TO
Thomas D. Otto
SoftwarebioinformaticsGenome, ProtozoanPlasmodium falciparummicrobiologyMalaria, FalciparummalariaMalariaTranscriptomeEvolution, Molecular
On Valency
published · living versionsW_26xzgw86·v1 · currentpublished
Assemblathon 2: evaluating de novo methods of genome assembly in three vertebrate species
with Keith R. Bradnam, Joseph N. Fass, Anton Alexandrov, Paul Baranay +86
1 version
Preprints & journals
183 papers in the corpus · 1999–2026Cell DiffErential Expression by Pooling (CellDEEP) highlights issues in differential gene expression in scRNA-seq.42909367 · Cheng, Yiyi, Kettlewell, Toby, Laidlaw, Ross F et al.2026 · 1 citationNAR genomics and bioinformatics. 2026;8(4):lqag128
Erratum for Pires et al., "Plasmodium falciparum leucine-rich repeat 5 disruption alters the transcription progression during asexual and sexual stage development".42644621 · Pires, Camilla V, Wang, Changqi C Q, Zhang, Min et al.2026 · 0 citationsmSphere. 2026;11(9):e0059226
The genome of the avian malaria parasite Haemoproteus majoris (lineage WW2) and its relationship to other Plasmodium species10.64898/2026.07.13.738139v2 · Bardil, A., Berthomieu, A., Dainat, J. et al.2026 · 0 citationsbioRxiv
BLASE: bulk linkage analysis for single cell experiments - teasing out the secrets of bulk transcriptomics with trajectory analysis.42781706 · McCluskey, Andrew, Kettlewell, Toby, Smith, Adrian M et al.2026 · 0 citationsBMC methods. 2026;3(1)
Plasmodium falciparum leucine-rich repeat 5 disruption alters the transcription progression during asexual and sexual stage development.42294623 · Pires, Camilla V, Wang, Chengqi C Q, Zhang, Min et al.2026 · 0 citationsmSphere. 2026;11(7):e0018626
Human Fibroblast-Myeloid Cell Tissue Atlas Across the Lungs, Synovium, Skin, and Heart.42223224 · MacDonald, Lucy, Apostolopoulou, Katerina, Hardy, Olympia et al.2026 · 1 citationArthritis & rheumatology (Hoboken, N.J.). 2026
Trypanosoma cruzi cell atlas as a single-cell resource for understanding parasite population heterogeneity and differentiation.42185256 · Laidlaw, Ross F, García-Sánchez, Marta, Da Silva Pacheco, Juliana et al.2026 · 10 citationsNature communications. 2026;17(1)
upsML: A high-accuracy machine learning classifier for predicting Plasmodium falciparum var gene upstream groups.41990100 · Pangilinan, Elcid Aaron, Quenu, Mathieu, Claessens, Antoine et al.2026 · 0 citationsPloS one. 2026;21(4):e0344557
ZINBGT: Exploratory Data Analysis of Single-Cell Transcriptomic Expression Using Mixture Models2604.09319v1 · Toby Kettlewell, Yiyi Cheng, Thomas D. Otto et al.2026 · 0 citationsarXiv
A partition-based spatial entropy for co-occurrence analysis with broad application.10.64898/2026.02.23.707425v1 · Otto, T., Nemri, A., Claessens, A. et al.2026 · 0 citationsbioRxiv
Synovial lining expressed mechanosensor PIEZO1 drives inflammation-permissive macrophage phenotypes and joint inflammation10.64898/2026.01.12.699005v1 · Simakou, T., Doohan, M., Huesa, C. et al.2026 · 1 citationbioRxiv
Exploring homology detection via k-means clustering of proteins embedded with a large language model.40857396 · Minotto, Thomas, Claessens, Antoine, Otto, Thomas D2025 · 1 citationBioinformatics (Oxford, England). 2025;41(10)
PROS1 released by lung basal cells limits inflammation in epithelial and monocytes during SARS-CoV-2 infection.40980495 · Simakou, Theodoros, Szemiel, Agnieszka M, MacDonald, Lucy et al.2025 · 2 citationsDiscovery immunology. 2025;4(1):kyaf012
Spatial transcriptomics elucidates localized immune responses in atherosclerotic coronary artery.40847214 · Campos, Joana, McMurray, Jack L, Certo, Michelangelo et al.2025 · 16 citationsEMBO molecular medicine. 2025;17(10):2827-2846
Phenotypic screens reveal Plasmodium falciparum genetic factors associated with infection of sickle-trait cells.40782493 · Pires, Camilla V, Oberstaller, Jenna, Wang, Chengqi et al.2025 · 0 citationsBlood cells, molecules & diseases. 2025;115:102951
upsAI: A high-accuracy machine learning classifier for predicting Plasmodium falciparum var gene upstream groups10.1101/2025.05.19.654848v1 · Pangilinan, E. A., Quenu, M., Claessens, A. et al.2025 · 1 citationbioRxiv
RNAcare: integrating clinical data with transcriptomic evidence using rheumatoid arthritis as a case study.40399884 · Tang, Mingcan, Haese-Hill, William, Morton, Fraser et al.2025 · 2 citationsBMC medical genomics. 2025;18(1):93
The dynamic transcriptome of Plasmodium malariae in the mosquito10.1101/2025.05.05.652270v1 · Ruiz, J. L., Diaz-Terenti, B., Lefevre, T. D. et al.2025 · 1 citationbioRxiv
Seasonal transcriptional profiling of malaria parasites using a new single-cell atlas of a Malian Plasmodium falciparum isolate10.1101/2025.04.14.648697v1 · Votborg-Novel, L., Kampmann, M., Carrasquilla, M. et al.2025 · 2 citationsbioRxiv
TrAGEDy-trajectory alignment of gene expression dynamics.40065693 · Laidlaw, Ross F, Briggs, Emma M, Matthews, Keith R et al.2025 · 10 citationsBioinformatics (Oxford, England). 2025;41(3)
paraCell: a novel software tool for the interactive analysis and visualization of standard and dual host-parasite single-cell RNA-seq data.39988320 · Agboraw, Edward, Haese-Hill, William, Hentzschel, Franziska et al.2025 · 4 citationsNucleic acids research. 2025;53(4)
Supersaturation mutagenesis reveals adaptive rewiring of essential genes among malaria parasites.39913589 · Oberstaller, Jenna, Xu, Shulin, Naskar, Deboki et al.2025 · 23 citationsScience (New York, N.Y.). 2025;387(6734):eadq7347
Identification of novel PfEMP1 variants containing domain cassettes 11, 15 and 8 that mediate the Plasmodium falciparum virulence-associated rosetting phenotype.39804943 · McLean, Florence E, Omondi, Brian R, Diallo, Nouhoum et al.2025 · 6 citationsPLoS pathogens. 2025;21(1):e1012434
scRNA-seq reveals elevated interferon responses and TNF-α signaling via NFkB in monocytes in children with uncomplicated malaria.39830896 · Morang'a, Collins M, Drake, Riley S, Miao, Vincent N et al.2025 · 4 citationsExperimental biology and medicine (Maywood, N.J.). 2024;249:10233
Genetic factors regulating Plasmodium falciparum gametocytogenesis identified by phenotypic screens.39730700 · Pires, Camilla V, Chawla, Jyotsna, Sollelis, Lauriane et al.2024 · 1 citationScientific reports. 2024;14(1):31010
Synovial tissue myeloid dendritic cell subsets exhibit distinct tissue-niche localization and function in health and rheumatoid arthritis.39609125 · MacDonald, Lucy, Elmesmari, Aziza, Somma, Domenico et al.2024 · 63 citationsImmunity. 2024;57(12):2843-2862.e12
Spatially resolved single-cell atlas unveils a distinct cellular signature of fatal lung COVID-19 in a Malawian population.39567718 · Nyirenda, James, Hardy, Olympia M, Silva Filho, João Da et al.2024 · 7 citationsNature medicine. 2024;30(12):3765-3777
Distinct tissue-niche localization and function of synovial tissue myeloid DC subsets in health, and in active and remission Rheumatoid Arthritis10.1101/2024.07.17.600758v1 · MacDonald, L., Elmesmari, A., Somma, D. et al.2024 · 0 citationsbioRxiv
Annotation and visualization of parasite, fungi and arthropod genomes with Companion.38752499 · Haese-Hill, William, Crouch, Kathryn, Otto, Thomas D2024 · 15 citationsNucleic acids research. 2024;52(W1):W39-W44
Annotation and visualisation of parasite, fungi and arthropod genomes with Companion10.1101/2024.02.19.580948v1 · Haese-Hill, W., Crouch, K., Otto, T. D.2024 · 0 citationsbioRxiv
Spatial transcriptomics reveals recasting of signalling networks in the small intestine following tissue invasion by the helminth parasite Heligmosomoides polygyrus10.1101/2024.02.09.579622v2 · Campillo Poveda, M., Hardy, O., Laidlaw, R. F. et al.2024 · 2 citationsbioRxiv
A novel computational pipeline for var gene expression augments the discovery of changes in the Plasmodium falciparum transcriptome during transition from in vivo to short-term in vitro culture.38270586 · Andradi-Brown, Clare, Wichers-Misterek, Jan Stephan, von Thien, Heidrun et al.2024 · 11 citationseLife. 2024;12
Sterile protection against P. vivax malaria by repeated blood stage infection in the Aotus monkey model.38158220 · Obaldía, Nicanor, Da Silva Filho, Joao Luiz, Núñez, Marlon et al.2024 · 4 citationsLife science alliance. 2024;7(3)
MalariaSED: a deep learning framework to decipher the regulatory contributions of noncoding variants in malaria parasites.37845769 · Wang, Chengqi, Dong, Yibo, Li, Chang et al.2023 · 6 citationsGenome biology. 2023;24(1):231
Double-negative-2 B cells are the major synovial plasma cell precursor in rheumatoid arthritis.37638026 · Wing, Elinor, Sutherland, Catherine, Miles, Katherine et al.2023 · 52 citationsFrontiers in immunology. 2023;14:1241474
From contigs towards chromosomes: automatic improvement of long read assemblies (ILRA).37406192 · Ruiz, José Luis, Reimering, Susanne, Escobar-Prieto, Juan David et al.2023 · 14 citationsBriefings in bioinformatics. 2023;24(4)
Author Correction: Cyclin-dependent kinase 12 is a drug target for visceral leishmaniasis.37402863 · Wyllie, Susan, Thomas, Michael, Patterson, Stephen et al.2023 · 0 citationsNature. 2023;619(7970):E48
The exception that proves the rule: Virulence gene expression at the onset of Plasmodium falciparum blood stage infections.37384799 · Wichers-Misterek, Jan Stephan, Krumkamp, Ralf, Held, Jana et al.2023 · 12 citationsPLoS pathogens. 2023;19(6):e1011468
A novel Modulator of Ring Stage Translation (MRST) gene alters artemisinin sensitivity in Plasmodium falciparum.37219373 · Simmons, Caroline, Gibbons, Justin, Wang, Chengqi et al.2023 · 3 citationsmSphere. 2023;8(4):e0015223
Profiling the bloodstream form and procyclic form Trypanosoma brucei cell cycle using single-cell transcriptomics.37166108 · Briggs, Emma M, Marques, Catarina A, Oldrieve, Guy R et al.2023 · 21 citationseLife. 2023;12
Phenotypic Screens Identify Genetic Factors Associated with Gametocyte Development in the Human Malaria Parasite Plasmodium falciparum.37154686 · Chawla, Jyotsna, Goldowitz, Ilana, Oberstaller, Jenna et al.2023 · 8 citationsMicrobiology spectrum. 2023;11(3):e0416422
Chemogenomic Profiling of a Plasmodium falciparum Transposon Mutant Library Reveals Shared Effects of Dihydroartemisinin and Bortezomib on Lipid Metabolism and Exported Proteins.37067430 · Pires, Camilla Valente, Oberstaller, Jenna, Wang, Chengqi et al.2023 · 10 citationsMicrobiology spectrum. 2023;11(3):e0501422
New technologies to study helminth development and host-parasite interactions.36931423 · Britton, Collette, Laing, Roz, McNeilly, Tom N et al.2023 · 27 citationsInternational journal for parasitology. 2023;53(8):393-403
peaks2utr: a robust Python tool for the annotation of 3' UTRs.36864613 · Haese-Hill, William, Crouch, Kathryn, Otto, Thomas D2023 · 23 citationsBioinformatics (Oxford, England). 2023;39(3)
A comprehensive analysis of rheumatoid arthritis B cells reveals the importance of CD11c+ve double-negative-2 B cells as the major synovial plasma cell precursor.10.1101/2023.02.15.526468v3 · Wing, E., Sutherland, C., Miles, K. et al.2023 · 1 citationbioRxiv
Repeated Plasmodium vivax blood stage infection provides sterile protection against homologous challenge in non-human primates10.1101/2023.02.13.528262v2 · Obaldia, N., da Silva Filho, J. L., Nunez, M. et al.2023 · 0 citationsbioRxiv
Protein KIC5 is a novel regulator of artemisinin stress response in the malaria parasite Plasmodium falciparum.36624300 · Simmons, Caroline F, Gibbons, Justin, Zhang, Min et al.2023 · 14 citationsScientific reports. 2023;13(1):399
Author Correction: Increased circulation time of Plasmodium falciparum underlies persistent asymptomatic infection in the dry season.35927582 · Andrade, Carolina M, Fleckenstein, Hannah, Thomson-Luque, Richard et al.2022 · 1 citationNature medicine. 2022;28(10):2216
Single cell and spatial transcriptomic analyses reveal microglia-plasma cell crosstalk in the brain during Trypanosoma brucei infection.36180478 · Quintana, Juan F, Chandrasegaran, Praveena, Sinton, Matthew C et al.2022 · 50 citationsNature communications. 2022;13(1):5752
Host cell maturation modulates parasite invasion and sexual differentiation in Plasmodium berghei.35476438 · Hentzschel, Franziska, Gibbins, Matthew P, Attipa, Charalampos et al.2022 · 32 citationsScience advances. 2022;8(17):eabm7348
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