Welcome to the eilslabs

The eilslabs form a joint research group between the division "Theoretical Bioinformatics" at the German Cancer Research Center (dkfz) and the department Bioinformatics and Functional Genomics at the Institute of Pharmacy and Molecular Biotechnology (IPMB) at Heidelberg University. The group is headed by Prof. Roland Eils.

 


The eilslabs bioinformatics groups have moved to Mathematikon

 

Mathematikon 400pxAs 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!

 

"Getting more than Mom's looks" - eilslabs LINA article featured in Science

Our recent article on epigenetic impact of smoking has been featured in Science:

MSB vol12 03 cover RGB RE IL 2 red 400pxZahn, L. M. (2016). Getting more than Mom's looks. Science, 352(6284), 425-426. doi:10.1126/science.352.6284.425-d

 

 

Roland Eils participates in German Research Summit in Berlin

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:

Forschungsgipfel-2016 600px

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

 

Maternal smoking is certainly harmful to the newborn child, but why?

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.

Maternal Smoking is Harmful!

Cover Image of Molecular Systems Biology featuring the study: Smoking during pregnancy causes epigenetic reprogramming in mothers and children. © Molecular Systems Biology, EMBOpress



Publication:

  • 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).

Press Coverage:

Further information:

Dr. Irina Lehmann
UFZ Department of Environmental Immunology
Department of Environmental Immunology
This email address is being protected from spambots. You need JavaScript enabled to view it.
and
Prof. Dr. Roland Eils
German Cancer Research Center and the University of Heidelberg
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eilslabs Synthetic Biology team publishes second optogenetic tool in Nature Communications

 

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.

optogenetik 460x175

Source: Dominik Niopek

Microscopy images of human embryonic kidney cells in culture. The cells were genetically modified to produce a glowing protein, which was linked to the new optogenetic tool (the LOV2-NES hybrid). Cells irradiated with a blue laser beam (blue arrows) show an efficient nuclear export of the protein. Non-irradiated cells (red arrows) show a constitutively nuclear localisation of the protein.

LEXY supplements the previously developed tool named LINuS (light-inducible nuclear localization signal), which allows the light-controlled nuclear import of proteins.

Further Reading:

 

ChIP-seq analysis tools on the test - publication by two eilslabs' Master Students in Briefings in Bioinformatics

 

2016-1 Steinhauser briefingsIn 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

A new gold standard to improve cancer genome analysis - Publication in Nature Communications

 

CNAG sequenceRecently, 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.

Further Information:

  • Publication:
    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

"Recently on the bench": iGEM Team writes about Aptabodies Method in Laborjournal

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!)

aptabody

Copyright: iGEM Team Heidelberg 2015

 

First HD-HuB Workshop on “Data Interpretation for Next Generation Sequencing Data in Cancer Research”

 

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).

Bioinfo-Workshop-HD-HuB-Gruppe-teachingThe 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.

 

“Catch it if you can” goes to the finals and wins iGEMer’s Prize – Heidelberg iGEM Team rocks again

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.
iGEM team 2015In 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.

Using systems biology models to understand diseases - Systems Biology of Human Disease Conference kicks off at DKFZ

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.DSC 0522 600px

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.

Further Information:

systembiologie.de issue 09 is out!

ausgabe09Recently 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.

 

MapMyFlu: visualizing influenza sequences based on geographical occurrence and dates

 

mapmyflu screenshot

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

Citations:

Nolte, N., Kurzawa, N., Eils, R., & Herrmann, C. (2015). MapMyFlu: visualizing spatio-temporal relationships between related influenza sequences. Nucleic Acids Research. doi: 10.1093/nar/gkv417

Matthias Schlesner and Roland Eils discuss new findings regarding the effect of genome hypermutation in cancerthe impact of genome hypermutation on the development of certain cancers. They describe a newA recent study by Shlien et al.

Research Highlight on Hypermutation in Cancer

 

Chromsomen-alleine

In a recent research highlight in Genome Medicine (1), Matthias Schlesner and Roland Eils discuss the impact of genome hypermutation on the development of certain cancers. A recent study by Shlien et al. (2) describes that tumors from children with congenital biallelic mismatch repair deficiency (bMMRD) show an extremely high mutation rate (named "ultra-hypermutation”), exceeding even highly mutated adult cancers by one order of magnitude. Together with other studies on genome hypermutation in cancer, e.g. the earlier work of the eilslabs on X-Chromosome hypermutation (3), these findings might lead to the development of new therapeutic approaches to combat cancer.

Citations:

  1. (1) Schlesner, M., & Eils, R. (2015). Hypermutation takes the driver's seat. Genome Med, 7(1), 31. doi: 10.1186/s13073-015-0159-x
  2. (2) Shlien, A., Campbell, B. B., de Borja, R., Alexandrov, L. B., Merico, D., Wedge, D., . . . Biallelic Mismatch Repair Deficiency, C. (2015). Combined hereditary and somatic mutations of replication error repair genes result in rapid onset of ultra-hypermutated cancers. Nat Genet, 47(3), 257-262. doi: 10.1038/ng.3202
  3. (3) Jäger, N., Schlesner, M., Jones, David T. W., Raffel, S., Mallm, J.-P., Junge, Kristin M., . . . Eils, R. (2013). Hypermutation of the Inactive X Chromosome Is a Frequent Event in Cancer. CELL, 155(3), 567-581. doi: 10.1016/j.cell.2013.09.042
Matthias Schlesner and Roland Eils discuss new findings regarding the effect of genome hypermutation in cancerthe impact of genome hypermutation on the development of certain cancers. They describe a newA recent study by Shlien et al.

More Articles...

  1. Measuring protein dynamics in living cells – New Publication in Nature Biotechnology
  2. Now online: Biotechnology Journal Special Issue on Synthetic Biology edited by Roland Eils, Julia Ritzerfeld and Wolfgang Wiechert
  3. “we are only at equilibrium when we are dead” – Comment on Recent Paper by Ahsendorf et. al in BMC Biology
  4. Study Based on Whole Exome Sequencing Identifies New Genetic Causes For Wilms Tumors
  5. Interview in F.A.Z.: Roland Eils and Christof von Kalle Discuss the Impact of Big Data on Cancer Medicine
  6. BAZ2A in prostate cancer: New epigenetic mechanism involved in prostate cancer published in Nature Genetics
  7. Roland Eils receives HMLS Investigator Award
  8. Stefan Kallenberger receives Roche Oncology Award
  9. Become part of the iGEM Team Heidelberg 2015!
  10. William J. Godinez receives the Thomas Gessmann PhD Prize 2014 for his outstanding work on probabilistic particle tracking
  11. iGEM-Team Heidelberg wins Grand Prize at Giant Jamboree in Boston
  12. iGEM 2014 Wiki Freeze - Have a Look at "The Ring of Fire"
  13. Natalie Jäger receives Helmholtz PhD Award for her outstanding achievements in uncovering genomic alterations in cancer
  14. iGEM-Team Heidelberg 2014 launches iGEM@home project
  15. Directing the cell by light: eilslabs Synthetic Biology group publishes light-inducible tool for controlling nucleocytoplasmic protein localization in Nature Communications
  16. sports@eilslabs: Heidelberg runs for cancer research - May 25, 2014
  17. Former eilslabs PhD Student Lei Gu receives China Scholarship Council (CSC) Award
  18. Excellent Result at Particle Tracking Challenge Published in Nature Methods
  19. New eilslabs publication on regulation of apoptosis in Science Signaling highlighted by Science Editor
  20. iGEM Team Heidelberg 2013 publishes Grand-Prize project in Molecular Biosystems
  21. Second edition of Computational Systems Biology out; edited by Roland Eils and Andres Kriete
  22. A long way to the $1000 genome - assessment of costs of whole genome sequencing published
  23. International Symposium on Synthetic Biology and BioArts Exhibition: not invented by nature
  24. iGEM Heidelberg featured on FAZ.NET: "Heidelberg Gold Rush"
  25. Heidelberg Team Receives Grand Prize at iGEM World Jamboree
  26. X-Chromosome Hypermutation: New Biological Phenomenon Discovered - Publication in Cell
  27. Segregation Mechanism of Bacterial Chromosomes described in Molecular Systems Biology
  28. New publication in Nature Protocols: whole-genome bisulfite sequencing with minute amounts of DNA
  29. not invented by nature: Bioarts project running at eilslabs
  30. New Publication in Nature Genetics indicates that pilocytic astrocytoma is predominantly a single-pathway disease
  31. Campus Report on Big Data features Jürgen Eils
  32. SplicingCompass: differential splicing detection using RNA-Seq data
  33. Publication in Cancer Cell - Large Feedback in German Newspapers
  34. Medicine in the context of Big Data
  35. eilslabs Retreat 2013
  36. Publication in Cell Death and Differentiation: Changing the model of CD95 induced apoptosis with a new tool
  37. New Publications in PLoS One and Cancer Letters on Neuroblastoma
  38. Indo-German Symposium on Systems Biology in Hyderabad, co-organized by Roland Eils
  39. Best Poster Award for Natalie Jäger
  40. Deciphering the genome of Burkitt-Lymphomas: Publication in Nature Genetics
  41. Workshop on Data Processing and Pipelines for Next Generation Sequencing in Granada
  42. eilslabs Apoptosis Research Featured by the Simons Foundation
  43. eilslabs Retreat 2012
  44. eilslabs Gatherings
  45. Nature Publication on Genomic Analysis of brain tumors
  46. New publication on Whole-Genome Analysis in Cardiovascular Research
  47. 3D-Image Analysis project of BMCV group presented in German parliament
  48. ICGC-Publication in Cell: PedBrain-Tumor consortium identifies linkage between p53 mutations and DNA-Rearrangements
  49. Roland Eils voted as Acting Director of BioQuant, Heidelberg University's Systems Biology Center
  50. Radio-Feature on Total Genome Sequencing Projects in Heidelberg: All my Genes