Anonymization of human sequence data for open sharing
Are you also disappointed not being able to share your nice (human) sequencing data because of donor's genetic privacy? We wrote a lightweight software to anonymize reads stored in regular .bam files! Available on biorxiv and tool is here: https://github.com/sandberg-lab/dataprivacy
Multi-modal analysis of neurons using Patch-seq
Massive efforts to monitor electrophysiology, morphology, and transcriptomes in over 1,000 cells. We found that, although broad families of transcriptomic types had distinct morpho-electric phenotypes, individual transcriptomic types within the same family were not well separated in the morpho-electric space. All transcriptomics made with Smart-seq2 all mastered by Leo! Published in Nature.
RNA counting and molecule reconstrution with Smart-seq3
scRNA-seq with improved sensitivity and unique abilities to reconstruct counted RNA molecules was published in nature biotechnology!
Single-cell RNA-sequencing of newly transcribed and pre-existing RNA
In collaboration with Patrick Cramers lab, we developed metabolic labelling for single-cell transcriptomics. Important for ongoing studies in the lab focusing on transcriptional dynamics. Published in Nature Communications.
Genomic encoding of transcriptional burst kinetics
Transcription occurs in bursts. In this paper, we used single-cell RNA-sequencing with allelic resolution to infer the kinetics of transcription for thousands of genes. We found a transcriptome-wide role of enhancers in dictating burst frequencies, whereas core promoter elements affected burst size. Published in Nature.
Analysis of allelic expression in clonal somatic cells
Recent literature have suggested that random monoallelic expression (RME) of autosomal genes is widespread. In this paper, we formally tested whether allelic expression is clonally maintained in somatic cells and we found that clonal RME is scarce, whereas stochastic RME due to transcriptional bursting is widespread.
Appointed Professor in Molecular Genetics at KI
Rickard has been appointed Professor in Molecular Genetics at Karolinska Institutet, starting Nov 1st 2015.
Daniel Ramsköld's PhD thesis awarded 2014
Daniel Ramsköld recieved his Phd in June 2014 and was recently awarded the Dimitris N. Chorafas prize for his contributions to medical research. Congrats Daniel!