April 22, 2022
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
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
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
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
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.