Kuijjer Lab

Recent Posts

  • June 01, 2022

    New group member

    We are very excited to announce that Ladislav Hovan has joined the lab as a postdoctoral fellow. Ladislav has a PhD in chemistry from University College London and previously did postdoctoral research in molecular dynamics at the University of Geneva, Switzerland. Ladislav's project will focus on developing approaches to model spatially resolved gene regulation.

  • April 22, 2022

    New publication

    We are happy to announce that Netbooks has been published in Nature Methods! Netbooks is a hosted collection of Jupyter notebooks that provide detailed and annotated step-by-step case studies of gene regulatory network analysis. The project is led by Marouen Ben Guebila from the Quackenbush group, with contributions from Romana. More information on the publication can be found here.

  • 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.