Our publications

2025

Harnessing Machine Learning for Agnostic Biodetection | Health Security
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, and N.A. Be

Potential Role of Malassezia restricta in Pterygium Development | International Journal of Molecular Sciences
M. Paradzik Simunovic, M. Degoricija, J. Korac-Prlic, M. Lesin, R. Stanic, L. Puljak, I. Olujic, J. Marin Lovric, A. Vucinovic, Z. Ljubic, J. Thissen, C. Reen Kok, C. Jaing, K. Bucan, and J. Terzic

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, and N.A. Be

2023

A Computational Pipeline to Identify and Characterize Binding Sites and Interacting Chemotypes in SARS-CoV-2 | ACS Omega
S.H. Sandholtz, J.A. Drocco, A.T. Zemla, M.W. Torres, M.S. Silva, and J.E. Allen

Efforts to enhance reproducibility in a human performance research project | F1000Research
J. Drocco, K. Halliday, B. Stewart, S. Sandholtz, M. Morrison, J. Thissen, N. Be, C. Zwilling, R. Wilcox, S. Culpepper, A. Barbey, and C. Jaing

2022

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, et. al

Evaluation of co-circulating pathogens and microbiome from COVID-19 infections | PLOS ONE
J.B. Thissen, M.D. Morrison, N. Mulakken, W.C. Nelson, C. Daum, S. Messenger, D.A. Wadford, and C. Jaing

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, and S. Chattopadhyay

Microbial Tracking-2, a metagenomics analysis of bacteria and fungi onboard the International Space Station | Microbiome
C. Urbaniak, M.D. Morrison, J.B. Thissen, F. Karouia, D.J. Smith, S. Mehta, C. Jaing, and K. Venkateswaran

Metagenomic features of bioburden serve as outcome indicators in combat extremity wounds | Scientific Reports
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, and N.A. Be

Extracellular matrix modulates T cell clearance of malignant cells in vitro | Biomaterials
C. Robertson, A. Sebastian, A. Hinckley, N.D. Rios-Arce, W.F. Hynes, S.A. Edwards, W. He, N.R. Hum, E.K. Wheeler, G.G. Loots, M.A. Coleman, and M.L. Moya

Plant-associated fungi support bacterial resilience following water limitation | The ISME Journal
R. Hestrin, M. Kan, M. Lafler, J. Wollard, J.A. Kimbrel, P. Ray, and J. Pett-Ridge

Bacterial response to spatial gradients of algal-derived nutrients in a porous microplate | The ISME Journal
H. Kim, J.A. Kimbrel, C.A., Vaiana, J.R. Wollard, X. Mayali, and C.R. Buie

HT-SIP: a semi-automated stable isotope probing pipeline identifies cross-kingdom interactions in the hyphosphere of arbuscular mycorrhizal fungi | Microbiome
E.E. Nuccio, S.J. Blazewicz, M. Lafler, A.N. Campbell, A. Kakouridis, J.A. Kimbrel, and J. Pett-Ridge

2021

Investigation of Spaceflight Induced Changes to Astronaut Microbiomes | Frontiers in Microbiology
M.D. Morrison, J.B. Thissen, F. Karouia, S. Mehta, C. Urbaniak, K. Venkateswaran, D.J. Smith, C. Jaing

Gut microbiome associations with outcome following co-infection with porcine reproductive and respiratory syndrome virus (PRRSV) and porcine circovirus type 2 (PCV2) in pigs immunized with a PRRS modified live virus vaccine | Veterinary Microbiology
L.A. Constance, J.B. Thissen, C.J. Jaing, K.S. McLoughlin, R.R.R. Rowland, N.V.L. Serão, A.G. Cino-Ozuna, and M.C. Niederwerder

2020

Sierra Nevada sweep: metagenomic measurements of bioaerosols vertically distributed across the troposphere. Scientific Reports | Scientific Reports
C. Jaing, J. Thissen, M. Morrison, M.B. Dillon, S.M. Waters, G.T. Graham, N.A. Be, P. Nicoll, S. Verma, T. Caro, and D.J. Smith

Crewmember microbiome may influence microbial composition of ISS habitable surfaces | PLOS ONE
J. Thissen, C. Urbaniak, N.A. Be, D.J. Smith, F. Karouia, S. Mehta, K. Venkateswaran, and C. Jaing

The influence of spaceflight on the astronaut salivary microbiome and the search for a microbiome biomarker for viral reactivation | Microbiome
C. Urbaniak, H. Lorenzi, J. Thissen, C. Jaing, B. Crucian, C. Sams, D. Pierson, K. Venkateswaran, and S. Mehta

Manipulation of the Gut Microbiome Alters Acetaminophen Biodisposition in Mice | Scientific Reports
M.A. Malfatti, E.A. Kuhn, D.K. Murugesh, M.E. Mendez, N. Hum, J.B. Thissen, C.J. Jaing, and G.G. Loots

Macromolecular gelatin properties affect fibrin microarchitecture and tumor spheroid behavior in fibrin-gelatin gels | Biomaterials
K. Dubbin, C. Robertson, A. Hinckley, J.A. Alvarado, S.F. Gilmore, W.F. Hynes, E.K. Wheeler, and M.L. Moya

Comparative Molecular Analysis of Cancer Behavior Cultured In Vitro, In Vivo, and Ex Vivo | Cancers
N.R. Hum, A. Sebastian, S.F. Gilmore, W. He, K.A.Martin, A. Hinckley, K.R. Dubbin, M.L. Moya, E.K. Wheeler, M.A. Coleman, G.G. Loots

2019

Profiling microbial communities with shotgun metagenomics | Notices of the American Mathematical Society
J. Allen and C. Jaing

Mosquito-Borne Viruses and Insect-Specific Viruses Revealed in Field-Collected Mosquitoes by a Monitoring Tool Adapted from a Microbial Detection Array | Applied and Environmental Microbiology
E. Martin, M.K. Borucki, J. Thissen, S. Garcia-Luna, M. Hwang, M. Wise de Valdez, C.J. Jaing, G.L. Hamer, and M. Frank

Axiom Microbiome Array, the next generation microarray for high-throughput pathogen and microbiome analysis | PLOS ONE
N.A. Be, K. McLoughlin, S. Gardner, P.G. Rack, M.H. Shapero, R.R.R. Rowland, T. Slezak, and C.J. Jaing

Putative parapoxvirus-associated foot disease in the endangered huemul deer (Hippocamelus bisulcus) in Bernardo O'Higgins National Park, Chile | PLOS ONE
R.A. Vila, C. Briceno, D. McAloose, T.A. Seimon, A.G. Armien, E.A. Mauldin, N.A. Be, J.B. Thissen, A. Hinojosa, M. Quezada, J. Paredes, I. Avendano, A. Silva, and M.M. Uhart

Characterizing chemoautotrophy and heterotrophy in marine archaea and bacteria with single-cell multi-isotope NanoSIP | Frontiers in microbiology
A. E. Dekas, A.E. P.X. Mayali, J.A. Fuhrman, J. Wollard, P.K. Weber, and J. Pett-Ridge

A novel variant of torque teno virus 7 identified in patients with Kawasaki Disease | PLOS ONE
J.B. Thissen, M. Isshiki, C. Jaing, Y. Nagao, D.L. Aldea, J.E. Allen, M. Izui, T.R. Slezak, T. Ishida, and T. Sano

Airborne Bacteria in Earth’s Lower Stratosphere Resemble Taxa Detected in the Troposphere: Results From a New NASA Aircraft Bioaerosol Collector (ABC) | Frontiers in Microbiology
D.J. Smith, D. Ravichandar, S. Jain, D.W. Griffin, H. Yu, Q. Tan, J. Thissen, T. Lusby, P. Nicoll, S. Shedler, P. Martinez, A. Osorio, J. Lechniak, S. Choi, K. Sabino, K. Iverson, L. Chan, C. Jaing and J. McGrath

Double-stranded viral RNA persists in vitro and in vivo during prolonged infection of porcine reproductive and respiratory syndrome virus | Virology
R. Guo, P. Shang, C.A. Carrillo, Z. Sun, Y.S. Lakshmanappa, X. Yan, G.J. Renukaradhya, J. McGill, C.J. Jaing, M.C. Niederwerder, R.R.R. Rowland, and Y. Fang

Detection of antimicrobial resistance genes associated with the International Space Station environmental surfaces | Scientific Reports
C. Urbaniak, A. Checinska, K.G. Frey, C.L. Redden, J.E. Allen, N. Singh, C. Jaing, K. Wheeler, and K. Venkateswaran

Nonstructural proteins nsp2TF and nsp2N of porcine reproductive and respiratory syndrome virus (PRRSV) play important roles in suppressing host innate immune responses | Virology
Y. Li, P. Shang, D. Shyu, C. Carrillo, P. Naraghi-Arani, C.J. Jaing, G.J. Renukaradhya, A.E. Firth, E.J. Snijder, Y. Fang

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