A deep learning based approach for prediction of Chlamydomonas reinhardtii phosphorylation sites

RF-MaloSite and DL-Malosite: Methods based on random forest and deep learning to identify malonylation sites

(2020) Hussam AL-barakati et al.   Computational and Structural Biotechnology Journal

DeepSuccinylSite: a deep learning based approach for protein succinylation site prediction

(2020) Niraj Thapa et al.   BMC BIOINFORMATICS

Photosynthetic Metabolism and Nitrogen Reshuffling Are Regulated by Reversible Cysteine Thiol Oxidation Following Nitrogen Deprivation in Chlamydomonas

(2020) Amanda L. Smythers et al.   Plants-Basel

Inhibition of TOR in Chlamydomonas reinhardtii Leads to Rapid Cysteine Oxidation Reflecting Sustained Physiological Changes

(2019) Megan M. Ford et al.   Cells

The phosphorylated redox proteome of Chlamydomonas reinhardtii : Revealing novel means for regulation of protein structure and function

(2018) Evan W. McConnell et al.   Redox Biology

Investigating the effect of target of rapamycin kinase inhibition on the Chlamydomonas reinhardtii phosphoproteome: from known homologs to new targets

(2018) Emily G. Werth et al.   NEW PHYTOLOGIST

DeepPhos: prediction of protein phosphorylation sites with deep learning

(2018) Fenglin Luo et al.   BIOINFORMATICS

From molecular manipulation of domesticated Chlamydomonas reinhardtii to survival in nature

(2018) Severin Sasso et al.   eLife

Quantitative Phosphoproteomic and System-Level Analysis of TOR Inhibition Unravel Distinct Organellar Acclimation in Chlamydomonas reinhardtii

(2018) Valentin Roustan et al.   Frontiers in Plant Science

Probing the global kinome and phosphoproteome in Chlamydomonas reinhardtii via sequential enrichment and quantitative proteomics

(2017) Emily G. Werth et al.   PLANT JOURNAL

PhosphoPredict: A bioinformatics tool for prediction of human kinase-specific phosphorylation substrates and sites by integrating heterogeneous feature selection

(2017) Jiangning Song et al.   Scientific Reports

TOR Signaling and Nutrient Sensing

(2016) Thomas Dobrenel et al.   Annual Review of Plant Biology

TORC1 and TORC2 work together to regulate ribosomal protein S6 phosphorylation in Saccharomyces cerevisiae

(2016) Seda Yerlikaya et al.   MOLECULAR BIOLOGY OF THE CELL

Synergism between Inositol Polyphosphates and TOR Kinase Signaling in Nutrient Sensing, Growth Control, and Lipid Metabolism in Chlamydomonas

(2016) Inmaculada Couso et al.   PLANT CELL

RF-Phos: A Novel General Phosphorylation Site Prediction Tool Based on Random Forest

(2016) Hamid D. Ismail et al.   Biomed Research International

The Arabidopsis TOR Kinase Specifically Regulates the Expression of Nuclear Genes Coding for Plastidic Ribosomal Proteins and the Phosphorylation of the Cytosolic Ribosomal Protein S6

(2016) Thomas Dobrenel et al.   Frontiers in Plant Science

Deep learning

(2015) Yann LeCun et al.   NATURE

TheChlamydomonascell cycle

(2015) Frederick R. Cross et al.   PLANT JOURNAL

Rice_Phospho 1.0: a new rice-specific SVM predictor for protein phosphorylation sites

(2015) Shoukai Lin et al.   Scientific Reports

The Global Phosphoproteome ofChlamydomonas reinhardtiiReveals Complex Organellar Phosphorylation in the Flagella and Thylakoid Membrane

(2014) Hongxia Wang et al.   MOLECULAR & CELLULAR PROTEOMICS

Chemical and biological methods to detect post-translational modifications of arginine

(2013) Daniel J. Slade et al.   BIOPOLYMERS

PhosphoRice: a meta-predictor of rice-specific phosphorylation sites

(2012) Shufu Que et al.   Plant Methods

PhosTryp: a phosphorylation site predictor specific for parasitic protozoa of the family trypanosomatidae

(2011) Antonio Palmeri et al.   BMC GENOMICS

The chloroplast proteome: a survey from the Chlamydomonas reinhardtii perspective with a focus on distinctive features

(2011) Mia Terashima et al.   CURRENT GENETICS

Machine learning approach to predict protein phosphorylation sites by incorporating evolutionary information

(2010) Ashis Biswas et al.   BMC BIOINFORMATICS

Analysis of Flagellar Phosphoproteins fromChlamydomonas reinhardtii

(2009) Jens Boesger et al.   EUKARYOTIC CELL