Scientist/Senior Scientist, Computational Oligonucleotide Design

The RNA Society; Indiana (PA); On-site; USD 117,000 - 180,000; Full time

Job summary

NATi in Singapore is seeking a Computational Scientist to build pipelines and predictive models for ASOs, siRNAs, and mRNA across therapeutic applications. You will scale bioinformatics and AI/ML capabilities to accelerate design and optimization of oligonucleotide candidates with translational potential.

Collaborating with chemists, biologists, and pharmacologists, you will translate computational insights into experimentally validated candidates, contribute to IP, and stay current with new

Qualifications

• PhD in Computational Chemistry, Biophysics, Bioinformatics, Biomedical Engineering, or related field.
• 4+ years (Scientist) or 8+ years (Senior Scientist) hands-on industry experience in computational oligonucleotide design or RNA-targeting therapeutics.
• Strong scripting in Python/R and ML frameworks; experience with reproducible research practices.
• Proficiency in RNA structure prediction and interaction modelling tools.
• Experience with nucleotide modification strategies and integrating into design workflows.

Responsibilities

• Drive RNA therapeutic design and computational optimisation, integrating RNA biology and chemistry.
• Develop automated data processing and visualization pipelines for drug property analyses.
• Apply AI/ML to explore chemical space and predict oligonucleotide properties.
• Analyze large biological datasets to inform design and modification strategies.
• Create models combining sequence, structure, and chemistry to predict target engagement.

Skills

Python

R scripting

ML frameworks

data pipelines

git

reproducible research

Education

PhD in Computational Chemistry/Biophysics/Bioinformatics/Biomedical Engineering

Tools

RNAstructure

ViennaRNA

IntaRNA

RNAhybrid

RNA-Seq

Job description

Position Overview

We are seeking a highly skilled and results oriented Computational Scientist to develop computational pipelines and predictive drug property models for the rational design of ASOs, siRNAs and mRNAs 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 and mRNA candidates with translational potential. The successful candidate will establish and scale bioinformatics and AI/ML capabilities to accelerate oligonucleotide and mRNA drug development, enhance predictive modelling, and explore novel chemical space in oligonucleotide and mRNA 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

• Drive RNA therapeutic design and computational optimisation, integrating RNA biology, transcript structure, RNA accessibility, and oligonucleotide chemistry, establishing and scaling computational pipelines to support rapid design and optimisation at scale.
• Develop automated data processing and visualization pipelines to support drug property analyses, including target specificity, cross-species targeting, and pharmacological properties.
• Develop and apply AI/ML frameworks to explore novel chemical space and to predict oligonucleotide drug properties, e.g. efficacy and toxicity, across diverse RNA targets.
• Analyze large biological datasets (e.g., transcriptomics, miRNA profiles, structural data) to inform oligonucleotide design and modification strategies.
• Develop models that integrate sequence, secondary/tertiary structure, and oligonucleotide chemistry to predict target engagement and guide binding assay design.
• Collaborate with oligonucleotide chemists, molecular biologists, and pharmacologists to translate computational predictions into experimentally validated oligonucleotide candidates, driving iterative design-test-learn cycles 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's leadership and stakeholders.

Qualifications & Experience

• 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.
• Strong computational skills, including hands‑on experience developing scripts or workflows in R or Python, and applying machine learning frameworks to biological/chemical datasets, and familiarity with scientific computing libraries, git, and reproducible research practices.
• Proficiency in RNA structure prediction and interaction modelling tools (e.g., RNAstructure, ViennaRNA, IntaRNA, RNAhybrid).
• Hands‑on experience with RNA‑seq and sequence analysis tools and oligonucleotide design platforms.
• 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, spanning early design through late‑stage candidate selection with strong understanding of risk assessment across discovery and development stages.
• Demonstrated experience combining physics‑based modelling with AI/ML models to predict oligonucleotide efficacy, off‑target effects and/or RNA structure‑function relationships using biological datasets is a plus.
• Proven ability to work independently and collaboratively in cross‑functional, 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.
• This position is based in Singapore. Successful candidates must be willing to relocate to Singapore.

Global Recruitment & Notes

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.