In‐depth and 3‐dimensional exploration of the budding yeast phosphoproteome

Illuminating the dark phosphoproteome

(2019) Elise J. Needham et al.   Science Signaling

Strong anion exchange‐mediated phosphoproteomics reveals extensive human non‐canonical phosphorylation

(2019) Gemma Hardman et al.   EMBO JOURNAL

Multilayered Control of Protein Turnover by TORC1 and Atg1

(2019) Zehan Hu et al.   Cell Reports

The functional landscape of the human phosphoproteome

(2019) David Ochoa et al.   NATURE BIOTECHNOLOGY

Phosphoproteome dynamics during mitotic exit in budding yeast

(2018) Sandra A Touati et al.   EMBO JOURNAL

Separable roles for Mec1/ATR in genome maintenance, DNA replication, and checkpoint signaling

(2018) Michael Charles Lanz et al.   GENES & DEVELOPMENT

An interactome perturbation framework prioritizes damaging missense mutations for developmental disorders

(2018) Siwei Chen et al.   NATURE GENETICS

Interactome INSIDER: a structural interactome browser for genomic studies

(2018) Michael J Meyer et al.   NATURE METHODS

Quantitative Phosphoproteomics Reveals the Signaling Dynamics of Cell-Cycle Kinases in the Fission Yeast Schizosaccharomyces pombe

(2018) Matthew P. Swaffer et al.   Cell Reports

Unification of Protein Abundance Datasets Yields a Quantitative Saccharomyces cerevisiae Proteome

(2018) Brandon Ho et al.   Cell Systems

UniProt: a worldwide hub of protein knowledge

(2018)   NUCLEIC ACIDS RESEARCH

15 years of PhosphoSitePlus®: integrating post-translationally modified sites, disease variants and isoforms

(2018) Peter V Hornbeck et al.   NUCLEIC ACIDS RESEARCH

The TRAPPIII complex activates the GTPase Ypt1 (Rab1) in the secretory pathway

(2017) Laura L. Thomas et al.   JOURNAL OF CELL BIOLOGY

Improved Method for Determining Absolute Phosphorylation Stoichiometry Using Bayesian Statistics and Isobaric Labeling

(2017) Matthew Y. Lim et al.   JOURNAL OF PROTEOME RESEARCH

Systematic identification of phosphorylation-mediated protein interaction switches

(2017) Matthew J. Betts et al.   PLoS Computational Biology

Systematic proteomic analysis of LRRK2-mediated Rab GTPase phosphorylation establishes a connection to ciliogenesis

(2017) Martin Steger et al.   eLife

mutation3D: Cancer Gene Prediction Through Atomic Clustering of Coding Variants in the Structural Proteome

(2016) Michael J. Meyer et al.   HUMAN MUTATION

Cell cycle–dependent phosphorylation of Sec4p controls membrane deposition during cytokinesis

(2016) Dante Lepore et al.   JOURNAL OF CELL BIOLOGY

GTPase cross talk regulates TRAPPII activation of Rab11 homologues during vesicle biogenesis

(2016) Laura L. Thomas et al.   JOURNAL OF CELL BIOLOGY

Rab1 in cell signaling, cancer and other diseases

(2016) X-Z Yang et al.   ONCOGENE

Evolution of protein phosphorylation across 18 fungal species

(2016) R. A. Studer et al.   SCIENCE

Why phosphoproteomics is still a challenge

(2015) Fiorella A. Solari et al.   Molecular BioSystems

Yeast PP4 Interacts with ATR Homolog Ddc2-Mec1 and Regulates Checkpoint Signaling

(2015) Nicole Hustedt et al.   MOLECULAR CELL

Phosphoproteomics Reveals Distinct Modes of Mec1/ATR Signaling during DNA Replication

(2015) Francisco Meirelles Bastos de Oliveira et al.   MOLECULAR CELL

A Cell-Signaling Network Temporally Resolves Specific versus Promiscuous Phosphorylation

(2015) Evgeny Kanshin et al.   Cell Reports

Rad53-Mediated Regulation of Rrm3 and Pif1 DNA Helicases Contributes to Prevention of Aberrant Fork Transitions under Replication Stress

(2015) Silvia Emma Rossi et al.   Cell Reports

Off-Line High-pH Reversed-Phase Fractionation for In-Depth Phosphoproteomics

(2014) Tanveer S. Batth et al.   JOURNAL OF PROTEOME RESEARCH

Dual Control of Yen1 Nuclease Activity and Cellular Localization by Cdk and Cdc14 Prevents Genome Instability

(2014) Miguel G. Blanco et al.   MOLECULAR CELL

Whole-genome sequence variation, population structure and demographic history of the Dutch population

(2014) Laurent C Francioli et al.   NATURE GENETICS

Ultradeep Human Phosphoproteome Reveals a Distinct Regulatory Nature of Tyr and Ser/Thr-Based Signaling

(2014) Kirti Sharma et al.   Cell Reports

A Massively Parallel Pipeline to Clone DNA Variants and Examine Molecular Phenotypes of Human Disease Mutations

(2014) Xiaomu Wei et al.   PLoS Genetics

MAFFT Multiple Sequence Alignment Software Version 7: Improvements in Performance and Usability

(2013) K. Katoh et al.   MOLECULAR BIOLOGY AND EVOLUTION

Mapping and analysis of phosphorylation sites: a quick guide for cell biologists

(2013) Noah Dephoure et al.   MOLECULAR BIOLOGY OF THE CELL

Global analysis of phosphorylation and ubiquitylation cross-talk in protein degradation

(2013) Danielle L Swaney et al.   NATURE METHODS

ClinVar: public archive of relationships among sequence variation and human phenotype

(2013) Melissa J. Landrum et al.   NUCLEIC ACIDS RESEARCH

Key issues in the acquisition and analysis of qualitative and quantitative mass spectrometry data for peptide-centric proteomic experiments

(2012) Andrew J. Thompson et al.   AMINO ACIDS

Systematic Functional Prioritization of Protein Posttranslational Modifications

(2012) Pedro Beltrao et al.   CELL

An integrated map of genetic variation from 1,092 human genomes

(2012)   NATURE

Three-dimensional reconstruction of protein networks provides insight into human genetic disease

(2012) Xiujuan Wang et al.   NATURE BIOTECHNOLOGY

Interactome3D: adding structural details to protein networks

(2012) Roberto Mosca et al.   NATURE METHODS

Protein abundance is key to distinguish promiscuous from functional phosphorylation based on evolutionary information

(2012) E. D. Levy et al.   PHILOSOPHICAL TRANSACTIONS OF THE ROYAL SOCIETY B-BIOLOGICAL SCIENCES

Evolution and Functional Impact of Rare Coding Variation from Deep Sequencing of Human Exomes

(2012) J. A. Tennessen et al.   SCIENCE

YeastMine—an integrated data warehouse for Saccharomyces cerevisiae data as a multipurpose tool-kit

(2012) Rama Balakrishnan et al.   Database-The Journal of Biological Databases and Curation

Universal and Confident Phosphorylation Site Localization Using phosphoRS

(2011) Thomas Taus et al.   JOURNAL OF PROTEOME RESEARCH

Systematic exploration of essential yeast gene function with temperature-sensitive mutants

(2011) Zhijian Li et al.   NATURE BIOTECHNOLOGY

A large-scale method to measure absolute protein phosphorylation stoichiometries

(2011) Ronghu Wu et al.   NATURE METHODS

Role of Rab GTPases in Membrane Traffic and Cell Physiology

(2011) Alex H. Hutagalung et al.   PHYSIOLOGICAL REVIEWS

Phosphorylation Provides a Negative Mode of Regulation for the Yeast Rab GTPase Sec4p

(2011) Christopher D. Heger et al.   PLoS One

Phosphorylation in Protein-Protein Binding: Effect on Stability and Function

(2011) Hafumi Nishi et al.   STRUCTURE

DNA Damage Signaling Recruits the Rtt107-Slx4 Scaffolds via Dpb11 to Mediate Replication Stress Response

(2010) Patrice Y. Ohouo et al.   MOLECULAR CELL

Checkpoint-dependent inhibition of DNA replication initiation by Sld3 and Dbf4 phosphorylation

(2010) Philip Zegerman et al.   NATURE

Quantitative Phosphoproteomics Reveals Widespread Full Phosphorylation Site Occupancy During Mitosis

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

BLAST+: architecture and applications

(2009) Christiam Camacho et al.   BMC BIOINFORMATICS

Global Analysis of Cdk1 Substrate Phosphorylation Sites Provides Insights into Evolution

(2009) L. J. Holt et al.   SCIENCE

Weak functional constraints on phosphoproteomes

(2009) Christian R. Landry et al.   TRENDS IN GENETICS

A Multidimensional Chromatography Technology for In-depth Phosphoproteome Analysis

(2008) Claudio P. Albuquerque et al.   MOLECULAR & CELLULAR PROTEOMICS

G1/S Cyclin-dependent Kinase Regulates Small GTPase Rho1p through Phosphorylation of RhoGEF Tus1p in Saccharomyces cerevisiae

(2008) Keiko Kono et al.   MOLECULAR BIOLOGY OF THE CELL

Non-functional phosphorylations?

(2008) Gustav E. Lienhard   TRENDS IN BIOCHEMICAL SCIENCES