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Postdoctoral Research Fellow in Computational Biology of Genome Structure and Fragility Uppsala Sweden,
Sci Life Lab (company)
Posted on : 13 May 2017
The research group
- A shared postdoctoral position in computational biology of genome structure and fragility is immediately available for Quantitative Biology and Technology
- Our lab is an interdisciplinary center for molecular bio-sciences with focus on health and environmental research, bringing under the same roof groups.
- The center features state-of-the-art technology platforms, including NGS, super-resolution microscopy, proteomics, image analysis, and bioinformatics.
- The 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 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 lab is specialized in the development of algorithms for integrative analyses of NGS data and focuses on quantitatively describing and functionally characterizing animal transcriptomes.
- 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 labs.
- The three groups together form a synergic and dynamic team of international researchers, including clinicians, biologists, bio-technologists, 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 labs, as well as in integrating the data with publicly available data-sets (e.g., from ENCODE). Examples include, but are not limited to:
- Data obtained with custom methods
- Genome-wide in situ DNA digestion profiles obtained by GPSeq (unpublished) and used to infer the radial nuclear localization of chromosomes and genes
- Genome-wide DNA double-strand breaks profiles obtained by BLESS (Crosetto 2013) or BLISS (Yan 2017)
Data obtained with standard method
- Genome-wide intra- and inter-chromosomal contacts detected by HiC or related methods (4C)
- Transcriptome profiles obtained by RNA-seq and nascent RNA sequencing (TT-seq)
- Genome-wide DNA accessibility profiles obtained by ATAC-seq
- Genome-wide histone modification profiles obtained by ChIP-seq
- Genome-wide replication timing profiles obtained by Repli-seq
- Genome-wide mutation and DNA copy number profiles
- 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
- 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
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