Magda Bienko

Karolinska Institutet

Key publications

Girelli G, Custodio J, Kallas T, Agostini F, Spanjaard B, Wernersson E, Mota A, Gelali E, Crosetto N, Bienko M. GPSeq reveals radial genome organization at high resolution. Nat Biotechnol. 2020

Asp M, Giacomello S, Larsson L, Wu C, Fürth D, Qian X, Wärdell E, Custodio J, Reimegård J, Salmén F, Österholm C, Ståhl PL, Sundström E, Åkesson E, Bergmann O, Bienko M, Månsson-Broberg A, Nilsson M, Sylvén C, Lundeberg J. A Spatiotemporal Organ-Wide Gene Expression and Cell Atlas of the Developing Human Heart. Cell. 2019

Zhang X, Garnerone S, Nicoś M, Marchiò C, Simonetti M, Mirzazadeh R, Harbers L, Hartman J, Venesio T, Sapino A, Bienko M, Crosetto N. CUTseq is a versatile method for preparing multiplexed DNA sequencing libraries from low-input samples. Nat Commun. 2019

Gelali E, Girelli G, Matsumoto M, Wernersson E, Custodio J, Mota A, Schweitzer M, Ferenc K, Li X, Mirzazadeh R, Agostini F, Schell JP, Lanner F, Crosetto N, Bienko M. iFISH is a free resource enabling versatile DNA FISH to study genome architecture in single cells. Nat Commun. 2019

Yan WX, Mirzazadeh R, Garnerone S, Scott D, Schneider MW, Kallas T, Custodio J, Wernersson E, Li Y, Gao L, Federova Y, Zetsche B, Zhang F, Bienko M, Crosetto N. BLISS is a versatile and quantitative method for genome-wide profiling of DNA double-strand breaks. Nat Commun. 2017

Vickovic S, Ståhl PL, Salmén F, Giatrellis S, Westholm JO, Mollbrink A, Navarro JF, Custodio J, Bienko M, Sutton LA, Rosenquist R, Frisén J, Lundeberg J. Massive and parallel expression profiling using microarrayed single-cell sequencing. Nat Commun2016

Kind J, Pagie L, de Vries SS, Nahidiazar L, Dey SS, Bienko M, Zhan Y, Lajoie B, de Graaf CA, Amendola M, Fudenberg G, Imakaev M, Mirny LA, Jalink K, Dekker J, van Oudenaarden A, van Steensel B. Genome-wide maps of nuclear lamina interactions in single human cells. Cell 2015

Dey SS, Kester L, Spanjaard B, Bienko M, van Oudenaarden A. Integrated genome and transcriptome sequencing of the same cell. Nat Biotechnol. 2015

Research Interests

Our research group focuses on understanding the fundamental principles that govern how the three-dimensional architecture of the human genome is established and maintained. To this end, we apply single-molecule DNA and RNA fluorescence in situ hybridization (FISH) techniques to visualize the position and structure of DNA loci and chromosomes, together with the expression of selected genes, at high resolution in thousands of individual cells. In parallel, we develop new methods based on next-generation sequencing, that allow us to measure the radial position of DNA loci genome-wide. We combine state-of-the-art cell culture techniques with genetic and chemical manipulation of genome structure and function, and then apply our methods to probe for structural and functional changes that occur genome-wide or at selected loci.

In the past four years, we have established a powerful platform—iFISH—that enables us to produce hundreds of oligonucleotide probes for DNA and RNA FISH at affordable cost, in a short time. We are now using iFISH to label all human chromosomes with DNA FISH probes evenly spaced every one megabase (Mb), and then build an atlas of chromosome structures and arrangements in different cell types and tissues. In parallel, we have developed a method for Genomic loci Positioning by Sequencing—GPSeq—that allows us to measure, genome-wide, the radial position that a DNA locus occupies in the nucleus, with respect to the nuclear periphery/center. We are now applying GPSeq to find out whether different cell types harbor different radial genome configurations, as well as to learn how chromosomal territories form and arrange themselves in the nucleus, at the end of each mitosis.

Group members

Magda Bienko, PhD, Principal Investigator
Emma Inns, Lab Administrator
Federico Agostini, Senior Researcher
Su Wang, Postdoc
Erik Wernersson, Senior Researcher
Eleni Gelali, PhD student
Gabriele Girelli, PhD student
Tomasz Kallas, PhD student
Ana Mota, PhD student

Open positions

We are always interested in recruiting talented and curious people, with a strong passion for science, in general, and genome biology, in particular.


Last updated: 2022-11-30

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