Rapid immunoprecipitation mass spectrometry of endogenous proteins (RIME) for analysis of chromatin complexes

The BioPlex Network: A Systematic Exploration of the Human Interactome

(2015) Edward L. Huttlin et al.   CELL

Formaldehyde cross-linking and structural proteomics: Bridging the gap

(2015) Savita Srinivasa et al.   METHODS

Progesterone receptor modulates ERα action in breast cancer

(2015) Hisham Mohammed et al.   NATURE

Assessment of a method to characterize antibody selectivity and specificity for use in immunoprecipitation

(2015) Edyta Marcon et al.   NATURE METHODS

Fgf and Esrrb integrate epigenetic and transcriptional networks that regulate self-renewal of trophoblast stem cells

(2015) Paulina A. Latos et al.   Nature Communications

Proteins that bind regulatory regions identified by histone modification chromatin immunoprecipitations and mass spectrometry

(2015) Erik Engelen et al.   Nature Communications

LMTK3 Represses Tumor Suppressor-like Genes through Chromatin Remodeling in Breast Cancer

(2015) Yichen Xu et al.   Cell Reports

FOXM1 binds directly to non-consensus sequences in the human genome

(2015) Deborah A. Sanders et al.   GENOME BIOLOGY

Affinity purification–mass spectrometry and network analysis to understand protein-protein interactions

(2014) John H Morris et al.   Nature Protocols

An improved toolbox to unravel the plant cellular machinery by tandem affinity purification of Arabidopsis protein complexes

(2014) Jelle Van Leene et al.   Nature Protocols

The forkhead transcription factor FOXK2 acts as a chromatin targeting factor for the BAP1-containing histone deubiquitinase complex

(2014) Zongling Ji et al.   NUCLEIC ACIDS RESEARCH

miR-155 augments CD8+T-cell antitumor activity in lymphoreplete hosts by enhancing responsiveness to homeostatic γccytokines

(2014) Yun Ji et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Transcription Factor Networks in Drosophila melanogaster

(2014) David Y. Rhee et al.   Cell Reports

Affinity Purification Strategies for Proteomic Analysis of Transcription Factor Complexes

(2013) Roberto Giambruno et al.   JOURNAL OF PROTEOME RESEARCH

The CRAPome: a contaminant repository for affinity purification–mass spectrometry data

(2013) Dattatreya Mellacheruvu et al.   NATURE METHODS

Chromatin proteins captured by ChIP–mass spectrometry are linked to dosage compensation in Drosophila

(2013) Charlotte I Wang et al.   NATURE STRUCTURAL & MOLECULAR BIOLOGY

Endogenous Purification Reveals GREB1 as a Key Estrogen Receptor Regulatory Factor

(2013) Hisham Mohammed et al.   Cell Reports

Locus-Specific Proteomics by TChP: Targeted Chromatin Purification

(2013) Farzin Pourfarzad et al.   Cell Reports

Mass Spectrometry–Based Proteomics and Network Biology

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

Resolving protein interactions and complexes by affinity purification followed by label-based quantitative mass spectrometry

(2012) Laura Trinkle-Mulcahy   PROTEOMICS

Affinity-purification coupled to mass spectrometry: Basic principles and strategies

(2012) Wade H. Dunham et al.   PROTEOMICS

ChAP-MS: A Method for Identification of Proteins and Histone Posttranslational Modifications at a Single Genomic Locus

(2012) Stephanie D. Byrum et al.   Cell Reports

Analysis of the Human Endogenous Coregulator Complexome

(2011) Anna Malovannaya et al.   CELL

A Protein Complex Network of Drosophila melanogaster

(2011) K.G. Guruharsha et al.   CELL

Streamlined analysis schema for high-throughput identification of endogenous protein complexes

(2010) A. Malovannaya et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Defining the Human Deubiquitinating Enzyme Interaction Landscape

(2009) Mathew E. Sowa et al.   CELL

ChIP-seq: Using high-throughput sequencing to discover protein–DNA interactions

(2009) Dominic Schmidt et al.   METHODS

A general pipeline for quality and statistical assessment of protein interaction data using R and Bioconductor

(2009) Tony Chiang et al.   Nature Protocols

Switching of chromatin-remodelling complexes for oestrogen receptor-α

(2008) Maiko Okada et al.   EMBO REPORTS

Identifying specific protein interaction partners using quantitative mass spectrometry and bead proteomes

(2008) Laura Trinkle-Mulcahy et al.   JOURNAL OF CELL BIOLOGY

Utility of formaldehyde cross-linking and mass spectrometry in the study of protein–protein interactions

(2008) Brent W. Sutherland et al.   JOURNAL OF MASS SPECTROMETRY

Network Analysis Tools: from biological networks to clusters and pathways

(2008) Sylvain Brohée et al.   Nature Protocols