The DOI matches its Crossref record; 1 of the 1 references it cites were found in a registry or an index.
Efficient encoding of large antigenic spaces by epitope prioritization with Dolphyn
Open accessPreprint — published as 10.1038/s41467-024-45601-8 · Paper page
Abstract
We investigated a relatively underexplored component of the gut-immune axis by profiling the antibody response to gut phages using Phage Immunoprecipitation Sequencing (PhIP-Seq). To enhance this approach, we developed Dolphyn, a novel method that uses machine learning to select peptides from protein sets and compresses the proteome through epitope-stitching. Dolphyn improves the fraction of gut phage library peptides bound by antibodies from 10% to 31% in healthy individuals, while also reducing the number of synthesized peptides by 78%. In our study on gut phages, we discovered that the immune system develops antibodies to bacteria-infecting viruses in the human gut, particularly E . coli -infecting Myoviridae . Cost-effective PhIP-Seq libraries designed with Dolphyn enable the assessment of a wider range of proteins in a single experiment, thus facilitating the study of the gut-immune axis.
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Highly accurate protein structure prediction with AlphaFold
Jumper, J., Evans, R., Pritzel, A., Green, T., Figurnov, M., Ronneberger, O., Tunyasuvunakool, K., Bates, R., Žídek, A., Potapenko, A., et al. (2021) · Nature · doi:10.1038/s41586-021-03819-2 · Cited by 43,764
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Research works printed but not linked: 18
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Metadata
- Authors
- Liebhoff, A.-M., Venkataraman, T., Morgenlander, W. R., Na, M., Kula, T., Waugh, K., Morrison, C., Rewers, M., Longman, R., Round, J., Elledge, S., Ruczinski, I., Langmead, B., & Larman, H. B.
- Affiliations
- Johns Hopkins University (US)
- Brigham and Women's Hospital (US)
- University of Colorado Denver (US)
- Family Health International 360 (US)
- Weill Cornell Medicine (US)
- University of Utah (US)
- Corresponding author
- Larman, H Benjamin
- ORCID
- Venue
- Nature Communications
- Publisher
- openRxiv
- Published
- 2023-07-31
- Volume
- 15
- Issue
- 1
- Pages
- 1577-1577
- ISSN
- 2041-1723 (ISSN-L)
- PMC
- PMC10881494
- OpenAlex
- W4391998003
- Cited by
- 10
- References
- 1
- Citations by year
- 2026: 3 · 2025: 4 · 2024: 3
- FWCI
- 1.36
- Type
- journal article
- Language
- en
- Open access
- gold
- doi.org
- Licence
- cc-by
- Locations
- Nature Communications (publishedVersion, cc-by)
- bioRxiv (Cold Spring Harbor Laboratory) (acceptedVersion, cc-by)
- PubMed Central (publishedVersion, cc-by)
- PubMed (publishedVersion)
- PubMed Central (submittedVersion, cc-by)
- RePEc: Research Papers in Economics (submittedVersion)
- DOAJ (DOAJ: Directory of Open Access Journals) (submittedVersion, cc-by-sa)
- Funders
- Howard Hughes Medical Institute
- Leona M. and Harry B. Helmsley Charitable Trust
- National Institutes of Health (DK032493)
- National Institute of General Medical Sciences (R01GM136724, GM136724, T32GM136577, R35GM139602)
- National Institute of Allergy and Infectious Diseases (UM1AI068613)
- National Institute of Diabetes and Digestive and Kidney Diseases (R01DK032493, R37DK032493, P30DK116073)
- Topics
- Life Sciences › Biochemistry, Genetics and Molecular Biology › Molecular Biology › vaccines and immunoinformatics approaches
- Life Sciences › Immunology and Microbiology › Virology › Bacteriophages and microbial interactions
- Physical Sciences › Chemistry › Spectroscopy › Advanced Proteomics Techniques and Applications
- Keywords
- phage immunoprecipitation sequencing, Myoviridae, gut-immune axis
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