Machine learning: a powerful tool for gene function prediction in plants

EH Mahood, LH Kruse… - Applications in Plant …, 2020 - Wiley Online Library
Recent advances in sequencing and informatic technologies have led to a deluge of publicly
available genomic data. While it is now relatively easy to sequence, assemble, and identify …

[HTML][HTML] Deep learning frameworks for protein–protein interaction prediction

X Hu, C Feng, T Ling, M Chen - Computational and structural …, 2022 - Elsevier
Protein-protein interactions (PPIs) play key roles in a broad range of biological processes.
The disorder of PPIs often causes various physical and mental diseases, which makes PPIs …

Population genomics of Populus trichocarpa identifies signatures of selection and adaptive trait associations

LM Evans, GT Slavov, E Rodgers-Melnick, J Martin… - Nature …, 2014 - nature.com
Forest trees are dominant components of terrestrial ecosystems that have global ecological
and economic importance. Despite distributions that span wide environmental gradients …

[HTML][HTML] ProtInteract: A deep learning framework for predicting protein–protein interactions

F Soleymani, E Paquet, HL Viktor… - Computational and …, 2023 - Elsevier
Proteins mainly perform their functions by interacting with other proteins. Protein–protein
interactions underpin various biological activities such as metabolic cycles, signal …

Machine-learning techniques for the prediction of protein–protein interactions

D Sarkar, S Saha - Journal of biosciences, 2019 - Springer
Protein–protein interactions (PPIs) are important for the study of protein functions and
pathways involved in different biological processes, as well as for understanding the cause …

Hub protein controversy: taking a closer look at plant stress response hubs

K Vandereyken, J Van Leene, B De Coninck… - Frontiers in plant …, 2018 - frontiersin.org
Plant stress responses involve numerous changes at the molecular and cellular level and
are regulated by highly complex signaling pathways. Studying protein-protein interactions …

Forest tree genomics: 10 achievements from the past 10 years and future prospects

C Plomion, C Bastien, MB Bogeat-Triboulot… - Annals of Forest …, 2016 - Springer
Key message This review highlights some of the discoveries and applications made
possible by “omics” technologies over the last 10 years and provides perspectives for …

Reconstruction and application of protein–protein interaction network

T Hao, W Peng, Q Wang, B Wang, J Sun - International journal of …, 2016 - mdpi.com
The protein-protein interaction network (PIN) is a useful tool for systematic investigation of
the complex biological activities in the cell. With the increasing interests on the proteome …

Green genes: bioinformatics and systems-biology innovations drive algal biotechnology

MJMF Reijnders, RGA van Heck, CMC Lam… - Trends in …, 2014 - cell.com
Many species of microalgae produce hydrocarbons, polysaccharides, and other valuable
products in significant amounts. However, large-scale production of algal products is not yet …

Integration of data‐independent acquisition (DIA) with co‐fractionation mass spectrometry (CF‐MS) to enhance interactome mapping capabilities

BN Hay, MO Akinlaja, TC Baker, AA Houfani… - …, 2023 - Wiley Online Library
Proteomics technologies are continually advancing, providing opportunities to develop
stronger and more robust protein interaction networks (PINs). In part, this is due to the ever …