Publications by authors named "Thomas D Otto"

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Phenotypic screens reveal Plasmodium falciparum genetic factors associated with infection of sickle-trait cells.
Camilla V Pires, Jenna Oberstaller, Chengqi Wang, Justin Gibbons, Chiara Micchelli, Thomas D Otto

Blood Cells Mol Dis· November 2025

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Spatial transcriptomics elucidates localized immune responses in atherosclerotic coronary artery.
Joana Campos, Jack L McMurray, Michelangelo Certo, Ketaki Hardikar, Chris Morse, Thomas D Otto

EMBO Mol Med· October 2025

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Exploring homology detection via k-means clustering of proteins embedded with a large language model.
Thomas Minotto, Antoine Claessens, Thomas D Otto

Bioinformatics· October 2025

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PROS1 released by lung basal cells limits inflammation in epithelial and monocytes during SARS-CoV-2 infection.
Theodoros Simakou, Agnieszka M Szemiel, Lucy MacDonald, Karen Kerr, Domenico Somma, Thomas D Otto

Discov Immunol· September 2025

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scRNA-seq reveals elevated interferon responses and TNF-α signaling via NFkB in monocytes in children with uncomplicated malaria.
Collins M Morang'a, Riley S Drake, Vincent N Miao, Nancy K Nyakoe, Dominic S Y Amuzu, Thomas D Otto

Exp Biol Med (Maywood)· May 2025

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RNAcare: integrating clinical data with transcriptomic evidence using rheumatoid arthritis as a case study.
Mingcan Tang, William Haese-Hill, Fraser Morton, Carl Goodyear, Duncan Porter, Thomas D Otto

BMC Med Genomics· May 2025

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TrAGEDy-trajectory alignment of gene expression dynamics.
Ross F Laidlaw, Emma M Briggs, Keith R Matthews, Amir Madany Mamlouk, Richard McCulloch, Thomas D Otto

Bioinformatics· March 2025

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Supersaturation mutagenesis reveals adaptive rewiring of essential genes among malaria parasites.
Jenna Oberstaller, Shulin Xu, Deboki Naskar, Min Zhang, Chengqi Wang, Thomas D Otto

Science· February 2025

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paraCell: a novel software tool for the interactive analysis and visualization of standard and dual host-parasite single-cell RNA-seq data.
Edward Agboraw, William Haese-Hill, Franziska Hentzschel, Emma Briggs, Dana Aghabi, Thomas D Otto

Nucleic Acids Res· February 2025

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Identification of novel PfEMP1 variants containing domain cassettes 11, 15 and 8 that mediate the Plasmodium falciparum virulence-associated rosetting phenotype.
Florence E McLean, Brian R Omondi, Nouhoum Diallo, Stanley Otoboh, Carolyne Kifude, Thomas D Otto

PLoS Pathog· January 2025

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Spatially resolved single-cell atlas unveils a distinct cellular signature of fatal lung COVID-19 in a Malawian population.
James Nyirenda, Olympia M Hardy, João Da Silva Filho, Vanessa Herder, Charalampos Attipa, Thomas D Otto

Nat Med· December 2024

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Synovial tissue myeloid dendritic cell subsets exhibit distinct tissue-niche localization and function in health and rheumatoid arthritis.
Lucy MacDonald, Aziza Elmesmari, Domenico Somma, Jack Frew, Clara Di Mario, Thomas D Otto

Immunity· December 2024

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Genetic factors regulating Plasmodium falciparum gametocytogenesis identified by phenotypic screens.
Camilla V Pires, Jyotsna Chawla, Lauriane Sollelis, Jenna Oberstaller, Min Zhang, Thomas D Otto

Sci Rep· December 2024

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Annotation and visualization of parasite, fungi and arthropod genomes with Companion.
William Haese-Hill, Kathryn Crouch, Thomas D Otto

Nucleic Acids Res· July 2024

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Sterile protection against malaria by repeated blood stage infection in the monkey model.
Nicanor Obaldía, Joao Luiz Da Silva Filho, Marlon Núñez, Katherine A Glass, Tate Oulton, Thomas D Otto

Life Sci Alliance· March 2024

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A novel computational pipeline for gene expression augments the discovery of changes in the transcriptome during transition from in vivo to short-term in vitro culture.
Clare Andradi-Brown, Jan Stephan Wichers-Misterek, Heidrun von Thien, Yannick D Höppner, Judith A M Scholz, Thomas D Otto

Elife· January 2024

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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, Thomas D Otto

Genome Biol· October 2023

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A novel Modulator of Ring Stage Translation (MRST) gene alters artemisinin sensitivity in .
Caroline Simmons, Justin Gibbons, Chengqi Wang, Camilla Valente Pires, Min Zhang, Thomas D Otto

mSphere· August 2023

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Double-negative-2 B cells are the major synovial plasma cell precursor in rheumatoid arthritis.
Elinor Wing, Catherine Sutherland, Katherine Miles, David Gray, Carl S Goodyear, Thomas D Otto

Front Immunol· August 2023

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Author Correction: Cyclin-dependent kinase 12 is a drug target for visceral leishmaniasis.
Susan Wyllie, Michael Thomas, Stephen Patterson, Sabrinia Crouch, Manu De Rycker, Thomas D Otto, Fabio Zuccotto

Nature· July 2023

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From contigs towards chromosomes: automatic improvement of long read assemblies (ILRA).
José Luis Ruiz, Susanne Reimering, Juan David Escobar-Prieto, Nicolas M B Brancucci, Diego F Echeverry, Thomas D Otto

Brief Bioinform· July 2023

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Chemogenomic Profiling of a Plasmodium falciparum Transposon Mutant Library Reveals Shared Effects of Dihydroartemisinin and Bortezomib on Lipid Metabolism and Exported Proteins.
Camilla Valente Pires, Jenna Oberstaller, Chengqi Wang, Debora Casandra, Min Zhang, Thomas D Otto

Microbiol Spectr· June 2023

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Phenotypic Screens Identify Genetic Factors Associated with Gametocyte Development in the Human Malaria Parasite Plasmodium falciparum.
Jyotsna Chawla, Ilana Goldowitz, Jenna Oberstaller, Min Zhang, Camilla Valente Pires, Thomas D Otto

Microbiol Spectr· June 2023

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The exception that proves the rule: Virulence gene expression at the onset of Plasmodium falciparum blood stage infections.
Jan Stephan Wichers-Misterek, Ralf Krumkamp, Jana Held, Heidrun von Thien, Irene Wittmann, Thomas D Otto

PLoS Pathog· June 2023

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Profiling the bloodstream form and procyclic form cell cycle using single-cell transcriptomics.
Emma M Briggs, Catarina A Marques, Guy R Oldrieve, Jihua Hu, Thomas D Otto

Elife· May 2023

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