Judith Boer, PhD, Assistant Professor
Laboratory of Pediatric Oncology/ Hematology, Erasmus Medical Centre, Sophia Children's Hospital, Rotterdam
Centre for Human and Clinical Genetics, Leiden University Medical Centre
1. What is the leading research theme in your group?
"I am an ‘embedded’ bioinformatician in the translational molecular research group headed by Dr. Monique den Boer. Our group works on childhood leukaemias and particularly on identifying molecular markers that can be used in diagnosis to establish the specific subtype of leukaemia or can be used to predict clinical outcomes in patients. My work focuses on developing and implementing smart models that allow integration of data on various biological levels. We look beyond gene expression data and besides patient gene expression profiles have access to copy number data, microRNA profiles and protein profiles. Integrating all this data to better understand the biology of the disease and to develop better classifiers is the main objective."
2. With what type of groups or organisations do you collaborate most and why?
"For one day a week I work at the LUMC and I collaborate with the group of Renée de Menezes at the VUmc and with the group of Lodewyk Wessels at the NKI on method and model development and implementation. Through my Leiden-connection, I'm also involved in a variety of biological projects that are not focused on leukaemia. In general, through NBIC, a lot of different collaborations have been established on different topics. But also on education activities, for example a course on expression analysis for biologists, which I started about 12 years ago. I try to get biologists to work with their data as much as possible, it really helps them to get more out of their data, which in the end they know the best."
3. From your research perspective, what are the main challenges in bioinformatics right now?
"Looking at my own work my main challenges relate to rather mundane issues like the different way patient information is recorded and stored here. Getting simple things like unique identifiers for each patient in place takes a lot of discussion and organising and convincing. And this does not yet involve the molecular information, let alone the downstream problem of analysis and interpretation. There is already a lot of work to be done before you can start concentrating on the problems relating to the actual integration of the data."
4. What is the most important task of a group leader?
"Right now, I am not in the position of group leader, but I operate in various projects in which I mostly act as an interpreter to bridge the worlds of the clinicians and biologists on one side and the biostatisticians and bioinformaticians on the other. My main role is to quickly determine what is important for both sides and where the opportunities for progress are."
5. How would you describe the atmosphere in your group?
"In the project teams I work with, the atmosphere is very positive. I have always found bioinformaticians to be very enthusiastic and willing to explain their methods and apply them on new datasets. Biologists sometimes require a little more convincing to take on a new approach and try a new method, but that is also part of my role in these projects."
Text by Esther Thole.