IRB Barcelona is seeking a talented and highly motivated Postdoctoral Researcher to join the Structural Bioinformatics and Network Biology group (https://sbnb.irbbarcelona.org), led by Dr. Patrick Aloy, to work on Generative Models to create Precision Drugs. The candidate will work on the project “Valorización de EGA para la Industria y la Sociedad” (VEIS) funded by the Secretariat of Universities and Research of the Ministry of Business and Knowledge (Government of Catalonia) and by the European Regional Development Fund (FEDER) with reference number 001-P-001647.
Biological data is accumulating at an unprecedented rate, escalating the role of data-driven methods in computational drug discovery. The urge to couple biological data to cutting-edge machine learning has spurred developments in data integration and knowledge representation, especially in the form of heterogeneous, multiplex and semantically-rich biological networks. Today, thanks to the propitious rise in knowledge embedding techniques, these large and complex biological networks can be converted to a vector format that suits the majority of machine learning implementations. Indeed, we have generated biological embeddings (i.e. bioactivity signatures) that capture complex relationships between small molecules and other biological entities such as targets or diseases (Duran-Frigola et al. 2020 Nat Biotechnol in press, available at bioRxiv). However, only a tiny fraction of the possible chemical space has been so far explored, meaning that most compounds able to modulate biological activities (i.e. drugs) are yet to be discovered. Accordingly, the main objective of this project is to couple our bioactivity signatures to inverse design algorithms to generate new chemical entities with a desired functionality. In particular, we aim at generating new chemical entities (NCEs) to modulate the activity of a specific set of targets, selected from a combination of perturbagen profiles, to revert the pathological state induced by Alzheimer´s disease (AD) and other complex disorders. All in all, the incorporation of machine learning methods to the drug discovery process will trigger the development of thousands of novel compounds, finally enabling precision medicine.
Duties:
The successful candidate shall be responsible for the implementation of ML-based Generative Models (i.e. cVAEs or GANs) to create new small molecules that fulfill the required polypharmacological properties to revert AD pathological signatures.
Profile:
Must Have – Required
- Education: Bachelor in Biosciences, Chemistry, Pharmacy or Engineering degree in Computer Sciences. PhD in Bioinformatics, machine learning or related areas.
- Experience: previous experience on the use of machine learning and data science techniques. Strong publications record according to his/her career stage.
- Skills:
- Excellent programming and scripting skills, with deep knowledge of Python.
- Excellent knowledge of machine learning techniques (TensorFlow/AdaNet).
- Competent in the use of HPC queue systems, virtual machines (OpenNebula) and Grid Containers (Docker, Singularity).
- Excellent interpersonal and communication skills. Highly motivated. Fluency in English.
Desirable
- Experience: Previous experience working with biological data and in an international environment.
- Skills: Knowledge of ML-based generative models (e.g. cVAEs, GANs, etc)
Remarks:
Working conditions: Employed in compliance with Spanish legislation and regulations under a full-time contract. Employees receive the benefits of the Spanish Social Security system covering sickness, maternity/paternity leaves and injuries at work.
Training and Career: Postdoctoral researchers joining IRB Barcelona gain access to the Institute’s advanced research training and career development opportunities, all within in a competitive international environment. Courses and workshops on themes of particular interest to postdocs are offered regularly by the Institute.
International environment: Nearly 90 Postdoctoral researchers (more than a half non-Spanish nationals) are currently working at IRB Barcelona.
How to apply:
- Applications for the above opening should include a CV and a letter of interest and should be sent by e-mail to: irbjobs@irbbarcelona.org with the Reference: PD/20/07
- Deadline for applications: 31/03/2020 If no suitable candidate is found, the deadline will be extended.
Selection process
- Pre-selection: Will be based on CV, motivation letter and experience.
- Interviews: Short-listed candidates will be interviewed.
- Job offer: Will be sent to the successful candidate after the interview.
Original souce: https://www.irbbarcelona.org/en/about-us/jobs/postdoctoral-fellow-in-biological-data-science-ref-pd2007