PEER-REVIEWED JOURNAL PUBLICATIONS (Primarily UO1 Supported)

COVID-19 Case and Mortality Surveillance using Daily SARS-CoV-2 in Wastewater Samples adjusting for Meteorological Conditions and Sample pH.

Abelson, S., Penso, J., Alsuliman, B., Babler, K., Sharkey, M., Stevenson, M., Grills, G., Mason, C. E., Solo-Gabriele, H., & Kumar, N., 2023. COVID-19 Case and Mortality Surveillance using Daily SARS-CoV-2 in Wastewater Samples adjusting for Meteorological Conditions and Sample pH. medRxiv : the preprint server for health sciences, 2023.07.12.23292570. https://doi.org/10.1101/2023.07.12.23292570. PMID: 37502918, PMCID: PMC10370245

Wastewater Based Surveillance Can Be Used to Reduce Clinical Testing Intensity on a University Campus.

Amirali, A., Babler, K.M., Sharkey, M.E., Beaver, C., Boone, M.M., Comerford, S., Cooper, D., Currall, B.B., Goodman, K., Grills, G.S., Kobetz, E., Kumar, N., Laine, J., Lamar, W.E., Mason, C.E., Reding, B.D., Roca, M.A., Ryon, K., Schürer, S.C., Shukla, B.S., Schaefer Solle, N., Stevenson, M., Tallon Jr., J.J., Vidović, D., Williams, S.L., Yin, X., Solo-Gabriele, H.M., 2024. Wastewater Based Surveillance Can Be Used to Reduce Clinical Testing Intensity on a University Campus. The Science of the Total Environment, 918, 170452. https://doi.org/10.1016/j.scitotenv.2024.170452.

Geospatially-Resolved Public-Health Surveillance via Wastewater Sequencing.

Tierney, B., Foox, J., Ryon, A., Butler, D., Damle, N., Young, B. G., Mozsary, C., Babler, K. M., Yin, X., Carattini, Y., Andrews, D., Solle, N., Kumar, N., Shukla, B., Vidovic, D., Currall, B., Williams, S. L., Schürer, S. C., Stevenson, M., Amirali, A., Beaver, C., Kobetz, E., Boone, M. M., Reding, B., Laine, J., Comerford, S., Lamar, W. E., Tallon, J. J., Hirschberg, J. W., Proszynski, J., Sharkey, M. E., Church, G. M., Grills, G.S., Solo-Gabriele, H. M., Mason, C. E. Geospatially-Resolved Public-Health Surveillance via Wastewater Sequencing. medRxiv 2023. https://doi.org/10.1101/2023.05.31.23290781.

Expanding a Wastewater-Based Surveillance Methodology for DNA Isolation from a Workflow Optimized for SARS-CoV-2 RNA Quantification.

Babler, K. M., Sharkey, M. E., Amirali, A., Boone, M. M., Comerford, S., Currall, B. B., Grills, G. S., Laine, J., Mason, C. E., Reding, B., Schürer, S., Stevenson, M., Vidović, D., Williams, S. L., & Solo-Gabriele, H. M., 2023. Expanding a Wastewater-Based Surveillance Methodology for DNA Isolation from a Workflow Optimized for SARS-CoV-2 RNA Quantification. Journal of Biomolecular Techniques. 2023;34(4). https://doi.org/10.7171/3fc1f5fe.dfa8d906.

Correlative analysis of wastewater trends with clinical cases and hospitalizations through five dominant variant waves of COVID-19.

Zhan, Q., Solo-Gabriele, H.M., Sharkey, M.E., Amirali, A., Beaver, C.C., Boone, M.M., Comerford, S., Cooper, D., Cortizas, E.M., Cosculluela, G.A., Currall, B., Grills, G.S., Kobetz, E., Kumar, N., Laine, J., Lamar, W.E., Lyu, J., Mason, C.E., Reding, B.D., Roca, M.A., Schürer, S.C., Shukla, B., Schaefer Solle, N., Suarez, M., Stevenson, M., Tallon Jr., J.J., Thomas, C., Vidovic, D., Williams, S.L. Yin, X., Zarnegarnia, Y., Babler, K., 2023. Correlative analysis of wastewater trends with clinical cases and hospitalizations through five dominant variant waves of COVID-19.  ACS ES&T-Water, 3, 2849-2862.  https://doi.org/10.1021/acsestwater.3c00032.

Detection of the clinically persistent, pathogenic yeast spp. Candida auris from hospital and municipal wastewater in Miami-Dade County, Florida.

Babler, K., Sharkey, M., Arenas, S., Amirali, A., Beaver, C., Comerford,S., Goodman, K., Grills, G., Holung, M., Kobetz, E., Laine, J., Lamar, W., Mason, C.,  Pronty, D., Reding, B, Schürer, S., Schaefer Solle, N., Stevenson, M., Vidović, D., Solo-Gabriele, H., Shukla, B., 2023. Detection of the clinically persistent, pathogenic yeast spp. Candida auris from hospital and municipal wastewater in Miami-Dade County, Florida, Science of The Total Environment, 898, 165459, https://doi.org/10.1016/j.scitotenv.2023.165459. PMID: 37442462; PMCID: PMC10543605.

Monkeypox viral nucleic acids detected using both DNA and RNA extraction workflows. 

Sharkey, M. E., Babler, K. M., Shukla, B. S., Abelson, S., Alsuliman, B., Amirali, A., Comerford, S., Grills, G. S., Kumar, N., Laine, J., Lee, J.,Lamar, W. E., Mason, C. E., Penso, J., Reding, B. D., Schürer, S. C., Stevenson, M., Vidović, D., Solo-Gabriele, H. M., 2023. Monkeypox viral nucleic acids detected using both DNA and RNA extraction workflows.  The Science of the Total Environment, 890, 164289. https://doi.org/10.1016/j.scitotenv.2023.164289. PMID: 37216988; PMCID: PMC10213602

Degradation rates influence the ability of composite samples to represent 24-hourly means of SARS-CoV-2 and other microbiological target measures in wastewater.

Babler, K. M.; Sharkey, M. E.; Abelson, S.; Amirali, A.; Cosculluela, G. A.; Grills, G. S.; Kumar, N.; Laine, J.; Lamar, W. E.; Lamm, E. D.; Lyu, J.; Mason, C. E.; McCabe, P. M.; Raghavender, J.; Reding, B. D.; Roca, M. A.; Schurer, S. C.; Stevenson, M.; Szeto, A.; Tallon, J. J.; Vidovic, D.; Zarnegarnia, Y.; Solo-Gabriele, H. M., Degradation rates influence the ability of composite samples to represent 24-hourly means of SARS-CoV-2 and other microbiological target measures in wastewater.Sci Total Environ. 2023 Apr 1;867:161423. doi:10.1016/j.scitotenv.2023.161423. Epub 2023 Jan 6. https://pubmed.ncbi.nlm.nih.gov/36623667/ PMID: 36623667; PMCID: PMC9817413

MINI: A high-throughput point-of-care device for performing hundreds of nucleic acid tests per day.

McCloskey, D., Boza, J., Mason, C.E., Erickson, D. MINI: A high-throughput point-of-care device for performing hundreds of nucleic acid tests per day. Biosensors and Bioelectronics. 2022 216, 15: 114654, https://doi.org/10.1016/j.bios.2022.114654. PMID: 36084523

Relationships between SARS-CoV 2 in Wastewater and COVID-19 Clinical Cases and Hospitalizations, with and without Normalization against Indicators of Human Waste

Comparison of Electronegative Filtration to Magnetic Bead-Based Concentration and V2G-qPCR to RT-qPCR for Quantifying Viral SARS-CoV-2 RNA from Wastewater

Predicting COVID-19 cases using SARS-CoV-2 RNA in air, surface swab and wastewater samples

A Rapid, Isothermal, and Point-of-Care System for COVID-19 Diagnostics

Loop-Mediated Isothermal Amplification Detection of SARS-CoV-2 and Myriad Other Applications

Received outstanding paper of the year award

Danko, D.C., Sierra, M.A., Benardini, J.N. et al. A comprehensive metagenomics framework to characterize organisms relevant for planetary protection. Microbiome 9, 82 (2021). https://doi.org/10.1186/s40168-021-01020-1

Characterization of the public transit air microbiome and resistome reveals geographical specificity

Leung, M.H.Y., Tong, X., Bøifot, K.O. et al. Characterization of the public transit air microbiome and resistome reveals geographical specificity. Microbiome 9, 112 (2021). https://doi.org/10.1186/s40168-021-01044-7

A global metagenomic map of urban microbiomes and antimicrobial resistance

David Danko, Daniela Bezdan, Evan E. Afshin, Sibo Zhu, Christopher E. Mason, et al. A global metagenomic map of urban microbiomes and antimicrobial resistance, Cell Vol. 184, Issue 13, pp. 3376-3393, June 24, 2021. Published by Elsevier Inc.  https://doi.org/10.1016/j.cell.2021.05.002

Performance assessment of DNA sequencing platforms in the ABRF Next-Generation Sequencing Study

Foox, J., Tighe, S.W., Nicolet, C.M. et al. Performance assessment of DNA sequencing platforms in the ABRF Next-Generation Sequencing Study. Nat Biotechnol 39, 1129–1140 (2021). https://doi.org/10.1038/s41587-021-01049-5

The SEQC2 epigenomics quality control (EpiQC) study

Foox, J., Nordlund, J., Lalancette, C. et al. The SEQC2 epigenomics quality control (EpiQC) study. Genome Biol 22, 332 (2021). https://doi.org/10.1186/s13059-021-02529-2

Curated variation benchmarks for challenging medically relevant autosomal genes

Wagner, J., Olson, N.D., Harris, L. et al. Curated variation benchmarks for challenging medically relevant autosomal genes. Nat Biotechnol 40, 672–680 (2022). https://doi.org/10.1038/s41587-021-01158-1

System-wide transcriptome damage and tissue identity loss in COVID-19 patients

Park, J., Foox, J., Hether, T. et al. System-wide transcriptome damage and tissue identity loss in COVID-19 patients. Cell Press, 3, 2, 100522 (2022) https://doi.org/10.1016/j.xcrm.2022.100522

Integrating Virus Monitoring Strategies for Safe Non-Potable Water Reuse

Jiang SC, Bischel HN, Goel R, Rosso D, Sherchan SP, Whiteson KL, Yan T, Solo-Gabriele HM. Integrating Virus Monitoring Strategies for Safe Non-Potable Water Reuse. Water. 2022; 14(8):1187. https://doi.org/10.3390/w14081187

A metagenomic DNA sequencing assay that is robust against environmental DNA contamination

Mzava, O., Cheng, A.P., Chang, A. et al. A metagenomic DNA sequencing assay that is robust against environmental DNA contamination. Nat Commun 13, 4197 (2022). https://doi.org/10.1038/s41467-022-31654-0

Machine learning algorithm to characterize antimicrobial resistance associated with the International Space Station surface microbiome

Madrigal, P., Singh, N.K., Wood, J.M. et al. Machine learning algorithm to characterize antimicrobial resistance associated with the International Space Station surface microbiome. Microbiome 10, 134 (2022). https://doi.org/10.1186/s40168-022-01332-w

Supervised Machine Learning Enables Geospatial Microbial Provenance

Bhattacharya, C.; Tierney, B.T.; Ryon, K.A.; Bhattacharyya, M.; Hastings, J.J.A.; Basu, S.; Bhattacharya, B.; Bagchi, D.; Mukherjee, S.; Wang, L.; Henaff, E.M.; Mason, C.E. Supervised Machine Learning Enables Geospatial Microbial Provenance. Genes 2022, 13, 1914.  https://doi.org/10.3390/genes13101914 

Highly host-linked viromes in the built environment possess habitat-dependent diversity and functions for potential virus-host coevolution.

Du, S., Tong, X., Lai, A.C.K. et al. Highly host-linked viromes in the built environment possess habitat-dependent diversity and functions for potential virus-host coevolution. Nat Commun 14, 2676 (2023). https://doi.org/10.1038/s41467-023-38400-0. PMID: 37160974, PMCID: PMC10169181 https://pubmed.ncbi.nlm.nih.gov/37160974/

Structured Ethical Review for Wastewater-Based Testing in Support of Public Health. Environmental science & technology

Bowes, D. A., Darling, A., Driver, E. M., Kaya, D., Maal-Bared, R., Lee, L. M., Goodman, K., Adhikari, S., Aggarwal, S., Bivins, A., Bohrerova, Z., Cohen, A., Duvallet, C., Elnimeiry, R. A., Hutchison, J. M., Kapoor, V., Keenum, I., Ling, F., Sills, D., Tiwari, A., … Mansfeldt, C. (2023). Structured Ethical Review for Wastewater-Based Testing in Support of Public Health. Environmental science & technology, 57(35), 12969–12980. https://doi.org/10.1021/acs.est.3c04529. PMID: 37611169,  PMCID: PMC10484207 https://pubmed.ncbi.nlm.nih.gov/37611169/

Unlocking capacities of genomics for the COVID-19 response and future pandemics. Nature methods

Knyazev, S., Chhugani, K., Sarwal, V., Ayyala, R., Singh, H., Karthikeyan, S., Deshpande, D., Baykal, P. I., Comarova, Z., Lu, A., Porozov, Y., Vasylyeva, T. I., Wertheim, J. O., Tierney, B. T., Chiu, C. Y., Sun, R., Wu, A., Abedalthagafi, M. S., Pak, V. M., Nagaraj, S. H., … Mangul, S. (2022). Unlocking capacities of genomics for the COVID-19 response and future pandemics. Nature methods, 19(4), 374–380. https://doi.org/10.1038/s41592-022-01444-z. PMID: 35396471; PMCID: PMC9467803 https://pubmed.ncbi.nlm.nih.gov/35396471/

Shotgun transcriptome, spatial omics, and isothermal profiling of SARS-CoV-2 infection reveals unique host responses, viral diversification, and drug interactions

Butler D, Mozsary C, Meydan C, Foox J, Rosiene J, Shaiber A, Danko D, Afshinnekoo E, MacKay M, Sedlazeck FJ, Ivanov NA, Sierra M, Pohle D, Zietz M, Gisladottir U, Ramlall V, Sholle ET, Schenck EJ, Westover CD, Hassan C, Ryon K, Young B, Bhattacharya C, Ng DL, Granados AC, Santos YA, Servellita V, Federman S, Ruggiero P, Fungtammasan A, Chin CS, Pearson NM, Langhorst BW, Tanner NA, Kim Y, Reeves JW, Hether TD, Warren SE, Bailey M, Gawrys J, Meleshko D, Xu D, Couto-Rodriguez M, Nagy-Szakal D, Barrows J, Wells H, O’Hara NB, Rosenfeld JA, Chen Y, Steel PAD, Shemesh AJ, Xiang J, Thierry-Mieg J, Thierry-Mieg D, Iftner A, Bezdan D, Sanchez E, Campion TR Jr, Sipley J, Cong L, Craney A, Velu P, Melnick AM, Shapira S, Hajirasouliha I, Borczuk A, Iftner T, Salvatore M, Loda M, Westblade LF, Cushing M, Wu S, Levy S, Chiu C, Schwartz RE, Tatonetti N, Rennert H, Imielinski M, Mason CE. Shotgun transcriptome, spatial omics, and isothermal profiling of SARS-CoV-2 infection reveals unique host responses, viral diversification, and drug interactions. Nature Communications. 2021. Mar 12;12(1):1660. https://doi.org/10.1038/s41467-021-21361-7

News Coverage:

• Weill Cornell Newsroom: Global Microbiome Study Discovers Thousands of New Species, Maps Urban Antimicrobial Resistance and Reveals New Drug Candidates
• The New York Times: Subway Swabbers Find a Microbe Jungle and Thousands of New Species