Today, we visited the primary school of SFB Melle and explained some biological and bio-informatics concepts to 11- and 12 year olds. They now know which immune cells reside in our lab, could pipette some beautiful colors, they looked at their own cheek cells through the microscope, did a flow cytometry experiment, extracted their own DNA and tried to let a robot eat a sandwich with "muizenstrontjes". A day filled with science!

Another Saeyslab PhD student graduated! We are sad to see you go and we will miss you in our cytometry team. Congratulations dr. Couckuyt!

Following tradition, we had our secret Santa Saeyslab dinner. We all wish you the best papers, research and love for 2024.

Despite their amazing performance across many tasks, deep neural networks are in fact very fragile: small and insignificant perturbations can cause them to produce wrong results. Much research has gone into this problem over the past decade, but we are still far from satisfactory solutions. In our recent survey paper, we discuss the history of the field and its most salient contributions. We pay particular attention to the shortcomings of existing methods and identify promising avenues for future research towards robust machine learning.

Each year, Clarivate recognizes “Highly Cited Researchers” who have demonstrated significant and broad influence in their field of research. Researchers are selected based on their exceptional contributions to their research field, as judged by papers that rank in the top 1% by citations for a field and publication year in the Web of Science™.

This year, Yvan is one of the less than 7125 or 0.1% of researchers worldwide who are recognized as “Highly cited researchers". Congratulations to Yvan!

We recently analyzed a 28-color cytometry dataset with data from more than 3000 healthy donors! While our computational pipeline was more sensitive to technical issues than the manual analysis pipeline, we still identified several immune populations correlating with age and discovered a distinct immune signature for patients with a CD45 SNP. Thanks to Thomas Liechti and Mario Roederer for the opportunity to work on this dataset!

Katrien recently got her paper published where she collaborated with clinicians from the Erasmus MC Cancer Institute in Rotterdam. 

In this study, a phase II clinical trial was conducted to evaluate adjuvant dendritic cell-based immunotherapy in patients with malignant peritoneal mesothelioma. The therapy was found to be feasible and safe, and showed promising survival outcomes. In addition, a comprehensive computational cytometry analysis revealed immune modulatory effect on lymphoid cells and induced memory T-cell activation.

Lotte spent a fruitful week at the ProbAI summer school in Trondheim thinking about how we can incorporate prior knowledge and uncertainties into our ML models.

Can you spot her?

Our FlowCore received the very first BD FACS Discover S8 which means that we will receive a large number of data in the future. Fortunately Sofie reassured us that we can handle this!

Annelies participated in the soapbox science event. She presented her research to people passing by using only a piece of cardboard and some LEGO blocks.

We are proud to present this new paper published on bioRxiv showing two improvements to our NicheNet ecosystem for studying cell communication. NicheNet-v2 is an update of our ligand-receptor-target model. MultiNicheNet is a new tool for differential communication analysis. 

It was time for another teambuilding where multiple colleagues succeeded in beating two escape rooms!

This weekend, SaeysLab was represented on the science festival "Nerdland". We brought our tiny flow sorter and giant decision tree to explain our diagnostic pipelines to fellow science enthusiasts.

The entire cytometry team visited Montréal to attend the CYTOmeeting. With 2 workshops (about preprocessing and collaboration), 4 talks and 2 posters, they were highly represented on the conferences. We learned a lot and spread the word about our computational cytometry tools and pipelines. The parties were of course a nice addition as well.

Today, we visited the primary school of SFB Melle and explained some biological and bio-informatics concepts to 11- and 12 year olds. They now know which immune cells reside in our lab, could pipette some beautiful colors, they looked at their own cheek cells through the microscope, did a flow cytometry experiment and extracted their own DNA and tried to let robot Arne eat a sandwich with "muizenstrontjes". A day filled with science!

It was that time of the year again. Our lab was unreachable for three days because of our teambuilding stay. Short recap: Wonderful food, home-made escape rooms, learning how to debug properly, an AI quiz, brainstorming about the future of SaeysLab and (fairly) competitive highland games. Conclusion: We are ready for the next year!

Louise was present at the scverse hackathon in Heidelberg where interesting talks and a lot of coding happened. One of the end products is a package that brings the power of anndata objects to R.

We are proud to announce that Robin Browaeys obtained his PhD in Bioinformatics. Our founder of NicheNet successfully presented and defended his thesis today. Congrats dr. Browaeys!  

On the 5th edition of the Revolutionizing Next-Generation Sequencing of VIBLifeSciences, three SaeysLab members displayed their work through posters and soaked up the single-cell atmosphere. 

The new benchmark Spotless on spatial deconvolution methods can now be found on BioRxiv! We compared 11 methods on synthetic and real spatial transcriptomics data.

We are so proud of Sarah who has been awarded a young investigator proof-of-concept grant by Crig.

Let's look for measurable residual disease in acute myeloid leukemia with spectral flow cytometry!

At SaeysLab we are proud of the women in our team tipping the scales in the gender balance and delivering outstanding scientific research!

Our very own post-doc Ruth, helped organizing the Statistical Methods for Post Genomic Data in Ghent. It was enlightening to soo all the work ranging from mathematical to applied statistics, but also new areas in high throughput biology that need new statistical developments.