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Postdoc in Proteogenomic bioinformatics

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Proteogenomic signatures for improved prognosis of locally recurring breast cancer

We are seeking a highly motivated bioinformatics postdoctoral scientist to join a collaborative project between three research groups headed by Emma Niméus and Johan Malmström respectively from Lund University and Lars Malmström from University of Zurich. The research collaboration involves scientists from Department of surgery at the Region Skåne University hospital in Lund, the Department of Oncology, the Lund University center of excellence in biological and medical mass spectrometry (CEBMMS) and S3IT a bioinformatics infrastructure unit at the University of Zurich. Through the formation of an interdisciplinary research activity including expertize ranging from physicians, mass spectrometry experts and bioinformatics, the goal of the project is to discover driver mutations behind development of local recurrences in breast cancer using novel proteogenomics research strategies.

Breast cancer is the most common malignancy among women in the Western world, affecting approximately every tenth woman. A local recurrence (LR) is a recurrence in the same breast as the primary tumor and implies an increased risk of both distant recurrences and mortality. Detection of local recurrences represents a therapeutic opportunity that can be exploited for treatment to prevent the development of distant recurrences, which is currently considered a non-curable disease.

In the outlined project we intend to develop novel bioinformatics strategies to merge previously established genomic sequences from highly clinically characterized individual tumors with quantitative mass spectrometry based proteomics. The goal is to detect driver mutations for the development of LR and to separate “true” LR from a new primary tumor, which may be the first step of systemic spread1. Comparative analysis will be performed in a pair-wise fashion from over 100 available tumors where primary tumor is used as internal control. The proteomics analysis will be performed using several quantitative mass spectrometry techniques2-6 using instruments available at CEBMMS. A protein profile distinguishing a LR from a new primary tumor would have a clinical impact on the treatment plan.

Work description
The focus of the position is to support the computational workflows used to process and analyze mass spectrometry data. Primary tasks include operating and develop a data management (openBIS) and workflow management (gc3pie/applicake) system that is already installed and running on national infrastructure (SweStore for storage, openstack-based SMOG cloud for custom-installations and web servers and SNIC national compute clusters). Major other tasks include supporting users in their scientific endeavor by developing new workflows and software tools as well as analyzing scientific data.

You accept new challenges arising from working in a high-paced scientific environment and you can solve them independently even under pressure. You are a good communicator and have the necessary organizational skills to work with users (i.e., PhD students, research associates, professors etc.) efficiently and in a solution-oriented manner.

Level of employment
100 % for 2 years with possibility of further extensions

Requested skills
Candidates should preferably have working experience in all of the following subjects:
· MSc or PhD in computer science, math, statistics, biology or similar
· Python programming
· Linux systems administration (Ubuntu)
· Database experience, ideally postgresql
· Experience with any of the following will be considered an advantage:
· C++ and Java
· Experience with large-scale computer system
· Scientific computing
· Scientific user support
· Computational biology or Computational proteomics

Language
Good command of written and spoken English is a must.

The Lab Infrastructure
The groups are embedded in a multidisciplinary and highly collaborative systems biology/molecular medicine and bioinformatics research environment providing access to state-of-the-art mass spectrometry and bioinformatics. Located in the BioMedical Centre in proximity to the University Hospital, CEBMMS (http://www.cebmms.lu.se/) physically joins investigators and instruments from eight laboratories representing the members of the Faculties of Science, Medicine, and Engineering and Region Skåne with a combined staff of over forty researchers. The Centre’s strong interdisciplinary infrastructure currently includes 22 modern mass spectrometer instruments and the strategic investment in the Region Skåne Biobank.

The South Swedish Breast cancer group collects all tumors from all hospitals from the south Swedish region. Samples for the current project have been collected in a paired fashion with tissue from both the primary tumor and the local recurrence. Full clinical follow up has been obtained for the patients and individual CRFs (clinical research form) have been created.

Our offering
We offer a dynamic work environment with friendly colleagues on BMC in direct contact with both the CEBMMS proteomics scientists and the majority of the University research groups. You will have the chance to be an integral part of a growing scientific IT facility where we hack interesting problems daily. You will be compensated according to the high living standards of Sweden. Working place is the Lund University, Sweden. Financing and employment conditions for this position are according to the regulations of Lund University, which is an equal opportunities employer.

Start date
Fall 2016 or upon agreement

For more information:
Emma Niméus, MD, PhD Johan Malmström, Ass. Prof.
Department of Surgery and Oncology Department of infectious disease
Lund University Lund University
Phone:+46-766322154 Phone: +46-46-2220830
Emma.nimeus@med.lu.se johan.malmstrom@med.lu.se
http://www.med.lu.se/english/klinvetlund/johan_malmstrom_lab

References
1. Nimeus-Malmstrom, E. et al. Gene expression profiling in primary breast cancer distinguishes patients developing local recurrence after breast-conservation surgery, with or without postoperative radiotherapy. Breast cancer research : BCR 10, R34 (2008).
2. Malmstrom, L. et al. Quantitative proteogenomics of human pathogens using DIA-MS. Journal of proteomics 129, 98-107 (2015).
3. Sjostrom, M. et al. A Combined Shotgun and Targeted Mass Spectrometry Strategy for Breast Cancer Biomarker Discovery. J Proteome Res 14, 2807-2818 (2015).
4. Malmstrom, J. et al. Proteome-wide cellular protein concentrations of the human pathogen Leptospira interrogans. Nature 460, 762-765 (2009).
5. Karlsson, C., Malmstrom, L., Aebersold, R. & Malmstrom, J. Proteome-wide selected reaction monitoring assays for the human pathogen Streptococcus pyogenes. Nature communications 3, 1301 (2012).
6. Malmstrom, E. et al. Large-scale inference of protein tissue origin in gram-positive sepsis plasma using quantitative targeted proteomics. Nature communications 7, 10261 (2016)….

Source: Nature Jobs

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