Evidence map›Paper›PMID 37845769›Full record

ArticleGenome biology2023

MalariaSED: a deep learning framework to decipher the regulatory contributions of noncoding variants in malaria parasites.

Chengqi Wang, Yibo Dong, Chang Li, Jenna Oberstaller, Min Zhang, Justin Gibbons, Camilla Valente Pires, Mianli Xiao, Lei Zhu, Rays H Y Jiang and 6 more

Abstract read
PubMed Full text at PMC Publisher
In one paragraph

Article in Genome biology, 2023. 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
–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

1 citing paper in PubMed.

  1. Pf8: an open dataset ofWellcome open research · 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

16 authors.

Chengqi WangCenter for Global Health and Infectious Diseases Research and USF Genomics Program, College of Public Health, University of South Florida, Tampa, FL, USA. chengqi@usf.edu.
Yibo DongCenter for Global Health and Infectious Diseases Research and USF Genomics Program, College of Public Health, University of South Florida, Tampa, FL, USA.
Chang LiCenter for Global Health and Infectious Diseases Research and USF Genomics Program, College of Public Health, University of South Florida, Tampa, FL, USA.
Jenna OberstallerCenter for Global Health and Infectious Diseases Research and USF Genomics Program, College of Public Health, University of South Florida, Tampa, FL, USA.
Min ZhangCenter for Global Health and Infectious Diseases Research and USF Genomics Program, College of Public Health, University of South Florida, Tampa, FL, USA.
Justin GibbonsCenter for Global Health and Infectious Diseases Research and USF Genomics Program, College of Public Health, University of South Florida, Tampa, FL, USA.
Camilla Valente PiresCenter for Global Health and Infectious Diseases Research and USF Genomics Program, College of Public Health, University of South Florida, Tampa, FL, USA.
Mianli XiaoCenter for Global Health and Infectious Diseases Research and USF Genomics Program, College of Public Health, University of South Florida, Tampa, FL, USA.
Lei ZhuSchool of Biological Sciences, Nanyang Technological University, Singapore, Singapore.
Rays H Y JiangCenter for Global Health and Infectious Diseases Research and USF Genomics Program, College of Public Health, University of South Florida, Tampa, FL, USA.
Kami KimDepartment of Internal Medicine, Morsani College of Medicine, Tampa, FL, USA.
Jun MiaoDepartment of Internal Medicine, Morsani College of Medicine, Tampa, FL, USA.
Thomas D OttoSchool of Infection & Immunity, MVLS, University of Glasgow, Glasgow, UK.
Liwang CuiDepartment of Internal Medicine, Morsani College of Medicine, Tampa, FL, USA.
John H AdamsCenter for Global Health and Infectious Diseases Research and USF Genomics Program, College of Public Health, University of South Florida, Tampa, FL, USA.
Xiaoming LiuCenter for Global Health and Infectious Diseases Research and USF Genomics Program, College of Public Health, University of South Florida, Tampa, FL, USA.

Funding

Southeast Asia Malaria Research CenterU19AI089672 · NIAID · UNIVERSITY OF SOUTH FLORIDA · PI CUI, LIWANG · 2010 to 2023
$28.9M
Chemogenomic Profiling of Plasmodium Falciparum Responses and ResistanceR01AI117017 · NIAID · UNIVERSITY OF SOUTH FLORIDA · PI ADAMS, JOHN H · 2015 to 2025
$6.9M
NIAID NIH HHS R01 AI117017NIAID NIH HHS U19 AI089672
6 · The paper itself

Abstract

Malaria remains one of the deadliest infectious diseases. Transcriptional regulation effects of noncoding variants in this unusual genome of malaria parasites remain elusive. We developed a sequence-based, ab initio deep learning framework, MalariaSED, for predicting chromatin profiles in malaria parasites. The MalariaSED performance was validated by published ChIP-qPCR and TF motifs results. Applying MalariaSED to ~ 1.3 million variants shows that geographically differentiated noncoding variants are associated with parasite invasion and drug resistance. Further analysis reveals chromatin accessibility changes at Plasmodium falciparum rings are partly associated with artemisinin resistance. MalariaSED illuminates the potential functional roles of noncoding variants in malaria parasites.

Indexed as

AntimalarialsDeep LearningMalariaMalaria, FalciparumParasitesAnimalsChromatinDrug ResistanceHumansPlasmodium falciparumProtozoan ProteinsAntimalarialsChromatinProtozoan Proteins

Identifiers

PMID37845769
PMCPMC10577899

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.