Sylvius Laboratories (room 6.4.13), Sylviusweg 72, 2333 BE Leiden, The Netherlands
Dr. Christiaan Henkel
+31 71 527 4759
The presence of large and complex data sets creates an enormous need for bioinformatics expertise and infrastructure in contemporary biology. Since biologists typically lack the necessary expertise in computer science, mathematics or statistics, they need expert bioinformatics support for advanced bioinformatics analyses.
The main objective of the BioIT initiative is to achieve functional bioinformatics support by the Leiden Institute of Advanced Computer Science (LIACS), initially focused on the life sciences researchers from the Faculty of Science of the University of Leiden, with an extension towards other organizations, whether they are research institutes or companies.
Our expertise includes the design of -omics experimentation, statistics, data and image analysis, visualizations and experiment interpretation, as well as developing new methods and tools for life science research applications. Furthermore, we support the building of data analysis pipelines and the use of IT infrastructures, with high-performance computing and data storage, data-analysis pipelines, specific bioinformatics tools and databases, to enable large data life-sciences research projects. We help biologists on their way with the right tools and expertise, whether they are at the early (writing grant proposal) or late (data analysis and interpretation, writing articles) stage of their research.
Collectively with the MAD@UvA, we have a whole range of bioinformatics skills, tools and expertise. We have also quite a bit of genomics-technology know-how. As it is impractical to list all our resources, please do contact us with your specific demands. Here below we indicate some topics, in which we have a lot of know-how.
(Molecular) biology, omics technologies (microarray technology (DNA, RNA), next generation sequencing (Gen-seq, RNA-seq, small-RNA-seq), 3rd generation sequencing (DNA)), design for omics experimentation, bioinformatics for microarray technology/next generation sequencing/(genetic) epidemiology, biostatistics, informatics (scripting [Perl, Python, R, Unix/Linux], software selection: R, SPSS, Matlab, SAS, GATK, IGV, Plink, etc, e-infrastructure [cloud, high performance computing], common sense.
- Biomedical & health
- Agri & Food
- Applied Bioinformatics
- Next-generation sequencing
- Developmental biology
Expertise and Track Record
We are bioinformaticians with a background in (molecular) biology. In contrast to “technical” biologist, we understand the biology behind the experiment/study and will adapt the bioinformatics analyses to this. As such we have a strict model of collaborative bioinformatics support. We start by helping with the design of experimentation, and we finish by helping writing the article.
We are a part of a wider expertise center and collectively with the MAD@UvA we have about 13 bioinformatics experts that cover a wide range of expertise from data visualization to high-performance computing.
Our track-record shows that collectively, we have supported hundreds of life-sciences researchers with their omics analysis by providing excellent, yet pragmatic bioinformatics support. We do know what it means to play a support role. Opposite to many bioinformatics groups that have support as a sideshow, it is our core business. We are used to placing the customer/partner in the middle and aim to get the job done in a customer-friendly fashion.
We have only limited experience with qualitative cross-technology integration.
- Girard G, Willemse J, Zhu H, Claessen D, Bukarasam K, Goodfellow M, van Wezel GP.Analysis of novel kitasatosporae reveals significant evolutionary changes in conserved developmental genes between Kitasatospora and Streptomyces. Antonie Van Leeuwenhoek. 2014 Aug;106(2):365-80
- Melis JPM, Derks KWJ, Pronk T, Wackers P, Schaap MM, Zwart E, van IJcken WF, Jonker M, Breit TM, Pothof J, van Steeg H, Luijten M In vivo murine hepatic microRNA and mRNA expression signatures predicting the (non-)genotoxic carcinogenic potential of chemicals. Archives of Toxicology 2014
- Girard G, Traag BA, Sangal V, Mascini N, Hoskisson PA, Goodfellow M, van Wezel GP. A novel taxonomic marker that discriminates between morphologically complex actinomycetes. Open Biol. 2013 Oct 23;3(10):130073
- Tulinski P; Duim B; Wittink FR; Jonker MJ; Breit TM; van Putten JP; Wagenaar JA; Fluit AC. Staphylococcus aureus ST398 gene expression profiling during ex vivo colonization of porcine nasal epithelium. BMC genomics
- Jonker MJ, Melis JPM, Kuiper RV, van der Hoeven TV, Robinson J, van der Horst GTJ, Breit TM, Vijg J, Dolle M, Hoeijmakers JHJ, van Steeg H Lifelong murine gene expression profiles in relation to chronological and biological aging in multiple organs. Aging Cell. 2013 Oct;12(5):901-9.
- Sasidharan R, Mustroph A, Boonman A, Akman M, Ammerlaan AM, Breit T, Schranz ME, Voesenek LA, van Tienderen P.Root transcript profiling of two Rorippa (Brassicaceae) species reveals gene clusters associated with extreme submergence tolerance. Plant Physiol. 2013 Nov;163(3):1277-92.
- Röschmann K, van Kuijen A-M, Luiten S; Jonker M, Breit T, Fokkens W, Petersen A, van Drunen . M Purified Timothy grass pollen major allergen Phl p 1 may contribute to the modulation of allergic responses through a pleiotropic induction of cytokines and chemokines from airway epithelial cells. Clin Exp Immunol. 2012 Mar;167(3):413-21.
- Doroszuk A, Jonker MJ, Pul N, Breit TM, Zwaan B. Transcriptome analysis of a long-lived natural Drosophila variant: a prominent role of stress- and reproduction-genes in lifespan extension. BMC Genomics 2012 May 4;13(1):167.
- Melis JPM, Hoogervorst EM, van Oostrom CThM, Zwart E, Breit TM, Pennings JLA, de Vries A, van Steeg H Strong selection for the truncated ΔN-p53 isoform in murine urinary bladder tumors. Oncogene 2011 Apr 14;30(15):1764-72
- Garinis GA, Uittenboogaard LM, Stachelscheid H, Fousteri M, van Ijcken W, Breit TM, van Steeg H, Mullenders LH, van der Horst GT, Brüning JC, Niessen CM, Hoeijmakers JH, Schumacher B. Persistent transcription-blocking DNA lesions trigger somatic growth attenuation associated with longevity. Nat Cell Biol. 2009 May;11(5):604-15.
We have a strategic collaboration with the MAD at UvA.
- Dedicated postdocs (2 FTE)
We will use all international repositories if and when applicable, such as in GEO.