Search Results - "Shean, Ryan"

VAPiD: a lightweight cross-platform viral annotation pipeline and identification tool to facilitate virus genome submissions to NCBI GenBank by Shean, Ryan C, Makhsous, Negar, Stoddard, Graham D, Lin, Michelle J, Greninger, Alexander L

“…With sequencing technologies becoming cheaper and easier to use, more groups are able to obtain whole genome sequences of viruses of public health and…”
Get full text

A retrospective observational study of mNGS test utilization to examine the role of diagnostic stewardship at two academic medical centers by Shean, Ryan C, Garrett, Elizabeth, Malleis, James, Lieberman, Joshua A, Bradley, Benjamin T

“…Given the cost and unclear clinical impact of metagenomic next-generation sequencing (mNGS), laboratory stewardship may improve utilization. This retrospective…”
Get more information

Repeat testing of mpox specimens with late CTs improves detection of potential false positive cases by Shean, Ryan C, Hymas, Weston C, Klein, Jeremy, Pyne, Michael, Hillyard, David R, Bradley, Benjamin T

“…The mpox pandemic necessitated the rapid development of clinical assays for monkeypox virus detection. While the majority of mpox specimens have high viral…”
Get full text

Metagenomic Analysis Reveals Clinical SARS-CoV-2 Infection and Bacterial or Viral Superinfection and Colonization by Peddu, Vikas, Shean, Ryan C, Xie, Hong, Shrestha, Lasata, Perchetti, Garrett A, Minot, Samuel S, Roychoudhury, Pavitra, Huang, Meei-Li, Nalla, Arun, Reddy, Shriya B, Phung, Quynh, Reinhardt, Adam, Jerome, Keith R, Greninger, Alexander L

“…Abstract Background More than 2 months separated the initial description of SARS-CoV-2 and discovery of its widespread dissemination in the United States…”
Get full text

Advances in Hematology Analyzers Technology by Shean, Ryan C., Williams, Margaret C., Rets, Anton V.

“…The evolution of complete blood count (CBC) methodology from manual calculations to sophisticated high throughput hematology analyzers is the focus of this…”
Get full text

CrAssphage and its bacterial host in cat feces by Li, Yanpeng, Gordon, Emilia, Shean, Ryan C., Idle, Amanda, Deng, Xutao, Greninger, Alexander L., Delwart, Eric

“…CrAssphages are a diverse group of related phages detected in human feces where they are the most prevalent and abundant prokaryotic virus. CrAssphages’…”
Get full text

Viral Entry Properties Required for Fitness in Humans Are Lost through Rapid Genomic Change during Viral Isolation by Iketani, Sho, Shean, Ryan C, Ferren, Marion, Makhsous, Negar, Aquino, Dolly B, des Georges, Amedee, Rima, Bert, Mathieu, Cyrille, Porotto, Matteo, Moscona, Anne, Greninger, Alexander L

“…Human parainfluenza viruses cause a large burden of human respiratory illness. While much research relies upon viruses grown in cultured immortalized cells,…”
Get full text

Prolonged Shedding of Human Coronavirus in Hematopoietic Cell Transplant Recipients: Risk Factors and Viral Genome Evolution by Ogimi, Chikara, Greninger, Alexander L., Waghmare, Alpana A., Kuypers, Jane M., Shean, Ryan C., Xie, Hu, Leisenring, Wendy M., Stevens-Ayers, Terry L., Jerome, Keith R., Englund, Janet A., Boeckh, Michael

“…Background. Recent data suggest that human coronavirus (HCoV) pneumonia is associated with significant mortality in hematopoietic cell transplant (HCT)…”
Get full text

Human parainfluenza virus evolution during lung infection of immunocompromised individuals promotes viral persistence by Greninger, Alexander L, Rybkina, Ksenia, Lin, Michelle J, Drew-Bear, Jennifer, Marcink, Tara C, Shean, Ryan C, Makhsous, Negar, Boeckh, Michael, Harder, Olivia, Bovier, Francesca, Burstein, Shana R, Niewiesk, Stefan, Rima, Bert K, Porotto, Matteo, Moscona, Anne

“…The capacity of respiratory viruses to undergo evolution within the respiratory tract raises the possibility of evolution under the selective pressure of the…”
Get full text

A Systematic Review of Dietary Supplements and Alternative Therapies for Weight Loss by Batsis, John A., Apolzan, John W., Bagley, Pamela J., Blunt, Heather B., Divan, Vidita, Gill, Sonia, Golden, Angela, Gundumraj, Shalini, Heymsfield, Steven B., Kahan, Scott, Kopatsis, Katherine, Port, Ava, Parks, Elizabeth Prout, Reilly, Clifford A., Rubino, Domenica, Saunders, Katherine H., Shean, Ryan, Tabaza, Luai, Stanley, Abishek, Tchang, Beverly G., Gundumraj, Shivani, Kidambi, Srividya

“…Objective Dietary supplements and alternative therapies are commercialized as a panacea for obesity/weight gain as a result of the minimal regulatory…”
Get full text

Distribution of Staphylococcus species in dairy cows, workers and shared farm environments by Roberts, Marilyn C, Garland-Lewis, Gemina, Trufan, Sally, Meschke, Scott J, Fowler, Heather, Shean, Ryan C, Greninger, Alexander L, Rabinowitz, Peter M

“…Dairy farming involves frequent contact among animals, workers and farm environments. To explore the Staphylococcus spp. diversity that occurs on dairy farms,…”
Get full text

Cell free DNA from respiratory pathogens is detectable in the blood plasma of Cystic Fibrosis patients by Barrett, Sara L. Rassoulian, Holmes, Elizabeth A., Long, Dustin R., Shean, Ryan C., Bautista, Gilbert E., Ravishankar, Sumedha, Peddu, Vikas, Cookson, Brad T., Singh, Pradeep K., Greninger, Alexander L., Salipante, Stephen J.

“…Diagnostically informative microbial cell-free DNA (cfDNA) can be detected from blood plasma during fulminant infections such as sepsis. However, the potential…”
Get full text

Advances and Challenges in Wearable Glaucoma Diagnostics and Therapeutics by Shean, Ryan, Yu, Ning, Guntipally, Sourish, Nguyen, Van, He, Ximin, Duan, Sidi, Gokoffski, Kimberly, Zhu, Yangzhi, Xu, Benjamin

“…Glaucoma is a leading cause of irreversible blindness, and early detection and treatment are crucial for preventing vision loss. This review aims to provide an…”
Get full text

Private collection: high correlation of sample collection and patient admission date in clinical microbiological testing complicates sharing of phylodynamic metadata by Shean, Ryan C, Greninger, Alexander L

“…Abstract Infectious pathogens are known for their rapid evolutionary rates with new mutations arising over days to weeks. The ability to rapidly recover whole…”
Get full text

Genome Sequences of Three Novel Bunyaviruses, Two Novel Rhabdoviruses, and One Novel Nyamivirus from Washington State Moths by Makhsous, Negar, Shean, Ryan C, Droppers, David, Guan, Jonathan, Jerome, Keith R, Greninger, Alexander L

“…We report draft genome sequences of three novel bunyaviruses, two novel rhabdoviruses, and one novel nyamivirus identified metagenomically from 10 moths in…”
Get full text

Draft Genome Sequences of Six Novel Picorna-Like Viruses from Washington State Spiders by Shean, Ryan C, Makhsous, Negar, Crawford, Rodney L, Jerome, Keith R, Greninger, Alexander L

“…We report draft genome sequences of six novel members from six different spider species found in Washington state. These six viral sequences distinctly…”
Get full text

Using Laboratory Documentation to Extend a Large Language Model to Serve as a Laboratory Assistant by Shean, Ryan, Ng, David

“…Abstract Demographic and structural changes in the workforce are resulting in ever smaller cohorts of laboratory medical professionals while medical…”
Get full text

Myeloablation-associated deletion of ORF4 in a human coronavirus 229E infection by Greninger, Alexander L., Pepper, Gregory, Shean, Ryan C., Cent, Anne, Palileo, Isabel, Kuypers, Jane M., Schiffer, Joshua T., Jerome, Keith R.

“…We describe metagenomic next-generation sequencing (mNGS) of a human coronavirus 229E from a patient with AML and persistent upper respiratory symptoms, who…”
Get full text

Validation of Resting Energy Expenditure Equations in Older Adults with Obesity by Griffith, Rachel, Shean, Ryan, Petersen, Curtis L., Al-Nimr, Rima I., Gooding, Tyler, Roderka, Meredith N., Batsis, John A.

“…It is unclear which energy expenditure prediction equation should guide weight loss interventions in older adults with obesity. We ascertained the validity of…”
Get full text

NCBI's Virus Discovery Hackathon: Engaging Research Communities to Identify Cloud Infrastructure Requirements by Connor, Ryan, Brister, Rodney, Buchmann, Jan P, Deboutte, Ward, Edwards, Rob, Martí-Carreras, Joan, Tisza, Mike, Zalunin, Vadim, Andrade-Martínez, Juan, Cantu, Adrian, D'Amour, Michael, Efremov, Alexandre, Fleischmann, Lydia, Forero-Junco, Laura, Garmaeva, Sanzhima, Giluso, Melissa, Glickman, Cody, Henderson, Margaret, Kellman, Benjamin, Kristensen, David, Leubsdorf, Carl, Levi, Kyle, Levi, Shane, Pakala, Suman, Peddu, Vikas, Ponsero, Alise, Ribeiro, Eldred, Roy, Farrah, Rutter, Lindsay, Saha, Surya, Shakya, Migun, Shean, Ryan, Miller, Matthew, Tully, Benjamin, Turkington, Christopher, Youens-Clark, Ken, Vanmechelen, Bert, Busby, Ben

“…A wealth of viral data sits untapped in publicly available metagenomic data sets when it might be extracted to create a usable index for the virological…”
Get full text