Computational RNA Biology
Where sequence
becomes structure.
Expert consulting at the intersection of RNA biophysics, computational design, and machine learning — translating molecular complexity into therapeutic and synthetic biology applications.
What We Do
Expert consulting across the RNA design pipeline
From raw sequence to functional RNA molecule — computational, structural, and experimental design support for academic labs, biotech startups, and pharma R&D.
RNA Secondary Structure Prediction
Minimum free energy folding, partition functions, and ensemble analysis using ViennaRNA, RNAfold, and custom pipeline development. Comparative and kinetic approaches included.
ViennaRNA · RNAfold · RNAalifold
Co-transcriptional Folding
Energy landscape analysis of RNA folding during transcription. Barriers algorithm, disconnectivity graphs, and kinetic pathway identification for riboswitches and regulatory elements.
Barriers · Treekin · Energy Landscapes
De Novo RNA Design
Computational design of functional RNA elements including xrRNAs, ribozymes, and PRF-inducing pseudoknots. Inverse folding, NUPACK, and structure-guided sequence optimization.
xrRNA · Pseudoknots · Inverse Folding
Machine Learning for RNA
Neural network approaches to RNA structure prediction, sequence-structure mapping, and fitness landscape modelling. Integration of ML models into wet-lab design pipelines.
Deep Learning · Structure Prediction · NLP
Comparative RNA Virology
Evolutionary analysis of viral RNA structures. Conservation-guided identification of functional elements in flavivirus, alphavirus, and other positive-sense RNA virus genomes.
Arboviruses · Structural Conservation · Phylogenetics
Grant & Manuscript Support
Computational strategy design for FWF, ERC, and NIH grant proposals. Manuscript co-authorship, peer review preparation, and figure production for RNA structure papers.
FWF · ERC · Collaboration
Featured Work
Recent research directions
Bridging rigorous biophysics with practical RNA engineering across therapeutic design and fundamental structural biology.
2026
Rational design of mechanically active RNAs: de novo engineering of functional exoribonuclease-resistant RNAs
Nucleic Acids Res.
2025
Identification of conserved RNA regulatory switches in living cells using RNA secondary structure ensemble mapping and covariation analysis
Nature Biotechnology
2025
From structure to function: Computational insights into Musashi-RNA complexes in the context of viral pathogenesis
Science Asia
Let's Collaborate
Have an RNA design challenge?
Whether you're designing therapeutic oligonucleotides, engineering riboswitches, or need an expert second opinion on your structural data — let's talk.
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