Scientist/Senior Scientist, Computational Oligonucleotide Design Full-time

Scientist/Senior Scientist, Computational Oligonucleotide Design

The Nucleic Acid Therapeutics Initiative (NATi), hosted by A*STAR, is Singapore's national platform dedicated to advancing RNA-based medicines and revolutionizing drug and vaccine development. NATi's mission is to establish Singapore as a globally recognized hub of excellence in nucleic acid therapeutics research, clinical translation, and commercialization. NATi focuses on key RNA modalities such as antisense oligonucleotides (ASOs), small interfering RNA (siRNA), and messenger RNA (mRNA). To drive this vision, NATi is building a biotech-like translational engine focused on asset and technology development spanning discovery to clinical development. We are actively seeking passionate and committed RNA scientists with deep translational expertise to join us in advancing the next generation of RNA-based therapeutics.

We are seeking a highly skilled and results oriented computational scientist with expertise in molecular dynamics (MD) to guide the rational design of synthetic oligonucleotides across multiple therapeutic applications. This role is central to NATi's strategy to build a differentiated RNA therapeutic platform through computational innovation, enabling rapid design and optimization of oligonucleotide candidates with translational potential. The successful candidate will establish and apply MD simulation and AI/ML capabilities to accelerate oligonucleotide drug development, enhance predictive modelling, and explore novel chemical space in oligonucleotide design. The selected candidate will work closely with cross-functional teams to translate computational insights into experimentally validated oligonucleotide candidates and contribute to NATi's platform innovation and IP portfolio.

Key Responsibilities

• Develop automated data processing and visualization pipelines to support high-throughput oligonucleotide design and performance analysis (e.g., target specificity, stability, pharmacological properties).
• Establish and implement molecular dynamics (MD) simulations to study RNA-protein interactions and elucidate mechanism(s) of target engagement.
• Develop and apply AI/ML frameworks to explore novel chemical space and predict oligo performance across diverse RNA targets.
• Analyze large biological datasets (e.g., transcriptomics, miRNA profiles, structural data) to inform oligo design and modification strategies.
• Develop models that integrate sequence, secondary/tertiary structure, and oligo chemistry to predict target engagement and guide binding assay design.
• Collaborate with oligonucleotide chemists, biologists, and pharmacologists to integrate computational designs with experimental workflows towards the identification of a Drug Candidate.
• Stay current with emerging computational tools, algorithms, and scientific literature relevant to the development of differentiated RNA therapeutics.
• Contribute to NATi's intellectual property (IP) portfolio through computational tools and novel drug candidates.
• Prepare appropriate summary reports and presentations to update NATi leadership and stakeholders.

Qualifications & Experience

• Ph.D. in Computational Chemistry, Biophysics, Bioinformatics, Biomedical Engineering, or a related field.
• Minimum of 4 (Scientist) or 8 (Senior Scientist) years of hands-on industry experience in computational oligonucleotide design or RNA-targeting therapeutics.
• Hands-on experience with MD simulation tools (e.g., GROMACS, AMBER, OpenMM) and applying machine learning frameworks (e.g., Python, TensorFlow, PyTorch) to biological/chemical datasets.
• Proficiency in RNA structure prediction and interaction modelling tools (e.g., RNAstructure, ViennaRNA, IntaRNA, RNAhybrid).
• Hands-on experience with transcriptome analysis tools (e.g., Bowtie, BLAST, STAR, Salmon) and oligo design platforms (e.g., siDirect, ASO Designer, CRISPRoff).
• Strong programming skills in Python and familiarity with scientific computing libraries; experience with Git and reproducible research practices.
• Strong understanding of RNA biology, including alternative splicing, polyadenylation, RNA editing, and RNA-binding proteins.
• Experience with nucleotide modification strategies (e.g., 2″-O-methyl, phosphorothioate, LNA) and their integration into computational design workflows to optimize oligonucleotide performance, including stability, specificity, and selective target engagement.
• Prior experience in applying free energy calculation methods (e.g., FEP, TI, MM/PBSA, MM/GBSA) for binding affinity prediction or selectivity profiling is desirable.
• Demonstrated experience combining physics-based modelling with AI/ML models to predict oligo efficacy, off-target effects, and/or RNA structure-function relationships using biological datasets is a plus.
• Proven ability to work independently and collaboratively in multidisciplinary teams, effectively communicating computational insights to experimental scientists.
• Demonstrated ability to troubleshoot complex scientific problems and adapt to shifting priorities in a fast-paced, quality-driven environment.

Global Recruitment & Competitive Compensation

NATi is conducting a global search for top-tier talent in RNA therapeutics. We welcome applications from leading pharmaceuticals scientists and biotech innovators worldwide.

This role provides a highly competitive compensation package aligned with global industry standards, including attractive benefits and long-term career growth opportunities within Singapore's thriving biomedical innovation ecosystem. Join us in shaping the future of RNA-based medicines and establishing Singapore as a world-class hub for nucleic acid therapeutics.