[SocBiN] Postdoctoral Research Fellow in Computational Biology of Genome Structure and Fragility

[Silvano Garnerone]

The research group:

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2013], BLISS [Yan et al., Nat Comm 2017] and unpublished methods).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 at 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


--
Silvano Garnerone, PhD
Project Leader
Department of Medical Biochemistry and Biophysics | Karolinska Institutet
17165 Solna | Tomtebodavägen 23A
-------------- next part --------------
An HTML attachment was scrubbed...
URL: <http://lists.su.se/pipermail/socbin-at-sbc.su.se/attachments/20170526/2d25b4dc/attachment.html>