Long-read and chromosome-scale assembly of the hexaploid wheat genome achieves high resolution for research and breeding

JM Aury, S Engelen, B Istace, C Monat… - …, 2022 - academic.oup.com
Background The sequencing of the wheat (Triticum aestivum) genome has been a
methodological challenge for many years owing to its large size (15.5 Gb), repeat content …

[HTML][HTML] Fast-bonito: A faster deep learning based basecaller for nanopore sequencing

Z Xu, Y Mai, D Liu, W He, X Lin, C Xu, L Zhang… - Artificial Intelligence in …, 2021 - Elsevier
Abstract Nanopore sequencing from Oxford Nanopore Technologies (ONT) is a promising
third-generation sequencing (TGS) technology that generates relatively longer sequencing …

Effective training of nanopore callers for epigenetic marks with limited labelled data

B Yao, C Hsu, G Goldner, Y Michaeli… - Open …, 2024 - royalsocietypublishing.org
Nanopore sequencing platforms combined with supervised machine learning (ML) have
been effective at detecting base modifications in DNA such as 5-methylcytosine (5mC) and …

Nanopore callers for epigenetics from limited supervised data

B Yao, C Hsu, G Goldner, Y Michaeli, Y Ebenstein… - bioRxiv, 2021 - biorxiv.org
Nanopore sequencing platforms combined with supervised machine learning (ML) have
been effective at detecting base modifications in DNA such as 5mC and 6mA. These ML …

Integration of Data Science Into Thermal-Fluids Engineering Education

H Hu, C Heo - ASME International Mechanical …, 2022 - asmedigitalcollection.asme.org
To improve the integration of data science into thermal fluids education, a technical elective
course is developed to introduce a wide range of machine learning and deep learning …

Fast-Bonito: a faster basecaller for nanopore sequencing

Z Xu, Y Mai, D Liu, W He, X Lin, C Xu, L Zhang, X Meng… - BioRxiv, 2020 - biorxiv.org
Abstract Oxford Nanopore Technologies (ONT) is a promising sequencing technology that
could generate relatively longer sequencing reads compared to the next generation …

LRDB: LSTM Raw data DNA Base-caller based on long-short term models in an active learning environment

A Rezaei, M Taheri, A Mahani… - arXiv preprint arXiv …, 2023 - arxiv.org
The first important step in extracting DNA characters is using the output data of MinION
devices in the form of electrical current signals. Various cutting-edge base callers use this …

[PDF][PDF] Nanopore Methylation Calling from Limited Training Data

B Yao, J Listgarten - 2022 - digitalassets.lib.berkeley.edu
Nanopore sequencing platforms combined with machine learning models have been shown
to be effective for detecting base modifications in DNA such as 5mC and 6mA. However, a …

[HTML][HTML] Basecalling of Nanopore sequencing data using modern Hopfield networks/Author Monika Heinzl

M Heinzl - 2021 - epub.jku.at
Nanopore sequencing becomes more and more popular nowadays especially after Oxford
Nanopore Technologies (ONT) developed its pocket-sized sequencer MinION, which …

[PDF][PDF] Improving Basecalling Accuracy With Transformers

F Gravila, M Pakanec - projekter.aau.dk
DNA sequencing has recently undergone rapid improvements due to the Oxford Nanopore
Technologies sequencing devices. These devices are fast and can read longer sequences …