Recent Posts

• June 06, 2023

  New BioRχiv pre-print

  We have a new BioRχiv pre-print as part of a collaboration with researchers from The Arctic University of Norway (UiT) in Tromsø, and contributions from several group members. We modeled co-expression networks to investigate the transcriptional response to tumor necrosis factor alpha in endothelial cells. The pre-print can be found here. For more information on the pre-print, see also our current list of preprints.

• March 22, 2023

  The Kuijjer group has been renewed

  We are delighted to announce that the group has been renewed for our second term at NCMM, starting on October 1, 2023. Great job everyone! And thanks for all the help and trust from collaborators, mentors, funding agencies, and all others who contributed to making our first four years at NCMM successful. Looking forward to continuing working together!

• March 10, 2023

  New publication

  Marouen Ben Guebila from the Quackenbush group developed NetZoo, multilingual package that includes various tools for network reconstruction and analysis, including PyPanda, PUMA, LIONESS, and SAMBAR, with contributions from former visiting student David van IJzendoorn and former student and Research Assistant Genís Calderer. NetZoo is available on github. The paper includes analyses to demonstrate the value of the integrated toolkit and is now...

• February 20, 2023

  New BioRχiv pre-print

  We have a new BioRχiv pre-print as part of a collaboration with researchers from the Institute of Biotechnology, National Autonomous University of Mexico (UNAM). Here, we used our network tools (PANDA and LIONESS) to investigate the reduced development of colitis in mice upon enrichment of their environment. This indicated a Myc-driven regulatory network is enhanced by colitis and is attenuated by exposure to an enriched environment, via downmodulation...

• January 23, 2023

  New BioRχiv pre-print

  We have posted a new BioRχiv pre-print by Daniel. Daniel developed SCORPION, or Single Cell Oriented Reconstruction of PANDA-based Individually Optimized Networks, an approach to reconstruct gene regulatory networks based on single cell transcriptomic data.