Cummings, M. J., Lutwama, J. J., Owor, N., Tomoiaga, A. S., Ross, J. E., Muwanga, M., Nsereko, C., Nayiga, I., Kyebambe, S., Shinyale, J., Ochar, T., Nie, K., Xie, H., Miake-Lye, S., Villagomez, B., Qi, J., Reynolds, S. J., Nakibuuka, M. C., Lu, X., … Bakamutumaho, B. (2025). Host Response Stratification in Malarial and Non-malarial Sepsis: A Prospective, Multicenter Analysis From Uganda. Critical Care Medicine. https://doi.org/10.1097/ccm.0000000000006591

Lasso, G., Grodus, M., Valencia, E., DeJesus, V., Liang, E., Delwel, I., Bortz, R. H., Lupyan, D., Ehrlich, H. Y., Castellanos, A. A., Gazzo, A., Wells, H. L., Wacharapluesadee, S., Tremeau-Bravard, A., Seetahal, J. F. R., Hughes, T., Lee, J., Lee, M.-H., Sjodin, A. R., … Anthony, S. J. (2025). Decoding the blueprint of receptor binding by filoviruses through large-scale binding assays and machine learning. Cell Host & Microbe. https://doi.org/10.1016/j.chom.2024.12.016

Mougari, S., Favède, V., Predella, C., Reynard, O., Durand, S., Mazelier, M., Pizzioli, E., Decimo, D., Bovier, F. T., Lapsley, L. M., Castagna, C., Lieberman, N. A. P., Noel, G., Mathieu, C., Malissen, B., Briese, T., Greninger, A. L., Alabi, C. A., Dorrello, N. V., … Horvat, B. (2025). Intranasally administrated fusion-inhibitory lipopeptides block SARS-CoV-2 infection in mice and enable long-term protective immunity. Communications Biology, 8(1). https://doi.org/10.1038/s42003-025-07491-4

Cummings, M. J., Lutwama, J. J., Tomoiaga, A. S., Owor, N., Lu, X., Ross, J. E., Muwanga, M., Nsereko, C., Nayiga, I., Nie, K., Kayiwa, J., Che, X., Wayengera, M., Kim-Schulze, S., Lipkin, W. I., O’Donnell, M. R., & Bakamutumaho, B. (2024). Molecular phenotypes of critical illness confer prognostic and biological enrichment in sub-Saharan Africa: a prospective cohort study from Uganda. Thorax, thorax-2024-222412. https://doi.org/10.1136/thorax-2024-222412

Moonga, L. C., Chipinga, J., Collins, J. P., Kapoor, V., Saasa, N., Nalubamba, K. S., Hang’ombe, B. M., Namangala, B., Lundu, T., Lu, X.-J., Yingst, S., Wickiser, J. K., & Briese, T. (2024). Application of a Sensitive Capture Sequencing Approach to Reservoir Surveillance Detects Novel Viruses in Zambian Wild Rodents. Viruses, 16(11), 1754. https://doi.org/10.3390/v16111754

Ross, J., Cummings, M. J., Bakamutumaho, B., Tokarz, R., Al Jubaer, S., Mathema, B., O’Donnell, M. R., & Larsen, M. H. (2024). Xpert MTB/RIF Ultra enables sensitive detection of Mycobacterium tuberculosis in blood. The International Journal of Tuberculosis and Lung Disease, 28(12), 594–596. https://doi.org/10.5588/ijtld.24.0118

Kané, F., Collins, J., Koné, A., Keita, N. Y., Cisse, I., Koné, K. M., Diallo, D., Konate, I., Dabitao, D. K., Diarra, B., Sanogo, I., Coulibaly, T. A., Diallo, M., Keita, D., Tangara, C. O., Diakité, M., Dao, S., Fouth-Tchos, K., Aboulhab, J., … Doumbia, S. (2024). Surveillance and agnostic capture sequencing of samples from individuals with rash-associated illness in Mali indicates regional transmission of measles virus from West and Central Africa. Infection, Genetics and Evolution, 126, 105691. https://doi.org/10.1016/j.meegid.2024.105691

Mechikoff, M. A., Collins, J. P., Golder, P., Ingersoll, C. M., McGarry, R. E., Lu, X.-J., Gokden, A., Cuff, A., Webber, B. J., Wallace, A. B., Steel, J. J., Wickiser, J. K., & Balboni, A. L. (2024). Application of Pan-Viral Metagenomic Sequencing on United States Air Force Academy Wastewater to Uncover Potential Causes of Acute Gastroenteritis. Military Medicine. https://doi.org/10.1093/milmed/usae518

Tokarz, R., Guo, C., Sanchez-Vicente, S., Horn, E., Eschman, A., Turk, S. P., Lipkin, W. I., & Marques, A. (2024). Identification of reactive Borrelia burgdorferi peptides associated with Lyme disease. MBio, 15(10). https://doi.org/10.1128/mbio.02360-24

Furfaro, D., Che, X., Gou, W., Cummings, M. J., Mishra, N., Brodie, D., Briese, T., Fiehn, O., Lipkin, W. I., & O’Donnell, M. R. (2024). Metabolomic profiling and prognostication in COVID-19 acute respiratory distress syndrome. Journal of Intensive Medicine. https://doi.org/10.1016/j.jointm.2024.04.001

Havdahl, A., Farmer, C., Surén, P., Øyen, A., Magnus, P., Susser, E., Lipkin, W. I., Reichborn‐Kjennerud, T., Stoltenberg, C., Bishop, S., & Thurm, A. (2023). Attainment and loss of early social‐communication skills across neurodevelopmental conditions in the Norwegian Mother, Father and Child Cohort Study. Journal of Child Psychology and Psychiatry, 65(5), 610–619. Portico. https://doi.org/10.1111/jcpp.13792

Cummings, M. J., Bakamutumaho, B., Tomoiaga, A. S., Owor, N., Jain, K., Price, A., Kayiwa, J., Namulondo, J., Byaruhanga, T., Muwanga, M., Nsereko, C., Nayiga, I., Kyebambe, S., Sameroff, S., Che, X., Lutwama, J. J., Lipkin, W. I., & O’Donnell, M. R. (2023). A Transcriptomic Classifier Model Identifies High-Risk Endotypes in a Prospective Study of Sepsis in Uganda*. Critical Care Medicine, 52(3), 475–482. https://doi.org/10.1097/ccm.0000000000006023

Cummings, M. J., Bakamutumaho, B., Lutwama, J. J., Owor, N., Che, X., Astorkia, M., Postler, T. S., Kayiwa, J., Kiconco, J., Muwanga, M., Nsereko, C., Rwamutwe, E., Nayiga, I., Kyebambe, S., Haumba, M., Bosa, H. K., Ocom, F., Watyaba, B., … Kikaire, B. (2024). COVID-19 immune signatures in Uganda persist in HIV co-infection and diverge by pandemic phase. Nature Communications, 15(1). https://doi.org/10.1038/s41467-024-45204-3

Guo, C., & Wu, J.-Y. (2024). Pathogen Discovery in the Post-COVID Era. Pathogens, 13(1), 51. https://doi.org/10.3390/pathogens13010051

Dubey, S., Chen, Z., Jiang, Y. J., Talis, A., Molotkov, A., Ali, A., Mintz, A., & Momen-Heravi, F. (2024). Small extracellular vesicles (sEVs)-based gene delivery platform for cell-specific CRISPR/Cas9 genome editing. Theranostics, 14(7), 2777–2793. https://doi.org/10.7150/thno.92133

Kapoor, V., Briese, T., Ranjan, A., Donovan, W. M., Mansukhani, M. M., Chowdhary, R., & Lipkin, W. I. (2024). Validation of the VirCapSeq-VERT system for differential diagnosis, detection, and surveillance of viral infections. Journal of Clinical Microbiology, 62(1). https://doi.org/10.1128/jcm.00612-23

Cross, R. W., Prasad, A. N., Woolsey, C. B., Agans, K. N., Borisevich, V., Dobias, N. S., Comer, J. E., Deer, D. J., Geisbert, J. B., Rasmussen, A. L., Lipkin, W. I., Fenton, K. A., & Geisbert, T. W. (2023). Natural history of nonhuman primates after conjunctival exposure to Ebola virus. Scientific Reports, 13(1). https://doi.org/10.1038/s41598-023-31027-7

Giloteaux, L., Li, J., Hornig, M., Lipkin, W. I., Ruppert, D., & Hanson, M. R. (2023). Proteomics and cytokine analyses distinguish myalgic encephalomyelitis/chronic fatigue syndrome cases from controls. Journal of Translational Medicine, 21(1). https://doi.org/10.1186/s12967-023-04179-3

Sanchez-Vicente, S., & Tokarz, R. (2023). Tick-Borne Co-Infections: Challenges in Molecular and Serologic Diagnoses. Pathogens, 12(11), 1371. https://doi.org/10.3390/pathogens12111371

Guo, C., Yi, B., Wu, J., & Lu, J. (2023). The microbiome in post-acute infection syndrome (PAIS). Computational and Structural Biotechnology Journal, 21, 3904–3911. https://doi.org/10.1016/j.csbj.2023.08.002

Boruah, A. P., Kroopnick, A., Thakkar, R., Wapniarski, A. E., Kim, C., Dugue, R., Harrigan, E., Lipkin, W. I., Mishra, N., & Thakur, K. T. (2023). Application of VirCapSeq-VERT and BacCapSeq in the diagnosis of presumed and definitive neuroinfectious diseases. Journal of NeuroVirology, 29(6), 678–691. https://doi.org/10.1007/s13365-023-01172-w

Yi, B., Deng, Q., Guo, C., Li, X., Wu, Q., Zha, R., Wang, X., & Lu, J. (2023). Evaluating the zoonotic potential of RNA viromes of rodents provides new insight into rodent-borne zoonotic pathogens in Guangdong, China. One Health, 17, 100631. https://doi.org/10.1016/j.onehlt.2023.100631

Brydges, C., Che, X., Lipkin, W. I., & Fiehn, O. (2023). Bayesian Statistics Improves Biological Interpretability of Metabolomics Data from Human Cohorts. Metabolites, 13(9), 984. https://doi.org/10.3390/metabo13090984

Komaroff, A. L., & Lipkin, W. I. (2023). ME/CFS and Long COVID share similar symptoms and biological abnormalities: road map to the literature. Frontiers in Medicine, 10. https://doi.org/10.3389/fmed.2023.1187163

McLaren, S. H., Mishra, N., Hijiya, N., Ng, J., Guo, C., Whittier, S., Mariani, E., Glaser, L., Frantzis, I., Vindas, M. T., Leu, C.-S., & Dayan, P. S. (2023). High-throughput Sequencing to Identify Bacteremia in Children with Cancer. Pediatric Infectious Disease Journal, 42(8), 695–697. https://doi.org/10.1097/inf.0000000000003948

Maximova, O. A., Weller, M. L., Krogmann, T., Sturdevant, D. E., Ricklefs, S., Virtaneva, K., Martens, C., Wollenberg, K., Minai, M., Moore, I. N., Sauter, C. S., Barker, J. N., Lipkin, W. I., Seilhean, D., Nath, A., & Cohen, J. I. (2023). Pathogenesis and outcome of VA1 astrovirus infection in the human brain are defined by disruption of neural functions and imbalanced host immune responses. PLOS Pathogens, 19(8), e1011544. https://doi.org/10.1371/journal.ppat.1011544

Briese, T., Tokarz, R., Bateman, L., Che, X., Guo, C., Jain, K., Kapoor, V., Levine, S., Hornig, M., Oleynik, A., Quan, P., Wong, W. H., Williams, B. L., Vernon, S. D., Klimas, N. G., Peterson, D. L., Montoya, J. G., & Ian Lipkin, W. (2023). A multicenter virome analysis of blood, feces, and saliva in myalgic encephalomyelitis/chronic fatigue syndrome. Journal of Medical Virology, 95(8). Portico. https://doi.org/10.1002/jmv.28993

Che, X., Roy, A., Bresnahan, M., Mjaaland, S., Reichborn-Kjennerud, T., Magnus, P., Stoltenberg, C., Shang, Y., Zhang, K., Susser, E., Fiehn, O., & Lipkin, W. I. (2023). Metabolomic analysis of maternal mid-gestation plasma and cord blood in autism spectrum disorders. Molecular Psychiatry, 28(6), 2355–2369. https://doi.org/10.1038/s41380-023-02051-w

Wu, Q., Guo, C., Li, X., Yi, B.-Y., Li, Q.-L., Guo, Z.-M., & Lu, J.-H. (2023). A meta-transcriptomic study of mosquito virome and blood feeding patterns at the human-animal-environment interface in Guangdong Province, China. One Health, 16, 100493. https://doi.org/10.1016/j.onehlt.2023.100493

Broger, T., Koeppel, L., Huerga, H., Miller, P., Gupta-Wright, A., Blanc, F.-X., Esmail, A., Reeve, B. W. P., Floridia, M., Kerkhoff, A. D., Ciccacci, F., Kasaro, M. P., Thit, S. S., Bastard, M., Ferlazzo, G., Yoon, C., Van Hoving, D. J., Sossen, B., García, J. I., … Fielding, K. (2023). Diagnostic yield of urine lipoarabinomannan and sputum tuberculosis tests in people living with HIV: a systematic review and meta-analysis of individual participant data. The Lancet Global Health, 11(6), e903–e916. https://doi.org/10.1016/s2214-109x(23)00135-3

Miquel, J., Martín-Carrillo, N., Ribas, A., Sánchez-Vicente, S., Feliu, C., & Foronda, P. (2023). Morphologic and Genetic Characterization of Protospirura canariensis n. sp. (Nematoda, Spiruridae), a Parasite of the Black Rat Rattus rattus (Rodentia, Muridae) from El Hierro Island (Canary Archipelago, Spain). Animals, 13(11), 1806. https://doi.org/10.3390/ani13111806

Raizen, D. M., Mullington, J., Anaclet, C., Clarke, G., Critchley, H., Dantzer, R., Davis, R., Drew, K. L., Fessel, J., Fuller, P. M., Gibson, E. M., Harrington, M., Ian Lipkin, W., Klerman, E. B., Klimas, N., Komaroff, A. L., Koroshetz, W., Krupp, L., Kuppuswamy, A., … Craig Heller, H. (2023). Beyond the symptom: the biology of fatigue. SLEEP, 46(9). https://doi.org/10.1093/sleep/zsad069

Cummings, M. J., Bakamutumaho, B., Jain, K., Price, A., Owor, N., Kayiwa, J., Namulondo, J., Byaruhanga, T., Muwanga, M., Nsereko, C., Nayiga, I., Kyebambe, S., Che, X., Sameroff, S., Tokarz, R., Wong, W., Postler, T. S., Larsen, M. H., Lipkin, W. I., … O’Donnell, M. R. (2023). Brief Report: Detection of Urine Lipoarabinomannan Is Associated With Proinflammatory Innate Immune Activation, Impaired Host Defense, and Organ Dysfunction in Adults With Severe HIV-Associated Tuberculosis in Uganda. JAIDS Journal of Acquired Immune Deficiency Syndromes, 93(1), 79–85. https://doi.org/10.1097/qai.0000000000003159

Cummings, M. J., Bakamutumaho, B., Jain, K., Price, A., Owor, N., Kayiwa, J., Namulondo, J., Byaruhanga, T., Muwanga, M., Nsereko, C., Sameroff, S., Ian Lipkin, W., Lutwama, J. J., & O’Donnell, M. R. (2023). Development of a Novel Clinicomolecular Risk Index to Enhance Mortality Prediction and Immunological Stratification of Adults Hospitalized with Sepsis in Sub-Saharan Africa: A Pilot Study from Uganda. The American Journal of Tropical Medicine and Hygiene, 108(3), 619–626. https://doi.org/10.4269/ajtmh.22-0483

Guo, C., Che, X., Briese, T., Ranjan, A., Allicock, O., Yates, R. A., Cheng, A., March, D., Hornig, M., Komaroff, A. L., Levine, S., Bateman, L., Vernon, S. D., Klimas, N. G., Montoya, J. G., Peterson, D. L., Lipkin, W. I., & Williams, B. L. (2023). Deficient butyrate-producing capacity in the gut microbiome is associated with bacterial network disturbances and fatigue symptoms in ME/CFS. Cell Host & Microbe, 31(2), 288-304.e8. https://doi.org/10.1016/j.chom.2023.01.004

Cummings, M. J., Bakamutumaho, B., Price, A., Owor, N., Kayiwa, J., Namulondo, J., Byaruhanga, T., Jain, K., Postler, T. S., Muwanga, M., Nsereko, C., Nayiga, I., Kyebambe, S., Che, X., Sameroff, S., Tokarz, R., Shah, S. S., Larsen, M. H., Lipkin, W. I., … O’Donnell, M. R. (2022). HIV infection drives pro-inflammatory immunothrombotic pathway activation and organ dysfunction among adults with sepsis in Uganda. AIDS, 37(2), 233–245. https://doi.org/10.1097/qad.0000000000003410

Lipkin, W. I., Bresnahan, M., & Susser, E. (2023). Cohort-guided insights into gene–environment interactions in autism spectrum disorders. Nature Reviews Neurology, 19(2), 118–125. https://doi.org/10.1038/s41582-022-00764-0

Miquel, J., Martín-Carrillo, N., Ribas, A., Sánchez-Vicente, S., Feliu, C., & Foronda, P. (2022). Morphologic and genetic characterization ofPterygodermatites(Mesopectines)valladaresin. sp. (Nematoda, Rictulariidae), a parasite of the mouseMus musculus(Rodentia, Muridae) from the Canary Islands (Spain). Parasite, 29, 57. https://doi.org/10.1051/parasite/2022057

Neeb, Z. T., Ritter, A. J., Chauhan, L. V., Katzman, S., Lipkin, W. I., Mishra, N., & Sanford, J. R. (2022). A potential role for SARS-CoV-2 small viral RNAs in targeting host microRNAs and modulating gene expression. Scientific Reports, 12(1). https://doi.org/10.1038/s41598-022-26135-9

Cheng, X., Zhang, Y., Li, Y., Wu, Q., Wu, J., Park, S.-K., Guo, C., & Lu, J. (2022). Meta-analysis of 16S rRNA microbial data identified alterations of the gut microbiota in COVID-19 patients during the acute and recovery phases. BMC Microbiology, 22(1). https://doi.org/10.1186/s12866-022-02686-9

Kuhn, J. H., Adkins, S., Alkhovsky, S. V., Avšič-Županc, T., Ayllón, M. A., Bahl, J., Balkema-Buschmann, A., Ballinger, M. J., Bandte, M., Beer, M., Bejerman, N., Bergeron, É., Biedenkopf, N., Bigarré, L., Blair, C. D., Blasdell, K. R., Bradfute, S. B., Briese, T., Brown, P. A., … Økland, A. L. (2022). 2022 taxonomic update of phylum Negarnaviricota (Riboviria: Orthornavirae), including the large orders Bunyavirales and Mononegavirales. Archives of Virology, 167(12), 2857–2906. https://doi.org/10.1007/s00705-022-05546-z

Li, Q., Zhang, F., Lu, Y., Hu, H., Wang, J., Guo, C., Deng, Q., Liao, C., Wu, Q., Hu, T., Chen, Z., & Lu, J. (2022). Highly potent multivalent VHH antibodies against Chikungunya isolated from an alpaca naïve phage display library. Journal of Nanobiotechnology, 20(1). https://doi.org/10.1186/s12951-022-01417-6

Deng, Q., Guo, Z., Hu, H., Li, Q., Zhang, Y., Wang, J., Liao, C., Guo, C., Li, X., Chen, Z., & Lu, J. (2022). Inhibition of Chikungunya virus early replication by intracellular nanoantibodies targeting nsP2 Epitope Rich Region. Antiviral Research, 208, 105446. https://doi.org/10.1016/j.antiviral.2022.105446

Cummings, M. J., Bakamutumaho, B., Price, A., Owor, N., Kayiwa, J., Namulondo, J., Byaruhanga, T., Muwanga, M., Nsereko, C., Sameroff, S., Tokarz, R., Wong, W., Shah, S. S., Larsen, M. H., Lipkin, W. I., Lutwama, J. J., & O’Donnell, M. R. (2022). Multidimensional analysis of the host response reveals prognostic and pathogen-driven immune subtypes among adults with sepsis in Uganda. Critical Care, 26(1). https://doi.org/10.1186/s13054-022-03907-3

Cummings, M. J., & Jacob, S. T. (2022). Equitable endotyping is essential to achieve a global standard of precise, effective, and locally-relevant sepsis care. EBioMedicine, 86, 104348. https://doi.org/10.1016/j.ebiom.2022.104348

Lipkin, W. I., & Briese, T. (2022). Building a global immune system. Human Vaccines & Immunotherapeutics, 18(4). https://doi.org/10.1080/21645515.2022.2036069

He, B., Wang, K., Xiang, J., Bing, P., Tang, M., Tian, G., Guo, C., Xu, M., & Yang, J. (2022). DGHNE: network enhancement-based method in identifying disease-causing genes through a heterogeneous biomedical network. Briefings in Bioinformatics, 23(6). https://doi.org/10.1093/bib/bbac405

Wells, H. L., Loh, E., Nava, A., Solorio, M. R., Lee, M. H., Lee, J., Sukor, J. R. A., Navarrete-Macias, I., Liang, E., Firth, C., Epstein, J. H., Rostal, M. K., Zambrana-Torrelio, C., Murray, K., Daszak, P., Goldstein, T., Mazet, J. A. K., Lee, B., Hughes, T., … Anthony, S. J. (2022). Classification of new morbillivirus and jeilongvirus sequences from bats sampled in Brazil and Malaysia. Archives of Virology, 167(10), 1977–1987. https://doi.org/10.1007/s00705-022-05500-z

Fernández-Alvarez, Á., Sánchez-Vicente, S., Feliu, C., Valladares, B., Miquel, J., Alves, J., Melero-Alcíbar, R., & Foronda, P. (2022). Myiasis by Cordylobia anthropophaga (Calliphoridae) in rodents from Cape Verde. Acta Parasitologica, 67(3), 1260–1264. https://doi.org/10.1007/s11686-022-00576-8

Tagliafierro, T., Joshi, S., Sameroff, S., Marques, A., Dumler, J. S., Mishra, N., Sanchez-Vicente, S., Wormser, G. P., Marcos, L. A., Lipkin, W. I., & Tokarz, R. (2022). Detection of antibodies to Anaplasma phagocytophilum and Babesia microti using linear peptides. Ticks and Tick-Borne Diseases, 13(5), 101999. https://doi.org/10.1016/j.ttbdis.2022.101999