2018 FIMM Summer Intern Research Program (SIRP) in Molecular Medicine and Bioinformatics
2018 FIMM SUMMER INTERN RESEARCH PROGRAM (SIRP) IN MOLECULAR MEDICINE AND BIOINFORMATICS
Description of the program
The Institute for Molecular Medicine Finland (FIMM) is an international research institute focusing on human genomics and personalised medicine at the Helsinki Institute of Life Science (HiLIFE) of the University of Helsinki. FIMM integrates molecular medicine research, technology centre and biobanking infrastructures under one roof, promoting translational research in grand challenge projects, specifically, the impact of genome information from the Finnish population in personalised health and medicine, individualised cancer medicine, and digital molecular medicine. 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.
The FIMM Summer Internship Program (SIRP) invites young scientists from all over the world to participate in a 3-month research training supervised by scientists of one of the FIMM research groups. During the internship, students will work on a research project that matches their scientific interests and skills.
In addition to the project research, summer interns will receive an introduction to research methods and technologies at FIMM and broaden their background at bi-weekly SIRP journal clubs. Towards the end of the training, interns will present their project results to all FIMM scientists at a SIRP Seminar.
In 2018, the candidates can opt for one of the following research projects to apply to:
1. Algorithms and data analysis for network pharmacology, Tang Group
The project involves developing network pharmacology methods to predict, test and understand drug combinations for personalized medicine. The summer intern will be mentored in topics related to the research, and will assist researchers adapting algorithms and processing numeric results.
Specific tasks may include:
- Adapt existing algorithms for specific needs (Graph search algorithms, genetic algorithms, etc.)
- Create sample test data and programs to test examples, and validate results.
- Port code from one computer language to other (Matlab/R/Python).
- Process numeric results.
- Experience with languages R, Phython, and Matlab. Or, alternatively, demonstrate experience with other languages and capability to quickly adapt to work with R, Phython, and Matlab.
- Approved basic courses in statistics and related to algorithms.
- Capability and willingness to solve problems.
- Communication in English.
Additional knowledge beneficial for the position:
- Course in graph theory.
- Knowledge of: advanced data structures, C language, databases programming, grid computing.
- Participated in some coding contest or in a significant project.
Methods to use: Problem solving, algorithms programming.
Results and potential findings will accelerate our understanding of drug combinations for personalized medicine.
2. Chemical biology approach to chemoresistance in ovarian cancer, Wennerberg Group
The project aims to investigate the mechanisms of chemoresistance in high-grade serous ovarian cancer, the most common and lethal gynecologic malignancy.
Less than 50% of high-grade serous ovarian cancer (HGSOC) patients survive within 5 years after diagnosis due to recurrent disease. Therefore, finding vulnerabilities for targeting the developing resistance mechanisms in ovarian cancer cells is essential to improve efficacy of the disease therapy. To explore effective combinations of targeted drugs with platinum-based chemotherapy, we will utilize high-throughput drug sensitivity and resistance testing in patient-isolated ovarian cancer cells. For drug combinations outperforming the efficacy of chemotherapeutics alone, we will investigate the molecular mechanisms underlying the effect of hit agents using CRISPR/Cas9-based gene editing and a range of molecular biology and cell biology assays.
3. Regulatory network assisted drug combination search for AML using single-cell RNA-seq data, Aittokallio Group
Acute myeloid leukemia involves a huge genetic and, epigenetic and other heterogeneity in its origin, thus the same therapy can result in drastically varying treatment responses in different patients by rewiring and activation of multiple, currently poorly known unappreciated regulatory network and pathways (Jennifer N. Saultz, J Clin Med. 2016). Combination therapy involving drugs targeting these pathways along with established therapy (intensive anthracycline and cytarabine induction therapy) can combat slow and partial response followed by the development of resistance seen in some sub-group of patients against primary treatments. Hence a network assisted search for drug combination is necessary in order to find appropriate therapy for AML. The overall aim of the current project is to find and test effective combination therapies among epigenetic drugs along with approved cancer drugs for AML using single-cell RNA-seq based regulatory network analysis. The single cell data for 3 patients before and after primary treatment (anthracycline and cytarabine) along with exome sequencing and the bulk RNA-seq information is available with the group (Aittokallio Group). This project will utilize a multidisciplinary expertise, including genetics, network biology along with expertise in systems medicine and high-throughput drug testing to find drug combination for AML.
Program Requirements and Eligibility
- Eligible candidates are Master’s and undergraduate students, who have not completed their degree by 1st of June 2018.
- Successful candidates are selected based on their scientific accomplishments and background, and the match to the project-specific skills.
- Proficiency in English is required. The working language of FIMM-SIRP is English.
- Applicants must be available to work full time (Mon-Fri, 40 hours per week) for the entire 3 month period. Candidates accepted to the program will receive a stipend of 1600 euros per month (gross).
- Students of all nationalities are accepted into the program. However, please note that the Program does not cover expenses related to an application for a Finnish residence permit and relocation to Finland.
If you are interested in an internship at our Institute and would like to apply, please complete the e-form, indicating 1 project that best matches your research interests. As an attachment to the e-form, submit a single pdf that contains your motivation letter (max 1 page) and CV (max 2 pages, including contact information, educational background, professional experience, the list of publications, and the contact details of 2 referees). The deadline for application is 31.03.2018, 23:59 (EET+2).
If you have questions about the application process, please contact the Program coordinators: Daria Bulanova (daria.bulanova (a) helsinki.fi) and Zia Rehman (zia.rehman (a) helsinki.fi