Raw Signal and Modification Detection at Oxford Nanopore Technologies
From June 24 to September 20, 2024, Eamon McAndrew, LongTREC Doctoral Candidate at IPMC (CNRS, Université Côte d’Azur), had the opportunity to carry out a research secondment at Oxford Nanopore Technologies, supervised by Aino Järvelin with scientific supervision support from Marcus Stoiber. This secondment offered valuable growth, both in scientific expertise and personal development.
My goal? Gaining a deeper understanding of how nanopore raw signal is translated into biological insight, how machine learning models are designed, trained and evaluated in a production environment, and how nucleotide modifications are detected and what biological relevance they hold.
Eamon reflects on his experience:
What I Learned 🎓
I worked with raw signal data and learned how it is translated into reads, and how information beyond canonical bases can be detected from it.
Takeaways 🌱
I took part in training and evaluating neural network models for modification detection. I met regularly with the people who design these algorithms, who guided me through the pipeline.
Impact 🌟
The original project goal was collaboration in isoform quantification using nanopore data. It was adjusted to strengthen areas where I had limited knowledge, such as nucleotide modifications, and to suit my interest in applying machine learning to sequencing data in an industry setting.
Overall, this secondment gave me direct experience of machine learning development in an industry production environment.
