We are falling behind on TB elimination targets: can whole-genome sequencing guide our efforts?

por Wheeler, Nicole
Publicado 2019

Machine learning identifies signatures of host adaptation in the bacterial pathogen Salmonella enterica

por Wheeler, Nicole E., Gardner, Paul P., Barquist, Lars
Publicado 2018

A profile-based method for identifying functional divergence of orthologous genes in bacterial genomes

por Wheeler, Nicole E., Barquist, Lars, Kingsley, Robert A., Gardner, Paul P.
Publicado 2016

Why so narrow: Distribution of anti-sense regulated, type I toxin-antitoxin systems compared with type II and type III systems

por Coray, Dorien S., Wheeler, Nicole E., Heinemann, Jack A., Gardner, Paul P.
Publicado 2017

Gauge your phage: benchmarking of bacteriophage identification tools in metagenomic sequencing data

por Ho, Siu Fung Stanley, Wheeler, Nicole E., Millard, Andrew D., van Schaik, Willem
Publicado 2023

Improved Prediction of Bacterial Genotype-Phenotype Associations Using Interpretable Pangenome-Spanning Regressions

por Lees, John A., Mai, T. Tien, Galardini, Marco, Wheeler, Nicole E., Horsfield, Samuel T., Parkhill, Julian, Corander, Jukka
Publicado 2020

Ten simple rules for the sharing of bacterial genotype—Phenotype data on antimicrobial resistance

por Chindelevitch, Leonid, van Dongen, Maarten, Graz, Heather, Pedrotta, Antonio, Suresh, Anita, Uplekar, Swapna, Jauneikaite, Elita, Wheeler, Nicole
Publicado 2023

Evaluation of parameters affecting performance and reliability of machine learning-based antibiotic susceptibility testing from whole genome sequencing data

por Hicks, Allison L., Wheeler, Nicole, Sánchez-Busó, Leonor, Rakeman, Jennifer L., Harris, Simon R., Grad, Yonatan H.
Publicado 2019

Safety by design: Biosafety and biosecurity in the age of synthetic genomics

por Hoffmann, Stefan A., Diggans, James, Densmore, Douglas, Dai, Junbiao, Knight, Tom, Leproust, Emily, Boeke, Jef D., Wheeler, Nicole, Cai, Yizhi
Publicado 2023

Increased power from conditional bacterial genome-wide association identifies macrolide resistance mutations in Neisseria gonorrhoeae

por Ma, Kevin C., Mortimer, Tatum D., Duckett, Marissa A., Hicks, Allison L., Wheeler, Nicole E., Sánchez-Busó, Leonor, Grad, Yonatan H.
Publicado 2020

Genomic, Transcriptomic, and Phenotypic Analyses of Neisseria meningitidis Isolates from Disease Patients and Their Household Contacts

por Ren, Xiaoyun, Eccles, David A., Greig, Gabrielle A., Clapham, Jane, Wheeler, Nicole E., Lindgreen, Stinus, Gardner, Paul P., MacKichan, Joanna K.
Publicado 2017

Genomic correlates of extraintestinal infection are linked with changes in cell morphology in Campylobacter jejuni

por Wheeler, Nicole E., Blackmore, Timothy, Reynolds, Angela D., Midwinter, Anne C., Marshall, Jonathan, French, Nigel P., Savoian, Matthew S., Gardner, Paul P., Biggs, Patrick J.
Publicado 2019

Evolution of Salmonella enterica serotype Typhimurium driven by anthropogenic selection and niche adaptation

por Bawn, Matt, Alikhan, Nabil-Fareed, Thilliez, Gaëtan, Kirkwood, Mark, Wheeler, Nicole E., Petrovska, Liljana, Dallman, Timothy J., Adriaenssens, Evelien M., Hall, Neil, Kingsley, Robert A.
Publicado 2020

Robust Identification of Noncoding RNA from Transcriptomes Requires Phylogenetically-Informed Sampling

por Lindgreen, Stinus, Umu, Sinan Uğur, Lai, Alicia Sook-Wei, Eldai, Hisham, Liu, Wenting, McGimpsey, Stephanie, Wheeler, Nicole E., Biggs, Patrick J., Thomson, Nick R., Barquist, Lars, Poole, Anthony M., Gardner, Paul P.
Publicado 2014

Population‐based hospitalization burden estimates for respiratory viruses, 2015–2019

por Zimmerman, Richard K., Balasubramani, G. K., D'Agostino, Helen E. A., Clarke, Lloyd, Yassin, Mohamed, Middleton, Donald B., Silveira, Fernanda P., Wheeler, Nicole D., Landis, Jonathan, Peterson, Alanna, Suyama, Joe, Weissman, Alexandra, Nowalk, Mary Patricia
Publicado 2022

Adaptation to the cervical environment is associated with increased antibiotic susceptibility in Neisseria gonorrhoeae

por Ma, Kevin C., Mortimer, Tatum D., Hicks, Allison L., Wheeler, Nicole E., Sánchez-Busó, Leonor, Golparian, Daniel, Taiaroa, George, Rubin, Daniel H. F., Wang, Yi, Williamson, Deborah A., Unemo, Magnus, Harris, Simon R., Grad, Yonatan H.
Publicado 2020

Rapid Genomic Characterization and Global Surveillance of Klebsiella Using Pathogenwatch

por Argimón, Silvia, David, Sophia, Underwood, Anthony, Abrudan, Monica, Wheeler, Nicole E, Kekre, Mihir, Abudahab, Khalil, Yeats, Corin A, Goater, Richard, Taylor, Ben, Harste, Harry, Muddyman, Dawn, Feil, Edward J, Brisse, Sylvain, Holt, Kathryn, Donado-Godoy, Pilar, Ravikumar, K L, Okeke, Iruka N, Carlos, Celia, Aanensen, David M
Publicado 2021

An African Salmonella Typhimurium ST313 sublineage with extensive drug-resistance and signatures of host adaptation

por Van Puyvelde, Sandra, Pickard, Derek, Vandelannoote, Koen, Heinz, Eva, Barbé, Barbara, de Block, Tessa, Clare, Simon, Coomber, Eve L., Harcourt, Katherine, Sridhar, Sushmita, Lees, Emily A., Wheeler, Nicole E., Klemm, Elizabeth J., Kuijpers, Laura, Mbuyi Kalonji, Lisette, Phoba, Marie-France, Falay, Dadi, Ngbonda, Dauly, Lunguya, Octavie, Jacobs, Jan, Dougan, Gordon, Deborggraeve, Stijn
Publicado 2019

Joint sequencing of human and pathogen genomes reveals the genetics of pneumococcal meningitis

por Lees, John A., Ferwerda, Bart, Kremer, Philip H. C., Wheeler, Nicole E., Serón, Mercedes Valls, Croucher, Nicholas J., Gladstone, Rebecca A., Bootsma, Hester J., Rots, Nynke Y., Wijmega-Monsuur, Alienke J., Sanders, Elisabeth A. M., Trzciński, Krzysztof, Wyllie, Anne L., Zwinderman, Aeilko H., van den Berg, Leonard H., van Rheenen, Wouter, Veldink, Jan H., Harboe, Zitta B., Lundbo, Lene F., de Groot, Lisette C. P. G. M., van Schoor, Natasja M., van der Velde, Nathalie, Ängquist, Lars H., Sørensen, Thorkild I. A., Nohr, Ellen A., Mentzer, Alexander J., Mills, Tara C., Knight, Julian C., du Plessis, Mignon, Nzenze, Susan, Weiser, Jeffrey N., Parkhill, Julian, Madhi, Shabir, Benfield, Thomas, von Gottberg, Anne, van der Ende, Arie, Brouwer, Matthijs C., Barrett, Jeffrey C., Bentley, Stephen D., van de Beek, Diederik
Publicado 2019

Effectiveness of Pfizer-BioNTech and Moderna Vaccines Against COVID-19 Among Hospitalized Adults Aged ≥65 Years — United States, January–March 2021

por Tenforde, Mark W., Olson, Samantha M., Self, Wesley H., Talbot, H. Keipp, Lindsell, Christopher J., Steingrub, Jay S., Shapiro, Nathan I., Ginde, Adit A., Douin, David J., Prekker, Matthew E., Brown, Samuel M., Peltan, Ithan D., Gong, Michelle N., Mohamed, Amira, Khan, Akram, Exline, Matthew C., Files, D. Clark, Gibbs, Kevin W., Stubblefield, William B., Casey, Jonathan D., Rice, Todd W., Grijalva, Carlos G., Hager, David N., Shehu, Arber, Qadir, Nida, Chang, Steven Y., Wilson, Jennifer G., Gaglani, Manjusha, Murthy, Kempapura, Calhoun, Nicole, Monto, Arnold S., Martin, Emily T., Malani, Anurag, Zimmerman, Richard K., Silveira, Fernanda P., Middleton, Donald B., Zhu, Yuwei, Wyatt, Dayna, Stephenson, Meagan, Baughman, Adrienne, Womack, Kelsey N., Hart, Kimberly W., Kobayashi, Miwako, Verani, Jennifer R., Patel, Manish M., Amosu, Omowunmi, Armbruster, Brent, Aston, Valerie, Bernardo, Marianne, Bowers, Robert, De Souza, Leslie, Friedel, Jennifer, Gardner, Kevin, Goff, Jennifer, Gordon, Alexandra June, Hendrickson, Audrey, Hicks, Madeline, Howell, Michelle, Johnson, Jakea, Jorgensen, Jeffrey, Karow, Sarah, Kozikowski, Lori, Krol, Olivia, Landreth, Leigha, LaRose, Mary, Lopez, Brenda, York, New, Luong, Andrea, McClellan, Bob, Maruggi, Ellen, Miller, Karen, Nair, Rahul, Parks, Lisa, Peers, Jennifer, Perez, Cynthia, Rivera, Adreanne, Roque, Jonasel, Santana, Andres, Scharber, Tyler, Silverman, Emma, Tozier, Michael, Tzehaie, Hiwet, Zouyed, Zachary, Arroliga, Alejandro, Bagiatis, Alicia, Balasubramani, GK, Cheng, Caroline K., Eng, Heather, Ghamande, Shekhar, Herrick, Judy, Hoffman, Eric, Hughes, Kailey, Lamerato, Lois E., Lauring, Adam S., McKillop, Amanda, McNeal, Tresa, McSpadden, E.J., Midturi, John, Mutnal, Manohar, Nowalk, Mary Patricia, Petrie, Joshua G., Raiyani, Chandni, Rao, Arundhati, Saul, Sean G., Sax, Theresa M., Segaloff, Hannah E., Stiefel, Lori, Volz, Marcus, Walker, Kimberly, Wheeler, Nicole, White, Heath, Williams, John V., Yassin, Mohamed, Zayed, Martha, Zunie, Tnelda
Publicado 2021