[HTML][HTML] De novo mutations (DNMs) in autism spectrum disorder (ASD): Pathway and network analysis

A Alonso-Gonzalez, C Rodriguez-Fontenla… - Frontiers in …, 2018 - frontiersin.org
Autism Spectrum Disorder (ASD) is a neurodevelopmental disorder (NDD) defined by
impairments in social communication and social interactions, accompanied by repetitive …

BIONIC: biological network integration using convolutions

DT Forster, SC Li, Y Yashiroda, M Yoshimura, Z Li… - Nature …, 2022 - nature.com
Biological networks constructed from varied data can be used to map cellular function, but
each data type has limitations. Network integration promises to address these limitations by …

Ferroptosis‐Related Long Noncoding RNAs Have Excellent Predictive Ability for Multiomic Characteristics of Bladder Cancer

J Liu, J Cui, S Zhao, M Wu, J Wang… - Oxidative Medicine …, 2022 - Wiley Online Library
Background. The role of ferroptosis‐related long non‐coding RNAs (lncRNAs) in bladder
cancer remains elusive. This study is aimed at examining the prognostic role of ferroptosis …

Transcriptomics in toxicogenomics, part III: data modelling for risk assessment

A Serra, M Fratello, L Cattelani, I Liampa, G Melagraki… - Nanomaterials, 2020 - mdpi.com
Transcriptomics data are relevant to address a number of challenges in Toxicogenomics
(TGx). After careful planning of exposure conditions and data preprocessing, the TGx data …

Robust normalization and transformation techniques for constructing gene coexpression networks from RNA-seq data

KA Johnson, A Krishnan - Genome biology, 2022 - Springer
Background Constructing gene coexpression networks is a powerful approach for analyzing
high-throughput gene expression data towards module identification, gene function …

Metabolomics-driven mining of metabolite resources: Applications and prospects for improving vegetable crops

DP Singh, MS Bisen, R Shukla, R Prabha… - International Journal of …, 2022 - mdpi.com
Vegetable crops possess a prominent nutri-metabolite pool that not only contributes to the
crop performance in the fields, but also offers nutritional security for humans. In the pursuit of …

Uncovering protein networks in cardiovascular proteomics

M Hasman, M Mayr, K Theofilatos - Molecular & Cellular Proteomics, 2023 - ASBMB
Biological networks have been widely used in many different diseases to identify potential
biomarkers and design drug targets. In the present review, we describe the main …

[HTML][HTML] De novo mutations from whole exome sequencing in neurodevelopmental and psychiatric disorders: from discovery to application

W Wang, R Corominas, GN Lin - Frontiers in genetics, 2019 - frontiersin.org
Neurodevelopmental and psychiatric disorders are a highly disabling and heterogeneous
group of developmental and mental disorders, resulting from complex interactions of genetic …

Updating genome annotation for the microbial cell factory Aspergillus niger using gene co-expression networks

P Schaepe, MJ Kwon, B Baumann… - Nucleic acids …, 2019 - academic.oup.com
A significant challenge in our understanding of biological systems is the high number of
genes with unknown function in many genomes. The fungal genus Aspergillus contains …

[HTML][HTML] Two's company: studying interspecies relationships with dual RNA-seq

T Wolf, P Kämmer, S Brunke, J Linde - Current opinion in microbiology, 2018 - Elsevier
Organisms do not exist isolated from each other, but constantly interact. Cells can sense the
presence of interaction partners by a range of receptors and, via complex regulatory …