Opportunities and obstacles for deep learning in biology and medicine

T Ching, DS Himmelstein… - Journal of the …, 2018 - royalsocietypublishing.org
Deep learning describes a class of machine learning algorithms that are capable of
combining raw inputs into layers of intermediate features. These algorithms have recently …

Molecular mechanisms of ROS production and oxidative stress in diabetes

P Newsholme, VF Cruzat, KN Keane… - Biochemical …, 2016 - portlandpress.com
Oxidative stress and chronic inflammation are known to be associated with the development
of metabolic diseases, including diabetes. Oxidative stress, an imbalance between oxidative …

Modulation of the apoptosis gene Bcl-x function through alternative splicing

M Stevens, S Oltean - Frontiers in Genetics, 2019 - frontiersin.org
Apoptosis plays a vital role in cell homeostasis during development and disease. Bcl-x, a
member of the Bcl-2 family of proteins, is a mitochondrial transmembrane protein that …

Disease-modifying therapies and features linked to treatment response in type 1 diabetes prevention: a systematic review

JL Felton, KJ Griffin, RA Oram, C Speake… - Communications …, 2023 - nature.com
Abstract Background Type 1 diabetes (T1D) results from immune-mediated destruction of
insulin-producing beta cells. Prevention efforts have focused on immune modulation and …

Deep learning for genomics: A concise overview

T Yue, Y Wang, L Zhang, C Gu, H Xue, W Wang… - arXiv preprint arXiv …, 2018 - arxiv.org
Advancements in genomic research such as high-throughput sequencing techniques have
driven modern genomic studies into" big data" disciplines. This data explosion is constantly …

A deep learning approach to identify gene targets of a therapeutic for human splicing disorders

D Gao, E Morini, M Salani, AJ Krauson… - Nature …, 2021 - nature.com
Pre-mRNA splicing is a key controller of human gene expression. Disturbances in splicing
due to mutation lead to dysregulated protein expression and contribute to a substantial …

Immune recognition of β-cells: neoepitopes as key players in the loss of tolerance

EA James, M Pietropaolo, MJ Mamula - Diabetes, 2018 - Am Diabetes Assoc
Prior to the onset of type 1 diabetes, there is progressive loss of immune self-tolerance,
evidenced by the accumulation of islet autoantibodies and emergence of autoreactive T …

The Characterization of GSDMB Splicing and Backsplicing Profiles Identifies Novel Isoforms and a Circular RNA That Are Dysregulated in Multiple Sclerosis

G Cardamone, EM Paraboschi, V Rimoldi… - International journal of …, 2017 - mdpi.com
Abnormalities in alternative splicing (AS) are emerging as recurrent features in autoimmune
diseases (AIDs). In particular, a growing body of evidence suggests the existence of a …

Deep learning for genomics: From early neural nets to modern large language models

T Yue, Y Wang, L Zhang, C Gu, H Xue, W Wang… - International Journal of …, 2023 - mdpi.com
The data explosion driven by advancements in genomic research, such as high-throughput
sequencing techniques, is constantly challenging conventional methods used in genomics …

Not only cancer: the long non-coding RNA MALAT1 affects the repertoire of alternatively spliced transcripts and circular RNAs in multiple sclerosis

G Cardamone, EM Paraboschi, G Soldà… - Human molecular …, 2019 - academic.oup.com
Long non-coding RNAs (lncRNAs) are post-transcriptional and epigenetic regulators, whose
implication in neurodegenerative and autoimmune diseases remains poorly understood. We …