, and I think this has to be the easiest transition I have ever had.”

Winnie chimes in, pointing out that Aalborg also has a thriving environment for junior scientists.

The rotation process poses a number of benefits, both to NAD fellows like Carolyn, but also to the Danish neuroscience community as a whole. While the NAD fellow is exposed to new techniques and research areas and has the chance to build their network, the PI and host lab can also benefit from the perspectives that the NAD fellow brings into the lab, potentially paving the ground for new collaborations.

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For her first lab rotation, Sofie Aarup Bach changed out the familiar streets of Copenhagen with those of Aarhus, working in the CNS Disease Modeling Group at Aarhus University led by Associate Professor Marina Romeo-Ramos. The group focuses on the neurodegenerative processes in Parkinson’s disease and the interplay with the immune system in this disease, mainly working with animal models and biosamples from patients.

New perspectives on existing knowledge

NAD fellows have a lot of freedom when choosing their rotation lab, and this means that they are also responsible for establishing contact and planning their rotation with their PI. Sofie took several things into account when choosing a lab for her first rotation, including scientific perspectives, work environment and supervision style:

“I looked into the techniques Marina was using and I could see that some of them overlapped with things I have done before, which made me think that I could both learn something new and contribute to the lab’s work. For me, it was also a priority when moving somewhere different that I would come to a place with structure and where things are under control, and that has also been my experience after coming here.”

As it is challenging to design a full project to be completed in just 10 weeks, especially when it involves working with animals, Sofie and her PI Marina agreed prior to the start of the rotation that Sofie should instead be involved in all the different projects in the lab:

“In the first week, I did animal behavior in the animal facility, and I have done immunostaining of mice and rat brains. I have also analysed blood samples from Parkinson’s patients. Lastly, I have been performing flow cytometry, which is a technique that allows us to separate different immune cells to see if there is a mismatch between immunity cells in Parkinson’s disease patients and other patients. I think it has been really good to get a sense of the entire lab.”

This first lab rotation has also shed new light on Sofie’s main research interests:

“I have previously worked with Parkinson’s disease with a more dopaminergic focus, thus the immune system as a contributing factor or even a driving factor in the disease has brought a new and interesting perspective to my already acquired knowledge. I would not mind pursuing this further or at the very least keep it in mind in my future research.”

A home away from home

Sofie, who is currently based in Copenhagen, stayed in Aarhus during the week for the duration of the 10-week rotation, going back to Copenhagen every weekend to spend time with her family. While she has sometimes found it challenging to combine working in another end of the country with family life, Sofie has also seized this opportunity to fully delve into life in the lab:

“Since I have moved away from most of the people I know, I was worried that there would not be enough things to fill out my day. I have been very positively surprised that I have always had something to do in the lab. I feel like I am actually contributing and not just sitting at my desk. (…) It has also been a good experience to be included in a social lab environment where I do not have to say no because I have to pick up my daughter at daycare. I can stay late in the lab, and I can always participate if someone decides to go out for pizza after work.”

Looking towards a PhD project

This first rotation has informed Sofie about her future PhD studies in more ways than one. Before starting her rotation, Sofie was hesitant about working with live animals, but after having a chance to try it out, she would like to include at least some in vivo work in her PhD project. She has also had a chance to reflect on her preferred supervision style:

“I think Marina seems like a very present supervisor who knows what the members of her lab are doing, and she knows the progress of their projects. Her door is always open for questions, and I have realized that I would also like a very involved supervisor who has time to answer questions and knows how it is going and the progress in a project. I think that a good aspect of this programme is that it is a great opportunity to get to know your own preferences in regards to supervision.”

Regardless of where Sofie chooses to do her PhD project, she has made lasting connections:

“I really like Marina and all the people in her lab, and I hope that we can collaborate in the future, even if I do not decide to come here for my PhD project.”

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Yes. Applications are open to candidates
anywhere, and you do not need to be in Denmark when you apply.
Relocation happens after an offer.

No. The pre-PhD year exists so that you can
rotate through three laboratories before choosing. You apply to the
programme, not to a group.

Fellows are employed by their host
university on standard Danish PhD terms. The salary is stated in the
call, which is where to read it: the figures follow the collective
agreement and change.

Yes. Applying again in a later round is
permitted and is not held against you.

You are not tied to a rotation laboratory.
The programme finds you a suitable group, and the grant follows you
wherever you land.

The most recent round drew 807 applications
for 16 fellowships. Read the call carefully and make sure you meet the
criteria before applying.