DNA in nanochannels: theory and applications

K Frykholm, V Müller, KK Sriram… - Quarterly Reviews of …, 2022 - cambridge.org
Nanofluidic structures have over the last two decades emerged as a powerful platform for
detailed analysis of DNA on the kilobase pair length scale. When DNA is confined to a …

Single-molecule optical genome mapping in nanochannels: multidisciplinarity at the nanoscale

J Jeffet, S Margalit, Y Michaeli… - Essays in …, 2021 - portlandpress.com
The human genome contains multiple layers of information that extend beyond the genetic
sequence. In fact, identical genetics do not necessarily yield identical phenotypes as evident …

Fluorescent polymer as a biosensing tool for the diagnosis of microbial pathogens

S Krishnan, S Jose, BK Periyasamy… - Scientific Reports, 2024 - nature.com
Diseases and diagnoses are predominant in the human population. Early diagnosis of
etiological agents plays a vital role in the treatment of bacterial infections. Existing standard …

Strain-level bacterial typing directly from patient samples using optical DNA mapping

M Nyblom, A Johnning, K Frykholm, M Wrande… - Communications …, 2023 - nature.com
Background Identification of pathogens is crucial to efficiently treat and prevent bacterial
infections. However, existing diagnostic techniques are slow or have a too low resolution for …

Design of optimal labeling patterns for optical genome mapping via information theory

Y Nogin, D Bar-Lev, D Hanania, T Detinis Zur… - …, 2023 - academic.oup.com
Motivation Optical genome mapping (OGM) is a technique that extracts partial genomic
information from optically imaged and linearized DNA fragments containing fluorescently …

DeepOM: single-molecule optical genome mapping via deep learning

Y Nogin, T Detinis Zur, S Margalit, I Barzilai… - …, 2023 - academic.oup.com
Motivation Efficient tapping into genomic information from a single microscopic image of an
intact DNA molecule is an outstanding challenge and its solution will open new frontiers in …

Combining dense and sparse labeling in optical DNA mapping

E Torstensson, G Goyal, A Johnning, F Westerlund… - Plos one, 2021 - journals.plos.org
Optical DNA mapping (ODM) is based on fluorescent labeling, stretching and imaging of
single DNA molecules to obtain sequence-specific fluorescence profiles, DNA barcodes …

Optical Mapping: Detecting Genomic Resistance Cassettes in MRSA

E Ruppeka-Rupeika, S Abakumov, M Engelbrecht… - ACS …, 2024 - ACS Publications
Methicillin-resistant Staphylococcus aureus (MRSA) is a multidrug-resistant bacterium with a
global presence in healthcare facilities as well as community settings. The resistance of …

OM2Seq: Learning retrieval embeddings for optical genome mapping

Y Nogin, D Sapir, TD Zur, N Weinberger… - Bioinformatics …, 2024 - academic.oup.com
Motivation Genomics-based diagnostic methods that are quick, precise, and economical are
essential for the advancement of precision medicine, with applications spanning the …

Fluorescence Microscopy of Nanochannel-Confined DNA

S Kk, F Persson, J Fritzsche, JP Beech… - … Analysis: Methods and …, 2023 - Springer
Stretching of DNA in nanoscale confinement allows for several important studies. The
genetic contents of the DNA can be visualized on the single DNA molecule level, and the …