Jensen Group (Cellular Network Biology ) – University of Copenhagen

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Jensen Group - Cellular Network Biology

(Group Leader: Professor Lars Juhl Jensen) 

Introduction

The Cellular Network Biology Group was established in January 2009 and is headed by Professor Lars Juhl Jensen. The group is purely computational, using data- and text-mining techniques to understand protein networks. This includes answering biological questions through reanalysis of existing data, developing and maintaining international community resources, and collaborating closely with wet-lab groups both inside and outside of CPR.

Areas of Research

Web resources

We believe that developing widely used web resources is an important way to contribute to science as bioinformaticians. We have developed or co-developed the web resources listed below, which every week are used by thousands of researchers around the world. The resources mainly relate to proteins and their evolution, interactions, regulation, localization and phenotypic consequences. A list of all the resources can be found in the box on the right.

Global studies of the eukaryotic cell cycle

One of the cellular processes in which phosphorylation plays a crucial role is the eukaryotic cell cycle. Over the past year, the group has had several collaborations on this front. This includes the analysis mass-spectrometry data on the human cell cycle produced by Prof. Jesper Olsen’s group, Department of Proteomics, CPR and the discovery of feed-forward loops of kinases and transcription factors that jointly regulate the temporal activity profiles of cell-cycle proteins.

Deciphering phosphorylation-dependent signaling

Phosphorylation of proteins by protein kinases is one of the primary regulatory mechanisms and is involved in the control of virtually every cellular process in eukaryotes, including human. A major ongoing effort is the analysis and interpretation of high-throughput data on phosphorylation-dependent signaling. In collaboration with Dr. Rune Linding’s group at the Center for Biological Sequence Analysis, we have developed an improved scoring scheme that will form the basis for upcoming versions of the  NetworKIN tool and is already being used for analysis of mass spectrometry data from collaborators.

Augmenting the web with biological information

The life sciences are scaling up and producing huge amounts of data and new literature at an amazing pace. To help researchers, teachers and students keep up-to-date with scientific literature on the web, the group of Prof. Lars Juhl Jensen and collaborators at the European Molecular Biology Laboratory have developed Reflect, a free, automated document annotation service. It pinpoints genes, proteins and small molecule names on any web page and with a single click provides access to information on domain structure, subcellular localisation, 3D structure and interaction partners in the case of proteins and the chemical structure and interaction partners in the case of small molecules. Reflect was published in Nature Biotechnology, June 2009 and was awarded the first prize in the Elsevier Grand Challenge: Knowledge enhancement in the life sciences, an international contest that attracted over 70 teams.