Our publications
2025
Microbiome dynamics in the congregate environment of U.S. Army Infantry training | Microbiol Spectr.
C.R. Kok, M.D. Morrison, J.B. Thissen, S. Mabery, M.L. Carson, J.A. Kimbrel, J.W. Bennett, D.R. Tribble, E.V. Millar, K. Mende, N.A. Be
Phylodynamics of SARS-CoV-2 Lineages B.1.1.7, B.1.1.529 and B.1.617.2 in Nigeria Suggests Divergent Evolutionary Trajectories | Pathogens
B.O. Motayo, O.O. Oluwasemowo, A.B. Onoja, P.A. Akinduti, A.O. Faneye
High-quality Acinetobacter genomes recovered from combat wounds via metagenomic sequencing resemble cultured isolate genomes | Microbiol Spectr.
J.A. Kimbrel, J.B. Thissen, F.A. Lisboa, S. Mabery, C.J. Jaing, E.A. Elster, S.A. Schobel, N.A. Be
Benchmarking Concentration and Extraction Methods for Wastewater-Based Surveillance of Eight Human Respiratory Viruses: Implications for Rapid Application to Novel Pathogens | Environ Sci Technol.
A.L. Wang, M. Jiang, A. Nguyen, S.R. Kane, M.K. Borucki, R.S. Kantor, K.L. Nelson
Design of cross-reactive antigens with machine learning and high-throughput experimental evaluation | Front Bioinform.
C. Chesterman, T. Desautels, L.J. Sierra, K.T. Arrildt, A. Zemla, E.Y. Lau, S. Sundaram, J. Laliberte, L. Chen, A. Ruby, M. Mednikov, S. Bertholet, D. Yu, K. Luisi, E. Malito, C.P. Mallett, M.J. Bottomley, R.A. van den Berg, D. Faissol.
Early immune response to Coccidioides is characterized by robust neutrophil and fibrotic macrophage recruitment and differentiation | Microbiol Spectr.
N. Miranda, O.A. Davalos, A. Sebastian, M.V. Rangel, N.F. Leon, B.M. Gorman, D.K. Murugesh, N.R. Hum, G.G. Loots, K.K. Hoyer, D.R. Weilhammer
Harnessing Machine Learning for Agnostic Biodetection | Health Secur.
S.H. Sandholtz, C. Valdes, N. Mulakken, M.W. Torres, A. Avila-Herrera, J.A. Drocco, J.M. Martí, J.E. Allen, U. Tipnis, C.J. Jaing, N.A. Be
Field expedient stool collection methods for gut microbiome analysis in deployed military environments | mSphere
C.R. Kok, J.B. Thissen, M. Cerroni, D.R. Tribble, A. Cancio, S. Tran, C. Schofield, R.E. Colombo, T. Troth, C. Joya, T. Lalani, N.A. Be
Preemptive optimization of a clinical antibody for broad neutralization of SARS-CoV-2 variants and robustness against viral escape | Sci Adv.
F. Zhu, S. Rajan, C.F. Hayes, K.Y. Kwong, A.R. Goncalves, A.T. Zemla, E.Y. Lau, Y. Zhang, Y. Cai, J.W. Goforth, M. Landajuela, P. Gilchuk, M. Kierny, A. Dippel, B. Amofah, G. Kaplan, V. Cadevilla Peano, C. Morehouse, B. Sparklin, V. Gopalakrishnan, K.M. Tuffy, A. Nguyen, J. Beloor, G. Kijak, C. Liu, A. Dijokaite-Guraliuc, J. Mongkolsapaya, G.R. Screaton, B.K. Petersen, T.A. Desautels, D. Bennett, S. Conti, B.W. Segelke, K.T. Arrildt, S. Kaul, E.A. Grzesiak, F.L. da Silva, T.W. Bates, C.G. Earnhart, S. Hopkins, S. Sundaram, M.T. Esser, J.R. Francica, D.M. Faissol, LLNL Generative Unconstrained Intelligent Drug Engineering (GUIDE) consortium
Addressing the dynamic nature of reference data: a new nucleotide database for robust metagenomic classification | mSystems
J.M. Martí, C.R. Kok, J.B. Thissen, N.J. Mulakken, A. Avila-Herrera, C.J. Jaing, J.E. Allen, N.A. Be
Direct effects of prolonged TNF-α and IL-6 exposure on neural activity in human iPSC-derived neuron-astrocyte co-cultures | Front Cell Neurosci.
N. Goshi, D. Lam, C. Bogguri, V.K. George, A. Sebastian, J. Cadena, N.F. Leon, N.R. Hum, D.R. Weilhammer, N.O. Fischer, H.A. Enright
Nanobody screening and machine learning guided identification of cross-variant anti-SARS-CoV-2 neutralizing heavy-chain only antibodies | PLoS Pathog.
P.R. McIlroy, L.T.M. Pham, T. Sheffield, M.A. Stefan, C.E. Thatcher, J. Jaryenneh, J.L. Schwedler, A. Sinha, C.A. Sumner, I.K.A. Jones, S. Won, R.C. Bruneau, D.R. Weilhammer, Z. Liu, S. Whelan, O.A. Negrete, K.L. Sale, B. Harmon
Combining computational modeling and experimental library screening to affinity-mature VEEV-neutralizing antibody F5 | Protein Sci.
C.A. Sumner, J.L. Schwedler, K.M. McCoy, J. Holland, V. Duva, D. Gelperin, V. Busygina, M.A. Stefan, D.V. Martinez, M.A. Juarros, A.M. Phillips, D.R. Weilhammer, G. Grigoryan, M.S. Kent, B.N. Harmon.
Improved Zika virus plaque assay using Vero/TMPRSS2 cell line | Microbiol Spectr.
O.O. Oluwasemowo, M.E. Graham, D.K. Murugesh, M.K. Borucki
Spatiotemporal analysis of lung immune dynamics in lethal Coccidioides posadasii infection | mBio
O.A. Davalos, A. Sebastian, N.F. Leon, M.V. Rangel, N. Miranda, D.K. Murugesh, A.M. Phillips, K.K. Hoyer, N.R. Hum, G.G. Loots, D.R. Weilhammer
2024
Single-cell and spatiotemporal transcriptomic profiling of brain immune infiltration following Venezuelan equine encephalitis virus infection | Front Immunol
M.V. Rangel, A. Sebastian, N.F. Leon, A.M. Phillips, B.M. Gorman, N.R. Hum, D.R. Weilhammer
Evaluation of Subetadex-α-methyl, a Polyanionic Cyclodextrin Scaffold, as a Medical Countermeasure against Fentanyl and Related Opioids | ACS Cent Sci
M.A. Malfatti, H.A. Enright, S. McCloy, E.A. Ubick, E. Kuhn, A. Subramanian, V.H.L. Lao, D. Lam, N.A. Be, S. Hok, E.Y. Lau, D.C. Kaseman, B.P. Mayer, C.A. Valdez
Improved Zika virus plaque assay using Vero/TMPRSS2 cell line | Microbiol Spectr
O.O. Oluwasemowo, M.E. Graham, D.K. Murugesh, M.K. Borucki
Spatiotemporal analysis of lung immune dynamics in lethal Coccidioides posadasii infection | mBio
O.A. Davalos, A. Sebastian, N.F. Leon, M.V. Rangel, N. Miranda, D.K. Murugesh, A.M. Phillips, K.K. Hoyer, N.R. Hum, G.G. Loots, D.R. Weilhammer
Cell-Free Screening, Production and Animal Testing of a STI-Related Chlamydial Major Outer Membrane Protein Supported in Nanolipoproteins | Vaccines (Basel)
M. Mohagheghi, A. Abisoye-Ogunniyan, A.C. Evans, A.E. Peterson, G.A. Bude, S. Hoang-Phou, B.D. Vannest, D. Hall, A. Rasley, D.R. Weilhammer, N.O. Fischer, W. He, B.V. Robinson, S. Pal, A. Slepenkin, L. de la Maza, M.A. Coleman
Efforts to enhance reproducibility in a human performance research project | F1000Res
J.A. Drocco, K. Halliday, B.J. Stewart, S.H. Sandholtz, M.D. Morrison, J.B. Thissen, N.A. Be, C.E. Zwilling, R.R. Wilcox, S.A. Culpepper, A.K. Barbey, C.J. Jaing
Host tracheal and intestinal microbiomes inhibit Coccidioides growth in vitro | Microbiol Spectr
S. Tejeda-Garibay, L. Zhao, N.R. Hum, M. Pimentel, A.L. Diep, B. Amiri, S.S. Sindi, D.R. Weilhammer, G.G. Loots, K.K. Hoyer
Computationally restoring the potency of a clinical antibody against Omicron | Nature
T.A. Desautels, K.T. Arrildt, A.T. Zemla, E.Y. Lau, F. Zhu, D. Ricci, S. Cronin, S.J. Zost, E. Binshtein, S.M. Scheaffer, B. Dadonaite, B.K. Petersen, T.B. Engdahl, E. Chen, L.S. Handal, L. Hall, J.W. Goforth, D. Vashchenko, S. Nguyen, D.R. Weilhammer, J.K. Lo, B. Rubinfeld, E.A. Saada, T. Weisenberger, T.H. Lee, B. Whitener, J.B. Case, A. Ladd, M.S. Silva, R.M. Haluska, E.A. Grzesiak, C.G. Earnhart, S. Hopkins, T.W. Bates, L.B. Thackray, B.W. Segelke, Tri-lab COVID-19 Consortium, A.M. Lillo, S. Sundaram, J.D. Bloom, M.S. Diamond, J.E. Crowe Jr, R.H. Carnahan, D.M. Faissol
Differential laboratory passaging of SARS-CoV-2 viral stocks impacts the in vitro assessment of neutralizing antibodies | PLoS One
A. Avila-Herrera, J.A. Kimbrel, J. Manuel Martí, J. Thissen, E.A. Saada, T. Weisenberger, K.T. Arrildt, B.W. Segelke, J.E. Allen, A. Zemla, M.K. Borucki
Evaluation of the Impact of Concentration and Extraction Methods on the Targeted Sequencing of Human Viruses from Wastewater | Environ. Sci. Technol.
M. Jiang, A.L.W. Wang, N.A. Be, N. Mulakken, K.L. Nelson, R.S. Kantor
Evaluation of Inactivation Methods for Rift Valley Fever Virus in Mouse Microglia | Pathogens
M.V. Rangel, F.A. Bourguet, C.I. Hall, D.R. Weilhammer
The influence of microbial colonization on inflammatory versus pro-healing trajectories in combat extremity wounds | Scientific Reports
S.A. Schobel, E.R. Gann, D. Unselt, S.F. Grey, F.A. Lisboa, M.M. Upadhyay, M. Rouse, S. Tallowin, N.A. Be, X. Zhang, C.L. Dalgard, M.D. Wilkerson, M. Hauskrecht, S.F. Badylak, R. Zamora, Y. Vodovotz, B.K. Potter, T.A. Davis, E.A. Elster
The military gear microbiome: risk factors surrounding the warfighter | Appl Environ Microbiol
C.R. Kok, Z. Bram, J.B. Thissen, T.S. Horseman, K.S.K. Fong, S.A. Reichert-Scrivner, C. Paguirigan, K. O'Connor, K. Thompson, A.E. Scheiber, V. Mabery, S. Ngauy, C.F. Uyehara, N.A. Be
Therapeutic efficacy of a potent anti-Venezuelan equine encephalitis virus antibody is contingent on Fc effector function | MAbs
J.L. Schwedler, M.A. Stefan, C.E. Thatcher, P.R. McIlroy, A. Sinha, A.M. Phillips, C.A. Sumner, C.M. Courtney, C.Y. Kim, D.R. Weilhammer, B. Harmon
2023
Coccidioidomycosis Osteoarticular Dissemination | J. Fungi
B.M. Moni, B.L. Wise, G.G. Loots, D.R. Weilhammer
Evaluation of 6-OxP-CD, an Oxime-based cyclodextrin as a viable medical countermeasure against nerve agent poisoning: Experimental and molecular dynamic simulation studies on its inclusion complexes with cyclosarin, soman and VX | PLoS One
E.Y. Lau, H.A. Enright, V. Lao, M.A. Malfatti, B.P. Mayer, A.M. Williams, C.A. Valdez
Improved chemical synthesis, identification and evaluation of prospective centrally active oxime antidotes for the treatment of nerve agent exposure | Tetrahedron
C.A. Valdez, D. Lam, V. Lao, A. Subramanian, H.A. Enright, M.A. Malfatti, N.A. Be, M.L. Dreyer
Targeted metagenomic assessment reflects critical colonization in battlefield injuries | Microbiol. Spectr.
C.R. Kok, N. Mulakken, J.B. Thissen, S.F. Grey, A. Avila-Herrera, M.M. Upadhyay, F.A. Lisboa, S. Mabery, E.A. Elster, S.A. Schobel, N.A. Be
2022
Domestic Dogs as Sentinels for West Nile Virus but not Aedes-borne Flaviviruses, Mexico | Emerg. Infect. Dis.
E. Davila, N.A. Fernández-Santos, J.G. Estrada-Franco, L. Wei, J.A. Aguilar-Durán, M. de J. López-López, R. Solís-Hernández, R. García-Miranda, D.D. Velázquez-Ramírez, J. Torres-Romero, S. Arellano Chávez, R. Cruz-Cadena, R. Navarro-López, A.A. Pérez de León, C. Guichard-Romero, E. Martin, W. Tang, M. Frank, M. Borucki, M.J. Turell, A. Pauvolid-Corrêa, M.A. Rodríguez-Pérez, H. Ochoa-Díaz-López, S.A. Hamer, G.L. Hamer
Large-scale application of free energy perturbation calculations for antibody design | Scientific Reports
F. Zhu, F.A. Bourguet, W.F.D. Bennett, E.Y. Lau, K.T. Arrildt, B.W. Segelke, A.T. Zemla, T.A. Desautels, and D.M. Faissol
MAVS mediates a protective immune response in the brain to Rift Valley fever virus | PLOS Pathogens
N.R. Hum, F.A. Bourguet, A. Sebastian, D. Lam, A.M. Phillips, K.R. Sanchez, A. Rasley, G.G. Loots, and D.R. Weilhammer
Metagenomic features of bioburden serve as outcome indicators in combat extremity wounds | Sci. Rep.
A. Avila-Herrera, J.B. Thissen, N. Mulakken, S.A. Schobel, M.D. Morrison, X. Zhou, S.F. Grey, F.A. Lisboa, D. Unselt, S. Mabery, M.M. Upadhyay, C.J. Jaing, E.A. Elster, N.A. Be
Multiple Mutations Associated with Emergent Variants Can Be Detected as Low-Frequency Mutations in Early SARS-CoV-2 Pandemic Clinical Samples | Viruses
J. Kimbrel, J. Moon, A. Avila-Herrera, J.M. Martí, J. Thissen, N. Mulakken, S.H. Sandholtz, T. Ferrell, C. Daum, S. Hall, B. Segelke, K.T. Arrildt, S. Messenger, D.A. Wadford, C. Jaing, J.E. Allen, M.K. Borucki
SARS-CoV-2 Monitoring in Wastewater Reveals Novel Variants and Biomarkers of Infection | Viruses
J. McGowan, M. Borucki, H. Omairi, M. Varghese, S. Vellani, S. Chakravarty, S. Fan, S. Chattopadhyay, M. Siddiquee, J.B. Thissen, N. Mulakken, J. Moon, J. Kimbrel, A.K. Tiwari, R.T. Taylor, D.W. Kang, C. Jaing, R. Chakravarti, S. Chattopadhyay
Tailored approach to study Legionella infection using a lattice light sheet microscope (LLSM) | Biomed Opt. Express
X. Yi, H. Miao, J.K. Lo, M.M. Elsheikh, T.H. Lee, C. Jiang, Y. Zhang, B.W. Segelke, K.W. Overton, P.T. Bremer, T.A. Laurence
2021
A Survey of Preclinical Studies Evaluating Nanoparticle-Based Vaccines Against Non-Viral Sexually Transmitted Infections | Front. Pharmacol.
A. Abisoye-Ogunniyan, M. Carrano, D.R. Weilhammer, S.F. Gilmore, N.O. Fischer, S. Pal, L.M. de la Maza, M.A. Coleman, A. Rasley
Development of a CNS-permeable reactivator for nerve agent exposure: an iterative, multi-disciplinary approach | Sci. Rep.
B.J. Bennion, M.A. Malfatti, N.A. Be, H.A. Enright, S. Hok, C.L. Cadieux, T.S. Carpenter, V. Lao, E.A. Kuhn, M.W. McNerney, F.C. Lightstone, T.H. Nguyen, C.A. Valdez
Development of potent and effective synthetic SARS-CoV-2 neutralizing nanobodies | mAbs
M.A. Stefan, Y.K. Light, J.L. Schwedler, P.R. McIlroy, C.M. Courtney, E.A. Saada, C.E. Thatcher, A.M. Phillips, F.A. Bourguet, C.M. Mageeney, S.A. McCloy, N.M. Collette, O.A. Negrete, J.S. Schoeniger, D.R. Weilhammer, B. Harmon
Discovery of Small-Molecule Inhibitors of SARS-CoV-2 Proteins Using a Computational and Experimental Pipeline | Front. Mol. Biosci.
E.Y. Lau, O.A. Negrete, W.F.D. Bennett, B.J. Bennion, M. Borucki, F. Bourguet, A. Epstein, M. Franco, B. Harmon, S. He, D. Jones, H. Kim, D. Kirshner, V. Lao, J. Lo, K. McLoughlin, R. Mosesso, D.K. Murugesh, E.A. Saada, B. Segelke, M.A. Stefan, G.A. Stevenson, M.W. Torres, D.R. Weilhammer, S. Wong, Y. Yang, A. Zemla, X. Zhang, F. Zhu, J.E. Allen, F.C. Lightstone
Performance of three-dimensional printed nasopharyngeal swabs for COVID-19 testing | MRS Bulletin
A. Tooker, M.L. Moya, D.N. Wang, D. Freeman, M. Borucki, E. Wheeler, G. Larsen, M. Shusteff, E.B. Duoss, C.M. Spadaccini Tooker
Quantitative Fit Evaluation of N95 Filtering Facepiece Respirators and Coronavirus Inactivation Following Heat Treatment | Ann. Work Expo. and Health
T.L. Massey, M.K. Borucki, S.Y. Paik, K.W. Fuhrer, M. Bora, S.R. Kane, R.M. Haque, S.H. Baxamusa
Shotgun Immunoproteomic Approach for the Discovery of Linear B-Cell Epitopes in Biothreat Agents Francisella tularensis and Burkholderia pseudomallei | Front. Immunol.
P. D’haeseleer, N.M. Collette, V. Lao, B.W. Segelke, S.S. Branda, M. Franco
The Eco-Bio-Social Factors That Modulate Aedes aegypti Abundance in South Texas Border Communities | Insects
J.G. Juarez, S.M. Garcia-Luna, M.C.I. Medeiros, K.L. Dickinson, M.K. Borucki, M. Frank, I. Badillo-Vargas, L.F. Chaves, G.L. Hamer
2020
Cell fusing agent virus (Flavivirus) infection in Aedes aegypti in Texas: seasonality, comparison by trap type, and individual viral loads | Arch. Virol.
E. Martin, W. Tang, C. Briggs, H. Hopson, J.G. Juarez, S.M. Garcia-Luna, M.W. de Valdez, I.E. Badillo-Vargas, M.K. Borucki, M. Frank, G.L. Hamer
Characterization of Bacillus anthracis Spore Proteins Using a Nanoscaffold Vaccine Platform | Front. Immunol.
D.R. Weilhammer, A.D. Dunkle, T. Boone, S.F. Gilmore, M. Khemmani, S.K.G. Peters, P.D. Hoeprich, N.O. Fischer, C.D. Blanchette, A. Driks, A. Rasley
Countermeasures for Preventing and Treating Opioid Overdose | Clin. Pharmacol. Ther.
C.P. France, G.P. Ahern, S. Averick, A. Disney, H.A. Enright, B. Esmaeli-Azad, A. Federico, L.R. Gerak, S.M. Husbands, B. Kolber, E.Y. Lau, V. Lao, D.R. Maguire, M.A. Malfatti, G. Martinez, B.P. Mayer, M. Pravetoni, N. Sahibzada, P. Skolnick, E.Y. Snyder, N. Tomycz, C.A. Valdez
Crewmember microbiome may influence microbial composition of ISS habitable surfaces | PLoS One
A Avila-Herrera, J Thissen, C Urbaniak, NA Be, DJ Smith, F Karouia, S Mehta, K Venkateswaran, C. Jaing
High Rate of Non-Human Feeding by Aedes aegypti Reduces Zika Virus Transmission in South Texas | Viruses
M.F. Olson, M.L. Ndeffo-Mbah, J.G. Juarez, S. Garcia-Luna, E. Martin, M.K. Borucki, M. Frank, J.G. Estrada-Franco, M.A. Rodríguez-Pérez, N.A. Fernández-Santos, G.J. Molina-Gamboa, S.D. Carmona Aguirre, B.L. Reyes-Berrones, L.J. Cortés-De la Cruz, A. García-Barrientos, R.E. Huidobro-Guevara, R.M. Brussolo-Ceballos, J. Ramirez, A. Salazar, L.F. Chaves, I.E. Badillo-Vargas, G.L. Hamer
Sierra Nevada sweep: metagenomic measurements of bioaerosols vertically distributed across the troposphere | Sci. Rep.
C. Jaing, J. Thissen, M. Morrison, M.B. Dillon, S.M. Waters, G.T. Graham, N.A. Be, P. Nicoll, S. Verma, T. Caro, D.J. Smith
Single Amino Acid Mutations Affect Zika Virus Replication In Vitro and Virulence In Vivo | Viruses
N.M. Collette, V.H.I. Lao, D.R. Weilhammer, B. Zingg, S.D. Cohen, M. Hwang, L.L. Coffey, S.L. Grady, A.T. Zemla, M.K. Borucki
Two Sides of a Coin: a Zika Virus Mutation Selected in Pregnant Rhesus Macaques Promotes Fetal Infection in Mice but at a Cost of Reduced Fitness in Nonpregnant Macaques and Diminished Transmissibility by Vectors | J. Virol.
D. Lemos, J.B. Stuart, W. Louie, A. Singapuri, A.L. Ramírez, J. Watanabe, J. Usachenko, R.I. Keesler, C. Sanchez-San Martin, T. Li, C. Martyn, G. Oliveira, S. Saraf, N.D. Grubaugh, K.G. Andersen, J. Thissen, J. Allen, M. Borucki, K.A. Tsetsarkin, A.G. Pletnev, C.Y. Chiu, K.K.A. Van Rompay, L.L. Coffey
