Bienko group members


Current team members: 11

Current nationalities: 7


Magda Bienko
(Principal Investigator)
Email: magda.bienko

I studied biotechnology at Jagiellonian University in Krakow, Poland, where I was trained to be the experimentalist I am today, with a deep appreciation for the art of methodology used in life sciences. My journey in academia has always been marked by a common underlying theme: pursuing a fundamental biological question, while developing innovative technologies to address it.
As a master student, I got interested in signal transduction, which led me to join the lab of Ivan Dikic in Frankfurt, where I explored the role of ubiquitin in DNA damage repair. During that period, together with my colleagues, I demonstrated that novel ubiquin-binding domains (UBDs) present in the Y-family DNA polymerases are required for replication of damaged DNA in a process called translesion synthesis (TLS) (Bienko et al., Science 2005). I then went on to study the function of monoubiquitylation of such proteins, and discovered a complex network of monoubiquitylation and ubiquitin-binding events playing a central regulatory role in DNA translesion synthesis (Bienko et al., Mol Cell 2010).
In order to broaden my horizons and expand my expertise, I then switched research field and joined the Systems Biology lab of Alexander van Oudenaarden lab at MIT for my postdoctoral training. The prestigious Human Frontier Science Program recognized my aspiration to change field by awarding me with a postdoctoral fellowship. In Alexander’s lab we developed a powerful pipeline for high-definition DNA FISH (HD-FISH) combined with single-molecule RNA FISH (Bienko et al., Nature Methods 2013), which my group is now actively using to characterize various exciting aspects of RNA and DNA biology in single cells. In 2013, I moved with Alexander’s Lab to the Hubrecht Institute in the Netherlands, were I became enthusiastic about single-cell sequencing technologies and started developing novel approaches for integrated sequencing and microscopy in single cells. In 2015, I became an Assistant Professor at Karolinska Institutet and one of 16 Research Fellows at the Science for Life Laboratory, where I lead a team aiming at developing a comprehensive conceptual framework that explains how the key molecule of life is organized in the 3D confinement of the cell’s nucleus and how this arrangement shapes cells identity.


Silvano Garnerone
(Project Leader)
Bienko/Crosetto Labs

Have you ever come across this sentence: “If the 20th century was the century of physics, the 21st century will be the century of biology”? Well…I decided to see how and why this might be the case.
I defended my PhD thesis in Physics in 2007 at the Politecnico di Torino (Italy); since then I have worked at the Universite’ Pierre et Marie Curie in Paris, at the University of Southern California in Los Angeles, and at the Institute for Quantum Computing in Waterloo. My area of research has focused on quantum physics, information theory, and network science; my major contributions to these fields have been the development of new algorithms for the solution of hard computational problems, and of new techniques for the study of complex systems and big data.
In 2014 I felt the need to start a new career adventure and, excited by the big data revolution, I looked for an environment where my analytic and computational skills could be useful in approaching new fascinating problems. Biology, an old passion of mine, presented itself as the perfect arena where I could help tackling scientific and clinically relevant questions whose answers hide in the increasing flood of data coming from new sequencing and microscopy technologies.
From January 2015 I work in the Bienko and Crosetto labs, where not only I take care of their computational infrastructure but, most importantly, I participate in the delicate process of shaping questions, experiments and data-analysis pipelines according to the tools and techniques that the two groups use and develop.


Lei Xu
Bienko lab

I am from Zhangshu, a small town located in southeast of China. In 2006, I got my bachelor degree in Biological Engineering in Chang’an University located in Xi’an.I pursued master education in Biological Physics at Kungliga Tekniska Högskolan in Stockholm, Sweden. In September 2007, I joined Lene Oddershede‘s Optical Tweezers group at Niels Bohr Institute, University of Copenhagen for my master thesis for a year. Then I joined Jerker Widengren‘s group in Stockholm for my PhD focusing on both technical development and application of single molecule sensitive fluorescence spectroscopy and super-resolution STED microscopy for biochemical and biomedical studies. After defending my PhD thesis in June 2014, I continued in his lab for two years as a researcher. In September 2016, I went to the industry and worked at Vanadis Diagnostics (a company of PerkinElmer) in Stockholm as a Principal Optical Design Engineer, developing fully automated fluorescence imaging system. In September 2017, I came back to academia as a researcher. I enjoy taking challenges in science and technology.


Federico Agostini
Bienko/Crosetto Labs

I was born in Fano, Italy, where I learned how to swim before I could walk. Instead of listening to the ones that wanted me to be either an engineer or a medical doctor, I decided to mash up things and move to Rome to study biotechnologies. After completing my bachelor studies at Tor Vergata university, I attended the university of Bologna for my master in molecular and industrial biotechnologies. For the final thesis, I worked with NMR, and it was then that I decided that I was more interested in the computational side of biology, rather than the lab. To pursue this, I once again changed city, and moved to Barcelona for my PhD. During this time I worked under the supervision of Gian Gaetano Tartaglia at the CRG, studying the interaction between proteins and RNA. Since I was not sick of moving around yet, I went to London for my first postdoc experience, where I worked with Nick Luscombe and Jernej Ule at the Francis Crick Institute on neurodegenerative diseases using NGS data . Now I’m here in Sweden, where I joined the BiCro lab to widen even further my skills in data analysis.


Joaquín Custodio
Bienko Lab

I was born between 80s and 90s in a small city called Mollet del Vallès, located at 10 km from the nice city of Barcelona. Some years later I obtained Bachelor’s degree in Biology, specialized in Microbiology and Sanitary Biology, from the Autonomous University of Barcelona. During those nice years I was enrolled at the Microbiology Department studying a potential role of Mycobacterium species in creating antifungal compounds. Afterwards, I obtained a Master’s degree in Immunology from the University of Barcelona, and had a great opportunity to work in the prestigious association of Banc de sang i teixits de Catalunya (Blood and tissues bank of Catalonia), where I was conducting a collaborative work in order to develop quick and cost-effective techniques for HLA genotyping, based on multiplex PCR. I then started my PhD in Miguel Angel Peinado’s group at the Institute for Predictive and Personalized Medicine against Cancer (IMPPC). My PhD project was focused on deciphering epigenetic changes occurring in the colorectal cancer formation and expansion, mainly DNA methylation, histone modifications as well as chromatin conformational changes. I also worked on leukemia or pre-leukemic malignancies, such as MDS or AML, focusing on the complex epigenetic effects behind the administration of azacitidine or deoxy-azacitidine.
Recently, I joined Magda’s group as a Postdoc at the SciLifeLab Institute. My current projects in the lab include development of new techniques that allow us to get a better picture on how chromosome organization modulates genome expression. Personally, I am interested in applying these new techniques to study how genome organization is affected in various disease models, for example in cancer.


Su Wang
Bienko lab

I was born in the countryside of Wenzhou, which locates in the southeast of China. While growing up with abundant sun, heat, and seafood, I was always intrigued by science. I obtained the degree of B.Eng in Material Science at Zhejiang University of Technology (2012). During which, I found myself developing an appetite towards interdisciplinary subjects. With the urge to expand my mind and view, I started my master study in Biophysics and Biochemistry at the University of Leuven (KU Leuven), Belgium. It was my participation in the iGEM 2013 competition as a member of KU Leuven team that ignited my quest to become a researcher. Later on, my master thesis on the topic of “Identification of Single Synapses in C.elegans by Super-resolution Microscopy” in the laboratory of Prof. Hideaki Mizuno entranced me with this fascinating and engrossing world of microscopy. Therefore, I continued my journey with the pursuit of a Ph.D. degree with the topic of “Strategies and Applications for Sequence-specific Functionalization of DNA by Methyltransferases” in the laboratory of Prof. Johan Hofkens (KU Leuven) in 2014. During which, my fondness towards microscopy in biophysics and biochemistry related topics kept growing. I went on learning expansion microscopy to elucidate the bacterial genomic architecture at the laboratory of my Ph.D. co-supervisor, Dr. Robert K. Neely (University of Birmingham, UK), in 2017. Now (February 2019), I embarked on a new adventure as a postdoc researcher in Prof. Magda Bienko’s laboratory at Science for Life Laboratory / Karolinska Institutet, I wish to apply FISH and fluorescent microscopy to pave into the study of genomic architecture in eukaryotes.


Erik Wernersson
Bienko lab

I earned a M.Sc. degree in engineering physics from Lund University, Faculty of Engineering in 2008 with a major in mathematics. After that, I moved to Uppsala and joined the Centre for Image Analysis where I studied under supervision from Gunilla Borgefors, Cris L. Luengo Hendriks and Anders Brun until I defended my thesis in December 2014. I’m now applying methods from physics, mathematics, machine learning and image analysis to reveal the inner structure of the nucleus. At the same time learning a great deal about cell biology. The Swedish Society for Medical Research funds me until 2017.


Eleni Gelali
(PhD student)
Bienko Lab

I was born in Larisa, Greece and at 2012 I obtained my degree in Molecular Biology and Genetics from Democritus University of Thrace. At 2013, I moved to Stockholm since I was admitted to the Master’s Program in Biomedicine of Karolinska Institute from which I graduated at 2015. During this time, I had the opportunity to perform my rotations at Hong’s Qian lab in the Center of Hematology and Regenerative medicine (HERM), where I studied the multilineage differentiation capacity of the bone marrow Mesenchymal Stem Cells in myeloproliferative neoplasm mice, as well as the Leukotriene Receptors expression on the Leukemic Stem Cells in CML. It was during my master thesis that I joined Magda’s team, where we employed single cell and single molecule methods in an effort to characterize the expression and localisation of the FMR1 gene in Fragile X Spectrum Disorders. Fascinated by the enigma of the nuclear architecture, I am now starting my PhD, hoping to contribute to deciphering the design principles of genome organization and its interplay with gene expression.


Gabriele Girelli
(PhD student)
Bienko Lab

I was born near Verona, Italy and I obtained my B.Sc. (2012) and M.Sc. (2014) in Biotechnology at the University of Trento. There, I developed a passion for bioimaging and computational biology during two internships: first (2012) at Arosio’s Molecular Imaging Lab, where I analyzed images of HIV-infected cells, and then (2014) at Demichelis’ Computational Oncology Lab, where I gained experience in developing computational tools and on tumor heterogeneity and cancer progression. In 2013 I participated to the iGEM competition as a member of the UniTN-Trento team, engineering E. coli to control the fruit ripening process, and in 2014 I received a Summer Fellowship Grant from the Giovanni-Armenise Harvard Foundation to spend two months at Quackenbush’s Computational Biology and Functional Genomic Lab at the Dana-Farber Cancer Institute (Boston, MA), where I contributed to the development of a gene network visualization interface. After obtaining my M.Sc., I spent 6 more months at Demichelis’ Lab to study the association between prostate cancer genome lesions and Gleason Score. In september 2015, I joined Magda’s team at Science for Life Laboratory / Karolinska Institutet to uncover the nuclear 3D architecture principles and how this influences gene expression.


Tomek Kallas
(PhD student)
Bienko Lab

I come from Poland, where I graduated from Biotechnology at the West Pomeranian University of Technology. During my master program, I did an Erasmus summer internship in the lab of Professors Eva Klein and George Klein at Department of Microbiology, Tumor and Cell Biology at Karolinska Institutet, pursuing my interest in tumor biology. After my graduation, I was given the opportunity to join their group for a research project, where I tried to elucidate the effects of interferons on malignant hematopoietic cells. During that time, I observed that cells differ in their responses to various treatments even though they come from the same population, triggering my curiosity for cell-to-cell variability. To combine this with my interest in technologies that push biology forward, in January 2015 I joined the group of Magda Bienko at the Laboratory for Quantitative Biology of the Nucleus at Science for Life Laboratory / Karolinska Institutet, to study the interplay between gene expression and genome organization. Since that time, I have been involved in many rummy projects with the aim to develop new methods for better understanding of the nuclear architecture.


Ana Mota
(PhD student)
Bienko Lab

In my early studies I was thrilled by the fact that such small molecule could encode and command complex organisms and it had settled my interest’s foundation in studying chromatin. The genetic engineering’s recent achievements made me start a bachelor in Biotechnology at Aveiro University, in Portugal. Along the bachelor, Nanotechnology had caught my attention and inspired me to pursue a BSc thesis in drug development which was functionalized to a magnetic nanoparticle to combat tumours by light activation. The BSc thesis had spark my enthusiasm to keep learning nanotechnologies applied to biological systems. To complement my biological background, I started the master in Bioengineering and Nanosystems at Technical University of Lisbon with a deeper focus in physics, informatics, electronics and other engineering fields. It was granted the opportunity to develop my MSc thesis in Cees Dekker lab group at the Kavli Institute in TU Delft, the Netherlands. The project aimed to define the condensin model to compact DNA by using magnetic-tweezers, a single-molecule technique. In BiCroLab, I am relating specific genome events with diseases and learn about the genome organization.