Register for Postdocs & Researchers- Atlas Antibodies AB - Internship project VT23
This project is open to postdoctoral and early career researchers (PhD degree holders) with a fixed term employment at KI, or on a KI stipend, before and during the internship.
Atlas Antibodies AB
Target group
Postdocs and researchers (3 months)
About the organization
Atlas Antibodies AB was founded in 2006 by researchers from the prestigious Human Protein Atlas project with the mission to make the unique antibodies developed in the project available to fellow researchers worldwide. Atlas Antibodies has experienced significant growth over the years and currently consists of approximately 75 employees and a catalogue of more than 22 000 highly validated antibodies. Investor AB is the long-term owner, and the company is today part of the Atlas group, with offices in Stockholm, Zurich, and Newcastle. The group is centered around cutting-edge antibody technology and serves leading academic universities, biotech companies, and leading pharmaceutical companies worldwide.
The project
As an effort to find more sustainable production methods for our antibodies, we are investigating different approaches for developing recombinantly produced antibodies. In this project the focus will be on developing a sequencing strategy and analysis pipeline for evaluation of NGS data from sequenced antibody heavy and light chain cDNA amplified from rabbit B cells. The first step will be to evaluate and improve a suggested sequencing strategy and if necessary, investigate alternative strategies that could be better suited for the purpose of antibody discovery. The second step would be to combine solutions for an automated application, based on e.g. python or R, for easily scalable extraction of relevant immunoglobulin heavy and light chain sequences from NGS FASTQ files.
The expected outcome is to have a process that is easy use also for a person without experience in handling raw NGS data that can do the following:
Read FASTQ files from multiplex amplicon sequencing (or other sequencing approach) of antibody heavy and light chain variable domains
Process FASTQ files to find the most probable productive gene sequences for each clone
Calculate a reliability score for how well the sequencing results can be trusted
Map out framework and CDR regions in table or graphical format
Combine all the information into a clear and structured report per clone
The candidate will be based at the head office of Atlas Antibodies AB (Voltavägen 13, SE-168 69 Bromma, Sweden), but parts of the work can also be performed remotely.
The project would preferably start in the fall of 2023 at 50-100% pace.
The candidate
The candidate should have a background in bioinformatics, molecular biology or immunology with experience in analysis of NGS data for gene expression analysis or similar.
Contact information
Name: Björn Forsström
Email: bjorn.forsstrom@atlasantibodies.com Telephone: 08-54595850
Company website: https://www.atlasantibodies.com/
Last date of application has expired.