Job: Bioinformatician/Computational Life Scientist (m/f/d), Digital Health Centre, Berlin Institute of Health/Charite, Germany
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27 days ago by
naveed.ishaque0 wrote:

The eilslabs (http://www.eilslabs.de) has recently moved Berlin, where Prof. Roland Eils has established the Digital Health Centre on the Berlin Institute of Health in Berlin.

We are looking to rebuild our team of international and interdisciplinary computational researchers and technicians and are hiring a number of researchers at various levels of entry. Here we advertise research positions, but we are also looking for technical staff to help build hardware and software infrastructure.

Official application link: https://www.charite.de/service/stellenangebot/angebot/detailinfo/cc04_bih_0619_1_5_bioinformaticianscomputational_life_scientists_mf/

Salary: Based on Öffentlichen Dienst VKA E13. Final figure dependant on experience. Current range of E13 is €47.9k-€71.1k. 65% for PhD.

Deadline: 17th April 2019

Duration: Postdocs - 3 years, with possible extension. PhDs - 4 years. The position is a full time position (39 hours). Part time may also be possible.

Location: Central Berlin, Germany

Who we are

The Digital Health Centre, headed by Prof. Roland Eils, conducts innovative healthcare research with a strong focus on computational methods including application and development of big-data analytical methods, artificial intelligence and deep learning. We have recently moved our lab to Berlin and are looking rebuild our multi-disciplinary team of ambitious scientists to apply computational analytical methods to medical multi-omics, clinical and imaging data. We are leaders in international projects (Human Cell Atlas, International Cancer Genome Consortium) and European life science networks (de.NBI, ELIXIR, European Open Science Cloud). We have state-of-the-art computational resources including in-house HPC, cloud, GPGPU (2 x Nvidia DGX1) and FPGA technology. With access to vast amounts of data and computational resources, we aim to address important questions pertaining to precision medicine, interplay of multi-omics data and environmental/lifestyle factors, and methods development.

Example scientific projects

  • Single cell sequencing to unravel heterogeneity of cancer
  • Multi-omics integration to decipher molecular mechanisms of type 2 diabetes
  • Developing a multi-omics integration platform for single cell data
  • Investigating the role of environmental pollutants on the epigenome
  • Identifying the 'omic drivers behind pancreatic neuroendocrine tumors
  • Developing methods for analysis and visualisation of spatial 'omics data
  • Adaptation of cancer genomic workflows to graph based genomes
  • Identifying regulatory programs and immune receptor repertoires after vaccination
  • Implementation of hardware accelerated bioinformatics algorithms on FPGAs
  • Generating machine learning algorithms for diagnosing tumor type from 'omics data (e.g. from DNA methylation or NanoPore sequencing)
  • Investigating interplay of genome and epigenome and their downstream effects on regulatory networks

Responsibilities

The research group of Roland Eils provides a dynamic, challenging, and rewarding research environment. Your responsibilities are primarily to undertake excellent scientific research, while paying attention to career development and community engagement including the following:

  • Working in a highly collaborative research environment
  • Closely collaborate with other research scientist within and outside the group to develop methods and/or analyse biomedical data
  • Closely collaborate with other bioinformatics developers on system implementation and deployment on internal systems and the cloud
  • Focused on application and development of novel computational methods, and awareness of community standards (e.g. GA4GH)

Science communication

  • Publishing research papers in both peer-review and archival journals
  • Publishing novel methods arising from answering research questions

Training and professional development

  • Attend training courses as required, and presenting at international conferences/workshops
  • Generating own or adapting existing training material
  • Post-docs are expected to apply for third party funding as part of their own career development

Qualifications

  • Ambitious, self-driven, a thirst for answering scientific questions and aim to build a scientific career in biomedical data science research
  • A post-doc or Phd candidate with an academic background (PhD/Masters) in computer science, biotechnology, cancer genomics, physics, medicine, or similar
  • Strong quantitative skills and a keen interest in pursuing computational projects
  • Excellent programming proficiency especially in one modern language such as Python, R, Julia, Rust, Javascript, bash or similar
  • Experience with dimensionality reduction and machine learning methods (e.g. PCA, ICA, Random Forest, NMF, xNN, VAE)
  • Fluent in English (written and spoken)

Qualifications – desirable

  • Prior experience in working with single cell ‘omics data, liquid biopsies, or cancer genomics data
  • Experience in data visualization, integration and interpretation of large heterogeneous datasets
  • Able to work with code repositories (git, SVN) and literate programming platforms (e.g. Jupyter, R notebook)
  • Experience with machine learning frameworks (e.g. PyTorch, TensorFlow, Keras, Caffe)
  • Experience with next generation sequencing data analysis
  • Experience or interest in single cell 'omics and imaging applications to biomedical research
  • Experience with linux based HPC or cloud environments
  • Experience in designing and implementing data analysis pipelines
  • Grasp of CWL, WDL or another workflow language, and workflow management platforms (e.g. Cromwell, Funnel, snakemake)

Contact email: Please direct all enquires via the official email link. Informal enquiries should be sent to naveed.ishaque@charite.de

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