Congratulations Sophie Rabe

Sophie studied Molecular Biotechnology at the University of Heidelberg. She joined the Huber Group in Spring 2014 as student research assistant and worked on genomic biomarkers of drug sensitivity in primary blood cancer cells. For her PhD thesis, Sophie is now joining the group of Sascha Dietrich at NCT Heidelberg, where she will work on the SYMPATHY project, an integrated system medicine approach to personalized and targeted therapy in leukaemia and lymphoma. This multidisciplinary project is intended to have direct clinical impact on patient care in blood cancers.

Welcome Karsten Bach

Karsten Bach has a B.Sc. in Biology from the University of Bonn. He joined the Huber group in March 2016. At EMBL, he is finishing up his M.Sc. in Molecular Biotechnology and working on quantitative proteomics together with Dorothee Childs and Nikos Ignatiadis.

SOUND second consortium meeting

The second consortium meeting of the SOUND project, which is led by Wolfgang Huber, was hosted by our colleagues from IDMEC Lisbon. Principal investigators, postdocs and PhD students attended the meeting and presented recent results and progress in the work packages. All partners are well on track with their project aims and the atmosphere of sharing research developments was quite enthusiastic. Junyan Lu held a talk on “Mechanistic study of drug response using ex-vivo drug testing and multi-omics technology“ and Małgorzata Oleś provided a presentation on “Modulators of drug response identified by multivariate lasso regression”. Wolfgang Huber gave a lecture on “Data driven hypothesis weighting and false discovery rates”.

SOUND consortium

SOUND consortium







Photos from Lisbon by Junyan Lu.

Presentation by Dorothee

Dorothee Childs presented her work at the EMBL-Wellcome Genome Campus Conference “Target Validation using Genomics and Informatics 2015″, which took place from 8th to 10th December 2015 in Cambridge.
More than 200 people attended this ground-breaking conference. Dorothee gave a talk on “Screening for drug targets in intact cells by thermal proteome profiling”, a project in which she is involved as part of a collaboration between EMBL Heidelberg and GSK’s SME Cellzome, which is also based in Heidelberg.”


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Welcome Annika

Annika Gable has a B.Sc. in Molecular Biotechnology from the University of Heidelberg. She joined the Huber group in December 2015. At EMBL, she is finishing up her M.Sc. in Molecular Biotechnology (major: Bioinformatics) with a thesis on analyzing high-throughput chromatin conformation capture (Hi-C) data.

New paper: Thermal proteome profiling monitors ligand interactions with cellular membrane proteins

Abstract: We extended thermal proteome profiling to detect transmembrane protein–small molecule interactions in cultured human cells. When we assessed the effects of detergents on ATP-binding profiles, we observed shifts in denaturation temperature for ATP-binding transmembrane proteins. We also observed cellular thermal shifts in pervanadate-induced T cell–receptor signaling, delineating the membrane target CD45 and components of the downstream pathway, and with drugs affecting the transmembrane transporters ATP1A1 and MDR1.

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Welcome Junyan Lu

Junyan has a PhD in Computational Biology and Drug Design from Shanghai Institute of Materia Medica, Chinese Academy of Sciences. His previous research focused on understanding mechanisms of drug response using integrated multi-omics technology and large scale ex-vivo drug testing approaches. In November 2015, he joined the Huber Group as a postdoctoral fellow and is now working on the SOUND project.

Welcome Mike Smith

Mike joined EMBL in October 2015 as part of the de.NBI project where he is working on the development pipelines, workflows and computational approaches for large scale biological experiments. He has a PhD in computational biology from the University of Cambridge, UK.

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New paper: TimerQuant: A modelling approach to tandem fluorescent timer design and data interpretation for measuring protein turnover in embryos

Abstract: Studies on signalling dynamics in living embryos have been limited by a scarcity of in vivo reporters. Tandem fluorescent protein timers provide a generic method for detecting changes in protein population age and thus provide readouts for signalling events that lead to changes in protein stability or location. When imaged with quantitative dual-colour fluorescence microscopy, tandem timers offer detailed ‘snapshot’ readouts of signalling activity from subcellular to organismal scales, and therefore have the potential to revolutionize studies in developing embryos. Here we use computer modelling and embryo experiments to explore the behaviour of tandem timers in developing systems. We present a mathematical model of timer kinetics and provide software tools that will allow experimentalists to select the most appropriate timer designs for their biological question, and guide interpretation of the obtained readouts. Through the generation of a series of novel zebrafish reporter lines, we confirm experimentally that our quantitative model can accurately predict different timer responses in developing embryos and explain some less expected findings. For example, increasing the FRET efficiency of a tandem timer actually increases the ability of the timer to detect differences in protein half-life. Finally, while previous studies have used timers to monitor changes in protein turnover, our model shows that timers can also be used to facilitate the monitoring of gene expression kinetics in vivo.

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