Publications

2025

Radtke AJ, Anidi IU, Arakkal L, Arroyo-Mejias AJ, Beuschel RT, Börner K, Chu CJ, Clark B, Clatworthy MR, Colautti J, Coscia F, Croteau J, Denha S, Dever R, Dutra WO, Fritzsche S, Fullam S, Gerner MY, Gola A, Gollob KJ, Hernandez JM, Hor JL, Ichise H, Jing Z, Jonigk D, Kandov E, Kastenmüller W, Koenig JFE, Kortekaas RK, Kothurkar A, Kreins AY, Lamborn IT, Lin Y, Luciano Pereira Morais K, Lunich A, Luz JCS, MacDonald RB, Makranz C, Maltez VI, McDonough JE, Moriarty RV, Ocampo-Godinez JM, Olyntho VM, Oxenius A, Padhan K, Remmert K, Richoz N, Schrom EC, Shang W, Shi L, Shih RM, Speranza E, Stierli S, Teichmann SA, Veres TZ, Vierhout M, Wachter BT, Wade-Vallance AK, Williams M, Zangger N, Germain RN, Yaniv Z. The IBEX Knowledge-Base: A central resource for multiplexed imaging techniques. PLoS Biol. 2025 Mar 19;23(3):e3003070. doi: 10.1371/journal.pbio.3003070. PMID: 40106489; PMCID: PMC12135934.
Schrom EC, McCaffrey EF, Sreejithkumar V, Radtke AJ, Ichise H, Arroyo-Mejias A, Speranza E, Arakkal L, Thakur N, Grant S, Germain RN. Spatial Patterning Analysis of Cellular Ensembles (SPACE) finds complex spatial organization at the cell and tissue levels. Proc Natl Acad Sci U S A. 2025 Feb 11;122(6):e2412146122. doi: 10.1073/pnas.2412146122. Epub 2025 Feb 4. PMID: 39903116; PMCID: PMC11831171.
Nag J, Speranza E. Transcriptional Profiling of Filovirus-Infected Nonhuman Primate Samples. Methods Mol Biol. 2025;2877:369-385. doi: 10.1007/978-1-0716-4256-6_26. PMID: 39585635.

2024

Ichise H, Speranza E, La Russa F, Veres TZ, Chu CJ, Gola A, Germain RN. Rebalancing Viral and Immune Damage versus Tissue Repair Prevents Death from Lethal Influenza Infection. bioRxiv [Preprint]. 2024 Jul 7:2024.07.04.601620. doi: 10.1101/2024.07.04.601620. PMID: 39372755; PMCID: PMC11451654.
Radtke AJ, Postovalova E, Varlamova A, Bagaev A, Sorokina M, Kudryashova O, Meerson M, Polyakova M, Galkin I, Svekolkin V, Isaev S, Wiebe D, Sharun A, Sarachakov A, Perelman G, Lozinsky Y, Yaniv Z, Lowekamp BC, Speranza E, Yao L, Pittaluga S, Shaffer AL 3rd, Jonigk D, Phelan JD, Davies-Hill T, Huang DW, Ovcharov P, Nomie K, Nuzhdina E, Kotlov N, Ataullakhanov R, Fowler N, Kelly M, Muppidi J, Davis JL, Hernandez JM, Wilson WH, Jaffe ES, Staudt LM, Roschewski M, Germain RN. Multi-omic profiling of follicular lymphoma reveals changes in tissue architecture and enhanced stromal remodeling in high-risk patients. Cancer Cell. 2024 Mar 11;42(3):444-463.e10. doi: 10.1016/j.ccell.2024.02.001
Sturdevant GL, Meade-White KD, Best SM, Speranza E. Preservation of scRNA-Seq Libraries Using Existing Inactivation Protocols. Pathogens. 2024 Feb 13;13(2):167. doi: 10.3390/pathogens13020167

2023

Schrom EC, McCaffrey EF, Radtke AJ, Speranza E, Arakkal L, Thakur N, Grant S, Germain RN. Spatial Patterning Analysis of Cellular Ensembles (SPACE) enables statistically robust discovery of complex spatial organization at the cell and tissue level. bioRxiv [Preprint]. 2023 Dec 10:2023.12.08.570837. doi: 10.1101/2023.12.08.570837
Speranza, E. Understanding virus–host interactions in tissues. Nat Microbiol (2023). https://doi.org/10.1038/s41564-023-01434-7

2022

Speranza E*, Purushotham JN*, Port JR, Schwarz B, Flagg M, Williamson BN, Feldmann F, Singh M, Perez-Perez L, Sturdevant GL, Roberts LM, Carmody A, Schulz JE, van Doremalen N, Okumura A, Lovaglio J, Hanley P, Shaia C, Germain RN, Best SM, Munster VJ, Bosio CM, de Wit E. Age-related differences in immune dynamics during SARS-CoV-2 infection in rhesus macaques. Life Science Alliance Jan 2022, 5 (4) e202101314; DOI: 10.26508/lsa.202101314
Radtke AJ, Chu CJ, Yaniv Z, Yao L, Marr J, Beuschel RT, Ichise H, Gola A, Kabat J, Lowekamp B, Speranza E, Croteau J, Thakur N, Jonigk D, Davis JL, Hernandez JM, Germain RN. IBEX: an iterative immunolabeling and chemical bleaching method for high-content imaging of diverse tissues. Nat Protoc 17, 378–401 (2022). https://doi.org/10.1038/s41596-021-00644-9

2021

Roberts LM*, Schwarz B*, Speranza E*, Leighton I, Wehrly T, Best S, Bosio CM. Pulmonary infection induces persistent, pathogen-specific lipidomic changes influencing trained immunity. iScience. 2021 Aug 24;24(9):103025. doi: 10.1016/j.isci.2021.103025..
Strampe J, Asogun DA, Speranza E, Pahlmann M, Soucy A, Bockholt S, Pallasch E, Becker-Ziaja B, Duraffour S, Bhadelia N, Ighodalo Y, Oyakhilome J, Omomoh EO, Olokor T, Adomeh DI, Ikponwonsa O, Aire C, Tobin E, Akpede N, Okokhere P, Okogbenin S, Akpede G, Muñoz-Fontela C, Ogbaini-Emovon E, Günther S, Connor JH, Oestereich L. Factors associated with progression to death in patients with Lassa fever in Nigeria: an observational study. Lancet Infect Dis. 2021 Jun;21(6):876-886. doi: 10.1016/S1473-3099(20)30737-4.
Speranza E, Williamson BN, Feldmann F, Sturdevant GL, Pérez LP, Meade-White K, Smith BJ, Lovaglio J, Martens C, Munster VJ, Okumura A, Shaia C, Feldmann H, Best SM, de Wit E. SARS-CoV-2 infection dynamics in lungs of African green monkeys. Sci Transl Med. 2021 Jan 11:eabe8146. doi: 10.1126/scitranslmed.abe8146.

2020

Radtke AJ, Kandov E, Lowekamp B, Speranza E, Chu CJ, Gola A, Thakur N, Shih R, Yao L, Yaniv ZR, Beuschel RT, Kabat J, Croteau J, Davis J, Hernandez JM, Germain RN. IBEX: A versatile multiplex optical imaging approach for deep phenotyping and spatial analysis of cells in complex tissues. Proc Natl Acad Sci U S A. 2020 Dec 29;117(52):33455-33465. doi: 10.1073/pnas.2018488117.
Gola A, Speranza E*, Dorrington MG*, Sala C, Shih R, Radtke AJ, Wong HS, Baptista AP, Hernandez JM, Castellani G, Fraser IDC, Germain RN. Commensal-driven immune zonation of the liver promotes host defense. Nature. 2021 Jan;589(7840):131-136. doi: 10.1038/s41586-020-2977-2.
Speranza E, Caballero I, Honko AN, Johnson JC, Bohannon JK, Evans DeWald L, Gerhardt DM, Sword J, Hensley LE, Bennett RS, Connor JH. Previremic Identification of Ebola or Marburg Virus Infection Using Integrated Host-Transcriptome and Viral Genome Detection. mBio. 2020 Jun 16;11(3):e01157-20. doi: 10.1128/mBio.01157-20.