TY  - JOUR
A1  - Pandey, Prashant K.
A1  - Yu, Jing
A1  - Omranian, Nooshin
A1  - Alseekh, Saleh
A1  - Vaid, Neha
A1  - Fernie, Alisdair R.
A1  - Nikoloski, Zoran
A1  - Laitinen, Roosa A. E.
T1  - Plasticity in metabolism underpins local responses to nitrogen in Arabidopsis thaliana populations
JF  - Plant Direct
N2  - Nitrogen (N) is central for plant growth, and metabolic plasticity can provide a strategy to respond to changing N availability. We showed that two local A. thaliana populations exhibited differential plasticity in the compounds of photorespiratory and starch degradation pathways in response to three N conditions. Association of metabolite levels with growth-related and fitness traits indicated that controlled plasticity in these pathways could contribute to local adaptation and play a role in plant evolution.
KW  - Arabidopsis thaliana
KW  - natural variation
KW  - nitrogen availability
KW  - photorespiration
KW  - plasticity
Y1  - 2019
U6  - https://doi.org/10.1002/pld3.186
SN  - 2475-4455
VL  - 3
IS  - 11
PB  - John Wiley & sonst LTD
CY  - Chichester
ER  - 
TY  - JOUR
A1  - Hansen, Bjoern Oest
A1  - Meyer, Etienne H.
A1  - Ferrari, Camilla
A1  - Vaid, Neha
A1  - Movahedi, Sara
A1  - Vandepoele, Klaas
A1  - Nikoloski, Zoran
A1  - Mutwil, Marek
T1  - Ensemble gene function prediction database reveals genes important for complex I formation in Arabidopsis thaliana
JF  - New phytologist : international journal of plant science
N2  - Recent advances in gene function prediction rely on ensemble approaches that integrate results from multiple inference methods to produce superior predictions. Yet, these developments remain largely unexplored in plants. We have explored and compared two methods to integrate 10 gene co-function networks for Arabidopsis thaliana and demonstrate how the integration of these networks produces more accurate gene function predictions for a larger fraction of genes with unknown function. These predictions were used to identify genes involved in mitochondrial complex I formation, and for five of them, we confirmed the predictions experimentally. The ensemble predictions are provided as a user-friendly online database, EnsembleNet. The methods presented here demonstrate that ensemble gene function prediction is a powerful method to boost prediction performance, whereas the EnsembleNet database provides a cutting-edge community tool to guide experimentalists.
KW  - Arabidopsis thaliana
KW  - co-function network
KW  - complex I
KW  - ensemble prediction
KW  - gene function prediction
Y1  - 2017
U6  - https://doi.org/10.1111/nph.14921
SN  - 0028-646X
SN  - 1469-8137
VL  - 217
IS  - 4
SP  - 1521
EP  - 1534
PB  - Wiley
CY  - Hoboken
ER  -