Mining genomes to illuminate the specialized chemistry of life
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 …
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 …
organization, function and evolution of plant genes is essential to disentangle important …
Genome-wide prediction of metabolic enzymes, pathways, and gene clusters in plants
Plant metabolism underpins many traits of ecological and agronomic importance. Plants
produce numerous compounds to cope with their environments but the biosynthetic …
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 …
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 …
based on publicly available RNAseq and microarray data. One of the challenges in …
Effects of abiotic stress on plants: a systems biology perspective
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 …
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 …
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
Plants produce diverse specialized metabolites (SMs), but the genes responsible for their
production and regulation remain largely unknown, hindering efforts to tap plant …
production and regulation remain largely unknown, hindering efforts to tap plant …
Systematic multi-omics integration (MOI) approach in plant systems biology
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 …
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 …
requires precise spatiotemporal coordination throughout plant development and in response …