August 8, 2022. Publication in @MedCellPress (featuring on the cover!) where we demonstrate the feasibility and reliability of parallel lineage-assignment of select SARS-CoV-2 variants at population scale, tracking the dominant sublineage transition from BA.1 to BA.2 at day-to-day resolution. Importantly, we uncover nearly two-fold higher levels of viral RNA in cases infected with Omicron BA.2 relative to BA.1. Our data provide unique insights into the Omicron BA.1 to BA.2 transition that occurred in Sweden during early 2022, and later, across the world. This may help to understand the increased transmissibility of the BA.2 variant.

Funding: Funded by the SciLifeLab/KAW National COVID-19 Research Program Project Grant (2020.0182, 2020.0241, V-2020-0699), the Swedish Research Council (2017-01723), the Ragnar Söderberg Foundation (M16/17), and the Knut and Alice Wallenberg Foundation (KAW 2021.0142).

Article link:

KI news piece on the study:

May 16, 2022. Welcome to the team Ph.D. student Sebastian Wettersten! Sebastian has a bioinformatics background from Gothenburg University, where he worked on improving taxonomic classification software. At Karolinska Institutet, he will address key questions in gene-dosage compensation using single-cell genomics data. Great to have you onboard, Sebastian!

April 6, 2022. Our study "Elastic dosage compensation by X-chromosome upregulation", mapping the X-upregulation dynamics throughout the early mouse development, was published in Nature Communications. These new insights alter the established model of mammalian dosage compensation, bridging the allele-specific dynamics of X-chromosome upregulation and X-inactivation. Congratulations lead author Antonio Lentini and others who contributed to this landmark study!

Article link:

KI news piece on the study:

March 28, 2022. Read our preprint that may explain why the Omicron BA.2 variant outcompetes BA.1

"Throughout the SARS-CoV-2 pandemic, multiple waves of variants of concern have swept across populations, leading to a chain of new and yet more contagious lineages dominating COVID-19 cases. We tracked the remarkably rapid shift from Omicron BA.1 to BA.2 sub-variant dominance in the Swedish population during January-March 2022. By analysis of 174,933 clinical nasopharyngeal swab samples using a custom variant-typing RT-PCR assay, we uncover nearly two-fold higher levels of viral RNA in cases with Omicron BA.2. Importantly, increased viral load in the upper pharynx upon BA.2 infection may provide part of the explanation why Omicron BA.2 is more transmissible and currently outcompetes the BA.1 variant across populations."

Preprint link:

March 27, 2022. Collaborative work "Detection and isolation of airborne SARS‐CoV‐2 in a hospital setting" together with Antonio Gigliotti Rothfuchs (MTC, KI) published in Indoor Air. Article link:

Jan 13, 2022. A funded PhD position on the regulation of dosage compensation is available. Looking for a highly motivated student with computational and technical skills.

Contact: bjorn.reinius at

Apply here:

Dec 2, 2021. Björn Reinius is awarded a Wallenberg Academy Fellowship in Medicine funded by the Knut & Alice Wallenberg Foundation! This competitive five-year grant (with the possibility of extension yet 5 years) will allow the lab to study in-depth the mechanisms of dosage balance both on chromosome X and autosomal chromosomes upon aberrations. Read more here and here.

Aug 20, 2021. Read the Annual report of The Ragnar Söderberg Foundation on how we developed a streamlined Covid-19 testing procedure that helped to increase the RT-PCR-based diagnostic capacity globally, with >1,500,000 tests performed in Sweden alone via the Public Health System (as of Aug 2021). (text in Swedish)

July 15, 2021. Read our preprint: Allele-resolved single-cell multi-omics uncovers the dynamics and transcriptional kinetics of X-chromosome upregulation spearheaded by postdoctoral researcher Antonio Lentini. This study provides unprecedented insights into the dynamics of mammalian X-chromosome upregulation, prompting a revised model of the chain in events of allelic regulation by X-upregulation and X-inactivation in unitedly achieving stable cellular levels of X-chromosome transcripts.

May 25, 2021. Divergent clonal differentiation trajectories establish CD8+ memory T cell heterogeneity during acute viral infections in humans published in Cell Reports. Collaborative work led by Jakob Michaëlsson and Jonas Frisén (Karolinska Institutet).

May 4, 2021. Björn Reinius receives a Strategic Research Area Grant (Stem Cells and Regenerative Medicine) from Karolinska Institutet.

Mar 19, 2021. Our project Efficient Point-of-Care and Variant Detection of SARS CoV- 2 and Other Viruses (Phase 2) will be funded as part of the COVID-19 response program of the SciLifeLab and the Knut & Alice Wallenberg Foundation. Joint application with Vicent Pelechano and Aman Russom.

Feb 19, 2021. Continuous human uterine NK cell differentiation in response to endometrial regeneration and pregnancy published in Science Immunology. Collaborative work led by Niklas Björkström (Department of Medicine, Karolinska Institutet). Our study uncovers a continuous differentiation pathway of human NK cells in the uterus that is coupled to profound functional changes in response to local tissue regeneration and pregnancy

Feb 1, 2021. Welcome to the lab Erasmus+ grantee Fleur Vereijken (Van Hall-Larenstein Leeuwarden, the Netherlands). Fleur will study X-chromosome dosage compensation in the human pre- and per-implantation development.

Jan 19, 2021. Direct detection of SARS-CoV-2 using non-commercial RT-LAMP reagents on heat-inactivated samples published in Scientific Reports. Collaborative work led by Vicent Pelechano (SciLifeLab). We present the optimization of highly cost-effective in-house produced enzymes for RT-LAMP detection of Covid-19, and we benchmark their performance against commercial alternatives. We anticipate that optimized and affordable reagents for RT-LAMP will facilitate the expansion of SARS-CoV-2 testing globally, especially in sites and settings where the need for large-scale testing cannot be met by commercial alternatives.

Nov 20, 2020. The Faculty Board of Karolinska Institutet awards Björn Reinius with funding for the position as Senior Researcher.

Oct 30, 2020. Vetenskapsradion P1 (Science Radio, Radio Sweden) airs a 20 min program about extensive and rapid COVID-19 testing. Hear our collaborator Björn Högberg talk about our SARS-CoV-2 hid-RT-PCR method and other rapid COVID-19 tests - and their importance for infection control.

Oct 25, 2020. Computational postdoc position open. Apply here.

Oct 9, 2020. Reinius lab receives KID-funding 2020 (PhD salary funding from Committee of Doctoral Education) and will recruit PhD student(s) ahead. Ana Teixeira (Department of Medical Biochemistry and Biophysics) and Martin Enge (Department of Oncology-Pathology) will be co-supervisors for this PhD project.

Oct 8, 2020. Lab Event! Brain-storming session and team building. After a day of seminars and other curricular activities we solved an Escape Room ("Fox in a Box") and enjoyed a nice evening and dinner together.

Sept 26, 2020. Our simplified COVID-19 test featured in the main Swedish news outlets. Hear the original radio interview (in Swedish) at Sveriges Radio P1.

Other sources: Dagens Industri, Aftonbladet, Expressen, LäkemedelsVärlden

Research supported by the Knut and Alice Wallenberg Foundation

Sept 23, 2020. REMOVING BOTTLENECKS IN COVID-19 TESTING! Massive and rapid COVID-19 testing is feasible by extraction-free SARS-CoV-2 RT-PCR published in Nature Communications. We describe methods circumventing RNA extraction in COVID-19 testing by performing RT-PCR directly on heat-inactivated or lysed samples. Our data, including benchmarking using 597 clinical patient samples and a standardised diagnostic system, demonstrate that direct RT-PCR is viable option to extraction-based tests. This should aid the expansion of COVID-19 testing.

Link to Karolinska Institutet's press release: A cheaper, faster COVID-19 test

Aug 24, 2020. Detection of SARS-CoV-2 using non-commercial RT-LAMP regents and raw samples preprint available at Collaborative work led by Vicent Pelechano (Department of Microbiology, Karolinska Institutet). We present the optimization of highly cost-effective in-house produced enzymes for RT-LAMP detection of SART-CoV-2, and we benchmark their performance against commercial alternatives.

Aug 21, 2020. Natural killer cell immunotypes related to COVID-19 disease severity published in Science Immunity. Collaborative work led by Niklas Björkström (Department of Medicine, Karolinska Institutet). This study provides a detailed map of the Natural Killer Cell activation landscape in COVID-19 disease.

July 15, 2020. Postdoctoral researcher Jilin Zhang joins the lab (shared with Jussi Taipale's lab)! Jilin earned his PhD at Karolinska Institutet 2020, where he decoded the functions of genomic elements using RNA and DNA sequencing data and developed bioinformatics tools. Jilin will work on dosage compensation and transcriptional kinetics in ZW systems.

June 30, 2020. Welcome to the lab internship student Xian Xin! Xian (Lund University) will study dosage compensation in ZW systems using single-cell RNA-seq data.

June 7, 2020. We describe the developmental dynamics of X-chromosome upregulation and its link to X-inactivation - landmark results in chromosome-wide regulation. The interplay between X-chromosome upregulation (XCU) and X-chromosome inactivation (XCI) to balance allelic expression have remained poorly understood. We mapped XCU throughout early mouse embryonic development at cellular and allelic resolution, revealing sex- and lineage specific dynamics and an unappreciated flexibility of XCU. We provide a unified model of XCU and its link to XCI, and evidence for flexible balancing of allelic expression levels to compensate for dosage imbalance of the X chromosome.

Antonio Lentini (postdoc) spearheaded this amazing piece of work - congratulations!

Read our preprint: X-chromosome upregulation is dynamically linked to the X-inactivation state

May 5, 2020. Read our updated preprint Massive and rapid COVID-19 testing is feasible by extraction-free SARS-CoV-2 RT-qPCR, including the optimized protocol for direct SARS-CoV-2 RT-qPCR on heat-inactivated samples and benchmarking against the cobas 6800 (Roche Diagnostics) using nearly 600 samples.

Several labs and agencies have already contacted us with questions to aid in their implementation of the method. If your lab or organization have any questions whatsoever or need support in applying the method please do not hesitate to us by email: bjorn.reinius at

April 18, 2020. We describe methods to circumvent RNA extraction in COVID-19 testing by performing RT-qPCR directly on heat-inactivated subject samples as well as samples lysed with readily available detergents. Our data, including cross-comparisons with clinically diagnosed patient samples, suggest that direct RT-qPCR is a viable option to extraction-based COVID-19 diagnostics. We argue that significant savings in terms of time and cost can be achieved by embracing RNA-extraction-free protocols, that feeds directly into the established PCR-based testing pipeline. This could aid the expansion of COVID-19 testing. Read our preprint: Massive and rapid COVID-19 testing is feasible by extraction-free SARS-CoV-2 RT-qPCR

April 8, 2020. Our project Extraction-free high-sensitivity RT assay for SARS-CoV-2 RNA detection will be funded as part of the COVID-19 response program of the SciLifeLab and the Knut & Alice Wallenberg Foundation.

March 12, 2020. Given the increasing seriousness of the COVID-19 pandemic, and current bottlenecks in clinical testing, the lab will work to improve and simplify SARS-CoV-2 detection methods. In this work we will take a pragmatic approach, aiming to relieve current needs in clinical diagnostics. We will put major effort into moving this forward quickly.

March 6, 2020. Welcome to the lab postdoctoral researcher Joyce Noble! Joyce earned her PhD at Wesleyan University, Middletown, Connecticut, USA, where she studied the regulation of olfactory receptors (a classical example of autosomal random monoallelic gene expression). Joyce will establish stem cell lines in the lab and explore the mechanism of X-chromosome upregulation.

Feb 10, 2020. Jeroen Spruit from Van Hall-Larenstein Leeuwarden (Netherlands) joins the lab. Jeroen was awarded an Erasmus Grant to perform studies in our lab during the winter and spring. – Congratulations to your grant and welcome to the lab Jeroen! Jeroen will use CRISPR/Cas9 strategies to investigate the function of X-encoded elements in the establishment and maintenance of X-inactivation, together with PhD student Natali Papanicolaou.

Jan 7, 2020. We are very excited to welcome PhD student Natali Papanicolaou to the lab! Natalie's thesis will focus on the molecular regulation of X-chromosome inactivation. She will be digging into patterns of cell-type specificity in X-chromosome inactivation programs, among other exciting lines of research. Great to have you in the team Natalie!

Dec 10, 2019. The lab hosts Anke Sparmann, senior editor at Nature Structural & Molecular Biology (Springer Nature) for a day of visiting Researchers at the Karolinska Institute.

Oct 3, 2019. Our work on X-chromosome upregulation featured on the News Page of Karolinska Institutet: Breakthrough in sex-chromosome regulation. Also available in Swedish: Genombrott i förståelsen av könskromosomernas genreglering.

Oct 3, 2019. Our study X-chromosome upregulation is driven by increased burst frequency was published as an Article in Nature Structural & Molecular Biology! This paper was also highlighted in a News & Views article in the same issue: Rapid transcriptional bursts upregulate the X chromosome.

September 16, 2019. A funded PhD position is available in the lab! We hope to identify a highly motivated an talented student for PhD education at Karolinska Institutet (Reinius lab). The PhD student will characterize fundamental features of gene regulation, using the human and mouse X chromosome as model system.

More information about the research project and how to apply:

General information about doctoral education at Karolinska Institutet is found here:

Application deadline Oct 16.

August 14, 2019. Lab Event. Celebration of our work and team building event. After a day of seminars and other curricular activities, we solved an Escape Room ("Tesla's Mystery") together and enjoyed a nice evening at the restaurant Koh Phanang.

June 27, 2019. Preprint article Expression reduction of biallelically transcribed X-linked genes during the human female preimplantation development available at Paper under review.

June 19, 2019. Welcome postdoctoral researcher Antonio Lentini! Antonio has a background in molecular biology and bioinformatics and will work on the clonality of X-chromosome inactivation in human. He will also characterize previously unexplored features in various sex-chromosome systems...

Antonio earned his PhD at Linköping University, Sweden.

June 18, 2019. We welcome postdoctoral researcher Leyden Fernández Vidal to the lab! Leyden has a background in machine learning and will elucidate tissue-specific X-chromosome inactivation patterns and its regulation, among other exciting gene-regulatory patterns in vivo.

Leyden earned her PhD at University of Barcelona and Barcelona Supercomputing Center, Spain.

June 14, 2019. Erşen Kavak, the CEO of the biotech startup Genomize visits the lab. Genomize is specialized on genome-level data production and analysis, relevant for both Pharma or Academia.

May 24, 2019. Collaborative work investigating the theoretical extent of monoallelic expression resulting from transcriptional bursting and how it compares to the amounts of monoallelic expression of autosomal genes observed in single-cell RNA-sequencing data. Implications to random monoallelic expression. Preprint available at Paper under review.

April 1, 2019. The lab welcomes Eunkyoung Choi MSc.

March 14, 2019. Our Linux server is up and running! This computational resource is used to analyze high-throughput RNA/DNA sequencing data and to perform other intense calculations.

February 5, 2019. A MECHANISTIC BREAKTHROUGH to the major gene-regulation process of X-chromosome upregulation! We found that X-chromosome upregulation is achieved by elevated burst frequecies for X-linked genes. Preprint available at Paper under review.

Jan 2, 2019. Collaborative work with Rickard Sandberg's lab Genomic encoding of transcriptional burst kinetics. Published in Nature.

Dec 24, 2018. The lab is investing in a tailored computational server for in-house processing of sequencing data. Exciting times!

July 31, 2018. This is the warmest July ever recorded in Sweden.

July 2, 2018. The lab is stacking up on laboratory equipment.

June 25, 2018. The lab welcomes Postdoctoral Fellow Christos Coucoravas!

May 14, 2018. Collaborative work with Susana M. Chuva de Sousa Lopes' lab Parental haplotype-specific single-cell transcriptomics reveal incomplete epigenetic reprogramming in human female germ cells. Published in Nature Communications.

April 10, 2018. The Reinius lab opens. Access to the new KI facility Biomedicum. Starting to set up the lab...

Jan 1, 2018. Björn Reinius signs up with the Division of Biomaterials at the Department of Medical Biochemistry and Biophysics, Karolinska Institutet.

Dec 6, 2017. Björn Reinius receives a Grant from Åke Wiberg's Foundation.

Nov 16, 2017. Björn Reinius is appointed a Faculty Funded Career Position at Karolinska Institutet as Assistant Professor.

Nov 10, 2017. Björn Reinius receives a Starting Grant from the Swedish Research Council!

Oct 18, 2017. Björn Reinius is awarded a Ragnar Söderberg Fellowship in Medicine and a competitive Starting Grant from the Ragnar Söderberg Foundation!