ArticleNucleic acids research2014
Prospective identification of parasitic sequences in phage display screens.
Article in Nucleic acids research, 2014. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 75 papers.
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Who cites it
75 citing papers in PubMed.
- Phage Display as a Promising Platform for Peptide Drug Discovery.Pharmaceuticals (Basel, Switzerland) · 2026Review
- Serum-antibody Profiling of H3N2-infected Ferrets Using a Combinatorial Phage-display Random Peptide Library.Journal of molecular biology · 2026Article
- A suite of macrocyclic peptide inhibitors and substrate probes for arginine methyltransferases.Chemical science · 2026Article
- Universal Baseline forbioRxiv : the preprint server for biology · 2026Article
- Review
- Atom-level machine learning of protein-glycan interactions and cross-chiral recognition in glycobiology.Science advances · 2025Article
- Evaluation of multiplexed liquid glycan Array (LiGA) for serological detection of glycan-binding antibodies.Glycobiology · 2025Article
- Measuring carbohydrate recognition profile of lectins on live cells using liquid glycan array (LiGA).Nature protocols · 2025Review
- A comparative analysis of sequence composition in different lots of a phage display peptide library during amplification.Virology journal · 2025Article
- On the origin of non-specific binders isolated in the selection of phage display peptide libraries.Frontiers in microbiology · 2025Review
- De novo discovery of bicycles.Nature chemical biology · 2025Article
- Optimized Construction of a Yeast SICLOPPS Library for UnbiasedBiochemistry · 2024Article
- Next Generation SICLOPPS Screening for the Identification of Inhibitors of the HIF-1α/HIF-1β Protein-Protein Interaction.ACS chemical biology · 2024Article
- Using NGS to Uncover the Corruption of a Peptide Phage Display Selection.Current issues in molecular biology · 2024Article
- Diversification of Phage-Displayed Peptide Libraries with Noncanonical Amino Acid Mutagenesis and Chemical Modification.Chemical reviews · 2024Review
- Phage libraries screening on P53: Yield improvement by zinc and a new parasites-integrating analysis.PloS one · 2024Article
- Depth of Sequencing Plays a Determining Role in the Characterization of Phage Display Peptide Libraries by NGS.International journal of molecular sciences · 2023Article
- Combination of Experimental and Bioinformatic Approaches for Identification of Immunologically Relevant Protein-Peptide Interactions.Biomolecules · 2023Article
- Phage-based peptides for pancreatic cancer diagnosis and treatment: alternative approach.Frontiers in microbiology · 2023Review
- Pattern enrichment analysis for phage selection of stapled peptide ligands.Chemical science · 2022Article
15 more citing papers are in PubMed but not listed here.
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Authors and funding
4 authors.
Funding
No grant is acknowledged in the PubMed record.
Abstract
Phage display empowered the development of proteins with new function and ligands for clinically relevant targets. In this report, we use next-generation sequencing to analyze phage-displayed libraries and uncover a strong bias induced by amplification preferences of phage in bacteria. This bias favors fast-growing sequences that collectively constitute <0.01% of the available diversity. Specifically, a library of 10(9) random 7-mer peptides (Ph.D.-7) includes a few thousand sequences that grow quickly (the 'parasites'), which are the sequences that are typically identified in phage display screens published to date. A similar collapse was observed in other libraries. Using Illumina and Ion Torrent sequencing and multiple biological replicates of amplification of Ph.D.-7 library, we identified a focused population of 770 'parasites'. In all, 197 sequences from this population have been identified in literature reports that used Ph.D.-7 library. Many of these enriched sequences have confirmed function (e.g. target binding capacity). The bias in the literature, thus, can be viewed as a selection with two different selection pressures: (i) target-binding selection, and (ii) amplification-induced selection. Enrichment of parasitic sequences could be minimized if amplification bias is removed. Here, we demonstrate that emulsion amplification in libraries of ∼ 10(6) diverse clones prevents the biased selection of parasitic clones.
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Read under generation 80e0d062 · epoch 390. Bibliography from PubMed, PubMed Central and OpenAlex; grants from NIH RePORTER; trial links from ClinicalTrials.gov; estimates, votes and beliefs from the OpenQuestion graph.