Integrated pathogen load and dual transcriptome analysis of systemic host-pathogen interactions in severe malaria

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STAR: ultrafast universal RNA-seq aligner

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The immunopathology of sepsis and potential therapeutic targets

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In silico identification of potential inhibitors against human 2’-5’-oligoadenylate synthetase (OAS) proteinsPreprint

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Three hallmarks of malaria-induced selection in human genomesPreprint

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Publicly available transcriptomes provide the opportunity for dual RNA-Seq meta-analysis in Plasmodium infectionPreprint

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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 culturePreprint

Andradi-Brown, C., Wichers-Misterek, J. S., von Thien, H., Höppner, Y. D., Scholz, J. A. M., Hansson, H. S., Hocke, E. F., Gilberger, T., Duffy, M. F., Lavstsen, T., et al. (2023) · eLife · doi:10.7554/elife.87726.1 · Cited by 1

A Pan-Cancer Analysis Reveals OAS2 as a Biomarker for Cancer Prognosis and ImmunotherapyPreprint

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Anemia and tissue hypoxia are major determinants of malarial hypelactatemiaPreprint

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Innate immune responses to Plasmodium falciparum disrupt the blood-brain barrierPreprint

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Genome-wide expression in neonatal encephalopathy

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Transcriptome analysis of diverse Plasmodium falciparum clinical isolates identifies genes correlating with highly variable expression of merozoite surface protein MSPDBL2Preprint

Hocking, S. E., Stewart, L. B., Tarr, S. J., Fréville, A., Tetteh, K. K. A., Ahouidi, A. D., Amambua‐Ngwa, A., Diakité, M., Awandare, G. A., & Conway, D. J. (2022) · bioRxiv (Cold Spring Harbor Laboratory) · doi:10.1101/2022.02.18.481051

RNAseq of Infected Erythrocyte Surface Antigen-Encoding Genes

Nguyen, H. H. T., Azizan, S., Yeoh, L. M., Tang, J., & Duffy, M. F. (2022) · Methods in molecular biology · doi:10.1007/978-1-0716-2189-9_15

Reply to: Relationship of circulating Plasmodium falciparum lifecycle stage to circulating parasitemia and total parasite biomass

Thomson-Luque, R., Votborg-Novél, L., Osório, N. S., & Portugal, S. (2022) · Nature Communications · doi:10.1038/s41467-022-32998-3

Gene expression of macaques infected with malaria species of zoonotic concernPreprint

Trujillo, A. E., & Bergey, C. M. (2023) · bioRxiv (Cold Spring Harbor Laboratory) · doi:10.1101/2023.01.19.524806

Reviewer #3 (Public Review): 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

(2023) · eLife · doi:10.7554/elife.87726.1.sa0

eLife Assessment: 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

Krzych, U. (2023) · eLife · doi:10.7554/elife.87726.1.sa3

Reviewer #2 (Public Review): 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

(2023) · eLife · doi:10.7554/elife.87726.1.sa1

Reviewer #1 (Public Review): 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

(2023) · eLife · doi:10.7554/elife.87726.1.sa2

Author Response: 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

Andradi-Brown, C., Wichers-Misterek, J. S., von Thien, H., Höppner, Y. D., Scholz, J. A. M., Hansson, H. S., Hocke, E. F., Gilberger, T., Duffy, M. F., Lavstsen, T., et al. (2023) · eLife · doi:10.7554/elife.87726.1.sa4

Interactions shaping the interactome

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Neutrophils cultured ex vivo from CD34 + stem cells are immature and genetically tractablePreprint

Naveh, C. A., Roberts, K., Rice, C. M., Fleming, K., Thompson, M., Panyapiean, N., Diezmann, S., Moura, P. L., Toye, A. M., & Amulic, B. (2023) · medRxiv · doi:10.1101/2023.07.12.23292345

Gene expression analyses reveal differences in children’s response to malaria according to their agePreprint

Tebben, K., Yirampo, S., Coulibaly, D. M., Kone, A. K., Laurens, M. B., Stucke, E. M., Dembélé, A., Tolo, Y., Traoré, K., Niangaly, A., et al. (2023) · bioRxiv (Cold Spring Harbor Laboratory) · doi:10.1101/2023.10.24.563751

Gene expression analyses reveal differences in children’s response to malaria according to their agePreprint

Tebben, K., Yirampo, S., Coulibaly, D. M., Kone, A. K., Laurens, M. B., Stucke, E. M., Dembélé, A., Tolo, Y., Traoré, K., Niangaly, A., et al. (2023) · Research Square · doi:10.21203/rs.3.rs-3487114/v1

Additional file 12 of Multicohort transcriptome analysis of whole blood identifies robust human response signatures in Plasmodium falciparum infections

Zhang, Y., Su, X., Li, J., Shi, J., & Xie, L. (2022) · Figshare · doi:10.6084/m9.figshare.21563882

Additional file of A comprehensive RNA handling and transcriptomics guide for high-throughput processing of Plasmodium blood-stage samples

Kucharski, M., Tripathi, J., Nayak, S., Zhu, L., Wirjanata, G., van der Pluijm, R. W., Dhorda, M., Dondorp, A. M., & Bozdech, Z. (2021) · Figshare · doi:10.6084/m9.figshare.14433542

Additional file 10 of Multicohort transcriptome analysis of whole blood identifies robust human response signatures in Plasmodium falciparum infections

Zhang, Y., Su, X., Li, J., Shi, J., & Xie, L. (2022) · Figshare · doi:10.6084/m9.figshare.21563876

Additional file 11 of Multicohort transcriptome analysis of whole blood identifies robust human response signatures in Plasmodium falciparum infections

Zhang, Y., Su, X., Li, J., Shi, J., & Xie, L. (2022) · Figshare · doi:10.6084/m9.figshare.21563879

The Host Response to Infections: The “-omics” Revolution

Mejías, A., & Ramilo, O. (2025) · Elsevier eBooks · doi:10.1016/b978-0-323-82763-8.00003-0

Host Transcriptomics

Mejías, A., & Ramilo, O. (2025) · Wiley eBooks · doi:10.1002/9781683674597.ch8

Additional file 2 of Comparison of leucocyte profiles between healthy children and those with asymptomatic and symptomatic Plasmodium falciparum infections

Prah, D. A., Amoah, L. E., Gibbins, M. P., Bediako, Y., Cunnington, A. J., Awandare, G. A., & Hafalla, J. C. R. (2020) · Figshare · doi:10.6084/m9.figshare.13076444

Additional file 1 of Neutrophils cultured ex vivo from CD34+ stem cells are immature and genetically tractable

Naveh, C. A., Roberts, K., Zakrzewski, P., Rice, C. M., Ponce-Garcia, F. M., Fleming, K., Thompson, M., Panyapiean, N., Jiang, H., Diezmann, S., et al. (2024) · Figshare · doi:10.6084/m9.figshare.26728399

Additional file 2 of A comprehensive RNA handling and transcriptomics guide for high-throughput processing of Plasmodium blood-stage samples

Kucharski, M., Tripathi, J., Nayak, S., Zhu, L., Wirjanata, G., van der Pluijm, R. W., Dhorda, M., Dondorp, A. M., & Bozdech, Z. (2021) · Figshare · doi:10.6084/m9.figshare.14433539

Additional file 8 of Multicohort transcriptome analysis of whole blood identifies robust human response signatures in Plasmodium falciparum infections

Zhang, Y.-H., Su, X.-Z., Li, J., Shi, J.-J., & Xie, L.-H. (2022) · Figshare · doi:10.6084/m9.figshare.21563906

Additional file 2 of Neutrophils cultured ex vivo from CD34+ stem cells are immature and genetically tractable

Naveh, C. A., Roberts, K., Zakrzewski, P., Rice, C. M., Ponce-Garcia, F. M., Fleming, K., Thompson, M., Panyapiean, N., Jiang, H., Diezmann, S., et al. (2024) · Figshare · doi:10.6084/m9.figshare.26728402

Additional file 5 of Multicohort transcriptome analysis of whole blood identifies robust human response signatures in Plasmodium falciparum infections

Zhang, Y.-H., Su, X.-Z., Li, J., Shi, J.-J., & Xie, L.-H. (2022) · Figshare · doi:10.6084/m9.figshare.21563897

Additional file 3 of Comparison of leucocyte profiles between healthy children and those with asymptomatic and symptomatic Plasmodium falciparum infections

Prah, D. A., Amoah, L. E., Gibbins, M. P., Bediako, Y., Cunnington, A. J., Awandare, G. A., & Hafalla, J. C. R. (2020) · Figshare · doi:10.6084/m9.figshare.13076447

Additional file 1 of A comprehensive RNA handling and transcriptomics guide for high-throughput processing of Plasmodium blood-stage samples

Kucharski, M., Tripathi, J., Nayak, S., Zhu, L., Wirjanata, G., van der Pluijm, R. W., Dhorda, M., Dondorp, A. M., & Bozdech, Z. (2021) · Figshare · doi:10.6084/m9.figshare.14433536

Additional file 4 of Comparison of leucocyte profiles between healthy children and those with asymptomatic and symptomatic Plasmodium falciparum infections

Prah, D. A., Amoah, L. E., Gibbins, M. P., Bediako, Y., Cunnington, A. J., Awandare, G. A., & Hafalla, J. C. R. (2020) · Figshare · doi:10.6084/m9.figshare.13076450

Additional file 1 of Comparison of leucocyte profiles between healthy children and those with asymptomatic and symptomatic Plasmodium falciparum infections

Prah, D. A., Amoah, L. E., Gibbins, M. P., Bediako, Y., Cunnington, A. J., Awandare, G. A., & Hafalla, J. C. R. (2020) · Figshare · doi:10.6084/m9.figshare.13076441

Additional file 7 of Multicohort transcriptome analysis of whole blood identifies robust human response signatures in Plasmodium falciparum infections

Zhang, Y.-H., Su, X.-Z., Li, J., Shi, J.-J., & Xie, L.-H. (2022) · Figshare · doi:10.6084/m9.figshare.21563903

Additional file 9 of Multicohort transcriptome analysis of whole blood identifies robust human response signatures in Plasmodium falciparum infections

Zhang, Y.-H., Su, X.-Z., Li, J., Shi, J.-J., & Xie, L.-H. (2022) · Figshare · doi:10.6084/m9.figshare.21563909

Additional file 4 of Multicohort transcriptome analysis of whole blood identifies robust human response signatures in Plasmodium falciparum infections

Zhang, Y.-H., Su, X.-Z., Li, J., Shi, J.-J., & Xie, L.-H. (2022) · Figshare · doi:10.6084/m9.figshare.21563894

Additional file 1 of Multicohort transcriptome analysis of whole blood identifies robust human response signatures in Plasmodium falciparum infections

Zhang, Y.-H., Su, X.-Z., Li, J., Shi, J.-J., & Xie, L.-H. (2022) · Figshare · doi:10.6084/m9.figshare.21563885

Additional file 3 of Multicohort transcriptome analysis of whole blood identifies robust human response signatures in Plasmodium falciparum infections

Zhang, Y.-H., Su, X.-Z., Li, J., Shi, J.-J., & Xie, L.-H. (2022) · Figshare · doi:10.6084/m9.figshare.21563891

Additional file 2 of Multicohort transcriptome analysis of whole blood identifies robust human response signatures in Plasmodium falciparum infections

Zhang, Y.-H., Su, X.-Z., Li, J., Shi, J.-J., & Xie, L.-H. (2022) · Figshare · doi:10.6084/m9.figshare.21563888

Additional file 6 of Multicohort transcriptome analysis of whole blood identifies robust human response signatures in Plasmodium falciparum infections

Zhang, Y.-H., Su, X.-Z., Li, J., Shi, J.-J., & Xie, L.-H. (2022) · Figshare · doi:10.6084/m9.figshare.21563900

Integrated co-expression analysis of host–parasite transcriptomes reveals mechanisms of host modulation in an ant–cestode system

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The Enzymatic Mechanism of OAS: How Metal Ions and Quantum Effects Help Activate Innate Immunity

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Identifying host-pathogen interactions which cause severe malaria

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Interactive transcriptome analysis of malaria patients and infectingPlasmodium falciparumPreprint

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Host and Parasite Transcriptomic Changes upon Successive Plasmodium falciparum Infections in Early Childhood

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Reply to: Relationship of circulating Plasmodium falciparum lifecycle stage to circulating parasitemia and total parasite biomass

Thomson-Luque, R., Votborg-Novél, L., Osório, N. S., & Portugal, S. (2022) · Nature Communications · doi:10.1038/s41467-022-32998-3

Plasmodium falciparum gene expression signatures and antibody profiling implicate the fikk, phist, and surf multigene families in severe malaria syndromes

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