Evidence map›Paper›PMID 37055610›Full record

ArticleNature microbiology2023

Babesia duncani multi-omics identifies virulence factors and drug targets.

Pallavi Singh, Stefano Lonardi, Qihua Liang, Pratap Vydyam, Eleonora Khabirova, Tiffany Fang, Shalev Gihaz, Jose Thekkiniath, Muhammad Munshi, Steven Abel and 17 more

Open access · hybridAbstract read
In one paragraph

Article in Nature microbiology, 2023. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 25 papers, 1 of them a synthesis that pooled it.

0numbers the graph read from it
0cells of the map it votes in
25citing papers in PubMed, 1 pooled it
10.7field-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

25 citing papers in PubMed, 1 synthesis or guideline pooled it, 38 citations in OpenAlex.

  1. Pooled it
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  9. A propidium iodide-basedAntimicrobial agents and chemotherapy · 2025
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  12. Research progress on diagnostic techniques for differentFrontiers in cellular and infection microbiology · 2025
    Review
  13. Insights into the evolution, virulence and speciation ofEmerging microbes & infections · 2024
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  15. Antimicrobial agents and chemotherapy · 2024
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  16. Review
  17. Transfection ofBio-protocol · 2024
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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

27 authors at 6 institutions in 4 countries.

Pallavi Singh *Department of Internal Medicine, Section of Infectious Diseases, Yale School of Medicine, New Haven, CT, USA.ORCID http://orcid.org/0000-0003-2318-5960
Stefano Lonardi *Department of Computer Science and Engineering, University of California, Riverside, CA, USA. stelo@cs.ucr.edu.ORCID http://orcid.org/0000-0002-2696-7274
Qihua LiangDepartment of Computer Science and Engineering, University of California, Riverside, CA, USA.
Pratap VydyamDepartment of Internal Medicine, Section of Infectious Diseases, Yale School of Medicine, New Haven, CT, USA.
Eleonora KhabirovaDepartment of Statistics, University of California, Riverside, CA, USA.ORCID http://orcid.org/0000-0002-5891-6789
Tiffany FangDepartment of Internal Medicine, Section of Infectious Diseases, Yale School of Medicine, New Haven, CT, USA.ORCID http://orcid.org/0000-0002-1844-2101
Shalev GihazDepartment of Internal Medicine, Section of Infectious Diseases, Yale School of Medicine, New Haven, CT, USA.ORCID http://orcid.org/0000-0001-7292-0808
Jose ThekkiniathDepartment of Internal Medicine, Section of Infectious Diseases, Yale School of Medicine, New Haven, CT, USA.ORCID http://orcid.org/0000-0001-6026-1737
Muhammad MunshiDepartment of Internal Medicine, Section of Infectious Diseases, Yale School of Medicine, New Haven, CT, USA.
Steven AbelDepartment of Molecular, Cell and Systems Biology, University of California, Riverside, CA, USA.
Loic CiampossinDepartment of Molecular, Cell and Systems Biology, University of California, Riverside, CA, USA.
Gayani BatugedaraDepartment of Molecular, Cell and Systems Biology, University of California, Riverside, CA, USA.
Mohit GuptaDepartment of Molecular, Cell and Systems Biology, University of California, Riverside, CA, USA.ORCID http://orcid.org/0000-0002-5082-9875
Xueqing Maggie LuDepartment of Molecular, Cell and Systems Biology, University of California, Riverside, CA, USA.
Todd LenzDepartment of Molecular, Cell and Systems Biology, University of California, Riverside, CA, USA.ORCID http://orcid.org/0000-0001-6209-7061
Sakshar ChakravartyDepartment of Computer Science and Engineering, University of California, Riverside, CA, USA.ORCID http://orcid.org/0009-0002-6002-5229
Emmanuel CornillotInstitut de Biologie Computationnelle (IBC), and Institut de Recherche en Cancérologie de Montpellier (IRCM - INSERM U1194), Institut régional du Cancer Montpellier (ICM) and Université de Montpellier, Montpellier, France.ORCID http://orcid.org/0000-0002-1202-1162
Yangyang HuDepartment of Computer Science and Engineering, University of California, Riverside, CA, USA.
Wenxiu MaDepartment of Statistics, University of California, Riverside, CA, USA.ORCID http://orcid.org/0000-0003-4097-1621
Luis Miguel GonzalezParasitology Reference and Research Laboratory, National Centre for Microbiology, Instituto de Salud Carlos III, Majadahonda, Madrid, Spain.ORCID http://orcid.org/0000-0002-9107-2450
Sergio SánchezReference and Research Laboratory on Food and Waterborne Bacterial Infections, National Centre for Microbiology, Instituto de Salud Carlos III, Majadahonda, Madrid, Spain.ORCID http://orcid.org/0000-0001-9903-6203
Karel EstradaUnidad Universitaria de Secuenciación Masiva y Bioinformática, Instituto de Biotecnología, Universidad Nacional Autónoma de México, Cuernavaca, México.
Alejandro Sánchez-FloresUnidad Universitaria de Secuenciación Masiva y Bioinformática, Instituto de Biotecnología, Universidad Nacional Autónoma de México, Cuernavaca, México.ORCID http://orcid.org/0000-0003-0476-3139
Estrella MonteroParasitology Reference and Research Laboratory, National Centre for Microbiology, Instituto de Salud Carlos III, Majadahonda, Madrid, Spain.ORCID http://orcid.org/0000-0002-3852-960X
Omar S HarbDepartment of Biology, University of Pennsylvania, Philadelphia, PA, USA.ORCID http://orcid.org/0000-0003-4446-6200
Karine G Le RochDepartment of Molecular, Cell and Systems Biology, University of California, Riverside, CA, USA. karinel@ucr.edu.ORCID http://orcid.org/0000-0002-4862-9292
Choukri Ben MamounDepartment of Internal Medicine, Section of Infectious Diseases, Yale School of Medicine, New Haven, CT, USA. choukri.benmamoun@yale.edu.ORCID http://orcid.org/0000-0001-5028-1400
University of California, Riverside · USYale University · USInstituto de Salud Carlos III · ESUniversidad Nacional Autónoma de México · MXInserm · FRUniversity of Pennsylvania · US

Funding

Chromatin structure and control of gene expression in the human malaria parasiteR01AI136511 · NIAID · UNIVERSITY OF CALIFORNIA RIVERSIDE · PI LE ROCH, KARINE GAELLE · 2018 to 2022
$3.4M
Rapid response for pandemics: single cell sequencing and deep learning to predict antibody sequences against an emerging antigenR01AI169543 · NIAID · KECK GRADUATE INST OF APPLIED LIFE SCIS · PI HERNANDEZ, JENIFFER BERTHA, LONARDI, STEFANO · 2021 to 2023
$3.1M
RAPs-mediated post-transcriptional control in Apicomplexan parasitesR01AI142743 · NIAID · UNIVERSITY OF CALIFORNIA RIVERSIDE · PI LE ROCH, KARINE GAELLE · 2018 to 2022
$2.8M
Development of endochin-like quinolones for babesiosis therapyR01AI123321 · NIAID · YALE UNIVERSITY · PI BEN MAMOUN, CHOUKRI · 2017 to 2020
$2.7M
An antigen-detection assay to diagnose Babesia microti infectionR44AI136118 · NIAID · L2 DIAGNOSTICS, LLC · PI LEDIZET, MICHEL · 2020 to 2022
$2.1M
Function and Inhibition of Plasmodium Lipid DecarboxylasesR01AI097218 · NIAID · YALE UNIVERSITY · PI BEN MAMOUN, CHOUKRI · 2012 to 2016
$2.0M
Synthesis and Study of Complex Antiproliferative and Antimalarial Natural ProductsR01GM110506 · NIGMS · YALE UNIVERSITY · PI HERZON, SETH B. · 2015 to 2018
$1.2M
Evolution of the 3D chromatin structure in apicomplexan parasitesR21AI142506 · NIAID · UNIVERSITY OF CALIFORNIA RIVERSIDE · PI LE ROCH, KARINE GAELLE · 2019 to 2020
$479k
An antigen-detection assay to diagnose Babesia microti infectionR43AI136118 · NIAID · L2 DIAGNOSTICS, LLC · PI LEDIZET, MICHEL · 2018 to 2018
$300k
NIAID NIH HHS R01 AI097218NIAID NIH HHS R01 AI123321NIAID NIH HHS R01 AI136511NIAID NIH HHS R01 AI142743NIAID NIH HHS R01 AI169543NIAID NIH HHS R21 AI142506NIAID NIH HHS R43 AI136118NIAID NIH HHS R44 AI136118NIGMS NIH HHS R01 GM110506
6 · The paper itself

Abstract

Babesiosis is a malaria-like disease in humans and animals that is caused by Babesia species, which are tick-transmitted apicomplexan pathogens. Babesia duncani causes severe to lethal infection in humans, but despite the risk that this parasite poses as an emerging pathogen, little is known about its biology, metabolic requirements or pathogenesis. Unlike other apicomplexan parasites that infect red blood cells, B. duncani can be continuously cultured in vitro in human erythrocytes and can infect mice resulting in fulminant babesiosis and death. We report comprehensive, detailed molecular, genomic, transcriptomic and epigenetic analyses to gain insights into the biology of B. duncani. We completed the assembly, 3D structure and annotation of its nuclear genome, and analysed its transcriptomic and epigenetics profiles during its asexual life cycle stages in human erythrocytes. We used RNA-seq data to produce an atlas of parasite metabolism during its intraerythrocytic life cycle. Characterization of the B. duncani genome, epigenome and transcriptome identified classes of candidate virulence factors, antigens for diagnosis of active infection and several attractive drug targets. Furthermore, metabolic reconstitutions from genome annotation and in vitro efficacy studies identified antifolates, pyrimethamine and WR-99210 as potent inhibitors of B. duncani to establish a pipeline of small molecules that could be developed as effective therapies for the treatment of human babesiosis.

Indexed as

BabesiaBabesiosisTicksAnimalsErythrocytesHumansMiceMultiomics

Identifiers

PMID37055610
PMCPMC10159843
OpenAlexW4365446654

What OpenQuestion holds

Textmetadata
LicenceCC BY
Read underepoch 390

Registered trials

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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.