SELECTED PREPRINTS:

Farjo M and Brooke CB. 2025.

The fitness consequences of coinfection and reassortment for segmented viruses depend upon viral genetic structure

biorxiv. doi: https://doi.org/10.1101/2025.07.22.666171

SELECTED PUBLICATIONS:

Farjo M and Brooke CB. 2026.

Heterogeneity and Collective Interactions Within Viral Populations

Annual review of virology. DOI: 10.1146/annurev-virology-092623-093749

Alnaji FG, Farjo F, Goh SH, Aw DZH, Lorenzini pa, Liu t, lin-zhen rc, lee c, vignuzzi m, and brooke cb. 2026

Longitudinal analysis of influenza A virus deletion-containing viral genomes reveals key determinants of co-evolutionary dynamics and interference

nature communications. DOI: 10.1038/s41467-026-74526-7

Thayer ea, shipman g, rivera-cardona j, mahajan t, teo qw, paez js, lederer j, chen j, wu nc, maslov s, and brooke cb. 2026.

Single-cell heterogeneity in interferon induction potential is heritable and governed by variation in cell state

cell systems. doi: 10.1016/j.cels.2026.101676

Rivera-Cardona J, Mahajan T, Thayer EA, Kakuturu NR, Teo QW, Lederer J, Rowland EF, Heimburger K, Sun J, McDonald CA, Mickelson CK, Langlois RA, Wu NC, Milenkovic O, Maslov S, and Brooke CB. 2025

Intrinsic OASL expression governs heterogeneity in interferon induction during influenza A virus infection.

PNAS. DOI: 10.1073/pnas.2509560123

Rivera-Cardona J, Kakuturu N, Rowland EF, Teo QW, Thayer EA, Tan TJC, Sun J, Kieffer C, Wu NC, and Brooke CB. 2024.

Seasonal influenza A virus lineages exhibit divergent abilities to antagonize interferon induction and signaling.

PLOS Pathogens. doi: 10.1371/journal.ppat.1012727.

Liu T, Reiser WK, Tan TJC, Lv H, Rivera-Cardona J, Heimburger K, Wu NC, and Brooke CB. 2024

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

Virus Evolution. doi: 10.1093/ve/veae046.

Farjo M, Koelle K, Martin MA, Gibson LL, Walden KKO, Rendon G, Fields CJ, Alnaji FG, Gallagher N, Luo CH, Mostafa HH, Manade YC, Pekosz A, Smith RL, McManus DD, and Brooke CB. 2024.

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

J. Virology. doi: 10.1128/jvi.01618-23

Rivera-Cardona J and Brooke CB

How influenza shuts down host transcription

Nature Microbiology. doi: 10.1038/s41564-023-01416-9

Farjo M and Brooke CB. 2023.

When influenza viruses don’t play well with others

Nature. doi: 10.1038/d41586-023-00983-5

Farjo M and Brooke CB. 2023.

Low Viral Diversity Limits the Effectiveness of Sequence-Based Transmission Inference for SARS-CoV-2

mSphere. doi: 10.1128/mSphere.00400-22.

Liu T, Wang Y, Tan TJC, Wu NC, and Brooke CB. 2022.

The evolutionary potential of the influenza A virus hemagglutinin is highly constrained by epistatic interactions with neuraminidase.

Cell Host & Microbe. doi: https://doi.org/10.1016/j.chom.2022.09.003.

Ke R, Martinez PP, Smith RL, Gibson LL, Mirza A, Conte M, Gallagher N, Luo CH, Jarrett J, Conte A, Liu T, Farjo M, Walden KKO, Rendon G, Fields CJ, Wang L, Fredrickson R, Edmonson DC, Baughman ME, Chiu KK, Choi H, Scardina KR, Bradley S, Gloss SL, Reinhart C, Yedetore J, Quicksall J, Owens AN, Broach J, Barton B, Lazar P, Heetderks WJ, Robinson ML, Mostafa HH, Manabe YC, Pekosz A, McManus DD, and Brooke CB. 2022.

Daily sampling of early SARS-CoV-2 infection reveals substantial heterogeneity in infectiousness

Nature Microbiology. doi: 10.1038/s41564-022-01105-z

Diefenbacher M, Tan TJC, Bauer DLV, Stadtmueller B, Wu NC, Brooke CB. 2022.

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

J. Virology. doi: 10.1128/jvi.00205-22

Ke R, Martinez PP, Smith RL, Gibson LL, Achenbach CJ, McFall S, Qi C, Jacob J, Dembele E, Bundy C, Simons LM, Ozer EA, Hultquist JF, Lorenzo-Redondo R, Opdycke AK, Hawkins C, Murphy RL, Mirza A, Conte M, Gallagher N, Luo CH, Jarrett J, Conte A, Farjo M, Rendon G, Fields CJ, Wang L, Fredrickson R, Baughman ME, Chiu KK, Choi H, Scardina KR, Owens AN, Broach J, Barton B, Lazar P, Robinson ML, Mostafa HH, Manabe YC, Pekosz A, McManus DD, and Brooke CB. 2022.

Longitudinal analysis of SARS-CoV-2 vaccine breakthrough infections reveal limited infectious virus shedding and restricted tissue distribution.

Open Forum Infect. Dis. doi: 10.1093/ofid/ofac192

Alnaji FG, Reiser WK, Rivera Cardona J, te Velthuis A, and Brooke CB. 2021.

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

mBio. doi: 10.1128/mBio.02959-21

Smith RL, Gibson LL, Martinez PP, Ke R, Mirza A, Conte M, Gallagher N, Conte A, Wang L, Fredrickson R, Edmonson DC, Baughman ME, Chiu KK, Choi H, Jensen TW, Scardina KR, Bradley S, Gloss SL, Reinhart C, Yedetore J, Owens AN, Broach J, Barton B, Lazar P, Henness D, Young T, Dunnett A, Robinson ML, Mostafa HH, Pekosz A, Manabe YC, Heetderks WJ, McManus DD, and Brooke CB. 2021.

Longitudinal assessment of diagnostic test performance over the course of acute SARS-CoV-2 infection.

J. Infect. Dis.. doi: 10.1093/infdis/jiab337/6311835

Martin BE, Harris JD, Sun J, Koelle K, and Brooke CB. 2020

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

PLOS Pathogens. doi: 10.1371/journal.ppat.1008974

Sun J, Vera JC, Drnevich J, Lin YT, Ke R, and Brooke CB. 2020.

Single cell heterogeneity in influenza A virus gene expression shapes the innate antiviral response to infection

PLOS Pathogens. doi: 10.1371/journal.ppat.1008671

Alnaji FG and Brooke CB. 2020.

Influenza virus DI particles: Defective interfering or delightfully interesting?

PLOS Pathogens. doi: 10.1371/journal.ppat.1008436

Alnaji FG, Holmes JR, Rendon G, Vera JC, Fields CJ, Martin, BE, and Brooke CB. 2019

Sequencing framework for the sensitive detection and precise mapping of defective interfering particle-associated deletions across influenza A and B viruses

J. Virology. doi:10.1128/JVI.00354-19

Martin BE and Brooke CB. 2019

Flu shows the power of diversity

Cell. doi:10.1016/j.cell.2018.12.017

Gallagher ME, Brooke CB, Ke R, and Koelle K. 2018

Causes and consequences of spatial within-host viral spread

Viruses. doi:10.3390/v10110627

Sun J and Brooke CB. 2018

Influenza A virus superinfection potential is regulated by viral genomic heterogeneity

mBio. doi:10.1128/mBio.01761-18

Diefenbacher M, Sun J, and Brooke CB. 2018

The parts are greater than the whole: the role of semi-infectious particles in influenza A virus biology

Current Opinion in Virology. doi:10.1016/j.coviro.2018.07.002

Kosik I*, Ince WL*, Gentles LE*, Oler AJ, Kosikova M, Angel M, Magadan JG, Xie H, Brooke CB^ and Yewdell JW^. 2018.

Influenza A virus hemagglutinin glycosylation compensates for antibody escape fitness costs

PLOS Pathogens. doi:10.1371/journal.ppat.1006796. *,^ Authors contributed equally

Brooke CB. 2017.

Population Diversity and Collective Interactions during Influenza Virus Infection

J. Virology. doi:10.1128/JVI.01164-17

Brooke CB*, Ince WL*, Wei J, Bennink JR, and Yewdell JW. 2014. 

Influenza A virus nucleoprotein selectively decreases neuraminidase gene segment packaging while enhancing fitness and transmissibility.

PNAS. 111(47): 16854-16859. *Authors contributed equally

Brooke CB. 2014. 

Biological activities of ‘noninfectious’ influenza A particles.

Future Virology. 9(1):41-51. 

Brooke CB, Ince WL, Wrammert J, Ahmed R, Wilson PC, Bennink JR, and Yewdell JW. 2013. 

Most influenza A virions fail to express at least one essential viral protein.

J. Virology. 87(6): 3155-62.

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