Network medicine in the age of biomedical big data

AR Sonawane, ST Weiss, K Glass, A Sharma - Frontiers in Genetics, 2019 - frontiersin.org
Network medicine is an emerging area of research dealing with molecular and genetic
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 …

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 …

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 …

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 …

Computational prediction of gene regulatory networks in plant growth and development

S Haque, JS Ahmad, NM Clark, CM Williams… - Current opinion in plant …, 2019 - Elsevier
Highlights•GRNs represent causal relationships among regulators and their downstream
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 …

Integrative analysis of the shikonin metabolic network identifies new gene connections and reveals evolutionary insight into shikonin biosynthesis

T Suttiyut, RP Auber, M Ghaste, CN Kane… - Horticulture …, 2022 - academic.oup.com
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 …

Identifying missing biosynthesis enzymes of plant natural products

TD de Bernonville, N Papon, M Clastre… - Trends in …, 2020 - cell.com
Elucidating plant-specialized biosynthetic pathways has always constituted a laborious task,
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

H Masoomy, B Askari, S Tajik, AK Rizi, GR Jafari - Scientific Reports, 2021 - nature.com
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 …