Accelerated Systems for Portable DNA Sequencing

H Sadasivan - 2023 - deepblue.lib.umich.edu
The MinION is a revolutionary handheld DNA sequencer that is inexpensive, portable, and
can perform real-time sequencing. MinION is increasingly used in Precision Medicine …

Novel transformer networks for improved sequence labeling in genomics

J Clauwaert, W Waegeman - IEEE/ACM Transactions on …, 2020 - ieeexplore.ieee.org
In genomics, a wide range of machine learning methodologies have been investigated to
annotate biological sequences for positions of interest such as transcription start sites …

[HTML][HTML] alignparse: A Python package for parsing complex features from high-throughput long-read sequencing

KHD Crawford, JD Bloom - Journal of open source software, 2019 - ncbi.nlm.nih.gov
Advances in sequencing technology have made it possible to generate large numbers of
long, highaccuracy sequencing reads. For instance, the new PacBio Sequel platform can …

Visualizing complex feature interactions and feature sharing in genomic deep neural networks

G Liu, H Zeng, DK Gifford - BMC bioinformatics, 2019 - Springer
Background Visualization tools for deep learning models typically focus on discovering key
input features without considering how such low level features are combined in intermediate …

A survey of deep learning for scientific discovery

M Raghu, E Schmidt - arXiv preprint arXiv:2003.11755, 2020 - arxiv.org
Over the past few years, we have seen fundamental breakthroughs in core problems in
machine learning, largely driven by advances in deep neural networks. At the same time, the …

Mayday SeaSight: combined analysis of deep sequencing and microarray data

F Battke, K Nieselt - PLoS One, 2011 - journals.plos.org
Recently emerged deep sequencing technologies offer new high-throughput methods to
quantify gene expression, epigenetic modifications and DNA-protein binding. From a …

DeepBIO: an automated and interpretable deep-learning platform for high-throughput biological sequence prediction, functional annotation and visualization analysis

R Wang, Y Jiang, J Jin, C Yin, H Yu… - Nucleic acids …, 2023 - academic.oup.com
Here, we present DeepBIO, the first-of-its-kind automated and interpretable deep-learning
platform for high-throughput biological sequence functional analysis. DeepBIO is a one-stop …

[HTML][HTML] No more hidden solutions in bioinformatics

M Vihinen - Nature, 2015 - nature.com
No more hidden solutions in bioinformatics | Nature Skip to main content Thank you for visiting
nature.com. You are using a browser version with limited support for CSS. To obtain the best …

DeepMetabolism: a deep learning system to predict phenotype from genome sequencing

W Guo, Y Xu, X Feng - arXiv preprint arXiv:1705.03094, 2017 - arxiv.org
Life science is entering a new era of petabyte-level sequencing data. Converting such big
data to biological insights represents a huge challenge for computational analysis. To this …

A brief review on deep learning applications in genomic studies

X Shen, C Jiang, Y Wen, C Li, Q Lu - Frontiers in Systems Biology, 2022 - frontiersin.org
Deep learning is a powerful tool for capturing complex structures within the data. It holds
great promise for genomic research due to its capacity of learning complex features in …