Our research aims at revealing design principles governing the interplay between genome organization in the three-dimensional space of eukaryotic nucleus and the emergence of specific gene expression profiles. We are trying to understand how certain DNA topologies, both at the level of a single chromosome as well as chromosome assemblies, influence and are influenced by transcription. We do this in a variety of model systems, including healthy primary human cells as well as various pathological conditions characterized by nuclear malformations, such as a premature aging syndromes and cancer.
We are developing and applying state-of-the-art quantitative methods to measure DNA and RNA molecules at high-resolution in hundreds of single cells as well as tissues. We are building upon powerful methods for in situ quantification of DNA and RNA molecules, and integrating them with newly developed single-cell genomic assays to measure chromosome positioning, epigenetic states, and gene expression in a high-throughput fashion. We are combining technology development and experimental work with mathematical modeling and quantitative analyses to cast light on the fascinating question how two meters of DNA can fit in the microscopic volume of a cell’s nucleus.
Our group is a multicultural and multidisciplinary blend of people, willing to join forces and share their knowledge to make meaningful scientific advancements in a creative and collaborative work atmosphere.
Postdoctoral position in bioinformatics available
We are seeking a bioinformatician with very strong programming skills, a background in genomics and statistics, and with good experience with Python, R and shell scripting. The main responsibilities will be designing, implementing, validating and maintaining bioinformatics pipelines for our next-generation sequencing efforts.
Our group develops novel NGS-based technologies to study three-dimensional structure of human genome and the candidate will be expected to be skilled in a thorough and independent mining of the novel type of data our group will be generating.
Magda Bienko, Group Leader
Silvano Garnerone, Project leader
Joaquin Custodio, Post doc
Erik Wernersson, Post doc
Tomasz Kallas, PhD student candidate
Eleni Gelali, PhD student candidate
Dey SS, Kester L, Spanjaard B, Bienko M, van Oudenaarden A. Integrated genome and transcriptome sequencing from the same cell. Nat Biotechnology, Jan 2015
Crosetto* N, Bienko* M, van Oudenaarden A. Spatially resolved transcriptomics and beyond. Nat Rev Gen, Dec 2014
Bienko M*, Crosetto N*, Teytelman L, Klemm S, Itzkovitz S, van Oudenaarden A. A versatile genome-scale PCR-based pipeline for high-definition DNA FISH. Nat Methods. Feb 2013
Bienko M, Green CM, Sabbioneda S, Crosetto N, Matic I, Hibbert RG, Begovic T, Niimi A, Mann M, Lehmann AR, Dikic I. Regulation of translesion synthesis DNA polymerase η by Monoubiquitination. Molecular Cell Feb 2010
Bienko M, Green CM, Crosetto N, Rudolf F, Zapart G, Coull B, Kannouche P, Wider G, Peter M, Lehmann AR, Hofmann K, Dikic I. Ubiquitin-binding domains in Y-family polymerases regulate translesion synthesis. Science Dec 2005