Author

C. B. Brooke

Listed by name: these papers carry no ORCID for this author, so different people with the same name may be mixed together.

Biology Disciplines

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Microbiology· 12 Evolutionary Biology· 1

Signature Assays, Organisms & Methods

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Approach:experimental assay· 9 Organism:human· 8 Research Focus:host-pathogen & immune response· 7 Organism:virus· 5 Assay:proteomics· 4 Approach:statistical model· 4 Assay:bulk RNA-seq· 3 Research Focus:cell type annotation· 3

Frequent Co-Authors

N. C. Wu· 4 shared T. J. C. Tan· 4 shared F. G. Alnaji· 3 shared J. Sun· 3 shared J. Rivera-Cardona· 2 shared M. Diefenbacher· 2 shared R. Ke· 2 shared T. Liu· 2 shared

Activity by Year

2018-2024 · peak 3/yr

Co-Author Collaboration Network

10 top collaborators · 19 mutual co-author links

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4 shared papersMicrobiology

N. C. Wu

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Author profile →

13 papers

Recent·Most cited

Natural variation in neuraminidase activity influences the evolutionary potential of the seasonal H1N1 lineage hemagglutinin

T. Liu, W. K. Reiser, T. J. C. Tan, H. Lv, J. Rivera-Cardona, K. Heimburger, N. C. Wu, C. B. Brooke

This study shows that natural variation in neuraminidase activity affects the evolutionary potential of hemagglutinin in seasonal H1N1 influenza viruses.

bioRxiv · Mar 18, 2024Microbiology

Stratification of viral shedding patterns in saliva of COVID-19 patients

H. Park, Y. Raiki, S. Iwanami, K. Kim, K. Ejima, N. Nakamura, K. Aihara, Y. Miyazaki, T. Umeyama, K. Miyazawa, T. Morita, K. Watashi, C. B. Brooke, R. Ke, S. Iwami, T. Miyazaki

This study stratifies SARS-CoV-2 viral shedding patterns in saliva into three groups with distinct durations using a mathematical model and clustering, but finds no clear clinical or miRNA biomarkers explaining the differences.

bioRxiv · Jan 30, 2024Microbiology

Cryptic proteins translated from deletion-containing viral genomes dramatically expand the influenza virus proteome

J. N. Ranum, M. P. Ledwith, F. G. Alnaji, M. Diefenbacher, R. Orton, E. Sloan, M. Guereca, E. M. Feltman, K. Smollett, A. da Silva Filipe, M. Conley, A. B. Russell, C. B. Brooke, E. Hutchinson, A. Mehle

The paper identifies cryptic proteins from deletion-containing viral genomes that inhibit influenza virus replication and expand its proteome.

bioRxiv · Dec 12, 2023Microbiology

Within-host evolutionary dynamics and tissue compartmentalization during acute SARS-CoV-2 infection

M. Farjo, K. Koelle, M. A. Martin, L. L. Gibson, K. K. Walden, G. Rendon, C. J. Fields, F. Alnaji, N. Gallagher, C. H. Luo, H. H. Mostafa, Y. C. Manabe, A. Pekosz, R. L. Smith, D. D. McManus, C. B. Brooke

This study uses daily saliva and nasal samples to track SARS-CoV-2 genetic variants in infected individuals, revealing stochastic evolution, mutational hotspots, and compartmentalization between sample sites.

bioRxiv · Jun 21, 2022Microbiology

The evolutionary potential of the influenza A virus hemagglutinin is highly constrained by intersegment epistasis

T. Liu, Y. Wang, T. J. C. Tan, N. C. Wu, C. B. Brooke

This study shows that intersegment epistasis between hemagglutinin and neuraminidase constrains the evolutionary potential of the influenza A virus hemagglutinin gene.

bioRxiv · May 19, 2022 · PreprintMicrobiology

Interactions between influenza A virus nucleoprotein and gene segment UTRs facilitate selective modulation of viral gene expression

M. Diefenbacher, T. J. C. Tan, D. L. V. Bauer, B. Stadtmueller, N. C. Wu, C. B. Brooke

This study identifies how influenza A virus nucleoprotein interactions with gene segment UTRs selectively modulate viral gene expression, revealing a new role for NP in gene-segment specific regulation.

bioRxiv · Jan 9, 2022 · PreprintMicrobiology

Semi-continuous propagation of influenza A virus and its defective interfering particles: analyzing the dynamic competition to select candidates for antiviral therapy

L. Pelz, D. Ruediger, T. Dogra, F. G. Alnaji, Y. Genzel, C. B. Brooke, S. Y. Kupke, U. Reichl

This study investigates the competition between influenza A virus and its defective interfering particles (DIPs) during co-infection, identifying DIPs with superior antiviral efficacy as potential therapeutic candidates.

Journal of Virology · Nov 23, 2021Peer-reviewedEvolutionary Biology

Influenza A virus defective viral genomes are inefficiently packaged into virions relative to wild-type genomic RNAs

F. G. Alnaji, W. K. Reiser, A. te Velthuis, C. B. Brooke

The paper analyzes deletion-containing viral genomes (DelVGs) in influenza A virus infection, revealing packaging inefficiencies and deletion hotspots.

bioRxiv · May 13, 2021Microbiology

Sequence signatures of two IGHV3-53/3-66 public clonotypes to SARS-CoV-2 receptor binding domain

T. J. C. Tan, M. Yuan, K. Kuzelka, G. C. Padron, J. R. Beal, X. Chen, Y. Wang, J. Rivera-Cardona, X. Zhu, B. M. Stadtmueller, C. B. Brooke, I. A. Wilson, N. C. Wu

The paper identifies two public IGHV3-53/3-66 clonotypes with distinct CDR H3 motifs and shows Y58F mutation enhances binding affinity to SARS-CoV-2 RBD.

bioRxiv · Jan 26, 2021Microbiology

Cellular co-infection can modulate the efficiency of influenza A virus production and shape the interferon response

B. E. Martin, J. D. Harris, J. Sun, K. V. Koelle, C. B. Brooke

This study quantifies how cellular co-infection affects influenza A virus production and the interferon response in two cell lines, revealing cell-type-dependent effects on viral kinetics and immune signaling.

bioRxiv · Sep 6, 2020Microbiology

Drug repurposing screen identifies masitinib as a 3CLpro inhibitor that blocks replication of SARS-CoV-2 in vitro

N. Drayman, K. A. Jones, S.-A. Azizi, H. M. Froggatt, K. Tan, N. Ivanova Maltseva, S. Chen, V. Nicolaescu, S. Dvorkin, K. Furlong, R. S. Kathayat, M. R. Firpo, V. Mastrodomenico, E. A. Bruce, M. M. Schmidt, , S. Tay

The paper screens 1,900 drugs to find inhibitors of SARS-CoV-2 replication, identifies masitinib as a 3CLpro inhibitor effective in vitro, and shows its broad anti-viral activity.

bioRxiv · Aug 31, 2020Microbiology

A common pattern of influenza A virus single cell gene expression heterogeneity governs the innate antiviral response to infection

J. C. Vera, J. Sun, Y. T. Lin, J. Drnevich, R. Ke, C. B. Brooke

This study identifies a common pattern of viral gene expression heterogeneity in influenza A virus that influences host antiviral responses across subtypes.

bioRxiv · Dec 10, 2019Microbiology

Influenza A virus superinfection potential is regulated by viral genomic heterogeneity

J. Sun, C. B. Brooke

This study identifies that the number of viral genes expressed, not their identity, determines influenza A virus superinfection susceptibility.

bioRxiv · Mar 21, 2018Microbiology