Evidence map›Paper›PMID 34991452›Full record

ArticleBMC bioinformatics2022

STRIDE: a command-line HMM-based identifier and sub-classifier of Plasmodium falciparum RIFIN and STEVOR variant surface antigen families.

Albert E Zhou, Zalak V Shah, Katie R Bradwell, James B Munro, Andrea A Berry, David Serre, Shannon Takala-Harrison, Timothy D O'Connor, Joana C Silva, Mark A Travassos

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

Article in BMC bioinformatics, 2022. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 1 paper.

0numbers the graph read from it
0cells of the map it votes in
1citing papers in PubMed
0.4field-weighted citation impact, top 39% 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

1 citing paper in PubMed, 2 citations in OpenAlex.

  1. Diamonds in the rif: Alignment-free comparative genomics analysis reveals strain-transcendent Plasmodium falciparum antigens amidst extensive genetic diversity.Infection, genetics and evolution : journal of molecular epidemiology and evolutionary genetics in infectious diseases · 2025
    Article
4 · The record

Corrections and comments

PubMed lists nothing against this paper. Absence here is not a guarantee, only a check that was made.

5 · Who and what money

Authors and funding

10 authors at 1 institution in 1 country.

Albert E ZhouMalaria Research Program, Center for Vaccine Development and Global Health, University of Maryland School of Medicine, Baltimore, MD, USA.
Zalak V ShahMalaria Research Program, Center for Vaccine Development and Global Health, University of Maryland School of Medicine, Baltimore, MD, USA.
Katie R BradwellInstitute for Genome Sciences, University of Maryland School of Medicine, Baltimore, MD, USA.
James B MunroInstitute for Genome Sciences, University of Maryland School of Medicine, Baltimore, MD, USA.
Andrea A BerryMalaria Research Program, Center for Vaccine Development and Global Health, University of Maryland School of Medicine, Baltimore, MD, USA.
David SerreInstitute for Genome Sciences, University of Maryland School of Medicine, Baltimore, MD, USA.
Shannon Takala-HarrisonMalaria Research Program, Center for Vaccine Development and Global Health, University of Maryland School of Medicine, Baltimore, MD, USA.
Timothy D O'ConnorInstitute for Genome Sciences, University of Maryland School of Medicine, Baltimore, MD, USA.
Joana C SilvaInstitute for Genome Sciences, University of Maryland School of Medicine, Baltimore, MD, USA.
Mark A TravassosMalaria Research Program, Center for Vaccine Development and Global Health, University of Maryland School of Medicine, Baltimore, MD, USA. mtravass@som.umaryland.edu.ORCID http://orcid.org/0000-0002-6045-3322
University of Maryland, Baltimore · US

Funding

Technology CoreU19AI110820 · NIAID · UNIVERSITY OF MARYLAND BALTIMORE · PI WHITE, OWEN R · 2014 to 2023
$36.5M
Genome-wide sieve analysis and immunological validation to identify targets of protective efficacy in field trials of a whole-organism malaria vaccineR01AI141900 · NIAID · UNIVERSITY OF MARYLAND BALTIMORE · PI CARNEIRO DA SILVA, JOANA · 2019 to 2023
$3.9M
Variant surface antigens in cerebral malaria pathogenesisR01HL130750 · NHLBI · UNIVERSITY OF MARYLAND BALTIMORE · PI FISHER, STEVEN A., PLOWE, CHRISTOPHER V. · 2015 to 2018
$2.1M
Malaria variant surface antigen expression and vulnerability to disease in Malian children with Hemoglobin C traitR01HL146377 · NHLBI · UNIVERSITY OF MARYLAND BALTIMORE · PI TRAVASSOS, MARK A · 2019 to 2023
$1.9M
Protein microarray antibody responses to P. falciparum in a human challenge modelK23AI125720 · NIAID · UNIVERSITY OF MARYLAND BALTIMORE · PI BERRY, ANDREA · 2017 to 2021
$915k
The role of RIFINs and their interaction with blood type in vulnerability to severe malaria in Malian childrenF30HL146095 · NHLBI · UNIVERSITY OF MARYLAND BALTIMORE · PI ZHOU, ALBERT E · 2019 to 2021
$126k
NHLBI NIH HHS F30 HL146095NHLBI NIH HHS R01 HL130750NHLBI NIH HHS R01 HL146377NIAID NIH HHS K23 AI125720NIAID NIH HHS R01 AI141900NIAID NIH HHS U19 AI110820NIH HHS 1F30HL146095-01A1NIH HHS K23AI125720NIH HHS R01AI141900NIH HHS R01HL146377NIH HHS U19AI110820
6 · The paper itself

Abstract

backgroundRIFINs and STEVORs are variant surface antigens expressed by P. falciparum that play roles in severe malaria pathogenesis and immune evasion. These two highly diverse multigene families feature multiple paralogs, making their classification challenging using traditional bioinformatic methods.

resultsSTRIDE (STevor and RIfin iDEntifier) is an HMM-based, command-line program that automates the identification and classification of RIFIN and STEVOR protein sequences in the malaria parasite Plasmodium falciparum. STRIDE is more sensitive in detecting RIFINs and STEVORs than available PFAM and TIGRFAM tools and reports RIFIN subtypes and the number of sequences with a FHEYDER amino acid motif, which has been associated with severe malaria pathogenesis.

conclusionsSTRIDE will be beneficial to malaria research groups analyzing genome sequences and transcripts of clinical field isolates, providing insight into parasite biology and virulence.

Indexed as

Malaria, FalciparumPlasmodium falciparumAntigens, ProtozoanAntigens, SurfaceErythrocytesHumansProtozoan ProteinsAntigens, ProtozoanAntigens, SurfaceProtozoan ProteinsBioinformaticsHidden Markov modelsMalariaPlasmodium falciparumRIFINSTEVOR

Identifiers

PMID34991452
PMCPMC8733436
OpenAlexW4205797579

What OpenQuestion holds

Textmetadata
LicenceCC BY
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.