Research description
We are an enthusiastic and friendly group of young researchers in many different fields of computational biology applied to cancer research. We also carry out a few methodological projects in biomolecular modeling, simulations and biological network analysis.
More in details, CBL is focusing on different projects from structural biology, biomolecular simulations and modeling, biological network analyses, analyses of next generation sequencing data (mainly RNASEQ) and integrative -omics analyses. We recently established a small part of the group focusing on the experimental validation of our predictions.
We work in tight collaborations with experimentalists at the DCRC (Marja Jäättelä, Francesco Cecconi, Giuseppe Filomeni, Tuula Kallunki, Irina Gromova, Nils Brunner, Jan Stenvang, Jesper Nylandsted, Petra Hamerlik, Marin Barisic, Dorthe Helena Payne-Larsen, Jiri Bartek and Per Guldberg) in Denmark and abroad.
Indeed, in addition to several local collaborations (Birthe Kragelund, Kresten Lindorff-Larsen, Kaare Teilum, Anders Krogh, Lars Ellgaard and Rasmus Hartmann-Petersen at the University of Copenhagen, and Peter Røgen at the DTU) we have strong international collaborations including the groups of Francesco Gervasio (UCL, UK), Salvador Ventura (Universitat Autonoma de Barcelona, Spain), Ruth Nussinov (National Institute of Health, USA), Ilpo Vattulainen (Tampere University, Finland), Gary Shaw (University of West Ontario, Canada), Pablo Navarro (Institute Pasteur, France), Andrea Rasola (University of Padova, Italy), Richard Kriwacri (St. Jude Hospital, Memphis, USA), Gianluca Bontempi (Bruxelles University, Belgium) and Michele Ceccarelli (University of Sannio, Italy).
We focus on different key biological topics with a strong focus on cancer from intrinsic disorder, ubiquitination, cancer driver and passenger mutations, dual roles for oncogenes and tumour suppressors in cancer, post-translational modifications, chaperones, kinases/phosphatases, transcription factors, metal-binding, membrane proteins, microRNA, DNA damage/repair and autophagy. We are also interested, as side projects, in the understanding of the molecular determinants of cold adaptation in collaboration with colleagues at the University of Iceland and Tromsø University, which has been a focus of Elena's research since from her PhD studies and can also help us to identify the best methods to study impact of mutations on enzyme catalysis and function. We can translate what we learn from these studies to mutations identified in patients and occurring in genes that encode for enzymes.
In 2015, we also started and active and fruitful collaboration with the Chalmers University of Technology, Sweden (Lisbeth Olsson's group) to design new variants of an enzyme that can boost new directions in green environmental friendly chemistry.
Current major areas of interest for the research of the group, supported by different grants are: i) understanding lipid/protein interaction in a cancer context, ii) the study of non-conventional motifs for interaction with the Bcl2-family members, iii) the study mechanisms related to S-nitrosylation of proteins and its interplay with cancer mutations, iv) biomarker discovery from NGS and -omics data in breast and lung cancer, v) interplay between transcription-dependent and independent functions in cancer-related transcription factors, vi) cancer signature and structural biology of autophagy-related proteins, vi) cadmium toxicity in cancer.
Here a repository with the code developed by us:
We also recently contributed to Moonlight Bioconductor package for prediction of oncogenes and tumor suppressors:
http://www.bioconductor.org/packages/devel/bioc/vignettes/MoonlightR/inst/doc/Moonlight.html