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If you are looking for an intersting PhD position at the eilslabs focussing on Cancer Research and beyond, please apply via the DKFZ's Graduate School until January 5, 2017 via www.dkfz.de/phd
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As of April 28, you can find all bioinformatics groups of the eilslabs (Computational Oncology, Cancer Regulatory Genomics and Data Management) in the brand new Mathematikon building complex. The eilslabs office are in the central of the three Mathematikon building, the official entrance and adress is Berliner Straße 41. We are looking forward to welcome you soon!
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Our recent article on epigenetic impact of smoking has been featured in Science:
Zahn, L. M. (2016). Getting more than Mom's looks. Science, 352(6284), 425-426. doi:10.1126/science.352.6284.425-d
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The German Research Summit (Forschungsgipfel 2016) brings together top-ranking representatives from industy, politics and research. Topic of the 2016 edition on April 12 was "digitalization" as the main topic of our time influencing all areas of modern life. The event was jointly organized by the "Stifterverband für die Deutsche Wissenschaft", the German National Academy of Sciences Leopoldina and EFI, the expert commission for research and innovation of the German government.
During the summit, experts from industry, science and representatives of the civil society jointly discussed challenges and opportunities of the digital area for research in Germany. Most prominent participant was the German chancellor Angela Merkel.
Roland Eils, head of eilslabs, was invited to join the first discussion round featuring high-ranking officials such as Angela Merkel, Dieter Zetsche (CEO Daimler), Timotheus Höttges (CEO Deutsche Telekom), Jörg Hacker (Leopoldina) and Andreas Barner (CEO Boehringer Ingelheim). The proponents in the round discussed the broad implications which the digital revolution has on many aspects of modern life including amongst other autonomous driving, data security and digital health.
More on the Research Summit:
- Official Website http://www.forschungsgipfel.de/index.html
- Tweets #FoGIP16: https://twitter.com/hashtag/FoGip16?src=hash
- Storify of most interesting statements: https://storify.com/anderagadeib/forschungsgipfel-2016
First row: Dietmar Harhoff (Spokesperson EFI), Timotheus Höttges (CEO Deutsche Telekom), Dirk Ahlborn (CEO Jumpstart), Chancellor Angela Merkel, Andreas Barner (Deutscher Stifterverband and CEO of Böhringer Ingelheim), Roland Eils
Picture by: David Ausserhofer, http://www.forschungsgipfel.de/fotos/index.html
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New joint study of the eilslabs and the UFZ in Leipzig decrypts the epigenetic impact of smoking on the gene regulatory machinery
Numerous epidemiological studies have demonstrated that maternal smoking has a strong negative impact on the health of newborn child, for example laying the ground for later allergic affections. However, the molecular mechanisms involved remained so far obscure. Several members of the eilslabs under the lead of Roland Eils and Carl Herrmann have now published a study in Molecular Systems Biology in collaboration with a team from the UFZ Leipzig led by Irina Lehmann. In the study they describe the epigenetic mechanisms that are perturbed by maternal smoking, both in mothers and in children. Thanks to a comprehensive epigenetic dataset (whole genome bisulfite sequencing and ChIP-seq), they were able to show that enhancers, regulating the gene expression of distal genes, appear to be specifically targeted by DNA methylation changes. These hypo/hyper methylations modulate the activity of these regulatory elements, leading to downstream changes in the expression of genes involved in important developmental pathways such as the Wnt pathway. These results raise the intriguing hypothesis that distal regulatory hubs, rather than gene promoters, are prone to be perturbed by environmental cues, explaining their widespread downstream effects.
Cover Image of Molecular Systems Biology featuring the study: Smoking during pregnancy causes epigenetic reprogramming in mothers and children. © Molecular Systems Biology, EMBOpress
- Bauer T, Trump S, Ishaque N, Thürmann L, Gu L, Bauer M, Bieg M, Gu Z, Weichenhan D, Mallm J, Röder S, Herberth G, Takada E, Mücke O, Winter M, Junge KM, Grützmann K, Rolle-Kampczyk U, Wang Q, Lawerenz C, Borte M, Polte T, Schlesner M, Schanne M, Wiemann S, Geörg C, Stunnenberg HG, Plass C, Rippe K, Mizuguchi J, Herrmann C, Eils R, Lehmann I (2016). Environment-induced epigenetic reprogramming in genomic regulatory elements in smoking mothers and their children. Molecular Systems Biology http://dx.doi.org/10.15252/msb.20156520
This research was supported by the DKFZ’s Heidelberg Center for Personalized Oncology (DKFZ-HIPO).
- Feature in Science: Zahn, L. M. (2016). Getting more than Mom's looks. Science, 352(6284), 425-426. doi:10.1126/science.352.6284.425-d
- Augsburger Allgemeine
- Neue Osnabrücker Zeitung
- Joint Press Release of UFZ-Leipiz, DKFZ and Heidelberg University
Dr. Irina Lehmann
UFZ Department of Environmental Immunology
Department of Environmental Immunology
Prof. Dr. Roland Eils
German Cancer Research Center and the University of Heidelberg
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Using the LOV2 domain as a light-sensitive switch, the eilslabs team around PhD Student Dominik Niopek and group leader Barbara Di Ventura managed to induced spatial control of desired proteins in mammalian cells. The tool entitled LEXY (for light-inducible nuclear export system) combines the LOV2 domain with a nuclear export signal sequence (NES) and allows to trigger the nuclear export of attached proteins using blue light. Function of the tool was shown by the light-controlled regulation of synthetic repressors and the transcriptional activity of human p53 with light.
Source: Dominik Niopek
LEXY supplements the previously developed tool named LINuS (light-inducible nuclear localization signal), which allows the light-controlled nuclear import of proteins.
- Press Release of Heidelberg University "Using Light To Control Protein Transport From Cell Nucleus" (German Version)
- Citation: Niopek, D., Wehler, P., Roensch, J., Eils, R., & Di Ventura, B. (2016). Optogenetic control of nuclear protein export. Nature Communications, 7, 10624. doi: 10.1038/ncomms10624
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In this recently published work, Sebastian Steinhauser and Nils Kurzawa have benchmarked 14 available tools to determine differential enrichment of transcription factor binding between two conditions. The work was part of the Master thesis of Sebastian Steinhauser, which he carried out in the eilslabs under the supervision of Carl Herrmann in the Cancer Regulatory Genomics group.
Their analysis highlights significant differences between the produced results and emphasizes the need for selective choice of the correct tool.
Read more here:
Steinhauser, S., Kurzawa, N., Eils, R., & Herrmann, C. (2016). A comprehensive comparison of tools for differential ChIP-seq analysis. Briefings in Bioinformatics. doi: 10.1093/bib/bbv110
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Recently, researchers from the eilslabs have published together with colleagues from the DKFZ, the CNAG-CRG (Centro Nacional de Analisis Genómico) in Barcelona and the International Cancer Genome Consortium (ICGC) a benchmarking study in Nature Communications to evaluate experimental methods and bioinformatic analyses of next generation sequencing studies in the context of cancer genomics.
As a result of the study, the group, which was led by Ivo Gut from the CNAG-CRG, David Jones from the DKFZ and Roland Eils published a sequencing data record to serve as a “gold standard” for sequence analysis alongside with guidelines for bioinformatic evaluation. Laboratories that start out in the field of genome analysis can now use this data record as a basis to check whether the bioinformatic methods that they are using are capable of detecting all mutations concealed therein. This hopefully helps the international cancer genomics community to establish desperately needed standards for bioinformatics analysis.
Within the eilslabs, the study was driven forward by PhD student Ivo Buchhalter from the Computational Oncology group.
Alioto, T.S.*, Buchhalter, I.*, Derdak, S., Hutter, B., Eldridge, M.D., Hovig, E., Heisler, L.E., Beck, T.A., Simpson, J.T., Tonon, L., Sertier, A.S., Patch, A.M., Jager, N., Ginsbach, P., Drews, R., Paramasivam, N., Kabbe, R., Chotewutmontri, S., Diessl, N., Previti, C., Schmidt, S., Brors, B., Feuerbach, L., Heinold, M., Grobner, S., Korshunov, A., Tarpey, P.S., Butler, A.P., Hinton, J., Jones, D., Menzies, A., Raine, K., Shepherd, R., Stebbings, L., Teague, J.W., Ribeca, P., Giner, F.C., Beltran, S., Raineri, E., Dabad, M., Heath, S.C., Gut, M., Denroche, R.E., Harding, N.J., Yamaguchi, T.N., Fujimoto, A., Nakagawa, H., Quesada, V., Valdes-Mas, R., Nakken, S., Vodak, D., Bower, L., Lynch, A.G., Anderson, C.L., Waddell, N., Pearson, J.V., Grimmond, S.M., Peto, M., Spellman, P., He, M., Kandoth, C., Lee, S., Zhang, J., Letourneau, L., Ma, S., Seth, S., Torrents, D., Xi, L., Wheeler, D.A., Lopez-Otin, C., Campo, E., Campbell, P.J., Boutros, P.C., Puente, X.S., Gerhard, D.S., Pfister, S.M., McPherson, J.D., Hudson, T.J., Schlesner, M., Lichter, P., Eils, R.@, Jones, D.T. @, & Gut, I.G. @ (2015). A comprehensive assessment of somatic mutation detection in cancer using whole-genome sequencing. Nature Communications, 6, 10001. doi: 10.1038/ncomms10001
@: Joint Supervision; *: equal contribution
- DKFZ Press Release
- CNAG Press Release
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Jasmin Dehnen and Frieda Anna Sorgenfrei from the igem 2015 team have written a short essay about the creation of Aptabodies in the Laborjournal.
Read more at http://www.laborjournal.de/rubric/methoden/methoden/v159.lasso (only in German!)
Copyright: iGEM Team Heidelberg 2015
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The Heidelberg Center for Human Bioinformatics (HD-HuB) coordinated by Roland Eils and Chris Lawerenz has organized its first workshop on “Data Interpretation for Next Generation Sequencing Data in Cancer Research” on October 7-8, 2015 in the newly established computer teaching rooms at the Institute of Pharmacy and Molecular Biotechnology (IPMB).
The workshop was based on a joined initiative between HD-HuB and the DKTK School of Oncology and aimed at researchers working with larger datasets of next-generation sequencing (NGS) data arising from patient tumor samples. The curriculum of the course, which was attended by 20 scientists, included background knowledge on technologies used for data generation and gave an introduction to tools for data analysis and interpretation in the areas of whole genome sequencing, exome sequencing, whole genome bisulfite sequencing and RNASeq. The two-day course was run by Matthias Schlesner and Carl Herrmann from the eilslabs, as well as Benedikt Brors, former eilslabs member and now head of the Applied Bioinformatics division at DKFZ and NCT.
HD-HuB is part of the BMBF-funded German Network for Bioinformatics Infrastructure (de.NBI) and bundles bioinformatics expertise from the DKFZ, the EMBL and Heidelberg University.
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Following the tremendous success in last years (2013, 2014), the Heidelberg iGEM team, which was supervised by Roland Eils and Barbara Di Ventura from the eilslabs, has again made it to the final of this year’s iGEM competition in Boston and received the second runner up prize of over 260 teams from all over the world. Furthermore the project, carried out by ten talented students from Heidelberg University, received the iGEMer’s Prize, nominated by the over 2700 participants of the Giant Jamboree held in Boston over the last weekend.
In this year’s project, the team focused on the usage of functional nucleic acids as tools for synthetic biology. Over the summer months, the team was able to develop a new approach using a “twin ribozyme” with which they were able to repair in vitro the mRNA of the CFTR gene, which is the cause of cystic fibrosis. This result could lead to new avenues of gene therapeutic treatment of this and other genetic diseases.
Furthermore, the team focused on the development of software tools for the design and development of aptamers, RNA or DNA molecules, which specifically bind to other molecules. Via the development of two software tools, the team was able to develop intelligent combinations of aptamers with RNA-enzymes to generate sensors for small molecules that have a colorimetric readout. With this they could give a proof of concept for the fast and efficient detection of rape drugs in energy drinks. Finally, the team has developed a new aptamer-based method for fast and cheap detection of proteins on Western Blots without the need for antibodies.
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Since Monday, international researchers are meeting at the DKFZ to present the latest research results during the Systems Biology of Human Disease - SBHD conference organized by the eilslabs. Overarching topic of the conference is the use of mathematical methods and computer models to capture and study complex biological systems. Using this type of systems biology approaches, it is possible to recognize hidden relationships that are important for the emergence of complex diseases such as cancer.
The SBHD conference series was initiated by Peter Sorger from Harvard Medical School in Boston a few years ago and has since developed into a German-American which is held alternately in Boston and Heidelberg.
On Wednesday, the last day of the conference program, two awards will be presented:
- Karsten Rippe (DKFZ Heidelberg and BioQuant) will receive the CSB2 Price in Systems Biology (kindly sponsored by Merrimack Pharmaceuticals) for his interdisciplinary work on the structural organization of our genome and its influence on gene regulation and disease development.
- Kazuki Tainaka from Tokyo University will be awarded the Anne Heidenthal Prize for Fluorescence Research (kindly sponsored by Chroma Technology Corp.), for the development of CUBIC method (Clear, Unobstructed Brain Imaging cocktails and Computational Analysis). The CUBIC method is a newly developed imaging method using a combination of chemical discoloration and light-sheet fluorescent microscopy to achieve extremely detailed pictures of the inside of individual organs and even entire organisms.
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Recently the ninth issue of systembiologie.de has been released. The magazine is produced by the eilslabs together with German systems biology initiatives.
Topics of this issue include interviews with renowned systems biologists Gene Myers and Alexander Hoffmann, new insights into wound healing and optogenetics alongside many other interesting articles.
The electronic version can be downloaded here. The International Edition in English will be issued soon.
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In a new eilslabs publication from the Cancer Regulatory Genomics Group (headed by Carl Herrmann) bachelor students Nicholas Nolte and Nils Kurzawa are presenting a new tool – MapMyFlu - which allows to spatially and temporally display influenza viruses related to a query sequence on a Google Map. The analysis is based on BLAST results of the virus sequence against the NCBI Influenza Database. Based on this one can analyze temporal and geographical trends of the pandeminc, which may help in reconstructing the evolutionary history of a particular sequence. MapMyFlu is available at http://mapmyflu.ipmb.uni-heidelberg.de