News in 2015
STUDENT UPDATE: NYU CGSB - MDC BIMSB bilateral meeting
BIMSB researchers travelled to New York from December 4-5 for their annual exchange workshop with faculty of the Center for Genomics and Systems Biology of the New York University and the Developmental Genetics Symposium. Group leaders and graduate students presented latest results and discussed collaborative projects during the workshop. New faculty and exchange graduate students introduced their projects and found collaborative partners. BIMSB’s new group leader Jan Philipp Junker was invited to present his research at the Developmental Genetics Symposium with the focus on “Transcription regulation and cell fate”.
PUBLICATION: Watching the ribosome at work
A new statistical method could help to clarify the function of unknown genes. A research team under Uwe Ohler of the Berlin Institute for Medical Systems Biology (BIMSB) at the Max Delbrück Center for Molecular Medicine (MDC) has adapted and tested a filter method from speech signal processing that makes sequencing data more interpretable. First author of the study in Nature Methods is Lorenzo Calviello. “We can use this to watch the ribosome at work”, says group leader Ohler.
STUDENT UPDATE: Andranik Ivanov successfully defends his doctoral thesis
Andranik Ivanov, N Rajewsky group, has successfully defended his doctoral thesis "Cis-regulatory elements in transcription and splicing" with the grade magna cum laude at the Institute of Biology of the Humboldt-Universität zu Berlin on November 25, 2015.
Thesis reviewers: N. Rajewsky, C. Birchmeier, A. Pombo
Doctoral commission: N. Rajewsky, C. Birchmeier, A. Pombo, M. Selbach and A. Herrmann
This research was funded by the German-Israeli Foundation for Scientific Research and Development (GIF) and the German Ministry for Education (project SatNet).
SUMMER SCHOOL: Spot on - the computational genomics summer school
“Outstanding faculty… Amazingly well organized… Great people doing very good work… Extremely interesting, even and especially for a wet-lab biologist” – the participants only had superlatives when describing the 3rd International MDC-BIMSB Summer School, taking place at the Max Delbrück Center for Molecular Medicine (MDC) from October 18-24.
This time, the yearly Summer School was all about “Computational Genomics”. 20 participants chosen from 65 applications spent seven very intense days learning hands-on programming in R, statistics, NGS applications and Chip-seq/RNA-seq data analysis as well as working with multiple genomics data sets.
LECTURE SERIES: Scientific colleagues come together in Winter Semester 2015/16 to present lectures on the topic of Proteins & Proteomics. Please note that this series will be held on Campus Buch. All are welcome to attend.
COLLABORATION: 3rd MRC CSC - MDC BIMSB bilateral workshop
BIMSB hosted researchers from MRC Clinical Science Centre in London, UK, for the 3rd MRC CSC – MDC BIMSB bilateral workshop from October 6-7, 2015. This biannual activity brings together researchers from two leading European Systems Biology research institutions to discuss recent research and collaborative activities. Ongoing interactions will soon be extended with staff exchange.
This year’s workshop was accompanied by the Helmholtz International Fellow Award ceremony for Amanda Fisher, director of the MRC CSC, for her excellent research and to strengthen the collaboration between the MDC and the MRC CSC.
Full Professorship for Wei Chen
Geneticist and genome researcher Wei Chen of the Berlin Institute for Medical Systems Biology (BIMSB) at the Max Delbrück Center for Molecular Medicine in the Helmholtz-Association (MDC) has become full professor for “Functional Genomics and Systems Biology” at Charité - Universitätsmedizin Berlin. Professor Chen also heads a research group at the BIMSB in addition to the central core facility “Genomics“, which he has set up during the past few years.
Further information can be found in the MDC's press release.
STUDENT UPDATE: Jiaxuan Chen successfully defends his doctoral thesis
Jiaxuan Chen, Selbach group, has successfully defended his doctoral thesis "Analysis of protein-protein interaction by in vivo quantitative proteomics in Caenorhabditis elegans" with the grade magna cum laude at the Institute of Biology of the Humboldt-Universität zu Berlin on September 21, 2015.
Thesis reviewers: R. Lucius, M. Selbach, M. Landthaler
Doctoral commission: A. Herrmann, R. Lucius, M. Selbach, M. Landthaler, E. Klipp
RETREAT: BIMSB Retreat 2015 in Lindow
From September 9-11, the BIMSB gathered in Lindow for this year's retreat. About 120 participants joined a program packed with talks from all 15 research groups of the institute and two poster sessions, complemented by all kinds of social activities and sports in the beautiful surroundings of Brandenburg. Presentations and lively discussions revealed the high quality of research performed here, using cutting-edge technology focusing on microscopy and sequencing-based high-throughput methods. In addition to the scientific program, the retreat also fostered existing and created new collaborations – crucial for a field such as systems biology that heavily depends on collaborative research.
SEMINAR SERIES: Gideon Dreyfuss - Speaker in the BIMSB Seminar Series
On July 7, 2015, Gideon Dreyfuss from University of Pennsylvania visited BIMSB. He presented the lecture "An overarching RNA-controlled gene expression mechanism and cancer cell phenotype”.
Gideon, a HHMI investigator and Isaac Norris Professor of Biochemistry and Biophysics has been a key figure in the field of ribonucleoproteins and made important contribution to understanding their role in gene regulation and disease. His group focuses on the RNA-binding proteins that constitute premRNA-RNPs and noncoding small nuclear RNPs, the two key instruments of mRNA processing and gene regulation, whose perturbations underlie numerous diseases. Areas emerging from these studies are being pursued: the SMN complex, the RNA-protein chaperone required for snRNP assembly; and pre-mRNA protection, a crucial step that shapes the transcriptome. Recently, they discovered a crucial gene regulatory mechanism involving U1 snRNP, which protects the nascent transcriptome from destructive pre-mature termination and provides a tool to modulate cells’ response to stimuli and oncogenic phenotype.
Visit of Rahul Satija
On July 3, 2015, Rahul Satija from NYU visited BIMSB and gave a presentation on "Learning the 'metadata' of a cell - statistical methods for single cell genomics".
As a PostDoc at the Broad Institute, Rahul pioneered droplet based single cell sequencing methods and analyses (Shalek & Satija et al. Nature 2013; Shalek & Satija et al. Nature 2014; Macosko et al. Cell 2015). He applied this to zebrafish embryos and reconstructed a high-resolution spatial map of gene expression by computationally clustering thousands of single-cell sequencing data (Satija et al. Nat. Biotech. 2015). Amongst other insights, this approach identified new marker genes.
Rahul demonstrated the very forefront of method development, applications and analyses of single-cell transcriptome sequencing that he now develops in his own lab and at the New York Genome Center.
STUDENT UPDATE: Stefanie Grosswendt successfully defends her doctoral thesis
Stefanie Grosswendt, N Rajewsky group, has successfully defended her doctoral thesis "Identification of miRNA interactions by different types of ligation reactions" with the grade summa cum laude at the "Lebenswissenschaftliche Fakultät der Humboldt-Universität zu Berlin" on June 30, 2015.
Thesis reviewers: N. Rajewsky, T. Sommer and N. Blüthgen.
Doctoral commission: A. Herrmann, N. Rajewsky, T. Sommer, N. Blüthgen, U. Ohler
STUDENT UPDATE: Ana Babic successfully defends her doctoral thesis
Ana Babic, Chen group, has successfully defended her doctoral thesis "Profiling of synaptic transcriptome" at the Institute for Biology of Freie Universität Berlin on June 18, 2015.
Thesis reviewers: W. Chen, C. Scharff.
Doctoral commission: C. Scharff, W. Chen, H.-J. Pflueger, U. Koch
This research was funded by the BMBF and MDC.
CONFERENCE: Berlin Summer Meeting 2015 - Localization of Cellular Processes
From the June 4-6, 2015, the 8th annual Berlin Summer Meeting took place at the Umweltforum in Berlin Friedrichshain. This former church was a spectacular setting for an event that brought computational and experimental biologists together for intense scientific exchange on the "Localization of Cellular Processes".
Internationally renowned researchers spoke on recent developments and new challenges in areas such as the functional organization within the nucleus (e.g. Kerstin Bystriki, University of Toulouse, FR and Ana Pombo, MDC-Berlin, GER), mechanisms and consequences of RNA localization within cells (e.g. Anne Ephrussi, EMBL, GER and Steve Small, NYU, USA), local translation and protein localization in cellular function and disease (e.g. Joel Richter, U.Mass., USA and Antonella Riccio, MRC-UCL, UK), as well as localized signaling (e.g. Lionel Christiaen, NYU, USA and Sylvia Santos, MRC-CSC, UK).
The impressive keynote presentations were joined by shorter talks selected from submitted abstracts, which allowed further insights into new technologies and approach to understand the complex spatial organization of biological processes. During a lively poster session, younger scientists had a chance to discuss their results with over a hundred participants. The four best posters were awarded with poster prices, kindly sponsored by the Shering Stiftung. Thank you to all who participated and made this a successful, vibrant meeting.
For more information, please visit the Berlin Summer Meeting homepage and keep an eye out for the 9th Berlin Summer Meeting to be held in the summer of 2016!
PUBLICATION: Comprehensive new map helps understanding of gene regulation by the ribonuclease dicer
All the cells in our bodies, be they nerve or kidney cells, blood or skin cells, carry the same genetic information. And yet they all differ considerably. This is because different genes are transcribed in each cell type. In recent years, scientists have found a new class of molecules, so-called “microRNAs”, that play a crucial role in this gene regulation. An enzyme known as Dicer is involved in the formation of these microRNAs. A team of researchers led by Markus Landthaler and Nikolaus Rajewsky at the MDC’s Berlin Institute for Molecular Systems Biology (BIMSB) have recently compiled a comprehensive map of the RNA-binding and processing sites of Dicer, which they published in the journal Cell. Increased understanding of the basic mechanisms governing gene regulation could help in the search for targeted drugs and therapies.
Further information can be found in the MDC's Research Highlights section.
SEMINAR SERIES: Anders Krogh - Distinguished Speaker in the BIMSB Seminar Series
On May 26, 2015, Anders Krogh from the University of Copenhagen, presented a Distinguished Speaker Seminar on how “Bayesian transcriptome assembly improves detection and quantification of alternative transcripts in RNAseq”.
Anders, a theoretical physicist by training, is a pioneer in bioinformatics, having introduced the use of hidden Markov models to protein and nucleic acid sequence analysis. He is also well known to students for having co-authored a standard textbook in bioinformatics.
Recently, he focussed on analysis of data from high-throughput DNA sequencing with applications in post-transcriptional regulation, ancient genomics, metagenomics, and transcriptome analysis.
SEMINAR SERIES: Eric Westhof - Distinguished Speaker in the BIMSB Seminar Series
On May 5 and 6, 2015, Eric Westhof gave a lecture for the BIMSB seminar series “Distinguished Speakers” and for the BIMSB lecture series “RNA Biology”, organized by Marina Chekulaeva (BIMSB/MDC) and Benedikt Beckmann (IRI).
Eric, who directs the well known RNA focused institute IBMC in Strasbourg, is famous for his pioneering work to predict and model the structure of RNA. His lectures sparked inspiring discussions, and several students and postdocs enjoyed lunch discussions with him. Thanks Eric for the great visit!
SEMINAR SERIES: Matthias Hentze - Distinguished Speaker in the BIMSB Seminar Series
On the April 21, 2015, we had another highlight in our seminar series as Matthias Hentze, Director at the EMBL Heidelberg and Head of our Scientific Advisory Board, gave a Distinguished Speaker Seminar about “RNA binding proteins, metabolism and a new function of the genome”.
Matthias combines biochemical and systems level approaches to investigate the regulation of mRNAs via RNA-binding proteins and non-coding regulatory RNAs and recently identified all RNA-bindinding proteins in vivo using RNA interactome capture. As some of these RNA-binding proteins are ‘classic' enzymes carrying out housekeeping functions of intermediary metabolism, Matthias proposed the existence of post-transcriptional regulatory networks between intermediary metabolism and gene expression based on RNA, enzyme and metabolite interactions.
LECTURE SERIES: Scientific colleagues come together in Summer Semester 2015 to present lectures on the topic of RNA Biology. Please note that this series will be held on Campus Buch. All are welcome to attend.
STUDENT UPDATE: Jonas Maaskola successfully defends his doctoral thesis
Jonas Maaskola, N Rajewsky group, has successfully defended his doctoral thesis "Discriminative learning for probabilistic sequence analysis" at the Department of Mathematics and Computer Science of Freie Universität Berlin on April 16, 2015.
Thesis reviewers: M. Vingron and N. Rajewsky
Doctoral commission: M. Vingron, N. Rajewsky, B. Renard, and S. Andreotti
This research was funded by the DFG.
STUDENT UPDATE: Fabian Bindel successfully defends his doctoral thesis
Fabian Bindel, Kempa group, has successfully defended his doctoral thesis "Deciphering links between transcription factor signaling and cancer metabolism" with the grade magna cum laude at the Institute of Biology of the Humboldt-Universität zu Berlin on March 2, 2015.
Thesis reviewers: M. Landthaler, R. Bonneau and E. Klipp
Doctoral commission: E. Klipp, M. Landthaler, U. Ohler, R. Bonneau and A. Herrmann
This research was funded by the MDC-NYU PhD Exchange Program and was jointly conducted with the laboratory of Richard Bonneau at NYU.
PUBLICATION: New Insights on DNA Transcription: Start Region Shown to Be Directional
To bind enzymes that read a gene at the right place, the DNA contains so-called promoters, recognition sequences that are located near the transcription start sites of the genes. Since the advent of high-throughput sequencing technology, which enables the precise investigation of gene expression patterns, scientists had shown that a large percentage of promoters is not unidirectional and that the DNA is read on both opposing strands. Now, in the present study, Professor Uwe Ohler of the Max Delbrück Center for Molecular Medicine (MDC) and Professor James T. Kadonaga of the University of California in San Diego, USA have shown in human cells that a central part of promoters, the core promoter, is intrinsically unidirectional. Thus, transcripts of the opposing DNA strand arise from their own core promoters.
Further information can be found in the MDC's press release.
STUDENT UPDATE: Rina Ahmed successfully defends her doctoral thesis
Rina Ahmed, Dieterich group, has successfully defended her doctoral thesis “Bioinformatic analysis of microRNA genes in free-living and parasitic nematodes” at the Department of Mathematics and Computer Science of Freie Universität Berlin on February 26, 2015.
Thesis reviewers: M. Vingron and K. Gunsalus
This research was funded by the MDC-NYU PhD Exchange Program and was jointly conducted with the laboratory of Kris Gunsalus at NYU.
Helmholtz International Fellow Award for long-standing collaborator Professor Amanda Fisher
The British cell biologist Professor Amanda Gay Fisher of Imperial College London (ICL) has been honored with the Helmholtz International Fellow Award for her excellent research. She is one of seven outstanding researchers from abroad who received the award, each of which is endowed with 20,000 euros. Professor Fisher intends in particular to strengthen her existing collaborations with the Berlin Institute of Medical Systems Biology (BIMSB) of the Max Delbrück Center for Molecular Medicine (MDC) Berlin-Buch.
In her research, Professor Fisher focuses on gene regulation, a fundamental process of life which controls every biological function, including cell division, cell differentiation and regeneration. Professor Fisher, who started her research career in the 1980s, has earned an international reputation in this field. She is known for her pioneering work on HIV, the AIDS virus, describing the function of several of its genes. She also is an expert in epigenetic gene regulation - a process in which molecular biological information not contained in the DNA regulates which genes are turned on and which genes are kept silent. She also has an expertise in T lymphocyte development (immune cells) and in embryonic stem cells.
Further information can be found in the MDC's press release.