Oct14
The lab had a good summer. 3 publications were published: TriPepSVM is a machine learning approach to identify RNA-binding proteins de novo. This work was a great collaboration with the Marsico lab. You can find the paper here. Our in-depth discussion of PTex, a method to purify RNA-protein complexes in an unbiased fashion has been […]
Apr11
Accompanying our recently published PTex protocol, we have published another manuscript at bioRxiv: “Fast and unbiased purification of RNA-protein complexes after UV cross-linking” provides important background information for the understanding of biphasic extractions and UV cross-linking of RNA-protein complexes as prerequisite to apply PTex.
Apr11
Together with our collaborators from the group of Annalisa Marsico (MPI for Molecular Genetics, Berlin), we have just published our machine learning approach to predict RNA-binding proteins: TriPepSVM. Read more about it in Nucleic Acids Research (Open Access): https://academic.oup.com/nar/advance-article/doi/10.1093/nar/gkz203/5421814
Mar01
We are very happy to announce that our latest work has been published in Nature Communications. We developed PTex, an unbiased and fast method to purify cross-linked RNA-protein complexes from a variety of biological sources. We have a short summary of the method as well as other resources here. The article itself is […]
Nov09
Together with the RNA Bioinformatics group (MPI for Molecular Genetics, Berlin), we have just uploaded our latest work to bioRxiv: TriPepSVM is a new machine learning approach to predict RNA-binding proteins in human and bacteria. We use a radically reductionist approach by only using short amino acid motifs to train a support vector machine (SVM) to […]
May30
The Beckmann lab has its first work up on bioRxiv! Our manuscript “Purification of Cross-linked RNA-Protein Complexes by Phenol-Toluol Extraction” by Erika Urdaneta et al. describes a completely novel method to purify cross-linked RNA-protein complexes (RNPs) in an unbiased fashion. This new approach allow us now to investigate RNPs in human cell culture but to […]
May30
We are happy to announce that our lab will be part of the DFG-funded Graduate School IRTG 2290 “Crossing boundaries: Molecular Interactions in Malaria”. The International Research Training Group consists of 10 groups located in Berlin and 10 groups from Canberra, Australia. Up to 20 new PhD students will investigate diverse aspects of malaria in […]
Dec19
Finally, our method to purify RNA-binding proteins in yeast is out! The research paper in Methods gives a complete overview over all steps of the interactome capture approach and provides a comprehensive discussion on the background. The article is open access (CC-BY license) and can be found here.
May13
RNA-protein interactions have been studied intensively in recent years. Particularly novel methods such as mRNA interactome capture led to discovery of hundreds of novel RNA-binding proteins (RBPs). However, many of these recently identified RBPs lack classical RNA-binding domains. In our review The expanding universe of ribonucleoproteins: of novel RNA-binding proteins and unconventional interactions, we discuss features of RNA-protein […]
May13
We are proud to host two Bachelor students who are conducting their final thesis in our lab. Victoria Riebe (BSc Biology) is working on CRISPR/Cas9 in bacteria. Valentina Tovazzi (BSc Biophysics) is testing Salmonella proteins for RNA-binding activity.