Network medicine in the age of biomedical big data
Network medicine is an emerging area of research dealing with molecular and genetic
interactions, network biomarkers of disease, and therapeutic target discovery. Large-scale …
interactions, network biomarkers of disease, and therapeutic target discovery. Large-scale …
Co-expression networks for plant biology: why and how
X Rao, RA Dixon - Acta biochimica et biophysica Sinica, 2019 - academic.oup.com
Co-expression network analysis is one of the most powerful approaches for interpretation of
large transcriptomic datasets. It enables characterization of modules of co-expressed genes …
large transcriptomic datasets. It enables characterization of modules of co-expressed genes …
The Rauvolfia tetraphylla genome suggests multiple distinct biosynthetic routes for yohimbane monoterpene indole alkaloids
EA Stander, B Lehka, I Carqueijeiro, C Cuello… - Communications …, 2023 - nature.com
Monoterpene indole alkaloids (MIAs) are a structurally diverse family of specialized
metabolites mainly produced in Gentianales to cope with environmental challenges. Due to …
metabolites mainly produced in Gentianales to cope with environmental challenges. Due to …
Multi‐omics network‐based functional annotation of unknown Arabidopsis genes
T Depuydt, K Vandepoele - The Plant Journal, 2021 - Wiley Online Library
Unraveling gene function is pivotal to understanding the signaling cascades that control
plant development and stress responses. As experimental profiling is costly and labor …
plant development and stress responses. As experimental profiling is costly and labor …
MarpolBase Expression: A Web-Based, Comprehensive Platform for Visualization and Analysis of Transcriptomes in the Liverwort Marchantia polymorpha
S Kawamura, F Romani, M Yagura… - Plant and Cell …, 2022 - academic.oup.com
The liverwort Marchantia polymorpha is equipped with a wide range of molecular and
genetic tools and resources that have led to its wide use to explore the evo-devo aspects of …
genetic tools and resources that have led to its wide use to explore the evo-devo aspects of …
Computational prediction of gene regulatory networks in plant growth and development
Highlights•GRNs represent causal relationships among regulators and their downstream
genes.•Biological hypothesis drives data collection and the subsequent inferred …
genes.•Biological hypothesis drives data collection and the subsequent inferred …
Comprehensive and functional analysis of horizontal gene transfer events in diatoms
E Vancaester, T Depuydt… - Molecular Biology …, 2020 - academic.oup.com
Diatoms are a diverse group of mainly photosynthetic algae, responsible for 20% of
worldwide oxygen production, which can rapidly respond to favorable conditions and often …
worldwide oxygen production, which can rapidly respond to favorable conditions and often …
Integrative analysis of the shikonin metabolic network identifies new gene connections and reveals evolutionary insight into shikonin biosynthesis
Summary Plant specialized 1, 4-naphthoquinones present a remarkable case of convergent
evolution. Species across multiple discrete orders of vascular plants produce diverse 1, 4 …
evolution. Species across multiple discrete orders of vascular plants produce diverse 1, 4 …
Identifying missing biosynthesis enzymes of plant natural products
Elucidating plant-specialized biosynthetic pathways has always constituted a laborious task,
notably for natural products with high pharmaceutical values. Here, we discuss emerging …
notably for natural products with high pharmaceutical values. Here, we discuss emerging …
Topological analysis of interaction patterns in cancer-specific gene regulatory network: Persistent homology approach
In this study, we investigated cancer cellular networks in the context of gene interactions and
their associated patterns in order to recognize the structural features underlying this disease …
their associated patterns in order to recognize the structural features underlying this disease …