Integration of protein phosphorylation, acetylation, and methylation data sets to outline lung cancer signaling networks

Beyond histones - the expanding roles of protein lysine methylation

(2017) Zhouran Wu et al.   FEBS Journal

The NANCI–Nkx2.1 gene duplex buffers Nkx2.1 expression to maintain lung development and homeostasis

(2017) Michael J. Herriges et al.   GENES & DEVELOPMENT

Interrogating the Roles of Post-Translational Modifications of Non-Histone Proteins

(2017) Zakey Yusuf Buuh et al.   JOURNAL OF MEDICINAL CHEMISTRY

Multiplexed Phosphoproteomic Profiling Using Titanium Dioxide and Immunoaffinity Enrichments Reveals Complementary Phosphorylation Events

(2017) Anthony P. Possemato et al.   JOURNAL OF PROTEOME RESEARCH

PTMOracle: A Cytoscape App for Covisualizing and Coanalyzing Post-Translational Modifications in Protein Interaction Networks

(2017) Aidan P. Tay et al.   JOURNAL OF PROTEOME RESEARCH

How Hsp90 and Cdc37 Lubricate Kinase Molecular Switches

(2017) Kliment A. Verba et al.   TRENDS IN BIOCHEMICAL SCIENCES

Microarray-Based Gene Expression Analysis for Veterinary Pathologists: A Review

(2017) Barbara B. Raddatz et al.   VETERINARY PATHOLOGY

Post-translational Modifications and Protein Quality Control in Motor Neuron and Polyglutamine Diseases

(2017) Fabio Sambataro et al.   Frontiers in Molecular Neuroscience

Clustergrammer, a web-based heatmap visualization and analysis tool for high-dimensional biological data

(2017) Nicolas F. Fernandez et al.   Scientific Data

Bromodomain inhibitors and cancer therapy: From structures to applications

(2016) Montserrat Pérez-Salvia et al.   Epigenetics

Post-Translational Modification Control of Innate Immunity

(2016) Juan Liu et al.   IMMUNITY

Long non-coding RNAs: spatial amplifiers that control nuclear structure and gene expression

(2016) Jesse M. Engreitz et al.   NATURE REVIEWS MOLECULAR CELL BIOLOGY

The STRING database in 2017: quality-controlled protein–protein association networks, made broadly accessible

(2016) Damian Szklarczyk et al.   NUCLEIC ACIDS RESEARCH

The harmonizome: a collection of processed datasets gathered to serve and mine knowledge about genes and proteins

(2016) Andrew D. Rouillard et al.   Database-The Journal of Biological Databases and Curation

P300 acetyltransferase regulates fatty acid synthase expression, lipid metabolism and prostate cancer growth

(2016) Xiaokun Gang et al.   Oncotarget

Signaling Networks among Stem Cell Precursors, Transit-Amplifying Progenitors, and their Niche in Developing Hair Follicles

(2016) Amélie Rezza et al.   Cell Reports

On the Relationship of Protein and mRNA Dynamics in Vertebrate Embryonic Development

(2015) Leonid Peshkin et al.   DEVELOPMENTAL CELL

Targeting cancer with kinase inhibitors

(2015) Stefan Gross et al.   JOURNAL OF CLINICAL INVESTIGATION

Deep, Quantitative Coverage of the Lysine Acetylome Using Novel Anti-acetyl-lysine Antibodies and an Optimized Proteomic Workflow

(2015) Tanya Svinkina et al.   MOLECULAR & CELLULAR PROTEOMICS

The Roles of Post-translational Modifications in the Context of Protein Interaction Networks

(2015) Guangyou Duan et al.   PLoS Computational Biology

Neuroblastoma Tyrosine Kinase Signaling Networks Involve FYN and LYN in Endosomes and Lipid Rafts

(2015) Juan Palacios-Moreno et al.   PLoS Computational Biology

Large-Scale Analysis of Kinase Signaling in Yeast Pseudohyphal Development Identifies Regulation of Ribonucleoprotein Granules

(2015) Christian A. Shively et al.   PLoS Genetics

Connecting the speckles: Splicing kinases and their role in tumorigenesis and treatment response

(2015) Dale P Corkery et al.   Nucleus

Connecting the speckles: Splicing kinases and their role in tumorigenesis and treatment response

(2015) Dale P Corkery et al.   Nucleus

BAG6/BAT3 modulates autophagy by affecting EP300/p300 intracellular localization

(2014) Salwa Sebti et al.   Autophagy

BRG1/SMARCA4 Inactivation Promotes Non-Small Cell Lung Cancer Aggressiveness by Altering Chromatin Organization

(2014) T. Orvis et al.   CANCER RESEARCH

Subcellular mRNA localisation at a glance

(2014) Richard M. Parton et al.   JOURNAL OF CELL SCIENCE

Regulation of Autophagy by Cytosolic Acetyl-Coenzyme A

(2014) Guillermo Mariño et al.   MOLECULAR CELL

Targeting bromodomains: epigenetic readers of lysine acetylation

(2014) Panagis Filippakopoulos et al.   NATURE REVIEWS DRUG DISCOVERY

The rise of regulatory RNA

(2014) Kevin V. Morris et al.   NATURE REVIEWS GENETICS

PhosphoSitePlus, 2014: mutations, PTMs and recalibrations

(2014) Peter V. Hornbeck et al.   NUCLEIC ACIDS RESEARCH

Global absolute quantification reveals tight regulation of protein expression in single Xenopus eggs

(2014) Arne H. Smits et al.   NUCLEIC ACIDS RESEARCH

Systematic identification of signaling pathways with potential to confer anticancer drug resistance

(2014) C. A. Martz et al.   Science Signaling

RCytoscape: tools for exploratory network analysis

(2013) Paul T Shannon et al.   BMC BIOINFORMATICS

Enrichr: interactive and collaborative HTML5 gene list enrichment analysis tool

(2013) Edward Y Chen et al.   BMC BIOINFORMATICS

Protein post-translational modifications and regulation of pluripotency in human stem cells

(2013) Yu-Chieh Wang et al.   CELL RESEARCH

Threshold-controlled ubiquitination of the EGFR directs receptor fate

(2013) Sara Sigismund et al.   EMBO JOURNAL

Immunoaffinity Enrichment and Mass Spectrometry Analysis of Protein Methylation

(2013) Ailan Guo et al.   MOLECULAR & CELLULAR PROTEOMICS

Phosphotyrosine Signaling Proteins that Drive Oncogenesis Tend to be Highly Interconnected

(2013) Grigoriy Koytiger et al.   MOLECULAR & CELLULAR PROTEOMICS

Nkx2-1 Represses a Latent Gastric Differentiation Program in Lung Adenocarcinoma

(2013) Eric L. Snyder et al.   MOLECULAR CELL

The Cancer Genome Atlas Pan-Cancer analysis project

(2013) John N Weinstein et al.   NATURE GENETICS

Visualization of SNPs with t-SNE

(2013) Alexander Platzer   PLoS One

Dual Coordination of Post Translational Modifications in Human Protein Networks

(2013) Jonathan Woodsmith et al.   PLoS Computational Biology

Consecutive Proteolytic Digestion in an Enzyme Reactor Increases Depth of Proteomic and Phosphoproteomic Analysis

(2012) Jacek R. Wiśniewski et al.   ANALYTICAL CHEMISTRY

Mass Spectrometry–Based Proteomics and Network Biology

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

TiSH — a robust and sensitive global phosphoproteomics strategy employing a combination of TiO2, SIMAC, and HILIC

(2012) Kasper Engholm-Keller et al.   Journal of Proteomics

Comparison and applications of label-free absolute proteome quantification methods on Escherichia coli

(2012) L. Arike et al.   Journal of Proteomics

PTMScan Direct: Identification and Quantification of Peptides from Critical Signaling Proteins by Immunoaffinity Enrichment Coupled with LC-MS/MS

(2012) Matthew P. Stokes et al.   MOLECULAR & CELLULAR PROTEOMICS

PaxDb, a Database of Protein Abundance Averages Across All Three Domains of Life

(2012) M. Wang et al.   MOLECULAR & CELLULAR PROTEOMICS

The HSP90 inhibitor geldanamycin perturbs endosomal structure and drives recycling ErbB2 and transferrin to modified MVBs/lysosomal compartments

(2012) Katia Cortese et al.   MOLECULAR BIOLOGY OF THE CELL

Deciphering a global network of functionally associated post-translational modifications

(2012) Pablo Minguez et al.   Molecular Systems Biology

Evolution of SH2 domains and phosphotyrosine signalling networks

(2012) B. A. Liu et al.   PHILOSOPHICAL TRANSACTIONS OF THE ROYAL SOCIETY B-BIOLOGICAL SCIENCES

Combining many interaction networks to predict gene function and analyze gene lists

(2012) Sara Mostafavi et al.   PROTEOMICS

P-Bodies and Stress Granules: Possible Roles in the Control of Translation and mRNA Degradation

(2012) C. J. Decker et al.   Cold Spring Harbor Perspectives in Biology

Ten Years of Pathway Analysis: Current Approaches and Outstanding Challenges

(2012) Purvesh Khatri et al.   PLoS Computational Biology

Increasing phosphoproteomic coverage through sequential digestion by complementary proteases

(2011) Jason M. Gilmore et al.   ANALYTICAL AND BIOANALYTICAL CHEMISTRY

Multiobjective evolutionary algorithms to identify highly autocorrelated areas: the case of spatial distribution in financially compromised farms

(2011) Carlos R. García-Alonso et al.   ANNALS OF OPERATIONS RESEARCH

Ultra High Resolution Linear Ion Trap Orbitrap Mass Spectrometer (Orbitrap Elite) Facilitates Top Down LC MS/MS and Versatile Peptide Fragmentation Modes

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

Suppression of lung adenocarcinoma progression by Nkx2-1

(2011) Monte M. Winslow et al.   NATURE

An intuitive graphical visualization technique for the interrogation of transcriptome data

(2011) Natascha Bushati et al.   NUCLEIC ACIDS RESEARCH

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

Therapeutic strategies to overcome crizotinib resistance in non-small cell lung cancers harboring the fusion oncogene EML4-ALK

(2011) R. Katayama et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

A genome-wide map of human genetic interactions inferred from radiation hybrid genotypes

(2010) A. Lin et al.   GENOME RESEARCH

Heat Shock Protein 90 Inhibition in Lung Cancer

(2010) Takeshi Shimamura et al.   Journal of Thoracic Oncology

Pathway Commons, a web resource for biological pathway data

(2010) E. G. Cerami et al.   NUCLEIC ACIDS RESEARCH

The GeneMANIA prediction server: biological network integration for gene prioritization and predicting gene function

(2010) David Warde-Farley et al.   NUCLEIC ACIDS RESEARCH

Quantitative Phosphoproteomics Reveals Widespread Full Phosphorylation Site Occupancy During Mitosis

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

A penalized matrix decomposition, with applications to sparse principal components and canonical correlation analysis

(2009) D. M. Witten et al.   BIOSTATISTICS

Regulation of Epidermal Growth Factor Receptor Trafficking by Lysine Deacetylase HDAC6

(2009) Y. Lissanu Deribe et al.   Science Signaling

Endocytosis and intracellular trafficking of ErbBs

(2008) Alexander Sorkin et al.   EXPERIMENTAL CELL RESEARCH

Clathrin-independent endocytosis of ErbB2 in geldanamycin-treated human breast cancer cells

(2008) D. J. Barr et al.   JOURNAL OF CELL SCIENCE

Different phosphorylation states of the anaphase promoting complex in response to antimitotic drugs: A quantitative proteomic analysis

(2008) J. A. J. Steen et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA