Evidence map›Paper›PMID 37577562›Full record

ArticlebioRxiv : the preprint server for biology2023

Efficient encoding of large antigenic spaces by epitope prioritization with Dolphyn.

Anna-Maria Liebhoff, Thiagarajan Venkataraman, William R Morgenlander, Miso Na, Tomasz Kula, Kathleen Waugh, Charles Morrison, Marian Rewers, Randy Longman, June Round and 4 more

Abstract readPreprint
PubMed Full text at PMC Publisher
In one paragraph

Article in bioRxiv : the preprint server for biology, 2023. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Not yet cited in PubMed.

0numbers the graph read from it
0cells of the map it votes in
0citing papers in PubMed
–field-weighted citation impact
1 · What the graph read from it

What it found

Each row is one number read from the abstract, on the scale the paper reported it, with its interval. Left of the dashed line favours the treatment, right favours the comparator. Under each row is the sentence it came from. New to these charts? A ten-minute tutorial.

The abstract states no effect estimate the extractor could read, or names no intervention and outcome on the map, so this paper lights no cell and moves no belief. It is still indexed, cited and linked below.

2 · The registry

The trial behind it

Trials whose registry record cites this paper, or whose number appears in the abstract. A trial that started after this paper was published is citing it as background, not reporting it.

Neither the registry nor the abstract names a trial number. If this is a trial report, that itself is worth knowing.

3 · Its place in the literature

Who cites it

0 citing papers in PubMed.

No citing paper in PubMed yet.

4 · The record

Corrections and comments

5 · Who and what money

Authors and funding

14 authors.

Anna-Maria LiebhoffDepartment of Computer Science, Johns Hopkins University, Baltimore, MD, USA.
Thiagarajan VenkataramanDivision of Immunology, Department of Pathology, Johns Hopkins University, Baltimore, MD, USA.
William R MorgenlanderDivision of Immunology, Department of Pathology, Johns Hopkins University, Baltimore, MD, USA.
Miso NaDivision of Immunology, Department of Pathology, Johns Hopkins University, Baltimore, MD, USA.
Tomasz KulaDepartment of Genetics, Harvard Medical School, Boston, MA, USA.
Kathleen WaughBarbara Davis Center for Diabetes, University of Colorado Denver, Aurora, Colorado, USA.
Charles MorrisonBehavioral, Clinical and Epidemiologic Sciences, FHI 360, Durham, NC, USA.
Marian RewersBarbara Davis Center for Diabetes, University of Colorado Denver, Aurora, Colorado, USA.
Randy LongmanJill Roberts Institute for Research in IBD, Division of Gastroenterology and Hepatology, Department of Medicine, Weill Cornell Medicine, New York, NY, USA.
June RoundDepartment of Pathology, Division of Microbiology and Immunology, University of Utah School of Medicine, Salt Lake City, UT, USA.
Stephen ElledgeDepartment of Genetics, Harvard Medical School, Boston, MA, USA.
Ingo RuczinskiDepartment of Biostatistics, Johns Hopkins University, Baltimore, MD, USA.
Ben LangmeadDepartment of Computer Science, Johns Hopkins University, Baltimore, MD, USA.
H Benjamin LarmanDivision of Immunology, Department of Pathology, Johns Hopkins University, Baltimore, MD, USA.

Funding

Medical Scientist Training ProgramT32GM136577 · NIGMS · JOHNS HOPKINS UNIVERSITY · PI ANDREA L COX · 2020 to 2026
$13.4M
University of Colorado Anschutz Medical Campus DRCP30DK116073 · NIDDK · UNIVERSITY OF COLORADO DENVER · PI LORI SUSSEL · 2020 to 2026
$10.8M
Natural History of Pre-Diabetic Autoimmunity (DAISY)R01DK032493 · NIDDK · UNIVERSITY OF COLORADO DENVER · PI REWERS, MARIAN J · 1986 to 2024
$9.3M
Natural History of Pre-diabetic Autoimmunity (DAISY)R37DK032493 · NIDDK · UNIVERSITY OF COLORADO DENVER · PI REWERS, MARIAN J · 2001 to 2010
$8.0M
Methods for sequencing data analysis and archive-scale data science - RenewalR35GM139602 · NIGMS · JOHNS HOPKINS UNIVERSITY · PI Benjamin Thomas Langmead · 2021 to 2026
$5.0M
Design and Analysis of Displayed PeptidomesR01GM136724 · NIGMS · JOHNS HOPKINS UNIVERSITY · PI LARMAN, HARRY BENJAMIN, RUCZINSKI, INGO · 2020 to 2023
$1.9M
NIDDK NIH HHS P30 DK116073NIDDK NIH HHS R01 DK032493NIDDK NIH HHS R37 DK032493NIGMS NIH HHS R01 GM136724NIGMS NIH HHS R35 GM139602NIGMS NIH HHS T32 GM136577
6 · The paper itself

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

Indexed as

antibody profilinggut phagespeptides librariesPhIP-Seqpublic epitopes

Identifiers

PMID37577562
PMCPMC10418057

What OpenQuestion holds

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LicenceCC BY
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Registered trials

None linked

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.