Postdoc position

A shared postdoctoral position in computational biology of genome structure and fragility is immediately available in the Bienko and Crosetto laboratories for Quantitative Biology and Technology (https://bienkocrosettolabs.org/) jointly with the Friedländer laboratory for Computational RNA Biology (https://www.scilifelab.se/researchers/marc-friedlander/). The Bienko, Crosetto and Friedländer labs are located at the Science for Life Laboratory (SciLifeLab) situated at the Karolinska Institutet Solna campus. SciLifeLab is an interdisciplinary center for molecular biosciences with focus on health and environmental research, bringing under the same roof groups from Karolinska Institutet, Stockholm University, KTH Royal Institute of Technology and Uppsala University. The center features state-of-the-art technology platforms, including NGS, super-resolution microscopy, proteomics, image analysis, and bioinformatics.

The Bienko lab explores the fundamental design principles that regulate how chromatin is organized in the eukaryotic nucleus in normal and disease conditions, and how the 3D chromosome structure influences gene expression.

The Crosetto lab investigates the molecular basis of DNA fragility, trying to understand how the interplay between DNA replication and transcription is linked to the formation of DNA breaks genome-wide.

The Friedländer lab is specialized in the development of algorithms for integrative analyses of NGS data (e.g. miRDeep [Friedländer et al., Nat Biotech 2008, Genome Biol 2014]), and focuses on quantitatively describing and functionally characterizing animal transcriptomes.

Mission

The successful candidate will investigate the links between chromatin structure, gene expression, and DNA fragility by leading the analysis of various types of next-generation sequencing (NGS) data obtained with both standard techniques (e.g., whole-genome and targeted DNA sequencing, RNA-seq, HiC, ATAC-seq, Repli-seq, etc.) as well as custom methods developed in the Bienko and Crosetto labs (BLESS [Crosetto et al., Nat Meth 2013], BLISS [Yan et al., Nat Comm 2017] and unpublished methods).

The placement will be in the Friedländer lab, with daily interactions with members of the Bienko and Crosetto groups who will be responsible for data generation. Dr Bienko and Dr Crosetto will jointly supervise the successful candidate on issues related to the biology and experimental part of the projects, while Dr Friedländer will supervise all aspects related to data analysis and computational methods development. The three groups together form a synergic and dynamic team of international researchers, including clinicians, biologists, biotechnologists, computational biologists, and data scientists.

The main task will consist in processing, analyzing, and modeling standard as well as custom NGS data obtained in the frame of various projects run in the Bienko, Crosetto and Friedländer labs, as well as in integrating the data with publicly available datasets (e.g., from ENCODE). Examples include, but are not limited to:

Data obtained with custom methods

1) Genome-wide in situ DNA digestion profiles obtained by GPSeq (unpublished) and used to infer the radial nuclear localization of chromosomes and genes

2) Genome-wide DNA double-strand breaks profiles obtained by BLESS (Crosetto 2013) or BLISS (Yan 2017)

Data obtained with standard methods

1) Genome-wide intra- and inter-chromosomal contacts detected by HiC or related methods (4C)

2) Transcriptome profiles obtained by RNA-seq and nascent RNA sequencing (TT-seq)

3) Genome-wide DNA accessibility profiles obtained by ATAC-seq

4) Genome-wide histone modification profiles obtained by ChIP-seq

5) Genome-wide replication timing profiles obtained by Repli-seq

6) Genome-wide mutation and DNA copy number profiles

Your skills

A person is eligible for a position as postdoctoral research fellow if he or she has obtained a PhD no more than seven years before the deadline of the application.

The successful candidate will hold a PhD in bioinformatics or computational biology and must have a strong background in integrative analyses of different types of NGS data. Importantly, the candidate will have a keen interest in biology and in describing biology through modeling approaches. Proficiency in bash/Python/Pearl/R is mandatory and programming experience with for instance C versions is an advantage. A strong motivation to work in an interdisciplinary and collaborative environment, and a strong sense of mission and self-motivation are indispensable.

Practical information about the position

Location: Stockholm, Sweden

Start date: 2017-08-01

The position is for two years, with a reciprocal evaluation after one year, with potential for prolongation.

The position is funded by an ERC starting grant and will be paid as a stipend.

How to apply

The application must be written in English and sent to magda.bienko@scilifelab.se with the following items included:

Motivation letter

A complete curriculum vitae, including date of the thesis defence, title of the thesis, previous academic positions, academic title, current position, academic distinctions, and committee work
A complete list of publications
A summary of current work (no more than one page)
Application deadline: July 10