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Related Concept Videos

Protein Networks02:26

Protein Networks

An organism can have thousands of different proteins, and these proteins must cooperate to ensure the health of an organism. Proteins bind to other proteins and form complexes to carry out their functions. Many proteins interact with multiple other proteins creating a complex network of protein interactions.
These interactions can be represented through maps depicting protein-protein interaction networks, represented as nodes and edges. Nodes are circles that are representative of a protein,...
Next-generation Sequencing03:00

Next-generation Sequencing

The first human genome sequencing project cost $2.7 billion and was declared complete in 2003, after 15 years of international cooperation and collaboration between several research teams and funding agencies. Today, with the advent of next-generation sequencing technologies, the cost and time of sequencing a human genome have dropped over 100 fold.
Next-Generation Sequencing Methods
Although all next-generation methods use different technologies, they all share a set of standard features.
Genome Annotation and Assembly03:36

Genome Annotation and Assembly

The genome refers to all of the genetic material in an organism. It can range from a few million base pairs in microbial cells to several billion base pairs in many eukaryotic organisms. Genome assembly refers to the process of taking the DNA sequencing data and putting it all back together in a correct order to create a close representation of the original genome. This is followed by the identification of functional elements on the newly assembled genome, a process called genome annotation.
RNA-seq03:21

RNA-seq

RNA sequencing, or RNA-Seq, is a high-throughput sequencing technology used to study the transcriptome of a cell. Transcriptomics helps to interpret the functional elements of a genome and identify the molecular constituents of an organism. Additionally, it also helps in understanding the development of an organism and the occurrence of diseases. 
Before the discovery of RNA-seq, microarray-based methods and Sanger sequencing were used for transcriptome analysis. However, while microarray-based...
Protein-protein Interfaces02:04

Protein-protein Interfaces

Many proteins form complexes to carry out their functions, making protein-protein interactions (PPIs) essential for an organism's survival. Most PPIs are stabilized by numerous weak noncovalent chemical forces. The physical shape of the interfaces determines the way two proteins interact. Many globular proteins have closely-matching shapes on their surfaces, which form a large number of weak bonds. Additionally, many PPIs occur between two helices or between a surface cleft and a polypeptide...

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Updated: Jun 2, 2026

Label-Free Immunoprecipitation Mass Spectrometry Workflow for Large-scale Nuclear Interactome Profiling
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Label-Free Immunoprecipitation Mass Spectrometry Workflow for Large-scale Nuclear Interactome Profiling

Published on: November 17, 2019

Next-generation sequencing to generate interactome datasets.

Haiyuan Yu1, Leah Tardivo, Stanley Tam

  • 1Center for Cancer Systems Biology, Department of Cancer Biology, Dana-Farber Cancer Institute, Boston, Massachusetts, USA.

Nature Methods
|April 26, 2011
PubMed
Summary
This summary is machine-generated.

Researchers developed Stitch-seq, a new method using next-generation sequencing for protein-protein interactome mapping. This technique maintains interaction pair associations, enabling comprehensive network analysis.

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Interactome-Seq: A Protocol for Domainome Library Construction, Validation and Selection by Phage Display and Next Generation Sequencing
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Interactome-Seq: A Protocol for Domainome Library Construction, Validation and Selection by Phage Display and Next Generation Sequencing

Published on: October 3, 2018

Area of Science:

  • Biochemistry
  • Genomics
  • Bioinformatics

Background:

  • Protein-protein interactions (PPIs) are crucial for cellular functions.
  • Existing methods for mapping PPIs face limitations in scalability and maintaining interaction pair integrity.
  • Next-generation sequencing (NGS) has revolutionized biological data generation but hasn't been applied to interactome mapping due to data association challenges.

Purpose of the Study:

  • To develop a novel method for large-scale protein-protein interactome network mapping.
  • To overcome the challenge of maintaining interaction pair associations during high-throughput sequencing.
  • To generate a comprehensive human interactome dataset using the new method.

Main Methods:

  • Introduction of Stitch-seq, a massively parallel interactome-mapping pipeline.
  • Combination of Polymerase Chain Reaction (PCR) stitching with next-generation sequencing.
  • Application of the pipeline to generate a human interactome dataset.

Main Results:

  • Successful application of Stitch-seq to map protein-protein interactions.
  • Generation of a novel human interactome dataset.
  • Demonstration that Stitch-seq maintains the association between interacting protein pairs.

Conclusions:

  • Stitch-seq enables the application of next-generation sequencing to protein-protein interactome mapping.
  • The method is versatile and applicable to various interaction assays.
  • Stitch-seq is expected to significantly expand the scope and scale of interactome network mapping.