Postdoctoral Position in AI-Accelerated Oligonucleotide Drug Design

Chalmers University of Technology

Sweden

February 10, 2022

Description

This postdoctoral researcher position aims to improve the design of Oligonucleotide-based drugs using computational chemistry, biophysical simulation and AI methods. It is placed at the department of Computer Science and Engineering (CSE) at Chalmers/GU and is one of two postdoctoral positions in a joint project with Pharmacology at GU. The project is funded in a collaboration between the two largest research programs in Sweden, the Wallenberg AI, Autonomous Systems and Software Program (WASP) and the SciLifeLab and Wallenberg National Program for Data-Driven Life Science (DDLS), with the ultimate goal of solving ground-breaking research questions across disciplines.

Information about project The two postdoctoral researchers will closely collaborate and will be jointly supervised by both PIs, Alexander Schliep (CSE, University of Gothenburg Chalmers, https: // schlieplab.org) and Pär Matsson (Pharmacology, University of Gothenburg, https: // www. gu.se/en/research/cellular-and-molecular-pharmacokinetics), and spend time in both labs. Close ties to the OligoNova Hub at the University of Gothenburg (part of SciLifeLab's Drug Discovery and Development platform) and the considerable research activities at AstraZeneca R&D Gothenburg, provide a vibrant research environment in the exciting new area of computational design of oligonucleotide therapeutics. The PIs have extensive expertise in machine learning, AI for drug design, predicting oligonucleotide hybridization energies, as well as modeling and simulation of cellular pharmacology, measuring cellular drug disposition, and quantification of binding kinetics and –energetics of small-molecule and oligonucleotide therapeutics. Additionally, the project involves collaboration with Rula Zain's research group (Karolinska Institutet) to identify clinically relevant target genes in rare diseases and evaluate predicted oligonucleotide candidates in in vitro and in vivo models. Consequently, the postdoctoral position will position candidates uniquely to develop independent research programs and pursue distinguished careers in academia or industry.

Wallenberg AI, Autonomous Systems and Software Program (WASP) is Sweden's largest individual research program ever, a major national initiative for strategically motivated basic research, education and faculty recruitment. The program addresses research on artificial intelligence and autonomous systems acting in collaboration with humans, adapting to their environment through sensors, information and knowledge, and forming intelligent systems-of- systems. The vision of WASP is excellent research and competence in artificial intelligence, autonomous systems and software for the benefit of Swedish industry. Read more: https: // wasp- sweden.org/

The SciLifeLab and Wallenberg National Program for Data-Driven Life Science (DDLS) is a 12-year initiative that focuses on data-driven research, within fields essential for improving the people ́s lives, detecting and treating diseases, protecting biodiversity and creating sustainability. The programme will train the next generation of life scientists and create a strong computational and data science base. The program aims to strengthen national collaborations between universities, bridge the research communities of life sciences and data sciences, and create partnerships with industry, healthcare and other national and international actors. Read more: https: // www. scilifelab.se/data-driven.

Major responsibilities The postdoctoral researcher will develop and apply machine learning and bioinformatics methods to study the impact of chemical modification on the binding of therapeutic oligonucleotides to target nucleotide sequences and to cellular proteins. The development will be closely coordinated with complementary work on the molecular simulation and/or computational chemistry side.

Contract terms Full-time temporary employment. The employment is limited (temporary) for 24 months.

Qualifications Applicants must have a quantitative background with a doctorate, PhD or equivalent degree, in bioinformatics, computer science, mathematics, biophysics, biology or chemistry, with prior machine learning experience demonstrated through published research results. The degree should generally not be older than three years.

Excellent collaborative skills and oral as well as written proficiency in English are mandatory. Experience of studying nucleotide–nucleotide and/or nucleotide–protein interactions using bioinformatics or machine learning methods is highly meriting. The working language is English. Knowledge of Swedish is not a prerequisite for consideration.

The position requires sound verbal and written communication skills in English. Swedish is not a requirement.

We offer Chalmers offers a cultivating and inspiring working environment in the coastal city of Gothenburg. Read more about working at Chalmers and our benefits for employees. Chalmers offers Swedish courses.

Chalmers aims to actively improve our gender balance. We work broadly with equality projects, for example the GENIE Initiative on gender equality for excellence. Equality and diversity are substantial foundations in all activities at Chalmers.

Application procedure The application should be marked with Ref 20220005 and written in English. The application should be sent electronically and be attached as pdf-files, as below:

CV: (Please name the document as: CV, Surname, Ref. number) including: • CV, include complete list of publications • Previous teaching and pedagogical experiences • Two references that we can contact.

Personal letter: (Please name the document as: Personal letter, Family name, Ref. number) 1-3 pages where you: • Introduce yourself • Describe your previous research fields and main research results • Describe your future goals and future research focus

Other documents: • Attested copies of completed education, grades and other certificates.

Please use the button at the foot of the page to reach the application form. The files may be compressed (zipped).

Application deadline: 10th February, 2022

For questions, please contact: Dr. Alexander Schliep, DS&AI Division, alexander.schliep@cse.gu.s

Chalmers declines to consider all offers of further announcement publishing or other types of support for the recruiting process in connection with this position.

Information about the department The Department of Computer Science and Engineering is a joint department at Chalmers University of Technology and the University of Gothenburg, with activities on two campuses in the city of Gothenburg. The department has around 270 employees from over 30 countries. Our research has a wide span, from theoretical foundations to applied systems development. We provide high quality education at Bachelor's, Master's and graduate levels, offering over 120 courses each year. We also have extensive national and international collaborations with academia, industry and society.

The Data Science & AI division within CSE engages in research and education in this growing area, with a strong focus in biomedical applications and drug design. For more information about the department, see https: // www. chalmers.se/cse/en, and for the DSAI division, see https: // www. chalmers.se/en/departments/cse/organisation/dsai/Pages/default.aspx

Our aim is to actively improve our gender balance in both our department and division. We therefore strongly encourage female applicants for our positions. As an employee at Chalmers and the Department of Computer Science and Engineering, you are given the opportunity to contribute to our active work within the field of equality and diversity. We are working broadly with equality projects, for example the GENIE Initiative on gender equality for excellence. For more information,visit our website.

Chalmers University of Technology conducts research and education in engineering sciences, architecture, technology-related mathematical sciences, natural and nautical sciences, working in close collaboration with industry and society. The strategy for scientific excellence focuses on our six Areas of Advance; Energy, Health Engineering, Information and Communication Technology, Materials Science, Production and Transport. The aim is to make an active contribution to a sustainable future using the basic sciences as a foundation and innovation and entrepreneurship as the central driving forces. Chalmers has around 11,000 students and 3,000 employees. New knowledge and improved technology have characterised Chalmers since its foundation in 1829, completely in accordance with the will of William Chalmers and his motto: Avancez!

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