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Flint's Engineering Portfolio

DNA Barcode Identification
Genia Acquired by Roche

Before moving to the tunneling sequencing group, I worked with Roche’s nanopore sequencer. This technology sequenced strands of DNA by sampling the occlusion of current as nucleotides with attached moieties passed through protein nanopores. I was selected to work on a novel use of application of this sequencer to write an analysis pipeline that pulled the raw signal off of the sequencer and to search for barcodes within these signals. In order to do so I implemented the cumulative sum algorithm (CUSUM), a technique used to detect level changes in data. I implemented this algorithm iteratively in order to find large level changes in current, which corresponded to separate DNA molecules, smaller changes in current, which corresponded to barcodes or other DNA sequences within a given DNA molecule, and finally the smallest amplitude current changes, which corresponded to information about individual nucleotides (giving rise to statistics about how long a nucleotide and its attached moiety stayed in the constriction site of the nanopore and about its state while it remained there). This code was implemented by a variety of scientists in different bioinformatics and experimental groups and its success led to my being hired as an engineer in the tunneling sequencing group.

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