Mining genomes to illuminate the specialized chemistry of life

MH Medema, T de Rond, BS Moore - Nature Reviews Genetics, 2021 - nature.com
All organisms produce specialized organic molecules, ranging from small volatile chemicals
to large gene-encoded peptides, that have evolved to provide them with diverse cellular and …

Learning from co-expression networks: possibilities and challenges

EAR Serin, H Nijveen, HWM Hilhorst… - Frontiers in plant …, 2016 - frontiersin.org
Plants are fascinating and complex organisms. A comprehensive understanding of the
organization, function and evolution of plant genes is essential to disentangle important …

Genome-wide prediction of metabolic enzymes, pathways, and gene clusters in plants

P Schläpfer, P Zhang, C Wang, T Kim, M Banf… - Plant …, 2017 - academic.oup.com
Plant metabolism underpins many traits of ecological and agronomic importance. Plants
produce numerous compounds to cope with their environments but the biosynthetic …

ATTED-II in 2018: a plant coexpression database based on investigation of the statistical property of the mutual rank index

T Obayashi, Y Aoki, S Tadaka, Y Kagaya… - Plant and Cell …, 2018 - academic.oup.com
Abstract ATTED-II (http://atted. jp) is a coexpression database for plant species to aid in the
discovery of relationships of unknown genes within a species. As an advanced …

ATTED-II v11: a plant gene coexpression database using a sample balancing technique by subagging of principal components

T Obayashi, H Hibara, Y Kagaya, Y Aoki… - Plant and Cell …, 2022 - academic.oup.com
Abstract ATTED-II (https://atted. jp) is a gene coexpression database for nine plant species
based on publicly available RNAseq and microarray data. One of the challenges in …

Effects of abiotic stress on plants: a systems biology perspective

GR Cramer, K Urano, S Delrot, M Pezzotti… - BMC plant biology, 2011 - Springer
The natural environment for plants is composed of a complex set of abiotic stresses and
biotic stresses. Plant responses to these stresses are equally complex. Systems biology …

Gene regulatory network inference resources: A practical overview

D Mercatelli, L Scalambra, L Triboli, F Ray… - Biochimica et Biophysica …, 2020 - Elsevier
Transcriptional regulation is a fundamental molecular mechanism involved in almost every
aspect of life, from homeostasis to development, from metabolism to behavior, from reaction …

A global coexpression network approach for connecting genes to specialized metabolic pathways in plants

JH Wisecaver, AT Borowsky, V Tzin, G Jander… - The Plant …, 2017 - academic.oup.com
Plants produce diverse specialized metabolites (SMs), but the genes responsible for their
production and regulation remain largely unknown, hindering efforts to tap plant …

Systematic multi-omics integration (MOI) approach in plant systems biology

IN Jamil, J Remali, KA Azizan… - Frontiers in plant …, 2020 - frontiersin.org
Across all facets of biology, the rapid progress in high-throughput data generation has
enabled us to perform multi-omics systems biology research. Transcriptomics, proteomics …

The phenylpropanoid pathway is controlled at different branches by a set of R2R3-MYB C2 repressors in grapevine

E Cavallini, JT Matus, L Finezzo, S Zenoni… - Plant …, 2015 - academic.oup.com
Because of the vast range of functions that phenylpropanoids possess, their synthesis
requires precise spatiotemporal coordination throughout plant development and in response …