Scientist-II/Senior Software Engineer – In Silico and AI Department

Role Overview

We are seeking a highly skilled, preferably senior, software engineer with expertise in developing computational platforms within bioinformatics, immunology, or scientific computing to join the In Silico and AI Department at Nykode Therapeutics. In this role, you will collaborate with a team of experts to develop computational platforms for antigen identification and vaccine design, supporting treatments for cancer and autoimmune diseases.

As a (Senior) Software Engineer at Nykode, you will lead the development, implementation, and testing of computational software and databases to advance our vaccine technology and create new immunotherapies. Your work will ensure robust software development and bioinformatics analyses across Nykode's Research and Development programs.

Key Responsibilities

• Lead best practice software development by implementing robust CI/CD frameworks and collaborating with other employees in the In Silico and AI Department, IT and cross-functional teams to deliver scalable and maintainable solutions.
• Develop and implement algorithmic software based on prototype code from the bioinformatics team and Nykode's internal state-of-the-art computational platform NeoSELECTTM, for detection of patient specific neoantigens that give immune response.
• Oversee and maintain Nykode's computational research infrastructure, including managing relationships with vendors, consultants, CROs, and internal IT to ensure capabilities for research computational analysis and secure and effective processing of sensitive patient data.
• Collaborate with the Quality Assurance team to draft specifications and ensure software testing aligns with computerized system validation (GxP, GAMP5).
• Facilitate strong data management practices across Nykode functions to support data-driven research initiatives.
• Stay current with industry best practices in software development and contribute to continuous improvement efforts.

Qualifications and Experience

Required Qualifications

• Minimum Master's degree in computer science or a relevant scientific discipline
• 3+ years of experience in industry or academia architecting robust, maintainable, and scalable multi-tier software solutions (level of experience determines qualification as Scientist II or Senior Software Engineer)
• Proficiency in high- and low-level programming languages (Python, C++/C#, R), database programming (SQL), pipeline frameworks (Nextflow), and software development practices such as version control (Git, GitLab, GitHub), CI/CD, and code review
• Demonstrated experience developing, deploying, and managing software applications in cloud environments, particularly on AWS. Proficient in working with high-performance computing (HPC) Linux systems and implementing containerization solutions using technologies like Docker and Kubernetes for scalable and reproducible workflows.

Preferred Qualifications

• Experience developing bioinformatics pipelines and platforms
• Experience applying machine learning and AI in research and development, including the use of large language models and protein language models
• Knowledge of qualification and validation frameworks for computerized systems from a regulatory perspective (e.g., GAMP5, GxP)
• Familiarity with Infrastructure as Code (IaC) and experience working with IaC platforms like Terraform or AWS CloudFormation

Personal Traits

We are seeking an organized and proactive individual with excellent collaboration skills who takes ownership of responsibilities and drives analytical activities forward. The ideal candidate will possess strong interpersonal and communication abilities, working effectively with internal teams and external partners. High-level analytical and problem-solving skills are essential for resolving complex organizational challenges, as well as a proven ability to contribute within a team and foster a collaborative spirit.

Who Are We Looking For?

When hiring new employees, we look for people who are inspired by the Nykode technology and our quest to unlock the future of medicine. We embrace new ways of thinking and doing. When growing and building our teams, we look for the people inspired by our mission and those seeking to join a collaborative and value-based company culture. An eagerness to learn and continuously develop is a core characteristic of our highly skilled and competent individuals. Life at Nykode is an opportunity to take part in the journey to push the boundaries of human advancement. Our work is meaningful, and we care. We care about the patients, and we care about each other.

The Application Process

Due date: 28 Nov. We look forward to receiving your application Please note, we do not accept applications by mail. Should you have any further questions regarding the position, please reach out to us at

The recruitment process will be carried out in collaboration with AIMS International.