Our paper on rescuing reads as well as correcting reverse transcrition mediated bias in quantification of nucleotide conversion RNA-seq data is now published. Congrats Kevin for this really nice piece of work and thanks to all collaboration partners!
grandRescue/grandCorrect preprint online
Our preprint on rescuing previously unmappable reads as well as correcting reverse transcrition mediated bias in quantification of nucleotide conversion RNA-seq data is on bioRxiv. Thanks Kevin for a major effort!
Würzburg → Regensburg
Our lab moved from the Institute for Virology and Immunobiology at the University of Würzburg at the new Faculty for Informatics and Data Science at the University of Regensburg. We are absolutely excited and look forward to all future challenges.
5 new papers out
Collaboration with Cochain-lab: Integrated single-cell analysis-based classification of vascular mononuclear phagocytes in mouse and human atherosclerosis
Collaboration with Schlosser lab: Extending the Mass Spectrometry-Detectable Landscape of MHC Peptides by Use of Restricted Access Material
https://pubs.acs.org/doi/full/10.1021/acs.analchem.2c02198
Collaboration with Fischer lab: An unusual mode of baseline translation adjusts cellular protein synthesis capacity to metabolic needs
https://www.sciencedirect.com/science/article/pii/S2211124722013171
Collaboration with Dölken lab: Two murine cytomegalovirus microRNAs target the major viral immediate early 3 gene
https://www.microbiologyresearch.org/content/journal/jgv/10.1099/jgv.0.001804
Collaboration with Dölken lab: pUL36 Deubiquitinase Activity Augments Both the Initiation and the Progression of Lytic Herpes Simplex Virus Infection in IFN-Primed Cells
Review article on time-resolved single cell RNA-seq out
The combination of single-cell RNA sequencing (scRNA-seq) with metabolic RNA labelling approaches now enables time-resolved monitoring of transcriptional responses for thousands of genes in thousands of individual cells in parallel.
Preprint on grandR online
A preprint on our grandR package is now on bioRxiv. It offers easy access to all different kind of downstream analysis for nucleotide conversion RNA-seq data (such as SLAM-seq or TUC-seq), and introduced new computational methodology for quality control and temporal recalibration as well as a Bayesian hierarchical model to analyze synthesis and degradation rates from single snapshot experiments as well as changes thereof. Thanks Teresa and Lygeri for a major effort!
SPT6 paper online
Fantastic collaboration with the Wolf lab. Acute depletion of SPT6 analyzed with 4sU-seq, ChIP-seq, 4sUDRB-seq and SLAM-seq, including mathematical modeling and new computational concepts (LFC regression, DRB wave-front estimation / POL 2 termination zone decline via negative binomial regression, modeling transcriptional kinetics w/o steady-state using SLAM-seq)
https://authors.elsevier.com/sd/article/S1097-2765(21)00496-2
ZAP paper online
SLAM-seq and iCLIP identified the antiviral protein ZAP to bind and destabilize human cytomegalovirus UL4/5 transcripts. Very cool application of SLAM-seq to distinguish transcriptional regulation from RNA destabilization, and very nice collaboration with the Brinkmann lab and the Munschauer lab.
iTiSS paper online
Our paper on iTiSS is now online: https://academic.oup.com/bioinformatics/advance-article-abstract/doi/10.1093/bioinformatics/btab170/6171178
Congrats, Chris!
Identification of the Cryptic HLA-I Immunopeptidome
Our paper on de novo peptide sequencing and improved identification of MHC-I (a.k.a.) HLA-I immunopeptidomes is finally published at Cancer Immunology Research. Very nice collaboration with the Schlosser-lab!