Evidence map›Paper›PMID 31048489›Full record

ArticleScience (New York, N.Y.)2019

Structural topology defines protective CD8

Gaurav D Gaiha, Elizabeth J Rossin, Jonathan Urbach, Christian Landeros, David R Collins, Chioma Nwonu, Itai Muzhingi, Melis N Anahtar, Olivia M Waring, Alicja Piechocka-Trocha and 8 more

Open access · greenAbstract read
PubMed Full text at PMC Publisher
In one paragraph

Article in Science (New York, N.Y.), 2019. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 112 papers, 3 of them syntheses that pooled it.

0numbers the graph read from it
0cells of the map it votes in
112citing papers in PubMed, 3 pooled it
9.6field-weighted citation impact, top 1% of its field
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

112 citing papers in PubMed, 3 syntheses or guidelines pooled it, 146 citations in OpenAlex.

  1. Pooled it
  2. Pooled it
  3. Pooled it
  4. Trial
  5. Trial
  6. Article
  7. Article
  8. Renaissance of antiviral CD8Nature reviews. Immunology · 2026
    Review
  9. NK-like and networked CD8bioRxiv : the preprint server for biology · 2026
    Article
  10. Review
  11. Review
  12. Article
  13. Review
  14. Review
  15. Article
  16. Article
  17. Article
  18. Article
  19. Article
  20. Review

52 more citing papers are in PubMed but not listed here.

4 · The record

Corrections and comments

5 · Who and what money

Authors and funding

18 authors at 4 institutions in 1 country.

Gaurav D Gaiha *Ragon Institute of MGH, MIT and Harvard, Cambridge, MA 02139, USA.ORCID 0000-0001-6875-4472
Elizabeth J Rossin *The Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA.ORCID 0000-0002-0052-9575
Jonathan UrbachRagon Institute of MGH, MIT and Harvard, Cambridge, MA 02139, USA.ORCID 0000-0003-0597-2848
Christian LanderosRagon Institute of MGH, MIT and Harvard, Cambridge, MA 02139, USA.ORCID 0000-0002-6529-253X
David R CollinsRagon Institute of MGH, MIT and Harvard, Cambridge, MA 02139, USA.ORCID 0000-0001-7903-346X
Chioma NwonuRagon Institute of MGH, MIT and Harvard, Cambridge, MA 02139, USA.
Itai MuzhingiRagon Institute of MGH, MIT and Harvard, Cambridge, MA 02139, USA.
Melis N AnahtarRagon Institute of MGH, MIT and Harvard, Cambridge, MA 02139, USA.ORCID 0000-0003-0309-368X
Olivia M WaringRagon Institute of MGH, MIT and Harvard, Cambridge, MA 02139, USA.ORCID 0000-0001-9261-0516
Alicja Piechocka-TrochaRagon Institute of MGH, MIT and Harvard, Cambridge, MA 02139, USA.ORCID 0000-0002-1547-524X
Michael WaringRagon Institute of MGH, MIT and Harvard, Cambridge, MA 02139, USA.
Daniel P WorrallRagon Institute of MGH, MIT and Harvard, Cambridge, MA 02139, USA.ORCID 0000-0002-7760-9848
Musie S GhebremichaelRagon Institute of MGH, MIT and Harvard, Cambridge, MA 02139, USA.
Ruchi M NewmanRagon Institute of MGH, MIT and Harvard, Cambridge, MA 02139, USA.
Karen A PowerRagon Institute of MGH, MIT and Harvard, Cambridge, MA 02139, USA.
Todd M AllenRagon Institute of MGH, MIT and Harvard, Cambridge, MA 02139, USA.
James ChodoshDepartment of Ophthalmology, Massachusetts Eye and Ear, Boston, MA 02114, USA.ORCID 0000-0002-7463-1599
Bruce D WalkerRagon Institute of MGH, MIT and Harvard, Cambridge, MA 02139, USA. bwalker@mgh.harvard.edu.ORCID 0000-0001-6122-9245
Ragon Institute of MGH, MIT and Harvard · USHoward Hughes Medical Institute · USBroad Institute · USMassachusetts Eye and Ear Infirmary · US

Funding

Viral Sequencing CoreU19AI067854 · NIAID · DUKE UNIVERSITY · PI CRUMP, JOHN ANDREW · 2006 to 2011
$290.5M
Support Component D/Vaccine Discovery, Concept to ClinicUM1AI100663 · NIAID · SCRIPPS RESEARCH INSTITUTE, THE · PI BAROUCH, DAN H. · 2012 to 2018
$131.5M
The impact of HIV viral diversity and cellular immunity on HIV pathogenesisP30AI060354 · NIAID · HARVARD UNIVERSITY (MEDICAL SCHOOL) · PI ROBERT A. PARKER · 2004 to 2026
$94.4M
Vaccine Adjuvant/ Delivery Systems CoreP01AI104715 · NIAID · MASSACHUSETTS GENERAL HOSPITAL · PI ALLEN, TODD M · 2013 to 2017
$12.3M
Howard Hughes Medical InstituteNIAID NIH HHS P01 AI104715NIAID NIH HHS P30 AI060354NIAID NIH HHS U19 AI067854NIAID NIH HHS UM1 AI100663
6 · The paper itself

Abstract

Mutationally constrained epitopes of variable pathogens represent promising targets for vaccine design but are not reliably identified by sequence conservation. In this study, we employed structure-based network analysis, which applies network theory to HIV protein structure data to quantitate the topological importance of individual amino acid residues. Mutation of residues at important network positions disproportionately impaired viral replication and occurred with high frequency in epitopes presented by protective human leukocyte antigen (

Indexed as

Acquired Immunodeficiency SyndromeAIDS VaccinesAllelesCD8-Positive T-LymphocytesConserved SequenceEpitopes, T-Lymphocytegag Gene Products, Human Immunodeficiency VirusHistocompatibility Antigens Class IHIV-1HLA-B AntigensHumansMutationProteomeVirus ReplicationAIDS VaccinesEpitopes, T-Lymphocytegag Gene Products, Human Immunodeficiency VirusHistocompatibility Antigens Class IHLA-B57 antigenHLA-B AntigensProteome

Identifiers

PMID31048489
PMCPMC6855781
OpenAlexW2943694132

What OpenQuestion holds

Textmetadata
LicenceTDM
Read underepoch 390

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.