Dr. Magnus Palmblad

Head Bioinformatics

Area(s) of interest


Introduction

Dr. Magnus Palmblad received his PhD in Molecular Biotechnology from the Division of Ion Physics of Uppsala University in 2002 on the identification and characterization of peptides and proteins using Fourier transform ion cyclotron resonance (FTICR) mass spectrometry. After a 3-year postdoc at the Center for Accelerator Mass Spectrometry of the Lawrence Livermore National Laboratory, Dr. Palmblad was appointed as senior research fellow at the University of Reading BioCentre. In 2007, Dr. Palmblad joined the then Biomolecular Mass Spectrometry Unit of the Department of Parasitology and helped set up the mass spectrometry laboratories for high-throughput proteomics, pioneered proteomics population studies and developed automated data analysis pipelines using scientific workflows. Since 2015, Dr. Palmblad heads the Bioinformatics Research Group.

Internationally, Dr. Palmblad is involved in the annotation and dissemination of open source software for mass spectrometry data analysis (ms-utils.org, ELIXIR) and development of best practices for proteomics bioinformatics, currently chairing the Association of Biomolecular Resource Facilities Proteome Informatics Research Group (iPRG).

The research is funded by among others the NWO (VIDI grant “An Integrated Approach to Molecular Characterization of Zebrafish as a Biomedical Model” 2011-2016, NCF Parallellisatie grant “Parallelization of processing modules for analysis of liquid chromatography – mass spectrometry data” 2011-2012), EUREKA (ISCOS, “Towards Treatments For Premature Ageing Diseases” 2008-2011), the P.C. Flu Foundation, Amphia Hospital and the American Society for Mass Spectrometry.


Selected Publications

Scientific workflow optimization for improved peptide and protein identification. Holl S, Mohammed Y, Zimmermann O Palmblad M. BMC Bioinformatics. 2015 Sep 3;16:284. doi: 10.1186/s12859-015-0714-x.

Assessing the translational landscape of myogenic differentiation by ribosome profiling. de Klerk E, Fokkema IF, Thiadens KA, Goeman JJ, Palmblad M, den Dunnen JT, von Lindern M, 't Hoen PA. Nucleic Acids Res. 2015 May 19;43(9):4408-28. doi: 10.1093/nar/gkv281. Epub 2015 Apr 14.

PeptidePicker: a scientific workflow with web interface for selecting appropriate peptides for targeted proteomics experiments. Mohammed Y, Domanski D, Jackson AM, Smith DS, Deelder AM, Palmblad M, Borchers CH. J Proteomics. 2014 Jun 25;106:151-61. doi: 10.1016/j.jprot.2014.04.018. Epub 2014 Apr 22.

Identifying proteins in zebrafish embryos using spectral libraries generated from dissected adult organs and tissues. van der Plas-Duivesteijn SJ, Mohammed Y, Dalebout H, Meijer A, Botermans A, Hoogendijk JL, Henneman AA, Deelder AM, Spaink HP, Palmblad M. J Proteome Res. 2014 Mar 7;13(3):1537-44. doi: 10.1021/pr4010585. Epub 2014 Feb 5.

Identification of genetic variants influencing the human plasma proteome. Johansson Å, Enroth S, Palmblad M, Deelder AM, Bergquist J, Gyllensten U. Proc Natl Acad Sci U S A. 2013 Mar 19;110(12):4673-8. doi: 10.1073/pnas.1217238110. Epub 2013 Mar 4.

Scientific workflow management in proteomics. de Bruin JS, Deelder AM, Palmblad M. Mol Cell Proteomics. 2012 Jul;11(7):M111.010595. doi: 10.1074/mcp.M111.010595. Epub 2012 Mar 12.

A novel mass spectrometry cluster for high-throughput quantitative proteomics. Palmblad M, van der Burgt YE, Mostovenko E, Dalebout H, Deelder AM.  Am Soc Mass Spectrom. 2010 Jun;21(6):1002-11. doi: 10.1016/j.jasms.2010.02.001. Epub 2010 Feb 8.


Data/Resources


Contact

Leiden University Medical Center
Building 2
Room S7-022

Einthovenweg 20
2333 ZC Leiden
Tel: +31(0)715269582

Postalzone S3
P.O. Box 9600
2300 RC Leiden
The Netherlands

E-mail: n.m.palmblad@lumc.nl