PhosR enables processing and functional analysis of phosphoproteomic data

Reconstructing kinase network topologies from phosphoproteomics data reveals cancer-associated rewiring

(2020) Maruan Hijazi et al.   NATURE BIOTECHNOLOGY

Co-Phosphorylation Networks Reveal Subtype-Specific Signaling Modules in Breast Cancer

(2020) Marzieh Ayati et al.   BIOINFORMATICS

Illuminating the dark phosphoproteome

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

CoPhosK: A method for comprehensive kinase substrate annotation using co-phosphorylation analysis

(2019) Marzieh Ayati et al.   PLoS Computational Biology

INKA, an integrative data analysis pipeline for phosphoproteomic inference of active kinases

(2019) Robin Beekhof et al.   Molecular Systems Biology

A new normalization for Nanostring nCounter gene expression data

(2019) Ramyar Molania et al.   NUCLEIC ACIDS RESEARCH

Multi-omic Profiling Reveals Dynamics of the Phased Progression of Pluripotency

(2019) Pengyi Yang et al.   Cell Systems

AdaSampling for Positive-Unlabeled and Label Noise Learning With Bioinformatics Applications

(2018) Pengyi Yang et al.   IEEE Transactions on Cybernetics

The PRIDE database and related tools and resources in 2019: improving support for quantification data

(2018) Yasset Perez-Riverol et al.   NUCLEIC ACIDS RESEARCH

The Perseus computational platform for comprehensive analysis of (prote)omics data

(2016) Stefka Tyanova et al.   NATURE METHODS

KinasePA: Phosphoproteomics data annotation using hypothesis driven kinase perturbation analysis

(2016) Pengyi Yang et al.   PROTEOMICS

mTORC1 Is a Major Regulatory Node in the FGF21 Signaling Network in Adipocytes

(2016) Annabel Y. Minard et al.   Cell Reports

Elucidation of Signaling Pathways from Large-Scale Phosphoproteomic Data Using Protein Interaction Networks

(2016) Jan Daniel Rudolph et al.   Cell Systems

IKAP: A heuristic framework for inference of kinase activities from Phosphoproteomics data

(2015) Marcel Mischnik et al.   BIOINFORMATICS

Global Phosphoproteomic Analysis of Human Skeletal Muscle Reveals a Network of Exercise-Regulated Kinases and AMPK Substrates

(2015) Nolan J. Hoffman et al.   Cell Metabolism

Identification of AMPK Phosphorylation Sites Reveals a Network of Proteins Involved in Cell Invasion and Facilitates Large-Scale Substrate Prediction

(2015) Bethany E. Schaffer et al.   Cell Metabolism

Review, Evaluation, and Discussion of the Challenges of Missing Value Imputation for Mass Spectrometry-Based Label-Free Global Proteomics

(2015) Bobbie-Jo M. Webb-Robertson et al.   JOURNAL OF PROTEOME RESEARCH

High-throughput phosphoproteomics reveals in vivo insulin signaling dynamics

(2015) Sean J Humphrey et al.   NATURE BIOTECHNOLOGY

limma powers differential expression analyses for RNA-sequencing and microarray studies

(2015) Matthew E. Ritchie et al.   NUCLEIC ACIDS RESEARCH

Protein Phosphorylation: A Major Switch Mechanism for Metabolic Regulation

(2015) Sean J. Humphrey et al.   TRENDS IN ENDOCRINOLOGY AND METABOLISM

Large-scale models of signal propagation in human cells derived from discovery phosphoproteomic data

(2015) Camille D. A. Terfve et al.   Nature Communications

Prior AICAR Stimulation Increases Insulin Sensitivity in Mouse Skeletal Muscle in an AMPK-Dependent Manner

(2015) Rasmus Kjøbsted et al.   DIABETES

circlize implements and enhances circular visualization in R

(2014) Zuguang Gu et al.   BIOINFORMATICS

Normalization of RNA-seq data using factor analysis of control genes or samples

(2014) Davide Risso et al.   NATURE BIOTECHNOLOGY

KinomeXplorer: an integrated platform for kinome biology studies

(2014) Heiko Horn et al.   NATURE METHODS

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

(2014) Kirti Sharma et al.   Cell Reports

Direction pathway analysis of large-scale proteomics data reveals novel features of the insulin action pathway

(2013) Pengyi Yang et al.   BIOINFORMATICS

Dynamic Adipocyte Phosphoproteome Reveals that Akt Directly Regulates mTORC2

(2013) Sean J. Humphrey et al.   Cell Metabolism

Conventional Knockout ofTbc1d1in Mice Impairs Insulin- and AICAR-Stimulated Glucose Uptake in Skeletal Muscle

(2013) Janine Dokas et al.   ENDOCRINOLOGY

Kinase-Substrate Enrichment Analysis Provides Insights into the Heterogeneity of Signaling Pathway Activation in Leukemia Cells

(2013) P. Casado et al.   Science Signaling

clusterProfiler: an R Package for Comparing Biological Themes Among Gene Clusters

(2012) Guangchuang Yu et al.   OMICS-A JOURNAL OF INTEGRATIVE BIOLOGY

Uncaging Akt

(2012) S. J. Humphrey et al.   Science Signaling

Computational prediction of eukaryotic phosphorylation sites

(2011) B. Trost et al.   BIOINFORMATICS

Using control genes to correct for unwanted variation in microarray data

(2011) J. A. Gagnon-Bartsch et al.   BIOSTATISTICS

PhosphoSitePlus: a comprehensive resource for investigating the structure and function of experimentally determined post-translational modifications in man and mouse

(2011) P. V. Hornbeck et al.   NUCLEIC ACIDS RESEARCH

Phospho.ELM: a database of phosphorylation sites--update 2011

(2010) H. Dinkel et al.   NUCLEIC ACIDS RESEARCH

Global and Site-Specific Quantitative Phosphoproteomics: Principles and Applications

(2008) Boris Macek et al.   Annual Review of Pharmacology and Toxicology

Discovery of TBC1D1 as an Insulin-, AICAR-, and Contraction-stimulated Signaling Nexus in Mouse Skeletal Muscle

(2008) Eric B. Taylor et al.   JOURNAL OF BIOLOGICAL CHEMISTRY

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