Postdoctoral Researcher in Computational Genomics and Machine Learning through the NORPOD program

NORPOD is a collaborative postdoctoral program of the Nordic EMBL Partnership for Molecular Medicine. The partnership is a network of four national research centers across the Nordics and the European Molecular Biology Laboratory (EMBL), with complementary research expertise at the forefront of molecular medicine research. With the NORPOD program, the Nordic EMBL Partnership aims to foster the next generation of researchers in molecular medicine by implementing joint postdoctoral research projects to nurture strong competences and research excellence.

FIMM is currently seeking a Postdoctoral Researcher to join the Machine Learning in Biomedicine group, in collaboration with the Precision Cancer Epigenomics group at NCMM, through the NORPOD program.

Summary of the project
Human tumors are characterized by recurrent mutations in the well-defined cancer driver genes, but also non-mutational epigenetic reprogramming and phenotypic plasticity controlled by transcription factors (TF) are important contributors to tumorigenesis. Extensive consortium efforts have mapped the mutational and epigenetic landscapes of human cancers. However, the commonly used epigenomics methods such as ChIP-seq are correlative in nature and report a lot of spurious sites that might not be linked to gene expression, highlighting the need for novel innovative approaches to understand cancer genome and epigenome. Here, we will utilize cutting-edge long-read nanopore sequencing combined with deep machine learning approaches to model the epigenetic changes and mutational mechanisms in cancers originating from endodermal tissues. The goal is to reveal novel mechanistic details about the development of human cancer.

Tasks
The postdoctoral researcher will analyze NaNOME-seq, ATAC-seq and RNA-seq data to model the gene regulatory logic in epithelial cells. In addition, the researcher will investigate the effects of DNA adducts on methylome, transcriptome, and the gene regulatory logic.

Skills, expertise and/or qualifications
We expect a successful candidate to have a PhD degree from a relevant field with skills and experience in computational genomics and machine learning. Familiarity with the above-mentioned data types is an asset, as well as a strong publication record in a relevant field. Good written and oral communication skills in English are expected.

Research group descriptions
The Machine Learning in Biomedicine group led by Dr. Esa Pitkänen at FIMM develops novel machine learning methods and models to answer key questions in biomedicine: how do mutations arise and contribute to disease? How to accurately predict cancer patient outcomes? What is the role of inherited genetic factors in diseases? Together with our collaborators, we focus on answering these questions in cancers and hematological malignancies. We create scalable and multimodal machine learning techniques utilizing genome, transcriptome, epigenome and imaging data to build clinically useful computational tools.

The Precision Cancer Epigenomics group led by Dr. Biswajyoti Sahu at NCMM investigates the role of transcription factors in human diseases using modern genome-wide approaches for regulatory genomic features and chromatin architecture. We employ various model systems such as mammalian cell lines, 3D organoid cultures and stem cell-based methods as well as cutting-edge genome-wide approaches from ChIP-seq, CUT&RUN and HiChIP to single-nuclei multiome RNA-seq and ATAC-seq assays, epigenetics analysis using Illumina and single-molecule nanopore sequencing, and CRISPR-based approaches for genome editing. Our goal is to provide mechanistic understanding of the role of transcription factors and enhancer malfunction in development of enhanceropathies such as cancer.

Implementation 

The NORPOD Fellow will be employed at the Machine Learning in Biomedicine group (FIMM, University of Helsinki, Finland). To promote collaboration between the two groups, this position will involve regular visits to and communication with the Precision Cancer Epigenomics lab (NCMM, University of Oslo, Norway). Successful candidates are expected to travel between the labs to conduct work required for the research project, foster synergies and advance our goals. Expenses related to the research visits will be covered.

Contract & salary
The job is for a fixed term of 2.5 years. A trial period of 6 months will be applied. Salary will depend upon the applicant's level of skills, knowledge, and abilities and is based on the university salary system. The starting salary will be ca. 3,500 – 3,800 euros/month, depending on the appointee’s qualifications and experience and including a salary component based on personal performance. Standard Finnish pension benefits and occupational health care are provided for University employees. We welcome applicants from a variety of gender identities, linguistic and cultural backgrounds. 
 
Selection process

●    The collaborating PIs of the research project will shortlist and video interview the top candidates.

●    Top candidates will be invited for an online interview, conducted by an independent selection panel where they will also be given the opportunity to pitch the project plan.

●    NORPOD Fellowships will be awarded based on the recommendation of the selection panel.

How to apply: 
The application should include (i) CV with a complete list of scientific publications, (II) a one-page statement of motivation for applying for this position, (iii) contact information of at least two reference persons who have agreed to provide a written statement on behalf of the applicant.
 
To apply, please submit the application through the University of Helsinki electronic recruitment system by clicking on Apply for job. Internal applicants (i.e., current employees of the University of Helsinki) please submit your applications through SAP Fiori https://msap.sap.helsinki.fi.
 
Please apply no later than 31st of May 2024

The University of Helsinki is an international scientific community of 40,000 students and researchers. It is one of the leading multidisciplinary research universities and ranks among the top 100 international universities in the world.
 
The Institute for Molecular Medicine Finland (FIMM) is an international research unit focusing on human genomics and personalised medicine at the Helsinki Institute of Life Science (HiLIFE) of the University of Helsinki - a leading Nordic university with a strong commitment to life science research. As part of Academic Medical Center Helsinki in Meilahti campus FIMM collaborates locally with the Faculty of Medicine, Helsinki University Hospital and National Institute for Health and Welfare. FIMM is part of the Nordic EMBL Partnership for Molecular Medicine, composed of the European Molecular Biology Laboratory (EMBL) and the centres for molecular medicine in Norway, Sweden and Denmark, and the EU-LIFE Community.