Recent Posts

• April 15, 2022

  New BioRxiv pre-print

  We have a new BioRχiv pre-print, describing our latest tool PORCUPINE and its application to leiomyosarcoma, an aggressive soft-tissue sarcoma subtype. PORCUPINE, which was developed by Tatiana, analyzes complex, genome-wide, patient-specific regulatory networks directly on the network's edge weights. It does this by combining Principal Component Analysis (PCA) with permutations to identify pathways contributing to regulatory heterogeneity in a patient population. Importantly, instead of identifying discrete subtypes, it...

• April 04, 2022

  New BioRxiv pre-print

  We have a new BioRχiv pre-print, describing our latest tool retriever and its application to cancer. Retriever, which was developed by Daniel, integrates single-cell transcriptomes with drug response profiles to recommend drugs and drug combinations that can be used to revert disease profiles towards a more healthy-like state. In an application of retriever to triple-negative transcriptomes obtained from a large single-cell breast cancer atlas, we identified a combination...

• March 16, 2022

  New publication

  We are happy to announce that Marouen's tool gpuZoo has been published in Nucleic Acids Research Genomics and Bioinformatics! gpuZoo was developed in the Quackenbush group and leverages GPUs for cost-effective and fast running of netZoo algorithms such as PANDA, PUMA, and LIONESS. More information on the publication can be found here.

• March 14, 2022

  National Network for Breast Cancer meeting

  The group just got back from the National Network for Breast Cancer Research meeting in Tromsø, where Giulia presented a poster (below) on network modeling in the NeoAva study. After the conference, we visited the Arctic University of Norway to meet with collaborators.

• February 18, 2022

  Marieke joins the executive board of the FOSTER consortium

  Marieke was recently invited to join the executive board of the Fight OSteosarcoma Through European Research (FOSTER) consortium as biologist representative. The consortium brings together almost 200 oncologists, researchers, patients, parents, and others, who together will work on improving patient outcome and quality of life. See Pan Pantziarka (parent representative and researcher)'s blog post to learn more about this important initiative.