You are here: Home / External Files / People Pages / Erwin Schoof / Erwin Schoof - Research

Erwin Schoof - Research

My overall research goal is to combine experimental and computational methods in order to model cell behavior, and to investigate how disease phenotypes are established and could be therapeutically targeted. Network biology seems to be an extremely adept platform for exactly these purposes, as it allows the integration of genome-scale technologies such as Mass Spectrometry, Next-Generation Sequencing and siRNA screening.

Erwin Schoof, PhD student

Network Medicine Approaches targeting Cancer Metastasis
Using a wide variety of experimental and computational techniques, we are attempting to elucidate signaling network dynamics associated with cancer metastasis in several cancer types. Through the integration of different types of data (e.g. proteomics, genomics and imaging), we aim to gain a more complete understanding of underlying cellular processes which can be targeted therapeutically.
*Publications* - *Creixell et al. Navigating cancer network attractors for tumor-specific therapy.* Schoof et al., Experimental and computational tools for analysis of signaling networks in primary cells. Under Revision. Schoof, Cox et al., In Preparation.

Network Medicine Approaches targeting Cancer Metastasis

Using a wide variety of experimental and computational techniques, we are attempting to elucidate signaling network dynamics associated with cancer metastasis in several cancer types. Through the integration of different types of data (e.g. proteomics, genomics and imaging), we aim to gain a more complete understanding of underlying cellular processes which can be targeted therapeutically.

Publications

- Creixell et al. Navigating cancer network attractors for tumor-specific therapy.

Schoof et al., Experimental and computational tools for analysis of signaling networks in primary cells. Under Revision.

Schoof, Cox et al., In Preparation.

Computational Modeling of Kinase-Substrate Networks
	With current updated versions of our flagship algorithms NetPhorest and NetworKIN, we are modeling large-scale (phospho-) proteomics datasets in order to determine differential kinase and phosphatase activity profiles in different diseases, cell-lines and experimental conditions. These results can be used for diagnostic and/or therapeutic purposes. Through large-scale in vitro screening, we are deciphering novel kinase specificities in an attempt to obtain a kinome-wide modeling framework.
*Publications* - Zanivan et al., In Vivo SILAC-Based Proteomics Reveals Phosphoproteome Changes during Mouse Skin Carcinogenesis. *- Horn, Schoof, Kim et al., KinomeXplorer: A Novel Integrated Framework for Kinome Biology Studies. In Preparation*

Computational Modeling of Kinase-Substrate Networks

With current updated versions of our flagship algorithms NetPhorest and NetworKIN, we are modeling large-scale (phospho-) proteomics datasets in order to determine differential kinase and phosphatase activity profiles in different diseases, cell-lines and experimental conditions. These results can be used for diagnostic and/or therapeutic purposes. Through large-scale in vitro screening, we are deciphering novel kinase specificities in an attempt to obtain a kinome-wide modeling framework.

Publications

- Zanivan et al., In Vivo SILAC-Based Proteomics Reveals Phosphoproteome Changes during Mouse Skin Carcinogenesis.

- Horn, Schoof, Kim et al., KinomeXplorer: A Novel Integrated Framework for Kinome Biology Studies. In Preparation

Global (Phospho-)Proteomics using Mass Spectrometry
Mass Spectrometry is the method of choice when wanting to analyze global protein dynamics within a cell. We are deploying state-of-the-art instruments to get as in-depth a proteome coverage as possible, while allowing the utilization of quantitationtechniques such as SILAC or dimethyl labeling. Using fractionation techniques such as SCX, SAX and HILIC, combined with enrichment strategies such as Titanium Dioxide (TiO2) and immuno-precipitation (IP), we are constantly trying to push the envelope of gaining greater (phospho-) proteome coverage which allows for more accurate modeling of cell behaviour.
*Publications* - Schoof & Linding., Experimental and computational tools for analysis of signaling networks in primary cells. Under Revision. *- Press Release*

Global (Phospho-)Proteomics using Mass Spectrometry

Mass Spectrometry is the method of choice when wanting to analyze global protein dynamics within a cell. We are deploying state-of-the-art instruments to get as in-depth a proteome coverage as possible, while allowing the utilization of quantitationtechniques such as SILAC or dimethyl labeling. Using fractionation techniques such as SCX, SAX and HILIC, combined with enrichment strategies such as Titanium Dioxide (TiO2) and immuno-precipitation (IP), we are constantly trying to push the envelope of gaining greater (phospho-) proteome coverage which allows for more accurate modeling of cell behaviour.

Publications

- Schoof & Linding., Experimental and computational tools for analysis of signaling networks in primary cells. Under Revision.

- Press Release

Evolution of phosphorylation signaling
	The dynamics of signaling networks within a cell alter not only through longer periods of time, but has also been attributed to disease progression. Mutations occurring at the DNA level affect protein sequences at the proteome level, which in turn can significantly alter the cellular phenotype. Through computational studies, we have elucidated evolutionary patterns underlying these phenomena, and are attempting to deploy these in the study of human diseases.
*Publications* - Creixell et al. Mutational Properties of Amino Acid Residues - Implications for Evolvability of Phosphorylatable Residues - Tan et al. Response to Comment on “Positive Selection of Tyrosine Loss in Metazoan Evolution”

Evolution of phosphorylation signaling

The dynamics of signaling networks within a cell alter not only through longer periods of time, but has also been attributed to disease progression. Mutations occurring at the DNA level affect protein sequences at the proteome level, which in turn can significantly alter the cellular phenotype. Through computational studies, we have elucidated evolutionary patterns underlying these phenomena, and are attempting to deploy these in the study of human diseases.

Publications

- Creixell et al. Mutational Properties of Amino Acid Residues - Implications for Evolvability of Phosphorylatable Residues

- Tan et al. Response to Comment on “Positive Selection of Tyrosine Loss in Metazoan Evolution”

News: Moving to Germany Sep 19, 2019; Multiple new Publications & PREPRINTS Sep 19, 2019; Digital ‘Rosetta Stone’ Decrypts How Mutations Rewire Cancer Cells Sep 17, 2015; Enzyme paves the way for the spread of cancer cells to bones May 27, 2015; Linding Lab moves to BRIC@UCPH Jul 31, 2014; More news…

Navigation

Webservices