Strain-Level Typing of Streptococcus pyogenes Using Optical DNA Mapping Streptococcus pyogenes, also known as group A Streptococcus (GAS), is a Gram-positive bacterial pathogen responsible for approximately 500,000 deaths globally per year. Therefore, surveillance of invasive GAS infections is of critical importance in understanding societal transmission. In this study, we propose an optical DNA mapping (ODM)-based assay for strain-level typing of S. pyogenes. Fluorescently labeled DNA molecules of lengths >150 kbp are stretched in nanochannels and imaged to reveal genomic information. A core genome alignment-based typing scheme is then utilized for identification at the strain level. Although our technique lacks the nucleotide-level resolution of whole-genome sequencing, it excels at detecting patterns across long stretches of DNA that remain inaccessible to short-read sequencing methods. Using clinical isolates, we demonstrate that the ODM assay can identify S. pyogenes at both the species level and at even higher taxonomic resolutions with high accuracy. Our typing scheme also shows a high correlation with standard emm subtyping for the analyzed samples. We conclude that ODM has the potential to deliver timely and cost-efficient strain-level bacterial identification.

Happy to share that our latest paper on high resolution identification of Gram positive bacteria using optical DNA mapping is out, I am happy to have contributed to some data analysis/maths of this work! pubs.acs.org/doi/10.1021/...

Lights are off A tragedy has fallen upon us today.

I published a new poem on my substack: Lights are off open.substack.com/pub/astreamo...

Always nice to be acknowledged in a friend’s phd, especially for the sweet reasons

I've been fan of topological data analysis since I saw Gunnar Carsson in Laussane at YTM2015. Incredible that they still have the recordings of it mediaspace.epfl.ch/media/0_5f6p.... Back then I thought I will research pure math. 10 years of dna/bio/physics later, I'm still only a fan ..

My very first poster ever was an assembly of an assembly. Poster's must really be my phobia since that was the first one in my 15 years of university life.

June 2014 – is it Albertas? 1 post published by susirupines during June 2014

10 years ago I wrote an introduction on my blog. It starts like this: What I do here is what I want here and what I want here is what I do. What I post here is what I think of and what I think of I post here. What I say here is what I mean to and what I mean... isitalbertas.wordpress.com/2014/06/

Computational Algebraic Topology Lecture Videos - YouTube

youtube.com/playlist?lis... a great lecture series on computational algebraic topology

Beneath the sun, so warm and bright,
A pirate sails, in morning light.
His ship, a patchwork of the seas,
Cuts through the waves with whispered breeze.

The golden fish that swim below,
Glide through waters’ gentle flow.
They shimmer near his wooden hull,
Their scales a sight so colorful.