Dynamic protein interaction network construction and applications

Spatio-temporal analysis of type 2 diabetes mellitus based on differential expression networks

(2013) Shao-Yan Sun et al.   Scientific Reports

Network Medicine Strikes a Blow against Breast Cancer

(2012) Janine T. Erler et al.   CELL

Sequential Application of Anticancer Drugs Enhances Cell Death by Rewiring Apoptotic Signaling Networks

(2012) Michael J. Lee et al.   CELL

Quantitative Chemical Proteomics Approach To Identify Post-translational Modification-Mediated Protein–Protein Interactions

(2012) Xiang Li et al.   JOURNAL OF THE AMERICAN CHEMICAL SOCIETY

Advancing Cell Biology Through Proteomics in Space and Time (PROSPECTS)

(2012) Angus I. Lamond et al.   MOLECULAR & CELLULAR PROTEOMICS

Dynamic Protein-Protein Interaction Wiring of the Human Spliceosome

(2012) Anna Hegele et al.   MOLECULAR CELL

Next-generation proteomics: towards an integrative view of proteome dynamics

(2012) A. F. Maarten Altelaar et al.   NATURE REVIEWS GENETICS

Examining post-translational modification-mediated protein-protein interactions using a chemical proteomics approach

(2012) Xiang Li et al.   PROTEIN SCIENCE

Mass spectrometry-based targeted quantitative proteomics: Achieving sensitive and reproducible detection of proteins

(2012) Emily S. Boja et al.   PROTEOMICS

Construction and application of dynamic protein interaction network based on time course gene expression data

(2012) Jianxin Wang et al.   PROTEOMICS

Investigation of stable and transient protein-protein interactions: Past, present, and future

(2012) Armand G. Ngounou Wetie et al.   PROTEOMICS

A comparison of the functional modules identified from time course and static PPI network data

(2011) Xiwei Tang et al.   BMC BIOINFORMATICS

Combined gene expression and protein interaction analysis of dynamic modularity in glioma prognosis

(2011) Xiaoyu Zhang et al.   JOURNAL OF NEURO-ONCOLOGY

Full-length transcriptome assembly from RNA-Seq data without a reference genome

(2011) Manfred G Grabherr et al.   NATURE BIOTECHNOLOGY

NOA: a novel Network Ontology Analysis method

(2011) Jiguang Wang et al.   NUCLEIC ACIDS RESEARCH

Transient protein-protein interactions

(2011) S. E. Acuner Ozbabacan et al.   PROTEIN ENGINEERING DESIGN & SELECTION

Identifying transient protein-protein interactions in EphB2 signaling by blue native PAGE and mass spectrometry

(2011) Costel C. Darie et al.   PROTEOMICS

Less label, more free: Approaches in label-free quantitative mass spectrometry

(2011) Karlie A. Neilson et al.   PROTEOMICS

Discovering conditional co-regulated protein complexes by integrating diverse data sources

(2010) Fei Luo et al.   BMC Systems Biology

Toward the dynamic interactome: it's about time

(2010) T. M. Przytycka et al.   BRIEFINGS IN BIOINFORMATICS

Transcript assembly and quantification by RNA-Seq reveals unannotated transcripts and isoform switching during cell differentiation

(2010) Cole Trapnell et al.   NATURE BIOTECHNOLOGY

Super-SILAC for tumors and tissues

(2010) Thomas A Neubert et al.   NATURE METHODS

MapSplice: Accurate mapping of RNA-seq reads for splice junction discovery

(2010) Kai Wang et al.   NUCLEIC ACIDS RESEARCH

Quantitative proteomics for investigating psychiatric disorders

(2010) Michaela D. Filiou et al.   Proteomics Clinical Applications

Transient Protein-Protein Interactions: Structural, Functional, and Network Properties

(2010) James R. Perkins et al.   STRUCTURE

A Quantitative Proteomics Analysis of Subcellular Proteome Localization and Changes Induced by DNA Damage

(2009) François-Michel Boisvert et al.   MOLECULAR & CELLULAR PROTEOMICS

Dynamic modularity in protein interaction networks predicts breast cancer outcome

(2009) Ian W Taylor et al.   NATURE BIOTECHNOLOGY

Applying mass spectrometry-based proteomics to genetics, genomics and network biology

(2009) Matthias Gstaiger et al.   NATURE REVIEWS GENETICS

Repeated two-hybrid screening detects transient protein–protein interactions

(2009) Arunachalam Vinayagam et al.   THEORETICAL CHEMISTRY ACCOUNTS

Precision and recall estimates for two-hybrid screens

(2008) Hailiang Huang et al.   BIOINFORMATICS

Mapping multiprotein complexes by affinity purification and mass spectrometry

(2008) Mark O Collins et al.   CURRENT OPINION IN BIOTECHNOLOGY

Network medicine

(2008) Tony Pawson et al.   FEBS LETTERS

Protein networks in disease

(2008) T. Ideker et al.   GENOME RESEARCH

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

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

An empirical framework for binary interactome mapping

(2008) Kavitha Venkatesan et al.   NATURE METHODS

RNA-Seq: a revolutionary tool for transcriptomics

(2008) Zhong Wang et al.   NATURE REVIEWS GENETICS

Dynamic Proteomics of Individual Cancer Cells in Response to a Drug

(2008) A. A. Cohen et al.   SCIENCE

Dynamic Changes in Protein Functional Linkage Networks Revealed by Integration with Gene Expression Data

(2008) Shubhada R. Hegde et al.   PLoS Computational Biology