Convergence of Ubiquitylation and Phosphorylation Signaling in Rapamycin-treated Yeast Cells

Acetyl-Phosphate Is a Critical Determinant of Lysine Acetylation in E. coli

(2013) Brian T. Weinert et al.   MOLECULAR CELL

TNFα Levels and Macrophages Expression Reflect an Inflammatory Potential of Trigeminal Ganglia in a Mouse Model of Familial Hemiplegic Migraine

(2013) Alessia Franceschini et al.   PLoS One

Quantitative Phosphoproteomics Reveal mTORC1 Activates de Novo Pyrimidine Synthesis

(2013) A. M. Robitaille et al.   SCIENCE

Lysine Succinylation Is a Frequently Occurring Modification in Prokaryotes and Eukaryotes and Extensively Overlaps with Acetylation

(2013) Brian T. Weinert et al.   Cell Reports

Mass Spectrometry–Based Proteomics and Network Biology

(2012) Ariel Bensimon et al.   Annual Review of Biochemistry

Systematic Functional Prioritization of Protein Posttranslational Modifications

(2012) Pedro Beltrao et al.   CELL

mTOR Signaling in Growth Control and Disease

(2012) Mathieu Laplante et al.   CELL

Rapamycin increases lifespan and inhibits spontaneous tumorigenesis in inbred female mice

(2012) Vladimir N. Anisimov et al.   CELL CYCLE

Optimized Fast and Sensitive Acquisition Methods for Shotgun Proteomics on a Quadrupole Orbitrap Mass Spectrometer

(2012) Christian D. Kelstrup et al.   JOURNAL OF PROTEOME RESEARCH

Proteome-wide Analysis of Lysine Acetylation Suggests its Broad Regulatory Scope inSaccharomyces cerevisiae

(2012) Peter Henriksen et al.   MOLECULAR & CELLULAR PROTEOMICS

Proteomic Analyses Reveal Divergent Ubiquitylation Site Patterns in Murine Tissues

(2012) Sebastian A. Wagner et al.   MOLECULAR & CELLULAR PROTEOMICS

Internal Amino Acids Promote Gap1 Permease Ubiquitylation via TORC1/Npr1/14-3-3-Dependent Control of the Bul Arrestin-Like Adaptors

(2012) A. Merhi et al.   MOLECULAR AND CELLULAR BIOLOGY

Systems-wide analysis of ubiquitylation dynamics reveals a key role for PAF15 ubiquitylation in DNA-damage bypass

(2012) Lou K. Povlsen et al.   NATURE CELL BIOLOGY

Global Identification of Modular Cullin-RING Ligase Substrates

(2011) Michael J. Emanuele et al.   CELL

TORC1 Regulates Endocytosis via Npr1-Mediated Phosphoinhibition of a Ubiquitin Ligase Adaptor

(2011) Jason A. MacGurn et al.   CELL

mTOR signaling in disease

(2011) Eva Dazert et al.   CURRENT OPINION IN CELL BIOLOGY

Andromeda: A Peptide Search Engine Integrated into the MaxQuant Environment

(2011) Jürgen Cox et al.   JOURNAL OF PROTEOME RESEARCH

Mass Spectrometry-based Proteomics Using Q Exactive, a High-performance Benchtop Quadrupole Orbitrap Mass Spectrometer

(2011) Annette Michalski et al.   MOLECULAR & CELLULAR PROTEOMICS

GProX, a User-Friendly Platform for Bioinformatics Analysis and Visualization of Quantitative Proteomics Data

(2011) Kristoffer T. G. Rigbolt et al.   MOLECULAR & CELLULAR PROTEOMICS

Enhancing the Identification of Phosphopeptides from Putative Basophilic Kinase Substrates Using Ti (IV) Based IMAC Enrichment

(2011) Houjiang Zhou et al.   MOLECULAR & CELLULAR PROTEOMICS

A Proteome-wide, Quantitative Survey of In Vivo Ubiquitylation Sites Reveals Widespread Regulatory Roles

(2011) Sebastian A. Wagner et al.   MOLECULAR & CELLULAR PROTEOMICS

Systematic and Quantitative Assessment of the Ubiquitin-Modified Proteome

(2011) Woong Kim et al.   MOLECULAR CELL

Phosphoproteomic Analysis Identifies Grb10 as an mTORC1 Substrate That Negatively Regulates Insulin Signaling

(2011) Y. Yu et al.   SCIENCE

The mTOR-Regulated Phosphoproteome Reveals a Mechanism of mTORC1-Mediated Inhibition of Growth Factor Signaling

(2011) P. P. Hsu et al.   SCIENCE

The Rapamycin-sensitive Phosphoproteome Reveals That TOR Controls Protein Kinase A Toward Some But Not All Substrates

(2010) Alexandre Soulard et al.   MOLECULAR BIOLOGY OF THE CELL

Global analysis of lysine ubiquitination by ubiquitin remnant immunoaffinity profiling

(2010) Guoqiang Xu et al.   NATURE BIOTECHNOLOGY

Decoding signalling networks by mass spectrometry-based proteomics

(2010) Chunaram Choudhary et al.   NATURE REVIEWS MOLECULAR CELL BIOLOGY

Phosphoproteomic Analysis Reveals Interconnected System-Wide Responses to Perturbations of Kinases and Phosphatases in Yeast

(2010) B. Bodenmiller et al.   Science Signaling

Quantitative Phosphoproteomics Reveals Widespread Full Phosphorylation Site Occupancy During Mitosis

(2010) J. V. Olsen et al.   Science Signaling

The ubiquitin code of yeast permease trafficking

(2010) Elsa Lauwers et al.   TRENDS IN CELL BIOLOGY

Mechanisms of regulation of RNA polymerase III-dependent transcription by TORC1

(2009) Yuehua Wei et al.   EMBO JOURNAL

Characterization of the rapamycin-sensitive phosphoproteome reveals that Sch9 is a central coordinator of protein synthesis

(2009) A. Huber et al.   GENES & DEVELOPMENT

Combination of FASP and StageTip-Based Fractionation Allows In-Depth Analysis of the Hippocampal Membrane Proteome

(2009) Jacek R. Wiśniewski et al.   JOURNAL OF PROTEOME RESEARCH

ULK-Atg13-FIP200 Complexes Mediate mTOR Signaling to the Autophagy Machinery

(2009) Chang Hwa Jung et al.   MOLECULAR BIOLOGY OF THE CELL

Global analysis of the yeast osmotic stress response by quantitative proteomics

(2009) Boumediene Soufi et al.   Molecular BioSystems

Sfp1 Interaction with TORC1 and Mrs6 Reveals Feedback Regulation on TOR Signaling

(2009) Harri Lempiäinen et al.   MOLECULAR CELL

Rapamycin fed late in life extends lifespan in genetically heterogeneous mice

(2009) David E. Harrison et al.   NATURE

Improved visualization of protein consensus sequences by iceLogo

(2009) Niklaas Colaert et al.   NATURE METHODS

Systematic and integrative analysis of large gene lists using DAVID bioinformatics resources

(2009) Da Wei Huang et al.   Nature Protocols

Physiological functions of the HECT family of ubiquitin ligases

(2009) Daniela Rotin et al.   NATURE REVIEWS MOLECULAR CELL BIOLOGY

Global Analysis of Cdk1 Substrate Phosphorylation Sites Provides Insights into Evolution

(2009) L. J. Holt et al.   SCIENCE

A Genome-Wide Screen for Regulators of TORC1 in Response to Amino Acid Starvation Reveals a Conserved Npr2/3 Complex

(2009) Taavi K. Neklesa et al.   PLoS Genetics

Versatile role of the yeast ubiquitin ligase Rsp5p in intracellular trafficking: Figure 1

(2008) Naima Belgareh-Touzé et al.   BIOCHEMICAL SOCIETY TRANSACTIONS

Arrestin-Related Ubiquitin-Ligase Adaptors Regulate Endocytosis and Protein Turnover at the Cell Surface

(2008) Charles H. Lin et al.   CELL

Comprehensive mass-spectrometry-based proteome quantification of haploid versus diploid yeast

(2008) Lyris M. F. de Godoy et al.   NATURE

MaxQuant enables high peptide identification rates, individualized p.p.b.-range mass accuracies and proteome-wide protein quantification

(2008) Jürgen Cox et al.   NATURE BIOTECHNOLOGY